Aminotransferase and oxidoreductase nucleic acids and polypeptides and methods of using

INCORPORATION BY REFERENCE

A Sequence Listing is being filed concurrently with the filing of this application under PCT AI §801(a). The accompanying Sequence Listing, identified as 07_—0245WO01seq.txt, is herein incorporated by reference.

Appendix 1 is being filed concurrently with the filing of this application under PCT AI §801(a). The accompanying Appendix, identified as 07_—0245WO01app.txt, is a table related to the Sequence Listing and is herein incorporated by reference.

TECHNICAL FIELD

This invention relates to nucleic acids and polypeptides, and more particularly to nucleic acids and polypeptides encoding aminotransferases and oxidoreductases as well as methods of using such aminotransferases and oxidoreductases.

BACKGROUND

An aminotransferase enzyme catalyzes a transamination reaction between an amino acid and an alpha-keto acid. Alpha-aminotransferases catalyze a reaction that removes the amino group from an amino acid, forming an alpha-keto acid, and transferring the amino group to a reactant α-keto acid, converting the keto acid into an amino acid. Therefore, an aminotransferase is useful in the production of amino acids.

An oxidoreductase enzyme such as a dehydrogenase catalyzes a reaction that oxidizes a substrate by transferring one or more protons and a pair of electrons to an acceptor (e.g., transfers electrons from a reductant to an oxidant). Therefore, an oxidoreductase is useful in catalyzing the oxidative deamination of amino acids to keto acids or the reductive amination of keto acids to amino acids.

SUMMARY

This disclosure provides for a number of different aminotransferase and oxidoreductase polypeptides and the nucleic acids encoding such aminotransferase and oxidoreductase polypeptides. This disclosure also provides for methods of using such aminotransferase and oxidoreductase nucleic acids and polypeptides.

In one aspect, the invention provides for methods of converting tryptophan to indole-3-pyruvate (or, alternatively, indole-3-pyruvate to tryptophan). Such methods include combining tryptophan (or indole-3-pyruvate) with a) one or more nucleic acid molecules chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975, wherein the one or more nucleic acid molecules encode polypeptides having aminotransferase (AT) or oxidoreductase activity; b) a variant of a), wherein the variant encodes a polypeptide having AT or oxidoreductase activity; c) a fragment of a) or b), wherein the fragment encodes a polypeptide having AT or oxidoreductase activity; d) one or more polypeptides chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, 976, 1069, 1070, 1071, 1072 and 1073, wherein the one or more polypeptides has AT or oxidoreductase activity; e) a variant of d), wherein the variant has AT or oxidoreductase activity; or f) a fragment of d) or e), wherein the fragment has AT or oxidoreductase activity.

In another aspect, the invention provides methods of converting MP to monatin (or, alternatively, monatin to MP). Such methods generally include combining MP (or monatin) with a) one or more nucleic acid molecules chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975, wherein the one or more nucleic acid molecules encode polypeptides having aminotransferase (AT) or oxidoreductase activity; b) a variant of a), wherein the variant encodes a polypeptide having AT or oxidoreductase activity; c) a fragment of a) or b), wherein the fragment encodes a polypeptide having AT or oxidoreductase activity; d) one or more polypeptides chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, 976, 1069, 1070, 1071, 1072 and 1073, wherein the one or more polypeptides has AT or oxidoreductase activity; e) a variant of d), wherein the variant has AT or oxidoreductase activity; or f) a fragment of d) or e), wherein the fragment has AT or oxidoreductase activity.

In one embodiment, the one or more nucleic acid molecules are chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 969, 971, 973, and 975. In another embodiment, the one or more polypeptides are chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, and 976.

In certain embodiments, the nucleic acid molecule has a sequence selected from the group consisting of SEQ ID NOs:945, 891, 893, 219, 175, 1063, 1065, and 1067. In certain embodiments, the polypeptide has a sequence selected from the group consisting of SEQ ID NOs:946, 892, 894, 220, 176, 1064, 1066, and 1068. In certain embodiments, the polypeptide has a sequence that corresponds to the consensus sequence shown in SEQ ID NO:1069 or 1070. In certain embodiments, the polypeptide has a sequence that corresponds to the consensus sequence shown in SEQ ID NO:1071, 1072, and 1073.

In some embodiments, the variant is a nucleic acid molecule that has at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 99%) sequence identity to SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 969, 971, 973, and 975.

In some embodiments, the variant is a polypeptide that has at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 99%) sequence identity to SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, and 976.

In one embodiment, the variant is a polypeptide that has at least 65% (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99%) sequence identity to SEQ ID NO:220. In another embodiment, the variant is a polypeptide that has at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 99%) sequence identity to SEQ ID NO:870. In yet another embodiment, the variant is a polypeptide that has at least 65% (e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99%) sequence identity to SEQ ID NO:894.

In certain embodiments, the variant is a mutant. Representative mutants include, without limitation, a mutant having a mutation at the residue that aligns with residue 243 of DAT 4978 (e.g., SEQ ID NO:870 T242N, SEQ ID NO:220 G240N, or SEQ ID NO:220 T241N). In one embodiment, the variant is a nucleic acid molecule that has been codon optimized. In certain embodiments, the variant polypeptide is a chimeric polypeptide.

In certain embodiments, a nucleic acid molecule is contained within an expression vector and can be, for example, overexpressed. In certain embodiments, the aminotransferase or oxidoreductase polypeptide is immobilized on a solid support. In certain embodiments, the tryptophan or the MP is a substituted tryptophan or a substituted MP. A representative tryptophan is 6-chloro-D-tryptophan.

In another aspect, the invention provides methods of converting tryptophan to indole-3-pyruvate (or, alternatively, indole-3-pyruvate to tryptophan). Such methods typically include combining tryptophan (or indole-3-pyruvate) with a) one or more nucleic acid molecules chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 969, 971, 973, and 975, wherein the one or more nucleic acid molecules encode polypeptides having D-aminotransferase (DAT) activity; b) a variant of a), wherein the variant encodes a polypeptide having DAT activity; c) a fragment of a) or b), wherein the fragment encodes a polypeptide having DAT activity; d) one or more polypeptides chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, 976, 1069, 1070, 1071, 1072 and 1073, wherein the one or more polypeptides has DAT activity; e) a variant of d), wherein the variant has DAT activity; or f) a fragment of d) or e), wherein the fragment has DAT activity.

In still another aspect, the invention provides for methods of converting MP to monatin (or, alternatively, monatin to MP). Such methods generally include combining MP (or monatin) with a) one or more nucleic acid molecules chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 969, 971, 973, and 975, wherein the one or more nucleic acid molecules encode polypeptides having DAT activity; b) a variant of a), wherein the variant encodes a polypeptide having DAT activity; c) a fragment of a) or b), wherein the fragment encodes a polypeptide having DAT activity; d) one or more polypeptides chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, 976, 1069, 1070, 1071, 1072 and 1073, wherein the one or more polypeptides has DAT activity; e) a variant of d), wherein the variant has DAT activity; or f) a fragment of d) or e), wherein the fragment has DAT activity.

In certain embodiments, the nucleic acid molecule or polypeptide has a sequence selected from the group consisting of SEQ ID NO:945, 891, 893, 219, 175, 1063, 1065, and 1067. In certain embodiments, the polypeptide has a sequence that corresponds to a consensus sequence shown in SEQ ID NO:1069, 1070, 1071, 1072 or 1073. In some embodiments, the tryptophan or the MP is a substituted tryptophan or a substituted MP. A representative substituted tryptophan is 6-chloro-D-tryptophan.

In still another aspect, the invention provides methods of making monatin. Generally, such methods include contacting tryptophan, under conditions in which monatin is produced, with a C3 carbon source and a) one or more nucleic acid molecules chosen from the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 969, 971, 973, and 975, wherein the one or more nucleic acid molecules encode polypeptides having D-aminotransferase (DAT) activity; b) a variant of a), wherein the variant encodes a polypeptide having DAT activity; c) a fragment of a) or b), wherein the fragment encodes a polypeptide having DAT activity; d) one or more polypeptides chosen from the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 220 G240N, 220 T241N, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 870 T242N, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, 976, 1069, 1070, 1071, 1072 and 1073, wherein the one or more polypeptides has DAT activity; e) a variant of d), wherein the variant has DAT activity; or f) a fragment of d) or e), wherein the fragment has DAT activity.

In some embodiments, the nucleic acid molecule is chosen from the group consisting of SEQ ID NO: 945, 891, 893, 219, 175, 1063, 1065, and 1067. In some embodiments, the C3 carbon source is selected from the group consisting of pyruvate, oxaloacetate, and serine. In some embodiments, the method further comprises adding or including a synthase/lyase (EC 4.1.2.- or 4.1.3.-) polypeptide. Representative synthase/lyase (EC 4.1.2.- or 4.1.3.-) polypeptides include aldolases such as KHG aldolases (EC 4.1.3.16) or HMG aldolases (EC 4.1.3.16).

In some embodiments of the above-indicated methods, the monatin produced is R,R monatin. In some embodiments, the monatin produced is S,R monatin. In certain embodiments, the tryptophan is a substituted tryptophan such as, for example, 6-chloro-D-tryptophan.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the drawings and detailed description, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 is an alignment of SEQ ID NO:894, 1066, 1064, and 1068.

FIG. 2 is an alignment of SEQ ID NO:870, 910, and several Bacillus sequences. Consensus sequences A and B (SEQ ID NO:1069 and 1070, respectively) directed toward the novel portions of SEQ ID NO:870 were developed from this alignment.

FIG. 3 is an alignment of SEQ ID NO:946, 894, 892, 220, 176, 1064, 1066, and 1068. Consensus sequences C, D and E (SEQ ID NO:1071, 1072 and 1073, respectively) were developed from this alignment.

FIG. 4 is a model of 3DAA-D-amino acid aminotransferase, with numbered residues indicating those sites selected for TMCA^SMevolution, as described in detail below.

Like reference symbols in the various drawings indicate like elements.

DETAILED DESCRIPTION

Disclosed herein are a number of different nucleic acid molecules encoding polypeptides having aminotransferase (AT) activity (e.g., transaminase activity). Specifically disclosed are a number of D-aminotransferases (DATs). DATs catalyze a transamination reaction (e.g., D-alanine+2-oxoglutarate<=>pyruvate+D-glutamate). Also provided are a number of different nucleic acid molecules encoding polypeptides having oxidoreductase activity (e.g., dehydrogenase activity). Oxidoreductases such as dehydrogenases catalyze an oxidation-reduction reaction (e.g., D-amino acid+H₂O+acceptor<=>a 2-oxo acid+NH₃+reduced acceptor). The nucleic acids or polypeptides disclosed herein can be used to convert tryptophan to indole-3-pyruvate and/or 2-hydroxy 2-(indol-3-ylmethyl)-4-keto glutaric acid (“monatin precursor” or “MP”) to monatin.

Isolated Nucleic Acid Molecules and Purified Polypeptides

The present invention is based, in part, on the identification of nucleic acid molecules encoding polypeptides having aminotransferase (AT) activity, herein referred to as “AT” nucleic acid molecules or polypeptides, where appropriate. The present invention also is based, in part, on the identification of nucleic acid molecules encoding polypeptides having oxidoreductase activity, herein referred to as “oxidoreductase” nucleic acid molecules or polypeptides, where appropriate.

Particular nucleic acid molecules described herein include the sequences shown in SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975. As used herein, the term “nucleic acid molecule” can include DNA molecules and RNA molecules, analogs of DNA or RNA generated using nucleotide analogs. A nucleic acid molecule of the invention can be single-stranded or double-stranded, depending upon its intended use. Nucleic acid molecules of the invention include molecules that have at least 75% sequence identity (e.g., at least 80%, 85%, 90%, 95%, or 99% sequence identity) to any of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975 and that have functional AT or oxidoreductase activity.

In calculating percent sequence identity, two sequences are aligned and the number of identical matches of nucleotides or amino acid residues between the two sequences is determined. The number of identical matches is divided by the length of the aligned region (i.e., the number of aligned nucleotides or amino acid residues) and multiplied by 100 to arrive at a percent sequence identity value. It will be appreciated that the length of the aligned region can be a portion of one or both sequences up to the full-length size of the shortest sequence. It will be appreciated that a single sequence can align differently with other sequences and hence, can have different percent sequence identity values over each aligned region. It is noted that the percent identity value is usually rounded to the nearest integer. For example, 78.1%, 78.2%, 78.3%, and 78.4% are rounded down to 78%, while 78.5%, 78.6%, 78.7%, 78.8%, and 78.9% are rounded up to 79%. It is also noted that the length of the aligned region is always an integer.

The alignment of two or more sequences to determine percent sequence identity is performed using the algorithm described by Altschul et al. (1997, Nucleic Acids Res., 25:3389-3402) as incorporated into BLAST (basic local alignment search tool) programs, available at ncbi.nlm.nih.gov on the World Wide Web. BLAST searches can be performed to determine percent sequence identity between an AT nucleic acid molecule described herein and any other sequence or portion thereof aligned using the Altschul et al. algorithm. BLASTN is the program used to align and compare the identity between nucleic acid sequences, while BLASTP is the program used to align and compare the identity between amino acid sequences. When utilizing BLAST programs to calculate the percent identity between a sequence of the invention and another sequence, the default parameters of the respective programs are used.

Nucleic acid molecules of the invention, for example, those between about 10 and about 50 nucleotides in length, can be used, under standard amplification conditions, to amplify an AT or oxidoreductase nucleic acid molecule. Amplification of an AT or oxidoreductase nucleic acid can be for the purpose of detecting the presence or absence of an AT or oxidoreductase nucleic acid molecule or for the purpose of obtaining (e.g., cloning) an AT or oxidoreductase nucleic acid molecule. As used herein, standard amplification conditions refer to the basic components of an amplification reaction mix, and cycling conditions that include multiple cycles of denaturing the template nucleic acid, annealing the oligonucleotide primers to the template nucleic acid, and extension of the primers by the polymerase to produce an amplification product (see, for example, U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188). The basic components of an amplification reaction mix generally include, for example, each of the four deoxynucleoside triphosphates, (e.g., dATP, dCTP, dTTP, and dGTP, or analogs thereof), oligonucleotide primers, template nucleic acid, and a polymerase enzyme. Template nucleic acid is typically denatured at a temperature of at least about 90° C., and extension from primers is typically performed at a temperature of at least about 72° C. In addition, variations to the original PCR methods (e.g., anchor PCR, RACE PCR, or ligation chain reaction (LCR)) have been developed and are known in the art. See, for example, Landegran et al., 1988, Science, 241:1077-1080; and Nakazawa et al., 1994, Proc. Natl. Acad. Sci. USA, 91:360-364).

The annealing temperature can be used to control the specificity of amplification. The temperature at which primers anneal to template nucleic acid must be below the Tm of each of the primers, but high enough to avoid non-specific annealing of primers to the template nucleic acid. The Tm is the temperature at which half of the DNA duplexes have separated into single strands, and can be predicted for an oligonucleotide primer using the formula provided in section 11.46 of Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). Non-specific amplification products are detected as bands on a gel that are not the size expected for the correct amplification product.

Nucleic acid molecules of the invention, for example, those between about 10 and several hundred nucleotides in length (up to several thousand nucleotides in length), can be used, under standard hybridization conditions, to hybridize to an AT or oxidoreductase nucleic acid molecule. Hybridization to an AT or oxidoreductase nucleic acid molecule can be for the purpose of detecting or obtaining an AT or oxidoreductase nucleic acid molecule. As used herein, standard hybridization conditions between nucleic acid molecules are discussed in detail in Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, 2^ndEd., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Sections 7.37-7.57, 9.47-9.57, 11.7-11.8, and 11.45-11.57). For oligonucleotide probes less than about 100 nucleotides, Sambrook et al. discloses suitable Southern blot conditions in Sections 11.45-11.46. The Tm between a sequence that is less than 100 nucleotides in length and a second sequence can be calculated using the formula provided in Section 11.46. Sambrook et al. additionally discloses prehybridization and hybridization conditions for a Southern blot that uses oligonucleotide probes greater than about 100 nucleotides (see Sections 9.47-9.52). Hybridizations with an oligonucleotide greater than 100 nucleotides generally are performed 15-25° C. below the Tm. The Tm between a sequence greater than 100 nucleotides in length and a second sequence can be calculated using the formula provided in Sections 9.50-9.51 of Sambrook et al. Additionally, Sambrook et al. recommends the conditions indicated in Section 9.54 for washing a Southern blot that has been probed with an oligonucleotide greater than about 100 nucleotides.

The conditions under which membranes containing nucleic acids are prehybridized and hybridized, as well as the conditions under which membranes containing nucleic acids are washed to remove excess and non-specifically bound probe can play a significant role in the stringency of the hybridization. For example, hybridization and washing may be carried out under conditions of low stringency, moderate stringency or high stringency. Such conditions are described, for example, in Sambrook et al. section 11.45-11.46. The conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., G/C vs. A/T nucleotide content) and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. For example, washing conditions can be made more stringent by decreasing the salt concentration in the wash solutions and/or by increasing the temperature at which the washes are performed.

The amount of hybridization can be quantitated directly on a membrane or from an autoradiograph using, for example, a PhosphorImager or a Densitometer (Molecular Dynamics, Sunnyvale, Calif.). It is understood by those of skill in the art that interpreting the amount of hybridization can be affected by, for example, the specific activity of the labeled oligonucleotide probe, the number of probe-binding sites on the target nucleic acid, and the amount of exposure of an autoradiograph or other detection medium. It will be readily appreciated that, although any number of hybridization, washing and detection conditions can be used to examine hybridization of a probe nucleic acid molecule to immobilized target nucleic acids, it is more important to examine hybridization of a probe to target nucleic acids under identical hybridization, washing, and detection conditions. Preferably, the target nucleic acids are on the same membrane. It can be appreciated by those of skill in the art that appropriate positive and negative controls should be performed with every set of amplification or hybridization reactions to avoid uncertainties related to contamination and/or non-specific annealing of oligonucleotide primers or probes.

Oligonucleotide primers or probes specifically anneal or hybridize to one or more AT or oxidoreductase nucleic acids. For amplification, a pair of oligonucleotide primers generally anneal to opposite strands of the template nucleic acid, and should be an appropriate distance from one another such that the polymerase can effectively polymerize across the region and such that the amplification product can be readily detected using, for example, electrophoresis. Oligonucleotide primers or probes can be designed using, for example, a computer program such as OLIGO (Molecular Biology Insights Inc., Cascade, Colo.) to assist in designing oligonucleotides. Typically, oligonucleotide primers are 10 to 30 or 40 or 50 nucleotides in length (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides in length), but can be longer or shorter if appropriate amplification conditions are used.

Non-limiting representative pairs of oligonucleotide primers that were used to amplify D-aminotransferase (DAT) nucleic acid molecules are shown in Tables 2-8 (SEQ ID NOs:978-1062 and 1074-1083), Table 46 (SEQ ID NOs:1084-1103) and Table 54 (SEQ ID NOs:1104-1125). The sequences shown in SEQ ID NOs:978-1062 and 1074-1083 are non-limiting examples of oligonucleotide primers that can be used to amplify AT nucleic acid molecules. Oligonucleotides in accordance with the invention can be obtained by restriction enzyme digestion of an AT or oxidoreductase nucleic acid molecules or can be prepared by standard chemical synthesis and other known techniques.

As used herein, an “isolated” nucleic acid molecule is a nucleic acid molecule that is separated from other nucleic acid molecules that are usually associated with the isolated nucleic acid molecule. Thus, an “isolated” nucleic acid molecule includes, without limitation, a nucleic acid molecule that is free of sequences that naturally flank one or both ends of the nucleic acid in the genome of the organism from which the isolated nucleic acid is derived (e.g., a cDNA or genomic DNA fragment produced by PCR or restriction endonuclease digestion). Such an isolated nucleic acid molecule is generally introduced into a vector (e.g., a cloning vector, or an expression vector) for convenience of manipulation or to generate a fusion nucleic acid molecule. In addition, an isolated nucleic acid molecule can include an engineered nucleic acid molecule such as a recombinant or a synthetic nucleic acid molecule. A nucleic acid molecule existing among hundreds to millions of other nucleic acid molecules within, for example, a nucleic acid library (e.g., a cDNA, or genomic library) or a portion of a gel (e.g., agarose, or polyacrylamine) containing restriction-digested genomic DNA is not to be considered an isolated nucleic acid.

Isolated nucleic acid molecules described herein having AT or oxidoreductase activity can be obtained using techniques routine in the art, many of which are described in the Examples herein. For example, isolated nucleic acids within the scope of the invention can be obtained using any method including, without limitation, recombinant nucleic acid technology, the polymerase chain reaction (e.g., PCR, e.g., direct amplification or site-directed mutagenesis), and/or nucleic acid hybridization techniques (e.g., Southern blotting). General PCR techniques are described, for example in PCR Primer: A Laboratory Manual, Dieffenbach & Dveksler, Eds., Cold Spring Harbor Laboratory Press, 1995. Recombinant nucleic acid techniques include, for example, restriction enzyme digestion and ligation, which can be used to isolate an AT or oxidoreductase nucleic acid molecule as described herein. Isolated nucleic acids of the invention also can be chemically synthesized, either as a single nucleic acid molecule or as a series of oligonucleotides.

Techniques for the manipulation of nucleic acids, such as, e.g., subcloning, labeling probes (e.g., random-primer labeling using Klenow polymerase, nick translation, amplification), sequencing, hybridization, amplification and the like are well described in the scientific and patent literature, see, e.g., Sambrook et al., Eds., 1989, Molecular Cloning: A Laboratory Manual (2^ndEd.), Vols 1-3, Cold Spring Harbor Laboratory; Current Protocols in Molecular Biology, 1997, Ausubel, Ed. John Wiley & Sons, Inc., New York; Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization with Nucleic Acid Probes, Part I. Theory and Nucleic Acid Preparation, Tijssen, Ed. Elsevier, N.Y. (1993).

Purified AT or oxidoreductase polypeptides, as well as polypeptide fragments having AT or oxidoreductase activity, are within the scope of the invention. AT polypeptides refer to polypeptides that catalyze a reaction between an amino group and a keto acid. Specifically, a transamination reaction by a DAT involves removing an amino group from an amino acid leaving behind an alpha-keto acid, and transferring the amino group to the reactant alpha-keto acid, thereby converting the alpha-keto acid into an amino acid. The predicted amino acid sequences of AT polypeptides are shown in SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 970, 972, 974, and 976. An oxidoreductase polypeptide refers to a polypeptide that catalyzes an oxidation-reduction reaction, and the predicted amino acid sequences of oxidoreductase polypeptides are shown in SEQ ID NOs:252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 962, 964, 966 and 968.

The term “purified” polypeptide as used herein refers to a polypeptide that has been separated from cellular components that naturally accompany it. Typically, a polypeptide is considered “purified” when it is at least partially free from the proteins and naturally occurring molecules with which it is naturally associated. The extent of enrichment or purity of an AT or oxidoreductase polypeptide can be measured using any appropriate method, e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

The invention also provides for AT and oxidoreductase polypeptides that differ in sequence from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, and 976. For example, the skilled artisan will appreciate that changes can be introduced into an AT or oxidoreductase polypeptide (e.g., SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, and 976) or in an AT or oxidoreductase nucleic acid molecule (e.g., SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975), thereby leading to changes in the amino acid sequence of the encoded polypeptide. AT and oxidoreductase polypeptides that differ in sequence from SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, and 976 and that retain aminotransferase and oxidoreductase activity, respectively, readily can be identified by screening methods routinely used in the art.

For example, changes can be introduced into an AT or oxidoreductase nucleic acid coding sequence that lead to conservative and/or non-conservative amino acid substitutions at one or more amino acid residues in the encoded AT or oxidoreductase polypeptide. Changes in nucleic acid sequences can be generated by standard techniques, such as site-directed mutagenesis, PCR-mediated mutagenesis of a nucleic acid encoding such a polypeptide, or directed evolution. In addition, changes in the polypeptide sequence can be introduced randomly along all or part of the AT or oxidoreductase polypeptide, such as by saturation mutagenesis of the corresponding nucleic acid. Alternatively, changes can be introduced into a nucleic acid or polypeptide sequence by chemically synthesizing a nucleic acid molecule or polypeptide having such changes.

A “conservative amino acid substitution” is one in which one amino acid residue is replaced with a different amino acid residue having a similar side chain. Similarity between amino acid residues has been assessed in the art. For example, Dayhoff et al. (1978, in Atlas of Protein Sequence and Structure, 5(Suppl. 3):345-352) provides frequency tables for amino acid substitutions that can be employed as a measure of amino acid similarity. Examples of conservative substitutions include, for example, replacement of an aliphatic amino acid with another aliphatic amino acid; replacement of a serine with a threonine or vice versa; replacement of an acidic residue with another acidic residue; replacement of a residue bearing an amide group with another residue bearing an amide group; exchange of a basic residue with another basic residue; or replacement of an aromatic residue with another aromatic residue. A non-conservative substitution is one in which an amino acid residue is replaced with an amino acid residue that does not have a similar side chain.

Changes in a nucleic acid can be introduced using one or more mutagens. Mutagens include, without limitation, ultraviolet light, gamma irradiation, or chemical mutagens (e.g., mitomycin, nitrous acid, photoactivated psoralens, sodium bisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid). Other mutagens are analogues of nucleotide precursors, e.g., nitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine. Intercalating agents such as proflavine, acriflavine, quinacrine and the like can also be used.

Changes also can be introduced into an AT or oxidoreductase nucleic acid and/or polypeptide by methods such as error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, gene reassembly (e.g., GeneReassembly, see, e.g., U.S. Pat. No. 6,537,776), Gene Site Saturation Mutagenesis (GSSM), synthetic ligation reassembly (SLR), or a combination thereof. Changes also can be introduced into polypeptides by methods such as recombination, recursive sequence recombination, phosphothioate-modified DNA mutagenesis, uracil-containing template mutagenesis, gapped duplex mutagenesis, point mismatch repair mutagenesis, repair-deficient host strain mutagenesis, chemical mutagenesis, radiogenic mutagenesis, deletion mutagenesis, restriction-selection mutagenesis, restriction-purification mutagenesis, artificial gene synthesis, ensemble mutagenesis, chimeric nucleic acid multimer creation, or any combination thereof.

An AT or oxidoreductase nucleic acid can be codon optimized if so desired. For example, a non-preferred or a less preferred codon can be identified and replaced with a preferred or neutrally used codon encoding the same amino acid as the replaced codon. A preferred codon is a codon over-represented in coding sequences in genes in the host cell and a non-preferred or less preferred codon is a codon under-represented in coding sequences in genes in the host cell, thereby modifying the nucleic acid to increase its expression in a host cell. An AT or oxidoreductase nucleic acid can be optimized for particular codon usage from any host cell (e.g., any of the host cells described herein). See, for example, U.S. Pat. No. 5,795,737 for a representative description of codon optimization. In addition to codon optimization, a nucleic acid can undergo directed evolution. See, for example, U.S. Pat. No. 6,361,974.

Other changes also are within the scope of this disclosure. For example, one, two, three, four or more amino acids can be removed from the carboxy- and/or amino-terminal ends of an aminotransferase or oxidoreductase polypeptide without significantly altering the biological activity. In addition, one or more amino acids can be changed to increase or decrease the pl of a polypeptide. In some embodiments, a residue can be changed to, for example, a glutamate. Also provided are chimeric aminotransferase or oxidoreductase polypeptides. For example, a chimeric AT or oxidoreductase polypeptide can include portions of different binding or catalytic domains. Methods of recombining different domains from different polypeptides and screening the resultant chimerics to find the best combination for a particular application or substrate are routine in the art.

One particular change in sequence that was exemplified herein involves the residue corresponding to residue 243 in a DAT from ATCC Accession No. 4978 (DAT 4978). In one instance, the polypeptide sequence of the SEQ ID NO:870 DAT was aligned with DAT 4978 and the residue in SEQ ID NO:870 that aligns with position 243 in DAT 4978 was identified (residue 242) and changed from Thr to Asn (SEQ ID NO:870 T242N). In another instance, the polypeptide sequence of the SEQ ID NO:220 DAT was aligned with DAT 4978 and the residue in SEQ ID NO:220 that aligns with position 243 in DAT 4978 was identified (either residue 240 or 241) and changed from Gly to Asn or Thr to Asn, respectively (SEQ ID NO:220 G240N and SEQ ID NO:220 T241N). Those of skill in the art can readily identify the residue that corresponds to residue 243 from DAT 4978 in any of the DATs disclosed herein and introduce a change into the polypeptide sequence at that particular residue. A number of additional DAT mutants were made and are listed in Tables 43 and 52.

It is noted that SEQ ID NO:894 is a novel DAT, for which the closest sequence in the public databases exhibits only 60% sequence identity to the SEQ ID NO:894 polypeptide. Therefore, polypeptides of the invention include sequences that have at least, for example, 65% sequence identity (e.g., at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity) to SEQ ID NO:894 and that have functional DAT activity. In addition, SEQ ID NO:870 also is a novel DAT and has 76% sequence identity to a Bacillus DAT polypeptide and 69% sequence identity to a B. sphaericus DAT polypeptide. Therefore, polypeptides of the invention include sequences having at least 80% sequence identity (e.g., at least 85%, 90%, 95%, or 99% sequence identity) to SEQ ID NO:870 and that have DAT activity. Further, SEQ ID NO:220 is a novel DAT that has 62% sequence identity to a DAT polypeptide from C. beijerinckii. Therefore, polypeptides of the invention include sequences having at least 65% sequence identity (e.g., at least 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity) to SEQ ID NO:220.

In one instance, SEQ ID NO:870 and 910 were aligned with published DATs and a consensus sequence was determined. The consensus sequence for SEQ ID NO:870-like DAT polypeptides that make it unique from the rest of the group of Bacillus-like DAT polypeptides is shown in SEQ ID NO:1069 (consensus sequence A). In another instance, SEQ ID NO:176, 220, 892, 894 and 946 were aligned and a consensus sequence was determined. The consensus sequence for this group of DATs is shown in SEQ ID NO:1071 (consensus sequence C). SEQ ID NO:1070 (consensus sequence B) represents a slightly more conservative consensus sequence relative to SEQ ID NO:1069 (consensus sequence A), while SEQ ID NO:1072 (consensus sequence D) and SEQ ID NO:1073 (consensus sequence E) correspond to slightly more conservative consensus sequences relative to SEQ ID NO:1071 (consensus sequence C). It is expected that polypeptides having a consensus sequence that corresponds to consensus sequence A, B, C, D or E as disclosed herein would exhibit DAT activity.

A fragment of an aminotransferase and oxidoreductase nucleic acid or polypeptide refers to a portion of a full-length aminotransferase and oxidoreductase nucleic acid or polypeptide. As used herein, “functional fragments” are those fragments of an aminotransferase or oxidoreductase polypeptide that retain the respective enzymatic activity. “Functional fragments” also refer to fragments of an aminotransferase or oxidoreductase nucleic acid that encode a polypeptide that retains the respective anzymatic activity. For example, functional fragments can be used in in vitro or in vivo reactions to catalyze transaminase or oxidation-reduction reactions, respectively.

AT or oxidoreductase polypeptides can be obtained (e.g., purified) from natural sources (e.g., a biological sample) by known methods such as DEAE ion exchange, gel filtration, and hydroxyapatite chromatography. Natural sources include, but are not limited to, microorganisms such as bacteria and yeast. A purified AT or oxidoreductase polypeptide also can be obtained, for example, by cloning and expressing an AT or oxidoreductase nucleic acid (e.g., SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 557, 559, 561, 563, 565, 567, 569, 571, 573, 575, 577, 579, 581, 583, 585, 587 589, 591, 593, 595, 597, 599, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 671, 673, 675, 677, 679, 681, 683, 685, 687, 689, 691, 693, 695, 697, 699, 701, 703, 705, 707, 709, 711, 713, 715, 716, 719, 721, 723, 725, 727, 729, 731, 733, 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831, 833, 835, 837, 839, 841, 843, 845, 847, 849, 851, 853, 855, 857, 859, 861, 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921, 923, 925, 927, 929, 931, 933, 935, 937, 939, 941, 943, 945, 947, 949, 951, 953, 955, 957, 959, 961, 963, 965, 967, 969, 971, 973, and 975) and purifying the resultant polypeptide using, for example, any of the known expression systems including, but not limited to, glutathione S-transferase (GST), pGEX (Pharmacia Biotech Inc), pMAL (New England Biolabs, Beverly, Mass.) or pRIT5 (Pharmacia, Piscataway, N.J.)). In addition, a purified AT or oxidoreductase polypeptide can be obtained by chemical synthesis using, for example, solid-phase synthesis techniques (see e.g., Roberge, 1995, Science, 269:202; Merrifield, 1997, Methods Enzymol., 289:3-13).

A purified AT or oxidoreductase polypeptide or a fragment thereof can be used as an immunogen to generate polyclonal or monoclonal antibodies that have specific binding affinity for one or more AT or oxidoreductase polypeptides. Such antibodies can be generated using standard techniques that are used routinely in the art. Full-length AT or oxidoreductase polypeptides or, alternatively, antigenic fragments of AT or oxidoreductase polypeptides can be used as immunogens. An antigenic fragment of an AT or oxidoreductase polypeptide usually includes at least 8 (e.g., 10, 15, 20, or 30) amino acid residues of an AT or oxidoreductase polypeptide (e.g., having the sequence shown in SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, SEQ ID NO:220 having one or more of the mutations shown in Table 43 or Table 52, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, 848, 850, 852, 854, 856, 858, 860, 862, 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922, 924, 926, 928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, 950, 952, 954, 956, 958, 960, 962, 964, 966, 968, 970, 972, 974, and 976), and encompasses an epitope of an AT or oxidoreductase polypeptide such that an antibody (e.g., polyclonal or monoclonal; chimeric or humanized) raised against the antigenic fragment has specific binding affinity for one or more AT or oxidoreductase polypeptides.

Polypeptides can be detected and quantified by any method known in the art including, but not limited to, nuclear magnetic resonance (NMR), spectrophotometry, radiography (protein radiolabeling), electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, various immunological methods, e.g. immunoprecipitation, immunodiffusion, immuno-electrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immuno-fluorescent assays, gel electrophoresis (e.g., SDS-PAGE), staining with antibodies, fluorescent activated cell sorter (FACS), pyrolysis mass spectrometry, Fourier-Transform Infrared Spectrometry, Raman spectrometry, GC-MS, and LC-Electrospray and cap-LC-tandem-electrospray mass spectrometries, and the like. Novel bioactivities can also be screened using methods, or variations thereof, described in U.S. Pat. No. 6,057,103. Furthermore, one or more, or, all the polypeptides of a cell can be measured using a protein array.

Methods of Using DAT or Oxidoreductase Nucleic Acids and Polypeptides

The AT or oxidoreductase polypeptides or the AT or oxidoreductase nucleic acids encoding such AT and oxidoreductase polypeptides, respectively, can be used to facilitate the conversion of tryptophan to indole-3-pyruvate and/or to facilitate the conversion of MP to monatin (or the reverse reaction). It is noted that the reactions described herein are not limited to any particular method, unless otherwise stated. The reactions disclosed herein can take place, for example, in vivo, in vitro, or a combination thereof.

Constructs containing AT or oxidoreductase nucleic acid molecules are provided. Constructs, including expression vectors, suitable for expressing an AT or oxidoreductase polypeptide are commercially available and/or readily produced by recombinant DNA technology methods routine in the art. Representative constructs or vectors include, without limitation, replicons (e.g., RNA replicons, bacteriophages), autonomous self-replicating circular or linear DNA or RNA, a viral vector (e.g., an adenovirus vector, a retroviral vector or an adeno-associated viral vector), a plasmid, a phage, a phagemid, a cosmid, a fosmid, a bacteriophage or an artificial chromosome. The cloning vehicle can comprise an artificial chromosome comprising a bacterial artificial chromosome (BAC), a bacteriophage P1-derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome (MAC). Exemplary vectors include, without limitation, pBR322 (ATCC 37017), pKK223-3, pSVK3, pBPV, pMSG, and pSVL (Pharmacia Fine Chemicals, Uppsala, Sweden), GEM1 (Promega Biotec, Madison, Wis., USA) pQE70, pQE60, pQE-9 (Qiagen), pD10, psiX174 pBluescript II KS, pNH8A, pNH16a, pNH18A, pNH46A, pSV2CAT, pOG44, pXT1, pSG (Stratagene), ptrc99a, pKK223-3, pKK233-3, DR540, pRIT5 (Pharmacia), pKK232-8 and pCM7. See, also, U.S. Pat. No. 5,217,879 for a description of representative plasmids, viruses, and the like.

A vector or construct containing an AT or oxidoreductase nucleic acid molecule can have elements necessary for expression operably linked to the AT or oxidoreductase nucleic acid. Elements necessary for expression include nucleic acid sequences that direct and regulate expression of nucleic acid coding sequences. One example of an element necessary for expression is a promoter sequence. Promoter sequences are sequences that are capable of driving transcription of a coding sequence. A promoter sequence can be, for example, an AT or oxidoreductase promoter sequence, or a non-AT or non-oxidoreductase promoter sequence. Non-AT and non-oxidoreductase promoters include, for example, bacterial promoters such as lacZ, T3, T7, gpt, lambda PR, lambdaPL and trp as well as eukaryotic promoters such as CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein I. Promoters also can be, for example, constitutive, inducible, and/or tissue-specific. A representative constitutive promoter is the CaMV 35S; representative inducible promoters include, for example, arabinose, tetracycline-inducible and salicylic acid-responsive promoters.

Additional elements necessary for expression can include introns, enhancer sequences (e.g., an SV40 enhancer), response elements, or inducible elements that modulate expression of a nucleic acid. Elements necessary for expression can include a leader or signal sequence. See, for example, SEQ ID NO:156, which is a DAT polypeptide having a leader sequence. Elements necessary for expression also can include, for example, a ribosome binding site for translation initiation, splice donor and acceptor sites, and a transcription terminator. Elements necessary for expression can be of bacterial, yeast, insect, mammalian, or viral origin, and vectors or constructs can contain a combination of elements from different origins. Elements necessary for expression are described, for example, in Goeddel, 1990, Gene Expression Technology: Methods in Enzymology, 185, Academic Press, San Diego, Calif.

A vector or construct as described herein further can include sequences such as those encoding a selectable marker (e.g., genes encoding dihydrofolate reductase or genes conferring neomycin resistance for eukaryotic cells; genes conferring tetracycline or ampicillin resistance for E. coli; and the gene encoding TRP1 for S. cerevisiae), sequences that can be used in purification of an AT or oxidoreductase polypeptide (e.g., 6×His tag), and one or more sequences involved in replication of the vector or construct (e.g., origins of replication). In addition, a vector or construct can contain, for example, one or two regions that have sequence homology for integrating the vector or construct. Vectors and constructs for genomic integration are well known in the art.

As used herein, operably linked means that a promoter and/or other regulatory element(s) are positioned in a vector or construct relative to an AT or oxidoreductase nucleic acid in such a way as to direct or regulate expression of the AT or oxidoreductase nucleic acid. Generally, promoter and other elements necessary for expression that are operably linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. Some transcriptional regulatory sequences such as enhancers, however, need not be physically contiguous or located in close proximity to the coding sequences whose expression they enhance.

Also provided are host cells. Host cells generally contain a nucleic acid sequence of the invention, e.g., a sequence encoding an AT or an oxidoreductase, or a vector or construct as described herein. The host cell may be any of the host cells familiar to those skilled in the art such as prokaryotic cells or eukaryotic cells including bacterial cells, fungal cells, yeast cells, mammalian cells, insect cells, or plant cells. Exemplary bacterial cells include any species within the genera Escherichia, Bacillus, Streptomyces, Salmonella, Pseudomonas and Staphylococcus, including, e.g., E. coli, L. lactis, B. subtilis, B. cereus, S. typhimurium, P. fluorescens. Exemplary fungal cells include any species of Aspergillus, and exemplary yeast cells include any species of Pichia, Saccharomyces, Schizosaccharomyces, or Schwanniomyces, including P. pastoris, S. cerevisiae, or S. pombe. Exemplary insect cells include any species of Spodoptera or Drosophila, including Drosophila S2 and Spodoptera Sf9. Exemplary animal cells include CHO, COS, Bowes melanoma, C127, 3T3, HeLa and BHK cell lines. See, for example, Gluzman, 1981, Cell, 23:175. The selection of an appropriate host is within the abilities of those skilled in the art.

Techniques for introducing nucleic acid into a wide variety of cells are well known and described in the technical and scientific literature. A vector or construct can be introduced into host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer. Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis et al., 1986, Basic Methods in Molecular Biology). Exemplary methods include CaPO₄precipitation, liposome fusion, lipofection (e.g., LIPOFECTIN™), electroporation, viral infection, etc. The AT or oxidoreductase nucleic acids may stably integrate into the genome of the host cell (for example, with retroviral introduction) or may exist either transiently or stably in the cytoplasm (i.e. through the use of traditional plasmids, utilizing standard regulatory sequences, selection markers, etc.).

The content of host cells usually is harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. Microbial cells employed for expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or the use of cell lysing agents. Such methods are well known to those skilled in the art. The expressed polypeptide or fragment thereof can be recovered and purified from cell cultures by methods including, but not limited to, precipitation (e.g., ammonium sulfate or ethanol), acid extraction, chromatography (e.g., anion or cation exchange, phosphocellulose, hydrophobic interaction, affinity, hydroxylapatite and lectin). If desired, high performance liquid chromatography (HPLC) can be employed for final purification steps.

Cell-free translation systems can also be employed to produce a polypeptide of the invention. Cell-free translation systems can use mRNAs transcribed from a DNA construct comprising a promoter operably linked to a nucleic acid encoding the polypeptide or fragment thereof. In some aspects, the DNA construct may be linearized prior to conducting an in vitro transcription reaction. The transcribed mRNA is then incubated with an appropriate cell-free translation extract, such as a rabbit reticulocyte extract, to produce the desired polypeptide or fragment thereof.

An AT or oxidoreductase polypeptide, a fragment, or a variant thereof can be assayed for activity by any number of methods. Methods of detecting or measuring the activity of an enzymatic polypeptide generally include combining a polypeptide, fragment or variant thereof with an appropriate substrate and determining whether the amount of substrate decreases and/or the amount of product or by-product increases. The substrates used to evaluate the activity of DATs disclosed herein typically were tryptophan and/or R-MP, and the products were indole-3-pyruvate and/or R,R-monatin. In addition to a tryptophan or MP substrate, it is expected that polypeptides disclosed herein also will utilize substituted tryptophan and/or MP substrates such as, without limitation, chlorinated tryptophan or 5-hydroxytryptophan. In addition, a by-product of the conversion of MP to monatin (e.g., 4-hydroxy-4-methyl glutamic acid (HMG)) can be monitored or measured.

Methods for evaluating AT activity are described, for example, in Sugio et al., 1995, Biochemistry, 34:9661-9669; Ro et al., 1996, FEBS Lett., 398:141-145; or Gutierrez et al., 2000, Eur. J. Biochem., 267, 7218-7223. In addition, methods for evaluating dehydrogenase activity are described, for example, in Lee et al., 2006, AEM, 72(2):1588-1594; and Mayer, 2002, J. Biomolecular Screening, 7(2):135-140. In addition, methods of evaluating candidate polypeptides for DAT activity are described in Part A and Part B of the Example section herein. For the purposes of determining whether or not a polypeptide falls within the scope of the invention, the methods described in Part B of the Example section are employed.

Typically, an AT or oxidoreductase polypeptide exhibits activity in the range of between about 0.05 to 20 units (e.g., about 0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 19.5 or more units). As used herein, a unit equals one μmol of product released per minute per mg of enzyme. In one embodiment, one unit of activity for an AT polypeptide is one μmol of alpha-keto acid or ketone produced per minute per mg of enzyme (formed from the respective alpha-amino acid or amine). In an alternative embodiment, one unit of activity for an aminotransferase polypeptide is one μmol of alpha-amino acid or amine produced per minute per mg of enzyme (formed from the respective alpha-keto acid or ketone).

The conversion of tryptophan to indole-3-pyruvate or the conversion of MP to monatin using one or more of the AT or oxidoreductase nucleic acids or polypeptides disclosed herein can be performed in vitro or in vivo, in solution or in a host cell, in series or in parallel. When one or more reactions are performed in vitro, the desired ingredients for the reaction(s) can be combined by admixture in an aqueous reaction medium or solution and maintained for a period of time sufficient for the desired product(s) to be produced. Alternatively, one or more AT or oxidoreductase polypeptides used in the one or more of the reactions described herein can be immobilized onto a solid support. Examples of solid supports include those that contain epoxy, aldehyde, chelators, or primary amine groups. Specific examples of suitable solid supports include, but are not limited to, Eupergit® C (Rohm and Haas Company, Philadelphia, Pa.) resin beads and SEPABEADS® EC-EP (Resindion).

To generate indole-3-pyruvate from typtophan or monatin from MP in vivo, an AT or oxidoreductase nucleic acid (e.g., an expression vector) can be introduced into any of the host cells described herein. Depending upon the host cell, many or all of the co-factors (e.g., a metal ion, a co-enzyme, a pyridoxal-phosphate, or a phosphopanthetheine) and/or substrates necessary for the conversion reactions to take place can be provided in the culture medium. After allowing the in vitro or in vivo reaction to proceed, the efficiency of the conversion can be evaluated by determining whether the amount of substrate has decreased or the amount of product has increased.

In some embodiments, the activity of one or more of the AT or oxidoreductase polypeptides disclosed herein can be improved or optimized using any number of strategies known to those of skill in the art. For example, the in vivo or in vitro conditions under which one or more reactions are performed such as pH or temperature can be adjusted to improve or optimize the activity of a polypeptide. In addition, the activity of a polypeptide can be improved or optimized by re-cloning the AT or oxidoreductase nucleic acid into a different vector or construct and/or by using a different host cell. For example, a host cell can be used that has been genetically engineered or selected to exhibit increased uptake or production of tryptophan (see, for example, U.S. Pat. No. 5,728,555). Further, the activity of an AT or oxidoreductase polypeptide can be improved or optimized by ensuring or assisting in the proper folding of the polypeptide (e.g., by using chaperone polypeptides) or in the proper post-translational modifications such as, but not limited to, acetylation, acylation, ADP-ribosylation, amidation, glycosylation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, phosphorylation, prenylation, selenoylation, sulfation, disulfide bond formation, and demethylation as well as covalent attachment of molecules such as flavin, a heme moiety, a nucleotide or nucleotide derivative, a lipid or lipid derivative, and/or a phosphytidylinositol. In addition, the solubility of a polypeptide can be increased using any number of methods known in the art such as, but not limited to, low temperature expression or periplasmic expression.

A number of polypeptides were identified herein that exhibit DAT activity using tryptophan and/or MP as a substrate. Specifically, SEQ ID NO:950, 946, 948, 892, 894, 866, 870, 870 T242N, 872, 874, 878, 880, 882, 884, 902, 910, 918, 176, 178, 154, 220, 156, 216, 238, 224, 230, 232, 214, CbDAT, CaDAT and LsDAT exhibit DAT activity. Notably, SEQ ID NO:946, 892, 894, 220, 176, 1064, 1066 and 1068 exhibited very high activity under the conditions described in Part B of the Examples. It is noted that SEQ ID NO:220 and 894 produced low levels of the HMG by-product during the conversion of MP to monatin.

Use of Aminotransferase or Oxidoreductase Nucleic Acids or Polypeptides in the Production of Monatin

One or more of the DAT polypeptides disclosed herein can be used in the production of monatin. Monatin is a high-intensity sweetener having the chemical formula:

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Monatin includes two chiral centers leading to four potential stereoisomeric configurations. The R,R configuration (the “R,R stereoisomer” or “R,R monatin”); the S,S configuration (the “S,S stereoisomer” or “S,S monatin”); the R,S configuration (the “R,S stereoisomer” or “R,S monatin”); and the S,R configuration (the “S,R stereoisomer” or “S,R monatin”). As used herein, unless stated otherwise, the term “monatin” is used to refer to compositions including all four stereoisomers of monatin, compositions including any combination of monatin stereoisomers, (e.g., a composition including only the R,R and S,S, stereoisomers of monatin), as well as a single isomeric form (or any of the salts thereof). Due to various numbering systems for monatin, monatin is known by a number of alternative chemical names, including: 2-hydroxy-2-(indol-3-ylmethyl)-4-aminoglutaric acid; 4-amino-2-hydroxy-2-(1H-indol-3-ylmethyl)-pentanedioic acid; 4-hydroxy-4-(3-indolylmethyl)glutamic acid; and, 3-(1-amino-1,3-dicarboxy-3-hydroxy-but-4-yl)indole.

Methods of producing various stereoisomers of monatin (e.g., R,R monatin) are disclosed in, for example, WO 07/133,183 and WO 07/103,389. One or more of the DAT polypeptides disclosed herein, in the presence of tryptophan, can be used in methods known to those of skill in the art to make a monatin composition. As disclosed in both WO 07/133,183 and WO 07/103,389, the conversion of indole-3-pyruvate (or derivatives thereof; see, for example, WO 07/103,389) to 2-hydroxy 2-(indol-3-ylmethyl)-4-keto glutaric acid (“monatin precursor” or “MP”) dictates the first chiral center of monatin, while the conversion of MP to monatin dictates the second chiral center. In on embodiment, one or more of the conversions required to produce monatin is catalyzed by more than one enzyme, for example, a mixture of enzymes, so that the resulting composition or preparation contains a desired percentage (e.g., minimum and/or maximum) of one or more of the monatin stereoisomers (e.g., R,R monatin). Alternatively, monatin made by two separate engineered pathways according to the methods of the invention be combined to produce a composition or preparation containing such desired percentage of each monatin stereoisomer(s).

Monatin that is produced utilizing one or more of the AT polypeptides disclosed herein can be at least about 0.5-30% R,R-monatin by weight of the total monatin produced. In other embodiments, the monatin produced using one or more of the polypeptides or biosynthetic pathways disclosed herein, is greater than 30% R,R-monatin, by weight of the total monatin produced; for example, the R,R-monatin is 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% of the total monatin produced. Alternatively, various amounts of two or more preparations of monatin can be combined so as to result in a preparation that is a desired percentage of R,R-monatin. For example, a monatin preparation that is 30% R,R-monatin can be combined with a monatin preparation that is 90% R,R-monatin; if equal amounts of 30% and 90% R,R-monatin preparations are combined, the resulting monatin preparation would be 60% R,R-monatin.

Monatin produced using one or more of the DAT polypeptides disclosed herein can be for example, a derivative. “Monatin derivatives” have the following structure:

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wherein, R_a, R_b, R_c, R_d, and R_eeach independently represent any substituent selected from a hydrogen atom, a hydroxyl group, a C₁-C₃alkyl group, a C₁-C₃alkoxy group, an amino group, or a halogen atom, such as an iodine atom, bromine atom, chlorine atom, or fluorine atom. However, R_a, R_b, R_c, R_d, and R_ecannot simultaneously all be hydrogen. Alternatively, R_band R_c, and/or R_dand R_emay together form a C₁-C₄alkylene group, respectively. “Substituted monatin” refers to, for example, halogenated or chlorinated monatin or monatin derivatives. See, for example, U.S. Publication No. 2005/0118317.

Monatin derivatives also can be used as sweeteners. For example, chlorinated D-tryptophan, particularly 6-chloro-D-tryptophan, which has structural similarities to R,R monatin, has been identified as a non-nutritive sweetener. Similarly, halogenated and hydroxy-substituted forms of monatin have been found to be sweet. See, for example, U.S. Publication No. 2005/0118317. Substituted indoles have been shown in the literature to be suitable substrates for PLP-enzymes and have yielded substituted tryptophans. See, for example, Fukuda et al., 1971, Appl. Environ. Microbiol., 21:841-43. The halogen does not appear to sterically hinder the catalytic mechanism or the enantiospecificity of the enzyme. Therefore, halogens and hydroxyl groups should be substitutable for hydrogen, particularly on positions 1-4 of the benzene ring in the indole of tryptophan, without interfering in subsequent conversions to D- or L-tryptophan, indole-3-pyruvate, MP, or monatin.

One or more of the DAT polypeptides disclosed herein, with or without one or more additional polypeptides, can be used in the production of monatin. A DAT polypeptide (or nucleic acid molecule encoding such a DAT polypeptide) can be used in the conversion of tryptophan to indole-3-pyruvic acid (in the presence of an amino acceptor) and in the conversion of MP to monatin. The intermediate step between those two reactions is the conversion of indole-3-pyruvic acid to MP, which requires the presence of a C3 carbon source such as pyruvate, oxaloacetate or serine. The use of a DAT polypeptide in the conversion step from MP to monatin results in the R configuration at the second chiral center. It is noted that SEQ ID NO:946, 950, 220 and 948 produced high amounts of R,R monatin.

The conversion of indole-3-pyruvate (or indole-3-pyruvic acid) to MP can occur in the absence of an enzyme (i.e., an aldol condensation), but also can be facilitated by a polypeptide. The chirality at the first chiral center is determined by the enantiospecificity of the reaction converting indole-3-pyruvate to MP. If the MP formation reaction is not facilitated by an enzyme, a racemic mixture of R-MP and S-MP is typically formed in the absence of a chiral auxiliary. Enzymes that facilitate the conversion of indole-3-pyruvate to MP include, for example, a synthase/lyase (EC 4.1.3.- and 4.1.2.-), specifically those in classes EC 4.1.3.16 and EC 4.1.3.17. These classes include carbon-carbon synthases/lyases, such as aldolases that catalyze the condensation of two carboxylic acid substrates. Enzyme class EC 4.1.3.- are those synthases/lyases that form carbon-carbon bonds utilizing oxo-acid substrates (such as indole-3-pyruvate) as the electrophile, while EC 4.1.2.- are synthases/lyases that form carbon-carbon bonds utilizing aldehyde substrates (such as benzaldehyde) as the electrophile. For example, KHG aldolase (EC 4.1.3.16) and HMG aldolase (EC 4.1.3.17), are known to convert indole-3-pyruvate and pyruvate to MP. Herein, the term HMG aldolase is used to mean any polypeptide with 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity. Suitable examples of HMG aldolases include Comamonas testosteroni ProA and Sinorhizobium meliloti ProA (NCBI Accession No. CAC46344).

When one or more of the conversion reactions in the pathway to producing monatin are to be performed in vivo, a person of ordinary skill in the art may optimize production of monatin in a microorganism, including R,R monatin, by various routine methods. Such a microorganism can be one that naturally is better than other microorganisms in one or more of the following characteristics, or that has been modified to exhibit one or more of the following characterisitics, which typically result in improved production of monatin (relative to the microorganism before such modification). Such characteristics include, without limitation, an increase in the ability of a microorganism to take-up tryptophan (e.g., D-tryptophan); an increase in the ability of a microorganism to take-up indole-3-pyruvate; a decrease in the ability of a microorganism to secrete indole-3-pyruvate; a decrease in the amount of degradation of indole-3-pyruvate in the microorganism; and/or a decrease in the toxicity of D-tryptophan to a microorganism. Such characteristics and strategies for obtaining microorganisms exhibiting one or more such characteristics are described in, for example, WO 07/133,183 and WO 07/103,389.

Monatin, or an intermediate of the tryptophan to monatin biosynthetic pathway (including indole-3-pyruvate and MP) produced using one or more of the AT or oxidoreductase polypeptides disclosed herein can be purified from the components of the reaction. In one embodiment, the monatin or an intermediate can be purified simply by removing the substance that is to be purified from the enzyme preparation in which it was synthesized. In other embodiments, monatin or an intermediate is purified from a preparation in which it was synthesized so that the resulting “purified” composition or preparation is at least about 5-60% monatin by weight of total organic compounds. In another embodiment, the monatin or an intermediate can be purified to a degree of purity of at least about 70%, 80%, 90%, 95% or 99% by weight of total organic compounds. The monatin produced using one or more of the polypeptides or biosynthetic pathways disclosed herein can be purified from the components of the reaction by any method known to a person of ordinary skill in the art (e.g., repeatedly recrystallization).

In accordance with the present invention, there may be employed conventional molecular biology, microbiology, biochemical, and chemical techniques within the skill of the art. Such techniques are explained fully in the literature. The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

The aminotransferases and oxidoreductases described herein were obtained using a selection strategy. In this selection strategy, environmental DNA libraries were constructed in a bacterial host strain that exhibits L-tryptophan auxotrophy. Library clones were innoculated onto media containing D-tryptophan (but lacking L-tryptophan). The only clones that could grow are those that expressed a gene on one of the discrete environmental DNA fragments that encoded an enzyme active on D-tryptophan. For example, clones were identified that expressed an active tryptophan racemase and were able to convert D-tryptophan to L-tryptophan. Additionally, clones were identified that expressed an oxidoreductase (such as an amino acid oxidase or a dehydrogenase) that could convert D-tryptophan to an intermediate that the host cell could, in turn, convert to L-tryptophan. In the case of oxidoreductases such as amino acid oxidases and dehydrogenases, one such intermediate is indole-3-pyruvate.

The Examples in Part A describe the methodologies used for initial characterization of the candidate DAT and oxidoreductase nucleic acids and the encoded polypeptides. Further characterization of particular nucleic acids and polypeptides is described in Part B.

Part A
Example 1
Growth and Assay Procedures #1

Enzyme Preparation

Glycerol stocks were used to inoculate flasks containing 50 mL of LB medium with the appropriate antibiotic. The starter cultures were grown overnight at 37° C. with shaking at 230 rpm and the OD_600nmwas checked. The starter culture was used to inoculate 400 mL to OD_600nmof 0.05. The culture was incubated at 37° C. with shaking at 230 rpm.

Cultures were induced with 1 mM IPTG when the OD_600nm, was between 0.5 and 0.8 and incubated at 30° C. and 230 rpm overnight. Cultures were harvested by pelleting cells by centrifugation at 4000 rpm for 15 minutes. The supernatant was poured off and the pellet was either frozen for later use or resuspended in 20 mL of 50 mM sodium phosphate buffer (pH 7.5) supplemented with 26 U/mL of DNAse and lysed using a microfluidizer (Microfluidics Corporation, Newton, Mass.) per the manufacturer's instructions. The clarified lysate was collected and centrifuged at 11,000 rpm for 30 minutes. The supernatant was collected in a clean tube and filtered through a 0.2 μm filter. Five mL aliquots of the clarified lysate were placed in a vial and freeze-dried using a lyophilizer (Virtis Company, Gardinier, N.Y.) per the manufacturer's instructions. Approximately 1 mL of the clarified lysate was retained for protein quantitation using the Bio-Rad Protein Assay Reagent (Bio-Rad, Hercules, Calif.) and SDS-PAGE analysis. Then, the amount of protein in each lyophilized sample was calculated.

Activity Assay

Enzymes for activity assays were prepared in 50 mM sodium phosphate pH 7.5. DAT assays were usually performed using approximately 1 mg/mL total protein.

DAT Assay Using RR-Monatin Substrate

Twenty-five mM RR-monatin, 25 mM pyruvic acid sodium salt, 0.08 mM PLP, 90 mM sodium phosphate pH 8.0 and 0.8 mg/mL DAT (total protein) prepared as described above (under ‘Enzyme Preparation’ section) were combined and incubated at 30° C. at 300 rpm. At various timepoints (generally 0, 2, 4, and 24 hours), 50 μL of the reaction product was transferred to 150 μL of ice cold acetonitrile, and the sample vortexed for 30 seconds. Samples were centrifuged at 13,200 rpm for 10 minutes at 4° C., and the supernatant was passed through a 0.45 μm filter. The filtrate was diluted 10-fold in methanol, and samples were analyzed by LC/MS/MS to monitor the D-alanine formed (described in this Example below under ‘LC/MS/MS method for detecting D-alanine or R,R-monatin’ section).

DAT Assay Using Tryptophan Substrate

Ten mM D-tryptophan, 25 mM pyruvic acid sodium salt, 0.08 mM PLP, 90 mM sodium phosphate pH 8.0, and 0.8 mg/mL DAT (total protein) prepared as described above (under ‘Enzyme Preparation’ section) were combined and incubated at 30° C. and 300 rpm. At timepoints (generally 0, 2, 4, and 24 hours), 50 μL of the reaction product was transferred to 150 μL of ice cold acetonitrile, vortexed for 30 seconds, and centrifuged at 13,200 rpm for 10 minutes at 4° C. The supernatant was passed through a 0.45 μm filter and the filtrate was diluted 10-fold in methanol. Samples were analyzed by LC/MS/MS to monitor the D-alanine formed (described in this Example below under ‘LC/MS/MS method for detecting D-alanine or R,R-monatin’ section).

LC/MS/MS Method for Detecting D-Alanine or R,R-Monatin

LC/MS/MS screening was achieved by injecting samples from 96-well plates using a CTCPal auto-sampler (LEAP Technologies, Carrboro, N.C.) into a 30/70H₂O/Acn (0.1% formic acid) mixture provided by LC-10ADvp pumps (Shimadzu, Kyoto, Japan) at 1.0 mL/min through a Zorbax Eclipse XDB-C8 (2.1×50 mm) column and into the API4000 TurboIon-Spray triple-quad mass spectrometer (Applied Biosystems, Foster City, Calif.).

Ion spray and Multiple Reaction Monitoring (MRM) were performed for the analytes of interest in the positive ion mode. alanine: parent/daughter ions: 90.12/44.25 monatin: parent/daughter ions: 293.11/130.15.

Example 2
Activity of DATs Using Assay Procedures #1

The vector pSE420-cHis is a derivative of pSE420 (Invitrogen, Carlsbad, Calif.). For pSE420-cHis, the vector was cut with NcoI and Hind III, and ligated with C-His. C-His: 5′-CCA TGG GAG GAT CCA GAT CTC ATC ACC ATC ACC ATC ACT AAG CTT (SEQ ID NO:977). The expression of the His-tag in this vector depends on the choice of host and stop codon. That is, if a TAG stop codon and a supE host are used, the His-tag is expressed; if a TAG stop codon and a non supE host are used, the His-tag is not expressed. Unless indicated otherwise, the His-tag was not expressed in these experiments.

The DAT subclones were in the pSE420-cHis vector/E. coli HMS174 host (Novagen, San Diego, Calif.) with the exception of the following subclones: SEQ ID NO:930, 932, 936 were in the pET101 D-Topo vector/BL21Star(DE3) host (Invitrogen, Carlsbad, Calif.); SEQ ID NO:934 was in the pET101 D-Topo vector/BL21 Codon PlusRIL host (Stratagene, La Jolla, Calif.); SEQ ID NO:938, 942, 944, 946 were in the pSE420 vector/XL1Blue host (Stratagene, La Jolla, Calif.); SEQ ID NO:940, 948, 950, 962 and 966 were in the pSE420-c-His vector/XL1Blue host (Stratagene, La Jolla, Calif.); and SEQ ID NO:928 was in the pQET1 vector/M15pREP4 host (pQET1 described in U.S. Pat. Nos. 5,814,473 and 6,074,860; M15pREP4 from Qiagen; Valencia, Calif.).

The subclones were grown, lysed and lyophilized according to the procedures described in Example 1. Samples were tested for activity on R,R-monatin as well as D-tryptophan (as described in Example 1). For the monatin DAT assay, DATs were incubated with 25 mM R,R-monatin, 25 mM pyruvic acid sodium salt, and 0.08 mM PLP (pH 8) at 30° C. For the D-tryptophan DAT assay, DATs were incubated with 10 mM D-tryptophan, 25 mM pyruvic acid sodium salt, and 0.08 mM PLP (pH 8) at 30° C. All DATs were loaded at 0.8 mg/mL total protein in both assays.

At indicated timepoints, 50 μL of the reaction product was added to 150 μL of ice-cold acetonitrile. Samples were vortexed for 30 seconds and the supernatant was then diluted ten-fold in methanol. Samples were then analyzed by LC/MS/MS (as described in Example 1) to monitor the D-alanine formed. The tables below show the D-aminotransferase activity on both substrates.

TABLE 1

Activity of D-aminotransferase subclones

on R,R-monatin and D-tryptophan

Activity on
Activity on

R,R-monatin
D-tryptophan

μg/mL D-alanine
μg/mL D-alanine

formed at
formed at
Relative

SEQ ID NO:
indicated hour
indicated hour
Expression

928
30@24 hr
NT
+

938
122@24 hr
NT
++

940
5@24 hr
NT
ND

942
12@24 hr
NT
ND

944
75@24 hr
NT
ND

946
39@24 hr
NT
ND

948
200@0.5 hr
441@0.5 hr
ND

950
75@0.5 hr
452@0.5 hr
ND

962
NT
NT
+

964
7@24 hr
ND@24 hr
++

966
NT
NT
++

968
6.7@24 hr
52@24 hr
+++

886 (expressed in
NT
NT
++

XL1Blue cells)

886 (expressed in
15.4@24 hr
143@24 hr
+++

E. coli

HMS174 cells)

NT, not tested;

ND, not detected under conditions used;

+, low expression,

++, moderate expression,

+++, high expression

Activity on
Activity on

R,R-monatin
D-tryptophan

μg/mL D-alanine
μg/mL D-alanine

formed at
formed at
Relative

Subclone name
indicated hour
indicated hour
Expression

888 (expressed in
NT
NT
++

XL1 Blue cells)

888 (expressed in
7@24 hr
317@24 hr
+++

HMS174 cells)

890 (expressed in
NT
NT
++

XL1 Blue cells)

890 (expressed in
54@24 hr
278@24 hr
+++

HMS174 cells)

892 (expressed in
NT
NT
+

XL1 Blue cells)

892 (expressed in
113@24 hr
<5@24 hr
++

HMS174 cells)

894 (expressed in
NT
NT
ND

XL1 Blue cells)

894 (expressed in
16@24 hr
116@24 hr
+

HMS174 cells)

866
28@24 hr
NT
+++

868
<1@24 hr
NT
+++

970
10.8@24 hr
NT
+

870
123.5@24 hr
NT
+++

872
62.3@24 hr
NT
+++

874
46.5@24 hr
NT
+++

876
44@24 hr
NT
++

878
37@24 hr
NT
+++

972
<5@24 hr
NT
+

880
72.4@24 hr
79.6@24 hr
+

882
158.8@24 hr
344@2 hr
+++

884
290@24 hr
363@2 hr
++

896
54@24 hr
450@2 hr
+++

898
466@24 hr
300@24 hr
+

900
135@24 hr
154@24 hr
+

902
280@24 hr
130@24 hr
++

904
170@24 hr
140@24 hr
+

906
700@24 hr
500@24 hr
+++

908
55@24 hr
45@24 hr
+ insoluble

910
384@24 hr
240@24 hr
+++

912
NT
NT
ND

914
NT
NT
ND

916
NT
NT
ND

918
NT
NT
ND

920
NT
NT
ND

922
NT
NT
ND

924
NT
NT
ND

926
NT
NT
ND

974 (expressed in
NT
NT
ND

HMS174 cells)

974 (expressed in
NT
NT
ND

XL1 Blue cells)

930
NT
NT
ND

932
NT
NT
ND

934
NT
NT
ND

936
NT
NT
ND

976 (expressed in
NT
<5@24 hr
++

LX1 Blue cells)

NT, not tested;

ND, not detected;

+, low expression;

++, moderate expression;

+++, high expression

It should be noted that there are only very conservative differences between the subclones listed above and their native sequences that are also in the sequence listing. For example, quite often, a start or stop codon was modified to be more efficient for expression in E. coli. It is expected that cloning of the wildtype sequences would give similar results in terms of DAT activity. For clarification purposes, the following table shows the relationship between a number of the clones and subclones described herein.

Clone/

Sequence type

subclone
SEQ ID

(clone or

pair
NO:
Activity
subclone)

1
31, 32
D-AT
Clone

1
867, 868
D-AT
Subclone

2
955, 956
D-AT
Clone

2
929, 930
D-AT
Subclone

3
957, 958
D-AT
Clone

3
931, 932
D-AT
Subclone

4
959, 960
D-AT
Clone

4
935, 936
D-AT
Subclone

5
41, 42
D-AT
Clone

5
869, 870
D-AT
Subclone

6
7, 8
D-AT
Clone

6
943, 944
D-AT
Subclone

7
11, 12
D-AT
Clone

7
941, 942
D-AT
Subclone

8
83, 84
D-AT
Clone

8
879, 880
D-AT
Subclone

9
151, 152
D-AT
Clone

9
913, 914
D-AT
Subclone

10
951, 952
D-AT
Clone

10
933, 934
D-AT
Subclone

11
75, 76
D-AT
Clone

11
881, 882
D-AT
Subclone

12
87, 88
D-AT
Clone

12
883, 884
D-AT
Subclone

13
163, 164
D-AT
Clone

13
921, 922
D-AT
Subclone

14
145, 146
D-AT
Clone

14
919, 920
D-AT
Subclone

15
149, 150
D-AT
Clone

15
925, 926
D-AT
Subclone

16
147, 148
D-AT
Clone

16
915, 916
D-AT
Subclone

17
15, 16
D-AT
Clone

17
947, 948
D-AT
Subclone

18
17, 18
D-AT
Clone

18
949, 950
D-AT
Subclone

19
3, 4
D-AT
Clone

19
937, 938
D-AT
Subclone

20
5, 6
D-AT
Clone

20
939, 940
D-AT
Subclone

21
161, 162
D-AT
Clone

21
923, 924
D-AT
Subclone

22
953, 954
D-AT
Clone

22
927, 928
D-AT
Subclone

23
19, 20
D-AT
Clone

23
885, 886
D-AT
Subclone

24
21, 22
D-AT
Clone

24
891, 892
D-AT
Subclone

25
23, 24
D-AT
Clone

25
893, 894
D-AT
Subclone

26
13, 14
D-AT
Clone

26
945, 946
D-AT
Subclone

27
143, 144
D-AT
Clone

27
917, 918
D-AT
Subclone

28
43, 44
D-AT
Clone

28
871, 872
D-AT
Subclone

29
45, 46
D-AT
Clone

29
873, 874
D-AT
Subclone

30
49, 50
D-AT
Clone

30
897, 898
D-AT
Subclone

31
51, 52
D-AT
Clone

31
875, 876
D-AT
Subclone

32
37, 38
D-AT
Clone

32
877, 878
D-AT
Subclone

33
25, 26
D-AT
Clone

33
889, 890
D-AT
Subclone

34
27, 28
D-AT
Clone

34
887, 888
D-AT
Subclone

35
131, 132
D-AT
Clone

35
909, 910
D-AT
Subclone

36
53, 54
D-AT
Clone

36
865, 866
D-AT
Subclone

37
29, 30
D-AT
Clone

37
895, 896
D-AT
Subclone

38
125, 126
D-AT
Clone

38
907, 908
D-AT
Subclone

39
133, 134
D-AT
Clone

39
911, 912
D-AT
Subclone

40
127, 128
D-AT
Clone

40
899, 900
D-AT
Subclone

41
137, 138
D-AT
Clone

41
901, 902
D-AT
Subclone

42
139, 140
D-AT
Clone

42
903, 904
D-AT
Subclone

43
129, 130
D-AT
Clone

43
905, 906
D-AT
Subclone

44
33, 34
D-AT
Clone

44
969, 970
D-AT
Subclone

45
219, 220
D-AT
Clone

45
973, 974
D-AT
Subclone

46
39, 40
D-AT
Clone

46
971, 972
D-AT
Subclone

47
1, 2
D-AT
Clone

47
975, 976
D-AT
Subclone

48
253, 254
Dehydrogenase
Clone

48
961, 962
Dehydrogenase
Subclone

Part B
Example 3
Detection of Monatin, MP, Tryptophan, Alanine, and HMG

This example describes the analytical methodology associated with the further characterization of selected D-aminotransferase (DAT) enzymes.

LC/MS/MS Multiple Reaction Monitoring (MRM) Analysis of Monatin and Tryptophan

Analyses of mixtures for monatin and tryptophan derived from biochemical reactions were performed using a Waters/Micromass® liquid chromatography-tandem mass spectrometry (LC/MS/MS) instrument including a Waters 2795 liquid chromatograph with a Waters 996 Photo-Diode Array (PDA) absorbance monitor placed in series between the chromatograph and a Micromass® Quattro Ultima® triple quadrupole mass spectrometer. LC separations were made using an Xterra MS C8 reversed-phase chromatography column, 2.1 mm×250 mm at 40° C. The LC mobile phase consisted of A) water containing 0.3% formic acid and 10 mM ammonium formate and B) methanol containing 0.3% formic acid and 10 mM ammonium formate.

The gradient elution was linear from 5% B to 45% B, 0-8.5 min, linear from 45% B to 90% B, 8.5-9 min, isocratic from 90% B to 90% B, 9-12.5 min, linear from 90% B to 5% B, 12.5-13 min, with a 4 min re-equilibration period between runs. The flow rate was 0.27 mL/min, and PDA absorbance was monitored from 210 nm to 400 nm. All parameters of the ESI-MS were optimized and selected based on generation of protonated molecular ions ([M+H]+) of the analytes of interest, and production of characteristic fragment ions. The following instrumental parameters were used for LC/MS/MS Multiple Reaction Monitoring (MRM) analysis of monatin and tryptophan: Capillary: 3.5 kV; Cone: 40 V; Hex 1: 20 V; Aperture: 0 V; Hex 2: 0 V; Source temperature: 100° C.; Desolvation temperature: 350° C.; Desolvation gas: 500 L/h; Cone gas: 50 L/h; Low mass resolution (Q1): 12.0; High mass resolution (Q1): 12.0; Ion energy: 0.2; Entrance: −5 V; Collision Energy: 8; Exit: 1 V; Low mass resolution (Q2): 15; High mass resolution (Q2): 15; Ion energy (Q2): 3.5; Multiplier: 650. Four monatin-specific parent-to-daughter MRM transitions and one tryptophan specific parent-to-daughter transition are used to specifically detect monatin and tryptophan in in vitro and in vivo reactions. The transitions monitored are 293.08 to 157.94, 293.08 to 167.94, 293.08 to 130.01, and 293.08 to 256.77. Tryptophan is monitored with the MRM transition 205.0 to 146.0. For internal standard quantification of monatin and tryptophan, four calibration standards containing four different ratios of each analyte to d₅-tryptophan and d₅-monatin, are analyzed. These data are subjected to a linear least squares analysis to form a calibration curve for monatin and tryptophan. To each sample is added a fixed amount of d₅-tryptophan and d₅-monatin (d₅-monatin was synthesized from d₅-tryptophan according to the methods from WO 2003/091396 A2), and the response ratios (monatin/d₅-monatin; tryptophan/d₅-tryptophan) in conjunction with the calibration curves described above are used to calculate the amount of each analyte in the mixtures. Parent-to-daughter mass transitions monitored for d₅-tryptophan and d₅-monatin are 210.0 to 150.0, and 298.1 to 172.0 and 298.1 to 162.00 respectively.

Chiral LC/MS/MS (MRM) Measurement of Monatin

Determination of the stereoisomer distribution of monatin in biochemical reactions was accomplished by derivatization with 1-fluoro-2-4-dinitrophenyl-5-L-alanine amide (FDAA), followed by reversed-phase LC/MS/MS MRM measurement.

Derivatization of Monatin with FDAA

To 50 μL of sample or standard and 10 μL of internal standard was added 100 μL of a 1% solution of FDAA in acetone. Twenty μL of 1.0 M sodium bicarbonate was added, and the mixture was incubated for 1 h at 40° C. with occasional mixing. The sample was removed and cooled, and neutralized with 20 μL of 2.0 M HCl (more HCl may be required to effect neutralization of a buffered biological mixture). After degassing was complete, samples were ready for analysis by LC/MS/MS.

LC/MS/MS Multiple Reaction Monitoring for the Determination of the Stereoisomer Distribution of Monatin

Analyses were performed using the LC/MS/MS instrumentation described in the previous sections. The LC separations capable of separating all four stereoisomers of monatin (specifically FDAA-monatin) were performed on a Phenomenex Luna® 2.0×250 mm (3 μm) C18 reversed phase chromatography column at 40° C. The LC mobile phase consisted of A) water containing 0.05% (mass/volume) ammonium acetate and B) acetonitrile. The elution was isocratic at 13% B, 0-2 min, linear from 13% B to 30% B, 2-15 min, linear from 30% B to 80% B, 15-16 min, isocratic at 80% B 16-21 min, and linear from 80% B to 13% B, 21-22 min, with a 8 min re-equilibration period between runs. The flow rate was 0.23 mL/min, and PDA absorbance was monitored from 200 nm to 400 nm. All parameters of the ESI-MS were optimized and selected based on generation of deprotonated molecular ions ([M−H]⁻) of FDAA-monatin, and production of characteristic fragment ions.

The following instrumental parameters were used for LC/MS analysis of monatin in the negative ion ESI/MS mode: Capillary: 3.0 kV; Cone: 40 V; Hex 1: 15 V; Aperture: 0.1 V; Hex 2: 0.1 V; Source temperature: 120° C.; Desolvation temperature: 350° C.; Desolvation gas: 662 L/h; Cone gas: 42 L/h; Low mass resolution (Q1): 14.0; High mass resolution (Q1): 15.0; Ion energy: 0.5; Entrance: 0 V; Collision Energy: 20; Exit: 0 V; Low mass resolution (Q2): 15; High mass resolution (Q2): 14; Ion energy (Q2): 2.0; Multiplier: 650. Three FDAA-monatin-specific parent-to-daughter transitions were used to specifically detect FDAA-monatin in in vitro and in vivo reactions. The transitions monitored for monatin were 542.97 to 267.94, 542.97 to 499.07, and 542.97 to 525.04. Monatin internal standard derivative mass transition monitored was 548.2 to 530.2. Identification of FDAA-monatin stereoisomers was based on chromatographic retention time as compared to purified monatin stereoisomers, and mass spectral data. An internal standard was used to monitor the progress of the reaction and for confirmation of retention time of the S,S stereoisomer.

Liquid Chromatography-Post Column Fluorescence Detection of Amino Acids, Including Tryptophan, Monatin, Alanine, and HMG

Procedure for Trytophan, Monatin, and Alanine

Liquid chromatography with post-column fluorescence detection for the determination of amino acids in biochemical reactions was performed on a Waters 2690 LC system or equivalent combined with a Waters 474 scanning fluorescence detector, and a Waters post-column reaction module (LC/OPA method). The LC separations were performed on an Interaction-Sodium loaded ion exchange column at 60° C. Mobile phase A was Pickering Na 328 buffer (Pickering Laboratories, Inc.; Mountain View, Calif.). Mobile phase B was Pickering Na 740 buffer. The gradient elution was from 0% B to 100% B, 0-20 min, isocratic at 100% B, 20-30 min, and linear from 100% B to 0% B, 30-31 min, with a 20 min re-equilibration period between runs. The flow rate for the mobile phase was 0.5 mL/min. The flow rate for the OPA post-column derivatization solution was 0.5 mL/min. The fluorescence detector settings were EX 338 nm and Em 425 nm. Norleucine was employed as an internal standard for the analysis. Identification of amino acids was based on chromatographic retention time data for purified standards.

Procedure for HMG

Samples from biochemical reactions were cleaned up by solid phase extraction (SPE) cartridges containing C18 as the packing material and 0.6% acetic acid as the eluent. The collected fraction from SPE was then brought up to a known volume and analyzed using HPLC post-column O-Phthaladehyde (OPA) derivatization with a florescence detector. Chromatographic separation was made possible using a Waters 2695 liquid chromatography system and two Phenomenex AquaC18 columns in series; a 2.1 mm×250 mm column with 5 μm particles, and a 2.1 mm×150 mm column with 3 μm particles. The temperature of the column was 40° C. and the column isocratic flow rate was 0.18 mL/min. The mobile phase was 0.6% acetic acid. OPA post-column derivatization and detection system consists of a Waters Reagent Manager (RMA), a reaction coil chamber, a temperature control module for the reaction coil chamber, and a Waters 2847 Florescent detector. The OPA flow rate was set at 0.16 mL/min, and the reaction coil chamber was set to 80° C. The florescence detector was set with an excitation wavelength of 348 nm and an emission wavelength of 450 nm. Other parameters controlling detector sensitivity, such as signal gain and attenuation, were set to experimental needs. Quantification of HMG was based off of the molar response of glutamic acid.

Detection of MP by LC/MS

Liquid chromatography separations were made using Waters 2690 liquid chromatography system and a 2.1 mm×50 mm Agilent Eclipse XDB-C18 1.8 μm reversed-phase chromatography column with flow rate at 0.25 mL/min and gradient conditions as follows:

Time (min)
A %
B %

0.00
95
5

0.2
95
5

1.2
5
95

4.5
5
95

5.0
95
5

10
95
5

The mobile phase A was 0.3% (v/v) formic acid with 10 mM ammonium formate, and mobile phase B was 0.3% formic acid w/10 mM ammonium formate in 50:50 methanol/acetonitrile. The column temperature was 40° C.

Parameters for the Micromass ZQ quadrupole mass spectrometer operating in negative electrospray ionization mode (−ESI) were set as follows: Capillary: 2.2 kV; Cone: 35 V; Extractor: 4 V; RF lens: 1 V; Source temperature: 120° C.; Desolvation temperature: 380° C.; Desolvation gas: 600 L/h; Cone gas: Off; Low mass resolution: 15.0; High mass resolution: 15.0; Ion energy: 0.2; Multiplier: 650. Single ion monitoring MS experiment was set up to allow detection selectively for m/z 290.3, 210.3, 184.3, and 208.4. The m/z 208.4 is the deprotonated molecular [M−H]⁻ ion of the internal standard d₅-tryptophan.

Detection of MP by LC/MS/MS

LC separations were made using Waters HPLC liquid chromatography system and a 2.1 mm×50 mm Agilent Eclipse XDB-C18 1.8 μm reversed-phase chromatography column with flow rate at 0.25 mL/min and gradient conditions are as follows:

Time (min)
A %
B %

0.00
95
5

0.7
95
5

3.0
5
95

4.0
5
95

4.3
95
5

6.0
95
5

Mobile phase A was 0.3% (v/v) formic acid with 10 mM ammonium formate, and B was 0.3% formic acid with 10 mM ammonium formate in 50:50 methanol/acetonitrile. The column temperature was 40° C.

Parameters on Waters Premier XE triple quadrupole mass spectrometer for LC/MS/MS Multiple Reaction Monitoring (MRM) experiments operating in negative electrospray ionization mode (−ESI) were set as the following; Capillary: 3.0 kV; Cone: 25 V; Extractor: 3 V; RF lens: 0 V; Source temperature: 120° C.; Desolvation temperature: 350° C.; Desolvation gas: 650 L/hr; Cone gas: 47 L/hr; Low mass resolution (Q1): 13.5; High mass resolution (Q1): 13.5; Ion energy (Q1): 0.5 V; Entrance: 1 V; Collision Energy: 18 V; Exit 1: 19; Low mass resolution (Q2): 15; High mass resolution (Q2): 15; Ion Energy (Q2): 2.0; Multiplier: 650. Four parent-to-daughter MRM transitions were monitored to selectively detect Monatin precursor (MP) and d₅-Monatin precursor (d₅-MP); d₅-MP was used as an internal standard (I.S.). The four MRM transitions were 290.1 to 184.1, 290.1 to 210.1, 290.1 to 228.1, and 295.1 to 189.1. Two of these transitions, 290.1 to 184.1 for MP, and 295.1 to 189.1 for d₅-MP, were used for generating calibration curves and for quantification purposes. Transitions of 290.1 to 210.1 and 290.1 to 228.1 were used as qualitative secondary confirmation of MP.

Production of Monatin and MP for Standards and for Assays

Production of Monatin

A racemic mixture of R,R and S,S monatin was synthetically produced as described in U.S. Pat. No. 5,128,482. The R,R and S,S monatin were separated by a derivatization and a hydrolysis step. Briefly, the monatin racemic mixture was esterified, the free amino group was blocked with carbamazepine (CBZ), a lactone was formed, and the S,S lactone was selectively hydrolyzed using an immobilized protease enzyme. The monatin can also be separated as described in Bassoli et al., Eur. J. Org. Chem., 8:1652-1658, (2005).

MP Production

R-MP was produced by the transamination of R,R monatin using AT-103 broad range D-aminotransferase (BioCatalytics, Pasadena, Calif.) in 0.1 M potassium phosphate buffer, using sodium pyruvate as the amino acceptor. S-MP was produced by the transamination of S,S monatin using AT-102 L-aminotransferase (BioCatalytics) in 0.1 M potassium phosphate buffer, using sodium pyruvate as the amino acceptor. Both reactions were carried out at 30° C. and at a pH of approximately 8.0-8.3, for approximately 20 hours. Both compounds were purified using preparative scale HPLC with a Rohm and Haas (Philadelphia, Pa.) hydrophobic resin (XAD™ 1600), eluting in water. Samples containing greater than 90% purity monatin precursor were collected and freeze-dried.

Example 4
Protein Preparation Methods

This example describes the methodology used for cloning, expression, cell extract preparation, protein purification, and protein quantification for secondary characterization of selected DATs.

Those of skill in the art would realize that the presence of activity in a polypeptide encoded from a subcloned (e.g., a fragment) or otherwise modified (e.g., tagged) nucleic acid is considered predictive of the presence of activity in the corresponding polypeptide encoded from the full-length or wild type nucleic acid.

Amplification of DAT-Encoding Genes for Cloning into Topo Plasmids

PCR reactions for Topo cloning (using either Pfu Turbo or Cloned Pfu from Stratagene) were as follows: 1× recommended buffer for the polymerase enzyme, 0.2 mM dNTPs, 0.5 μM of each primer, and 1 μl per 50 μl of reaction of the polymerase (2.5 units). The reactions contained approximately 5-100 ng of template DNA per reaction. A 94° C. hot start for 2 minutes was used for PCRs, as well as a melting temperature of 94° C. The annealing temperature was dependent on the Tm of the primers, and was either 30 or 60 seconds. The extension time (at 72° C.) was at least 2 min per kb. The reaction products were normally separated on a 1×TAE 1% agarose gel, and bands of appropriate sizes were purified with QIAquick Gel Extraction Kit as recommend by the manufacturer except an elution volume of 10 to 50 μl was used. Volumes of 1 to 4 μl of the purified PCR product were used for ligation with the pCRII-Topo Blunt plasmid (Invitrogen, Carlsbad, Calif.) as recommended by the manufacturer.

Cloning of DATs in pET30a for Untagged Expression

The DATs having the sequence shown in SEQ ID NO:945, 947, 949, 891, 893, 869, 873, 877, 881, 883, and 895 (encoding the polypeptides having the sequence of SEQ ID NO:946, 948, 950, 892, 894, 870, 874, 878, 882, 884, and 896) were amplified from plasmids or PCR products with Pfu Turbo (Stratagene, La Jolla, Calif.) and primers adding a Nde I at the 5′ end and either a Not I or BamH I restriction site at the 3′ end. The PCR fragments were cloned into pCR-Blunt II-Topo (Invitrogen, Carlsbad, Calif.) as recommended by the manufacturer. The sequence was verified by sequencing (Agencourt, Beverly, Mass.) and inserts with the correct sequences were then released from the vector using the appropriate restriction enzymes and ligated into the Nde I and Not I (or BamH I) restriction sites of pET30a. See Table 2 for specific primers.

The DAT nucleic acid having the sequence of SEQ ID NO:155 (encoding the polypeptide having SEQ ID NO:156) was amplified with Pfu Turbo (Stratagene) and primers adding a Nde I and Hind III restriction site at the 5′ and 3′ end, respectively. The PCR fragments were digested using Nde I and Hind III restriction enzymes and ligated into the Nde I and Hind III restriction sites of pET30a. See Table 2 for specific primers. It should be noted that the polypeptide having the sequence of SEQ ID NO:156 appeared to contain the following leader sequence with a probability of 0.991 (as determined by SignalP, as discussed in Nielsen, 1997, Protein Engineering, 10:1-6): KNSPIIAAYRAATPGSAAA (SEQ ID NO:1084). The nucleic acid encoding this DAT polypeptide was cloned with the apparent leader sequence.

TABLE 2

Primers for amplification

Amplifies

SEQ

SEQ ID

ID

NO
PCR primers
NO:

945
5′-CCGCCCCATATGAACGCACTAGGATATTACAACGGAAAATGG-3′
978

5′-GGCGGATCCTTATCCAAAGAATTCGGCACGAGCTGTC-3′
979

947
5′-CCGCCCCATATGCGCGAAATTGTTTTTTTGAATGGG-3′
980

5′-CGGATCCCTAAACCATCTCAAAAAACTTTTGCTGAATAAACCGTG-3′
981

949
5′-CCGCCCCATATGTTGGATGAACGGATGGTGTTCATTAAC-3′
982

5′-GGCGGATCCCTAGTCCACGGCATAGAGCCACTCGG-3′
983

891
5′-GGCCGCATATGGACGCACTGGGATATTACAACGGAAAATG-3′
984

5′-GGCCGCGGCCGCCTATGCCTTTCTCCACTCAGGCGTGTAGC-3′
985

893
5′-GGCCGCATATGGACGCACTGGGATATTACAACGGAAAATG-3′
986

5′-GGCCGCGGCCGCCTATACTGTGCTCCACTCAGGCGTGTAGCC-3′
987

869
5′-CATATGTATTCATTATGGAATGATCAAATAGTGAAGG-3′
988

5′-GCGGCCGCCTATTTATTCGTAAAAGGTGTTGGAATTTTCG-3′
989

873
5′-CATATGAGCACCCCGCCGACCAATC-3′
990

5′-GCGGCCGCCTAGGCCGCCTTCACTTCACGCTC-3′
991

877
5′-CATATGAGCACCCCGCCAACCAATTC-3′
992

5′-GCGGCCGCCTACGCGGCCTTCACTTCGCGC-3′
993

881
5′-TCCAGGCATATGAGCACAGTATATTTAAATGGCC-3′
994

5′-CCAGTAGCGGCCGCCTAACACTCAACACTATACTTATGC-3′
995

883
5′-TCTAGGCATATGGTTTATCTGAACGGGCG-3′
996

5′-ACTGTAGCGGCGGCCTATCCGAGGGACGCGTTGG-3′
997

895
5′-CATATGAAAGAGCTGGGCTATTACAACGGAAAAATC-3′
998

5′-GCGGCCGCCTATGACCTCCACCCCTGATTTCCAAAATAC-3′
999

155
5′-CTAGGATTCCATATGAAGAATTCGCCGATCATC-3′
1000

5′-CGAAGCTTCAACAGCGGCCGCTTAAAG-3′
1001

Site-Directed Mutagenesis

Site-directed mutagenesis was performed using QuikChange Multi Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) according to the manufacturer's instructions. To generate the SEQ ID NO:870 T242N mutant, the pET30a untagged construct described in Example 10 was used as the template. To generate SEQ ID NO:220 G240N and SEQ ID NO:220 T241N mutants, the pET30a construct with a C-terminal his tag described in Example 10 was used as the template. The mutagenic primers used are listed below in Table 3. All the desired mutations were confirmed by DNA sequencing.

TABLE 3

Primer sequences

Mutant

polypeptide

designation

SEQ ID

(SEQ ID NO)
Sequence
NO:

870 T242N
5′-AATTATTTGTTTCATCAACAAATTCTGAAATTACGCCGGTTATTG-3′
1002

220 G240N
5′-CTTGTGTCCAGCAGCAACACACTCGGCCTTAG-3′
1003

220 T241N
5′-GTCCAGCAGCGGCAACCTCGGCCTTAGCGCC-3′
1004

Cloning of DAT PCR Products in pET30a for the Expression as Untagged Protein

DAT nucleic acids having the sequences shown in SEQ ID NO:177, 179, 153, 165, 181, 217, 187, 189, 207, 219, 215, 195, 199, 197, 209, 201, 221, 235, 203, 237, 239, 223, 225, 227, 229, 231, 245, 213, 155, 169, 171, 167, 173, and 175 (encoding DAT polypeptides having the sequence shown in SEQ ID NO:178, 180, 154, 166, 182, 218, 188, 190, 208, 220, 216, 196, 200, 198, 210, 202, 222, 236, 204, 238, 240, 224, 226, 228, 230, 232, 246, 214, 156, 170, 172, 168, 174, and 176) were received as PCR products with Nde I and Not I compatible ends, as well as extraneous nucleotides to improve cutting efficiencies.

The DAT PCR products contained an NdeI restriction enzyme site at the 5′ end and a NotI site at the 3′ end. The PCR fragments were first cloned into pCR4 TOPO or pCR-Blunt II-TOPO vector (Invitrogen). After the DNA sequences were verified by sequencing, the DAT genes were released from the TOPO plasmids by the digestion of NdeI and NotI and ligated into the pET30a vector which had been cut using the same restriction enzymes. DAT genes containing either an NdeI or NotI site internally were amplified using primers with compatible restriction enzyme sites and cloned into pET30a. For example, the DAT nucleic acid having the SEQ ID NO:155 (encoding the polypeptide having the sequence of SEQ ID NO:156) was reamplified from the original PCR product using NdeI and HindIII restriction sites for cloning into pET30a.

Cloning of DATs in pET30a for the Expression as the C-His-Tagged Fusion Protein

Nucleic acids encoding DAT 4978 and DAT 4978 T243N (described in Example 6), SEQ ID NO:870 (expressed from plasmid pSE420-cHis), and SEQ ID NO:870 T242N, SEQ ID NO:176 and SEQ ID NO:220 (untagged versions expressed from pET30) were re-amplified with Pfu Turbo (Stratagene) and primers that placed an XhoI site immediately upstream of the stop codons. PCR fragments were cloned into pCR-Blunt II-Topo (Invitrogen, Carlsbad, Calif.) as recommended by the manufacturer or directly cloned into the Nde I and Xho I restriction sites of pET30a The sequence was verified by sequencing (Agencourt, Beverly, Mass.) and an insert with the correct sequence was then released from the vector using Nde I and Xho I restriction enzymes and the insert was ligated into the Nde I and Xho I restriction sites of pET30a. See Table 4 for specific primers and plasmids names.

TABLE 4

Primer sequences

Polypeptide

SEQ

designation

ID

(SEQ ID NO)
Sequence
NO

870 and
5′-CATATGTATTCATTATGGAATGATCAAATAGTGAAGG-3′
1005

870 T242N
5′-CTCGAGTTTATTCGTAAAAGGTGTTGGAATTTTCGTTTC-3′
1006

DAT4978 and
5′-CATATGAGTTATAGCTTATGGAATGACCAAATTGTGAATG-3′
1007

DAT4978T243N
5′-CTCGAGTGCGCGAATACCTTTTGGGATTTTCGTATC-3′
1008

220
5′-CTAGGATCTCATATGGACGCACTGGGATATTAC-3′
1009

5′-GCCTCGAGTACCCTGCTCCACTCAGG-3′
1010

176
5′-CTAGGATTCCATATGGACGCGCTTGGCTATTAC-3′
1011

5′-GCCTCGAGTACCCTGCTCCACGCAG-3′
1012

Cloning of CbDAT and CaDAT

A Clostridium beijerinckii D-amino-transferase was PCR amplified using Pfu Turbo (Stratagene) and C. beijerinckii genomic DNA with PCR primers containing a 5′ NdeI and a 3′ NotI restriction site. Genomic DNA was extracted from C. beijerinckii (ATCC 51743) using the Purrgene genomic DNA purification kit (Gentra Systems, Minneapolis, Minn.) per the manufacturer's instructions.

The 824 bp PCR product was gel extracted using a Qiagen Gel Extraction Kit and TOPO cloned into pCR-Blunt II-Topo (Invitrogen). After verifying the sequence, the gene was ligated to Nde I/Not I cut pET28b and pET30a vectors using a Rapid Ligation kit (Roche).

The C. acetobutylicum DAT was amplified by PCR using genomic DNA (ATCC 824) and the Stratagene Optiprime PCR Kit with PCR primers containing a 5′ NdeI and a 3′ NotI restriction site. The successful PCR reaction was cloned into the pCR4 TOPO vector and TOPO clones were sequenced. A positive TOPO clone was digested with restriction enzymes NdeI and NotI and the DAT fragment ligated into pET30a vector digested with the same restriction enzymes.

TABLE 5

Primer sequences

Designation
Sequence
SEQ ID NO:

CbDAT1
5′-GGTTCATATGGAGAATTTAGGTTATTA-3′
1013

5′-GGAAGCGGCCGCATATTCTACCTCCTATTCTG-3′
1014

CaDAT2
5′-GGTTCATATGAAAGATTTAGGATATTACAATGGAGAATAC-3′
1015

5′GGAAGCGGCCGCTTAATTTGTTTCTTCCAAAAATTCATTAAG-3′
1016

In Vitro Synthesis of LsDAT

The Lactobacillus salivarius DAT was assembled using a revised method based on Stemmer et al., 1995, Gene, 164:49-53. Briefly, 43 oligonucleotides (primarily 40 mers) were ordered from IDT based on the gene sequence and its complementary DNA sequence, with 20 basepair overlaps between the sense and antisense strands. See Table 6 for the primer list. The primers were diluted to 250 μM in water and 5 μL of each primer was mixed together in a microfuge tube. PCR was carried out as follows: per 100 μL reaction, 1.5 μL of the primer pool, 4 μL dNTPs, 1×XL PCR buffer, 1 mM magnesium acetate, 2 μL rTth polymerase (Roche, Indianapolis, Ind.), and 0.25 μL Pfu polymerase (Stratagene, La Jolla, Calif.) were added. A 3 minute hot start was done at 94° C., followed by 15 cycles of 94° C. for 30 seconds, 42° C. for 30 seconds, and 68° C. for 15 seconds. Ten more cycles were done with an extension time of 30 seconds (at 68° C.). Ten more cycles were performed with an extension time of 75 seconds. Lastly, a chain extension step was done for seven minutes at 68° C.

TABLE 6

Oligos used to synthesis LsDAT

Designation
Sequence (5′ → 3′)
SEQ ID NO:

F1:
ATGAAGCAAG TTGGATACTA CAATGGTACT ATCGCTGATT
1017

F2:
TAAATGAACT TAAGGTGCCT GCTACTGATC GTGCACTTTA
1018

F3:
TTTTGGTGAT GGTTGCTACG ATGCAACTAC ATTTAAGAAC
1019

F4:
AATGTTGCAT TTGCCTTAGA AGATCATCTT GATCGTTTTT
1020

F5:
ATAATAGTTG TCGCCTACTA GAGATCGATT TCCCTTTAAA
1021

F6:
TCGCGATGAA CTTAAAGAAA AGCTTTACGC TGTTATTGAT
1022

F7:
GCTAACGAAG TTGATACTGG TATCCTTTAT TGGCAAACTT
1023

F8:
CACGTGGTTC TGGTTTACGT AACCATATTT TCCCAGAAGA
1024

F9:
TAGCCAACCT AATTTATTAA TTTTTACTGC TCCTTATGGT
1025

F10:
TTAGTTCCAT TTGATACTGA ATATAAACTT ATATCTCGCG
1026

F11:
AAGACACTCG CTTCTTACAT TGCAATATTA AAACTTTGAA
1027

F12:
TTTACTTCCA AACGTTATTG CAAGTCAAAA GGCTAATGAA
1028

F13:
AGTCATTGCC AAGAAGTGGT CTTCCATCGC GGTGACAGAG
1029

F14:
TTACAGAATG TGCACACTCT AACATCTTAA TTCTAAAAGA
1030

F15:
TGGCGTTCTT TGCTCCCCAC CTAGAGATAA TTTAATCTTG
1031

F16:
CCAGGAATTA CTTTGAAACA TCTCTTGCAA TTAGCAAAAG
1032

F17:
AAAATAATAT TCCTACTTCC GAAGCACCAT TCACTATGGA
1033

F18:
TGATCTTAGA AATGCTGATG AAGTTATTGT TAGTTCTTCA
1034

F19:
GCTTGTCTAG GTATTCGCGC AGTCGAGCTT GATGGTCAGC
1035

F20:
CTGTTGGTGG AAAAGATGGA AAGACTTTAA AGATCTTGCA
1036

F21:
AGATGCTTAT GCTAAGAAAT ATAATGCTGA AACTGTAAGT CGTTAA
1037

R1:
TAGTATCCAA CTTGCTTCAT
1038

R2:
AGGCACCTTA AGTTCATTTA AATCAGCGAT AGTACCATTG
1039

R3:
CGTAGCAACC ATCACCAAAA TAAAGTGCAC GATCAGTAGC
1040

R4:
TCTAAGGCAA ATGCAACATT GTTCTTAAAT GTAGTTGCAT
1041

R5:
TAGTAGGCGA CAACTATTAT AAAAACGATC AAGATGATCT
1042

R6:
TTTCTTTAAG TTCATCGCGA TTTAAAGGGA AATCGATCTC
1043

R7:
CCAGTATCAA CTTCGTTAGC ATCAATAACA GCGTAAAGCT
1044

R8:
ACGTAAACCA GAACCACGTG AAGTTTGCCA ATAAAGGATA
1045

R9:
TTAATAAATT AGGTTGGCTA TCTTCTGGGA AAATATGGTT
1046

R10:
TCAGTATCAA ATGGAACTAA ACCATAAGGA GCAGTAAAAA
1047

R11:
ATGTAAGAAG CGAGTGTCTT CGCGAGATAT AAGTTTATAT
1048

R12:
CAATAACGTT TGGAAGTAAA TTCAAAGTTT TAATATTGCA
1049

R13:
ACCACTTCTT GGCAATGACT TTCATTAGCC TTTTGACTTG
1050

R14:
AGAGTGTGCA CATTCTGTAA CTCTGTCACC GCGATGGAAG
1051

R15:
GTGGGGAGCA AAGAACGCCA TCTTTTAGAA TTAAGATGTT
1052

R16:
TGTTTCAAAG TAATTCCTGG CAAGATTAAA TTATCTCTAG
1053

R17:
GGAAGTAGGA ATATTATTTT CTTTTGCTAA TTGCAAGAGA
1054

R18:
CATCAGCATT TCTAAGATCA TCCATAGTGA ATGGTGCTTC
1055

R19:
GCGCGAATAC CTAGACAAGC TGAAGAACTA ACAATAACTT
1056

R20:
TCCATCTTTT CCACCAACAG GCTGACCATC AAGCTCGACT
1057

R21:
ATTTCTTAGC ATAAGCATCT TGCAAGATCT TTAAAGTCTT
1058

R22:
TTAACGACTT ACAGTTTCAG CATTAT
1059

A secondary amplification with primers L. sal DAT R Not I and L. sal DAT F Nde I (below) resulted in a band of the correct molecular weight. See Table 7 for these secondary amplification primer sequences.

TABLE 7

Primer sequences

Designation
Sequence (5′ → 3′)
SEQ ID NO:

L. sal DAT R NotI
TTGGCCAAGCGGCCGCTTAACGACTTACAGTTT
1060

L. sal DAT F NdeI
GGTTCCAAGGCATATGAAGCAAGTTGGATACTA
1061

The secondary PCR reaction was set up the same as above with the exception that only 2 primers were added. For the PCR template, 2.5 μl of the primary PCR reaction was used. A 3 minute hot start was done at 94° C., followed by 10 cycles of 94° C. for 30 seconds, 42° C. for 30 seconds, and 68° C. for 15 seconds. Ten more cycles were done with an increased annealing temp of 48° C. for 30 seconds with an extension time of 30 seconds (at 68° C.). Lastly, a chain extension step was done for seven minutes at 68° C.

The fragment was cloned into a pCR-BluntII-TOPO vector and the TOPO clones were sequenced. A positive TOPO clone was cut with NdeI and NotI and the DAT fragment ligated into pET30a vector digested with the same restriction enzymes.

Enzyme Preparation

E. coli strain BL21(DE3) was used as the host strain for the expression of DATs from pET-derived plasmids. E. coli strain TOP10 was used in all other DAT constructs. Single colonies of desired constructs were typically innoculated into Overnight Express II medium (Novagen) containing the appropriate amount of antibiotics. Following cultivation at 30° C. overnight, the cells were harvested by centrifugation when the OD₆₀₀was greater than 10. Alternatively, overnight cultures were utilized to innoculate cultures in LB medium containing the appropriate antibiotics. The cultures were grown at 30° C. to an OD₆₀₀of 0.5 to 0.9 and protein expression was induced with 1 mM IPTG for 4 h at the same temperature.

Cell extracts were prepared by adding 5 mL per g of cell pellet or 5 mL per 50 mL of overnight culture, of BugBuster® (primary amine-free) Extraction Reagent (EMD Biosciences/Novagen catalog #70923) with 5 μL/mL of Protease Inhibitor Cocktail II (EMD Bioscience/Calbiochem catalog #539132), 1 μl/ml of Benzonase® Nuclease (EMD Biosciences/Novagen catalog #70746), and 0.033 μl/ml of r-Lysozyme™ solution (EMD Biosciences/Novagen catalog #71110) to the cells. The cell resuspension was incubated at room temperature for 15 min with gentle shaking. Following centrifugation at 16,100 rcf for 20 min at 4° C., the supernatant was removed as the cell-free extract.

Prior to using the enzyme preparation for monatin reactions, detergents and low molecular weight compounds were removed from the cell-free extract by passage through a PD-10 column (GE Healthcare, Piscataway, N.J.) that was previously equilibrated with potassium phosphate buffer (100 mM, pH 7.8) or EPPS buffer (100 mM, pH 8.2) containing 0.05 mM of PLP. The protein was eluted using the equilibration buffer. Protein concentrations were typically determined using the BioRad Coomassie plate assay (also known as the Bradford assay) plate assay with BSA (Pierce) as the standard. Occasionally, the BCA (Pierce) microtiter plate assay was used for protein determination, where noted. To estimate the concentration of the D-aminotransferase in the cell-free extracts, 1 mg/mL samples were loaded on the Experion (Bio-Rad, Hercules, Calif.) electrophoresis system and the Experion Software (Version 2.0.132.0) was used to calculate the percentage of the soluble DAT protein in the cell-free extract. Alternatively, SDS-PAGE analysis was done and visual estimation was used to estimate percentage of expression.

The His-tagged fusion proteins were purified using either the GE Healthcare Chelating Sepharose Fast Flow resin or Novagen His-Bind columns. The purification using the Sepharose resin involved loading the cell-free extract onto a column that was previously equilibrated with potassium phosphate buffer (100 mM, pH 7.8) containing 200 mM of sodium chloride and 0.050 mM of PLP. The column was then washed successively using 3-5 column volumes of the equilibration buffer, 3-5 column volumes of the equilibration buffer containing 25 mM of imidazole and 3-5 column volumes of the equilibration buffer containing 50-100 mM of imidazole. The His-tagged protein was eluted off the column using 3-5 column volumes of the equilibration buffer containing 500 mM of imidazole. The eluate was concentrated using the Amicon (Billerica, Mass.) Centricon-70. The imidazole and sodium chloride salts in the concentrated protein solution were removed by passage through PD-10 desalting columns that were previously equilibrated using potassium phosphate buffer (100 mM, pH 7.8) (for DAT4978 and DAT4978 T243N) or EPPS buffer (100 mM, pH 8.2) (for SEQ ID NO:870 and SEQ ID NO:870 T242N) containing 50 μM of PLP. Protein concentrations were determined using Bio-Rad Protein Assay (Bio-Rad) and Albumin (Pierce) as a standard. Aliquots (0.5-1 mL) of the purified enzyme were stored at −80° C. until use. The purification of the His-tagged protein using the His-Bind columns followed the manufacture's instruction. The eluate from the column was desalted using the PD10 column as described above.

Example 5
Assay Procedures #2 for D-Aminotransferase Activity

Monatin Production Assay (Standard)

The following components were combined: 100 mM EPPS, pH 8.2; 200 mM sodium pyruvate; 100 mM of D-tryptophan; 50 μM PLP; 1 mM MgCl₂; 0.01% Tween-80; 50 μg/mL of aldolase described in Example 6 (cell-free extract was used; the aldolase concentration was estimated based on the percentage reading from Experion chip) and an appropriate amount of DAT (typically 0.1-1 mg/mL).

Except for the PLP stock solution and the protein solutions, all other reagents were made using oxygen-free deionized water and stored in the anaerobic chamber. The reactions were set up in the anaerobic chamber at room temperature with constant gentle mixing. To take a time point, formic acid was added into an aliquot of the reaction mixture to a final concentration of 2% (v/v). Following centrifugation at 16,100 RCF for 5 min using a bench-top microfuge, the supernantant was filtered through a 0.2 μm nylon membrane filter. Samples were then diluted 20- to 100-fold with water prior to analysis by LC/MS/MS.

D-Tryptophan Transamination Assay

To compare the D-tryptophan transamination activities of certain D-aminotransferases, the following assays were performed. The assay mix contained: 0.5 mg/mL of cellular extract protein containing D-AT; 40 mM potassium phosphate pH 8.0; 20 mM D-tryptophan; 100 mM sodium pyruvate; and 50 μM PLP. The assays were incubated at 37° C. for 30 minutes and then placed on ice.

The extent of reaction was followed by measuring the amount of indole-3-pyruvate formed using the following assay: to 5 μl, 10 μl and 20 μl of reaction mix, 200 μl of the following solution was added: 0.5 mM sodium arsenate; 0.5 mM EDTA; and 50 mM sodium tetraborate (pH 8.5). Absorbance of the indole-3-pyruvate enol-borate complex at 325 nm was compared to a standard curve of indole-3-pyruvate prepared in the same solution.

Alanine formation can also be used to follow the extent of the D-tryptophan transamination reactions. Alanine concentrations were determined as described in Example 3.

R,R Monatin Transamination Assay

Assay conditions (final volume 2 mL) included: 0.01% Tween; 100 mM EPPS pH 8.2; 100 mM sodium pyruvate; approximately 3 mM R,R monatin; 0.5 mg/mL DAT; and 50 μM PLP. The extent of reaction was monitored by detection of alanine or R-MP formed using the protocols described in Example 3.

Example 6
Method for Obtaining DATs and an Aldolase

This method described the cloning of the aldolase used in monatin formation reactions with the D-aminotransferases, and D-aminotransferases previously isolated that were used for comparative purposes.

Aldolase

The aldolase used in monatin production assays from D-tryptophan was isolated and subcloned into pET vectors as described in WO 2007/103389 (referred to in that application as the aldolase of SEQ ID NO:276 encoded by the nucleic acid of SEQ ID NO:275).

DAT and DAT4978 T243N

A D-aminotransferase from ATCC #4978 (DAT 4978) was cloned as described in U.S. Publication No. 2006/0252135. A T243N mutant was made using the pET30 (untagged) DAT 4978 construct.

The primer for mutagenesis was designed following the suggestions listed in the Stratagene Multi-Change kit (La Jolla, Calif.). The primer was 5′-phosphorylated. Mutagenesis was done using the Stratagene Multi-Change kit following the manufacturer's instructions. The mutagenic oligonucleotide sequence is shown in Table 8.

TABLE 8

Mutagenic oligonucleotide sequences

Mutant name
Amino acid change
Primer
SEQ ID NO:

DAT4978T243N
T243N
5′-GTGATTGTTTCATCAACGAATTCAGAAGTAACGCC-3′
1062

E. coli XL10-Gold cells (Stratagene) were transformed and the resultant purified plasmid preparations were sequenced to verify that the correct mutations were incorporated. The plasmid containing the DAT 4978 T243N was then transformed into E. coli BL21 (DE3) expression host B. sphaericus DAT

A D-aminotransferase from B. sphaericus (ATCC number 10208) was cloned as described in US 2006/0252135. The protein was prepared as described in the same reference.

Example 7
Analysis of DATs

DAT polypeptides having the sequence shown in SEQ ID NO:928, 930, 932, 934, 936, 938, 940, 942, 944, 946, 948, and 950 were produced by expressing the corresponding nucleic acid in the vectors and in the compatible E. coli expression hosts described in Example 2. One skilled in the art can synthesize the genes encoding these D-aminotransferases using assembly PCR techniques such as those described in Example 4. Overnight cultures in LB medium containing carbenicillin (100 μg/mL) were diluted 100× in 100 mL of the same medium and grown in a 500 mL baffled flask. The culture was grown at 30° C. to an OD₆₀₀of 0.5 to 0.9, and protein expression was induced with 1 mM IPTG for 4 h at the same temperature. Samples for total protein were taken immediately prior to harvesting. Cells were harvested by centrifugation and washed once with 10 mL of potassium phosphate buffer pH 7.8. Cells were immediately frozen at −80° C. until cell extracts were prepared.

Cell extracts were prepared and desalted as described in Example 4 using 100 mM potassium phosphate as the buffer to elute and equilibrate the PD10 column. Total protein and DAT concentrations were determined as described.

Transamination of R,R monatin with pyruvate as the amino acceptor were performed as described in Example 5 except that 10 mM R,R monatin was utilized. Initial analyses of alanine, monatin, and monatin precursor levels were not consistent with each other and results were considered qualitative. The DAT polypeptide having the sequence of SEQ ID NO:948 appeared to show monatin precursor formation.

For further confirmation of activity, a monatin formation assay was done as described in the methods with a DAT concentration of approximately 0.2 mg/mL. As a control, 0.2 mg/mL concentration of purified B. sphaericus DAT was evaluated. After 2 and 21 hr, an aliquot was taken and formic acid was added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using LC/MS/MS methodology and for tryptophan and alanine using the LC/OPA post-column fluorescence methodology described in Example 3. The DAT polypeptides having the sequence of SEQ ID NO:946 and 950 were capable of R,R monatin formation under the conditions tested. The DAT polypeptide having the sequence of SEQ ID NO:948 showed a loss of tryptophan and an increase in alanine formation, demonstrating its activity as a D-tryptophan transaminase. The DAT polypeptide having the sequence of SEQ ID NO:946 expressed well as determined by the amount of total protein but was not very soluble, which explains some inconsistent results. The DAT polypeptides having the sequence shown in SEQ ID NO:930, 932, 940, 942, and 944 did not yield visible bands on analysis with SDS-PAGE and, therefore, may be active if produced under different conditions. See Table 9 for results.

TABLE 9

Activity of DATs

Monatin [mM]
Monatin [mM]

DAT Polypeptide (SEQ ID NO)
Time = 2 hr
Time = 21 hr

928
nd
nd

930
nd
nd

932
nd
nd

934
nd
nd

936
nd
nd

938
nd
nd

940
nd
nd

942
nd
nd

944
nd
nd

946
0.1
0.6

948
nd
nd

950
0.4
3.1

B. sphaericus control DAT
0.8
4.4

nd = not detected under conditions tested

Analysis of DAT Polypeptides in pET30a

The DAT polypeptides having the sequence of SEQ ID NO:946, 948, and 950 were subcloned into pET30a as described in Example 4. Duplicate cultures of E. coli strain BL21 DE3 containing the DATs in pET30a were grown overnight in Overnight Express II (Solution 1-6, Novagen) at both 25 and 30° C. As a control, a strain containing pET30a plasmid without an insert was also grown. Cells were collected at an OD₆₀₀of 5-10. Cells were harvested by centrifugation and washed once with 10 mL of 100 mM potassium phosphate buffer pH 7.8. Cells were frozen at −80° C. until further processed.

Cell extracts were prepared as described in Example 4 using 100 mM potassium phosphate as the buffer to elute and equilibrate the PD10 columns. Total protein and DAT protein concentrations were determined as described. The DAT polypeptide having the sequence of SEQ ID NO:946 expressed well at 30° C. in the total protein fraction, but was not soluble as viewed by SDS-PAGE. The DAT polypeptides having the sequence of SEQ ID NO:948 and 950 expressed at the higher temperature also, but were soluble.

A monatin formation assay was done as described in Example 5 except with a DAT concentration of 0.1 mg/mL for the polypeptide of SEQ ID NO:946 (0.5 mg/mL for all others). As a positive control, purified B. sphaericus DAT at a 0.5 mg/mL concentration was also assayed. After 2 and 21 hr, an aliquot was taken, formic acid was added to a final concentration of 2%, and the samples were frozen until further processed. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using LC/MS/MS, and for tryptophan and alanine using LC/OPA post-column fluorescence detection methods described in Example 3. The results are shown in Table 10. D-tryptophan consumption and alanine formation were shown for all the D-aminotransferases tested indicating that they all have activity on D-tryptophan. Under these conditions, only DAT polypeptides having the sequence of SEQ ID NO:946 and 948 appeared to have activity for monatin formation. It is possible that expression or stability differences between the two host systems are the reason why activity is seen in some cases but not in others.

TABLE 10

Monatin [mM]
Monatin [mM]

DAT polypeptide (SEQ ID NO)
time = 2 hr
time = 21 hr

pET30 (negative control)
nd
nd

946
0.4
1.8

948
nd
0.2

950
nd
nd

B. sphaericus positive control
1.8
8.6

nd, not detected under conditions tested

Example 8
Analysis of DATs in pSE420-cHis

DAT polypeptides having the sequence shown in SEQ ID NOs:886, 888, 890, 892 and 894 DATs were produced from the pSE420-cHis vector in E. coli HMS174. One skilled in the art can synthesize the genes encoding these D-aminotransferases using assembly PCR techniques such as those described in Example 4. Overnight cultures of the various DAT constructs were grown in LB medium containing ampicillin (100 μg/mL) at 30° C. Fifty mL of the same medium was inoculated the next day with 1 mL of the overnight cultures. The cultures were grown at 30° C. until the OD_{600 nm}reached approximately 0.5 and then induced with 1 mM IPTG. The cultures were further incubated for 4 h at 30° C. and then harvested by centrifugation at 3800 rcf for 15 min. The cells were washed with 1.5 mL of 50 mM potassium phosphate, pH 7.0 and centrifuged again. The supernatant was decanted and the cell pellets were weighed.

Cell extracts were prepared as described in the methods using 100 mM potassium phosphate as the buffer to elute and equilibrate the column. Total and DAT concentrations were determined as described except BCA (Pierce) was used instead of Bradford for total protein determination. Two different vector only cultures were grown in the same E. coli hosts as the cloned DATs. All of the proteins produced visible bands on SDS-PAGE gels, but to differing degrees of solubility. Polypeptides having the sequence of SEQ ID NO:892 were not very soluble.

To compare the D-tryptophan transamination activities of each of the enzymes, the D-tryptophan transamination assay and the R,R monatin transamination assay described in Example 5 were performed. The D-tryptophan aminotransferase targeted using a final concentration of 0.5 mg/mL of cellular extract containing D-aminotransferase and 0.1 mg/mL of the purified B. sphaericus DAT as a control. Quantification of the DATs in the cellular extracts was difficult due to the low levels of soluble polypeptides. The DAT polypeptides having the sequence shown in SEQ ID NO:888, 892 and 894 showed good activity with D-tryptophan as a substrate during the 30 minute reaction. DAT polypeptides having the sequence shown in SEQ ID NO:886 and 890 had measurable activity above the no-enzyme control, but exhibited little activity under the conditions tested.

Monatin transamination experiments were performed at room temperature, taking samples after 0.5, 1 and 2 hours targeting 0.5 mg/mL of each DAT, including the purified positive control from B. sphaericus. The R,R monatin transamination samples were then analyzed for monatin and alanine. The amount of monatin remaining was quantified by LC/MS/MS; alanine formation was measured using the post-column derivatization method in Example 3. Under the conditions tested, the DAT polypeptides having the sequence shown in SEQ ID NOs:892 and 894 were active. The DAT polypeptide having the sequence of SEQ ID NO:894 appeared to have the highest activity for conversion of R,R monatin to R-MP. The trends were consistent when alanine formation was assayed. The alanine production numbers (in mM) for the various timepoints are shown in Table 11.

TABLE 11

Alanine formation (mM) from R,R monatin transamination reactions

DAT polypeptide (SEQ ID NO)
0.5 hr
1 hr
2 hr

vector control 1
0.139
0.185
0.215

vector control 2
0.179
0.242
0.301

886
0.128
0.203
0.242

888
0.13
0.203
0.275

890
0.112
0.153
0.176

892
1.034
1.587
2.167

894
2.2
2.52
2.663

BsphDAT(purified)
0.287
0.519
0.894

no enzyme
0.043
0.035
0.037

DAT nucleic acids having the sequence shown in SEQ ID NO:891 and 893 were subcloned into pET30 as described in Example 4. These constructs were transformed into a variety of E. coli hosts carrying the DE3 lysogen for expression from a T7 promoter, including both K-12 and B strains of E. coli, and one strain that carried the pLysS plasmid. The clones were expressed in OvernightExpress System II as described in Example 4, with and without the addition of 0.5 mM pyridoxine, and analyzed by SDS-PAGE or Experion for expression. From these experiments, it became apparent that the proteins were expressing mostly in the insoluble fraction. Pyridoxine helped improve solubility to a small degree as did lowering the temperature from 37 to 30° C. for induction. Further work was done in cloning systems designed to maximize soluble expression (see Example 16-22).

Example 9
Analysis of CaDAT, CbDAT, and LsDAT in pET30a

The amino acid sequence shown in SEQ ID NO:894 was used to search for similar proteins available in the public databases. Three DATs were found that had similarity to SEQ ID NO:894. They were from Lactobacillus salivarus (47% identical at the protein level), Clostridium beijerinckii (57% identical at the protein level), and Clostridium acetobutylicum (60% identical at the protein level). The gene and protein sequences and their accession numbers are shown at the end of this example. FIG. 1 is an alignment showing the consensus regions of these SEQ ID NO:894-like proteins. One can see a high degree of consensus regions indicating structural similarities.

These nucleic acids were cloned into pET30a, and the corresponding polypeptides expressed and tested for activity as described herein.

CbDAT

The D-aminotransferase from Clostridium beijerinckii (CbDAT) was cloned into pET30a (untagged) BL21 (DE3) and expressed using Overnight Express II (Novagen). The cells were collected at an optical density at 600 nm of approximately 9 and centrifuged at 4000 rcf for 15 min. The cells were washed once with 100 mM potassium phosphate pH 7.8 (cold), and spun again.

Cell extracts were prepared as described herein using 100 mM EPPS pH 8.2 as the buffer to elute and equilibrate the column. Total protein and DAT protein concentrations were determined as described except the BCA method (Pierce) was used instead of the Bradford (Coomassie) assay. The CbDAT expressed well but was only partially soluble.

A monatin formation assay was done as described in Example 5 but the activity of CbDAT (0.5 mg/mL) was also studied at pH 7.4 (with potassium phosphate as a buffer). As a control, purified B. sphaericus DAT (1 mg/mL) was assayed at pH 8.2. After 1, 2, 4, 8, and 23 hrs, aliquots were taken and formic acid was added to a final concentration of 2%. Samples were frozen at −80° C. until analyzed. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. Results are shown in Table 12. The amount of monatin produced were slightly higher for the assays carried out at pH 8.2. Similar experiments were performed with the polypeptides expressed from pET28 with an N-terminal His-tag. The activity of the tagged version appeared to be slightly less than that of the untagged, but still easily detectable.

TABLE 12

Activity over time

Monatin
Monatin
Monatin
Monatin
Monatin

(ppm)
(ppm)
(ppm)
(ppm)
(ppm)

DAT Enzyme
1 hr
2 hr
4 hr
8 hr
23 hr

CbDAT pET30
45
126
280
428
502

(7.4 mg/mL)

CbDAT pET30
67
189
344
436
568

(8.2 mg/mL)

B. sphaericus

531
968
1742
2310
3706

DAT (1 mg/mL)

CaDAT and LsDAT

The D-aminotransferases from Lactobacillus salivarus (LsDAT) and Clostridium acetobutylicum (CaDAT) were cloned into pET30a (untagged) BL21(DE3) and expressed using Overnight Express II (Novagen). The cells were collected when the culture reached an optical density at 600 nm of approximately 9 by centrifugation at 4000 rcf for 15 minutes.

Cell extracts were prepared as described herein using 100 mM EPPS pH 8.2 as the buffer to elute and equilibrate the column. Total protein and DAT protein concentrations were determined using the BCA (Pierce) protocol. Both enzymes expressed well and were soluble.

The assay was performed at room temperature under anaerobic conditions. As a control, purified B. sphaericus D-aminotransferase was assayed. Approximately 0.5 mg/mL of each DAT was used. After 0.5, 1, 2, 4, 6, 8 and 22 hr an aliquot was taken and formic acid added to a final concentration of 2% and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. Results are shown in Table 13.

TABLE 13

Monatin
Monatin
Monatin
Monatin
Monatin
Monatin

DAT
(ppm)
(ppm)
(ppm)
(ppm)
(ppm)
(ppm)
Monatin (ppm)

polypeptide
0.5 hr
1 hr
2 hr
4 hr
6 hr
8 hr
22 hr

B. sphaericus

76.6
194.4
457.6
860.8
1186
1770
2546

LsDAT
2.8
6.4
14.6
33
52
69.8
173

CaDAT
50.2
141.2
318.6
543.4
612
1144
668

The homologs of the DAT having the sequence shown in SEQ ID NO:894 were active. Since the homologs showing the conserved sequence above were all active in monatin formation assays, it is expected that any D-aminotransferase containing the consensus sequences described herein would also be active, although their primary sequence identity is as low as 47%. There has been no evidence before this work that these unique D-aminotransferases, with low homology to the more characterized Bacillus D-aminotransferase, would have activity for monatin or would be broad specificity enzymes.

DNA Sequence CaDAT (ACCESSION AE001437 AE007513-AE007868; VERSION

AE001437.1 GI: 25168256; nucleotides 914049 . . . 914891)

(SEQ ID NO: 1063)

1
atgaaagatt taggatatta caatggagaa tacgacttaa ttgaaaatat gaaaatacca

61
atgaatgatc gtgtatgcta ttttggtgat ggtgtttatg atgctactta tagtagaaac

121
cataatatat ttgcactaga tgagcatatt gaccgatttt ataatagtgc cgagctttta

181
agaattaaaa ttccatatac aaagaaggaa atgaaagagc ttttaaagga tatggttaaa

241
aaggttgata gcggagaaca atttgtatat tggcaggtta ctagaggtac tggcatgcgt

301
aatcatgctt ttttgagtga ggatgttaag gctaatattt ggattgtttt aaagccacta

361
aaggtaaaag atatgtcaaa aaaattaaaa ctaataacat tagaggatac tagattttta

421
cattgtaaca taaaaacctt aaatttgctt cctagtgtaa ttgcagcaca aaaaactgaa

481
gaagcaggct gccaggaagc agtatttcat agaggagata gagttactga atgtgctcat

541
agtaatgttt caattataaa ggatgagatt ttaaaaactg cgccaacaga taatcttatt

601
ttgccgggaa tagcaagggc gcatcttata aaaatgtgca aaaaatttga gatacctgta

661
gatgaaactc catttacatt aaaggagtta attaatgcgg atgaagttat agttacaagt

721
tcagggcaat tttgtatgac tgcttgtgag atagatggaa gacctgtagg cggaaaagcg

781
ccagatatta ttaaaaagct tcagactgcc ttacttaatg aatttttgga agaaacaaat

841
taa

Protein Sequence CaDAT (ACCESSION NP_347428; VERSION NP_347428.1 GI: 15894079)

(SEQ ID NO: 1064)

1
MKDLGYYNGE YDLIENMKIP MNDRVCYFGD GVYDATYSRN HNIFALDEHI DRFYNSAELL

61
RIKIPYTKKE MKELLKDMVK KVDSGEQFVY WQVTRGTGMR NHAFLSEDVK ANIWIVLKPL

121
KVKDMSKKLK LITLEDTRFL HCNIKTLNLL PSVIAAQKTE EAGCQEAVFH RGDRVTECAH

181
SNVSIIKDEI LKTAPTDNLI LPGIARAHLI KMCKKFEIPV DETPFTLKEL INADEVIVTS

241
SGQFCMTACE IDGRPVGGKA PDIIKKLQTA LLNEFLEETN

DNA Sequence CbDAT (ACCESSION CP000721 AALO01000000 AALO01000001-

AALO01000089 VERSION CP000721.1 GI: 149901357; nucleotides 3213484 . . . 3212636)

(SEQ ID NO: 1065)

1
atggagaatt taggttatta taatggaaag tttggattat tagaggaaat gacagtacca

61
atgcttgatc gtgtttgcta ttttggagat ggagtttatg atgctactta tagcagaaat

121
cacaagattt ttgcattgga ggagcatatt gaaagatttt acaacagcgc tggtttatta

181
ggaattaaaa ttccttattc aaaggagcaa gtaaaagaaa tccttaagga gatggtatta

241
aaggttgatt caggagaaca atttgtatat tggcaaatta ctagaggaac tggaatgaga

301
aatcatgctt ttcctggaga tgaggtccct gcaaatctat ggattatgtt aaagccttta

361
aatattaagg atatgtcaca aaaattaaag ttaatcactt tagaagacac tagattttta

421
cactgtaata tcaaaacctt aaatttatta ccaagtgtaa ttgcatctca aaaaactgaa

481
gaggcaggat gtcaggaagc tgtatttcat agaggggata gagtaactga atgtgcacat

541
agcaatgtat caattattaa ggatggtata ttaaaaactg ctccaacaga caatttaatt

601
ttaccaggta tagcaagagc tcaccttatt aaaatgtgta aatcctttaa tattcctgta

661
gatgaaacag catttacctt gaaggaatta atggaggcag atgaagttat agttactagt

721
tcaggtcaat tttgtatggc aaccagtgaa atagatggaa tacctgtagg gggaaaagca

781
ccagagcttg taaagaaatt acaagatgca ttgttaaatg agttcttaga agaaacaaaa

841
acagaatag

Protein Sequence CbDAT (ACCESSION YP_001309869 VERSION YP_001309869.1

GI: 150017615)

(SEQ ID NO: 1066)

1
MENLGYYNGK FGLLEEMTVP MLDRVCYFGD GVYDATYSRN HKIFALEEHI ERFYNSAGLL

61
GIKIPYSKEQ VKEILKEMVL KVDSGEQFVY WQITRGTGMR NHAFPGDEVP ANLWIMLKPL

121
NIKDMSQKLK LITLEDTRFL HCNIKTLNLL PSVIASQKTE EAGCQEAVFH RGDRVTECAH

181
SNVSIIKDGI LKTAPTDNLI LPGIARAHLI KMCKSFNIPV DETAFTLKEL MEADEVIVTS

241
SGQFCMATSE IDGIPVGGKA PELVKKLQDA LLNEFLEETK TE

DNA Sequence LsDAT (ACCESSION CP000233 VERSION CP000233.1 GI: 90820184;

nucleotides 1750082 . . . 1750927)

(SEQ ID NO: 1067)

1
atgaagcaag ttggatacta caatggtact atcgctgatt taaatgaact taaggtgcct

61
gctactgatc gtgcacttta ttttggtgat ggttgctacg atgcaactac atttaagaac

121
aatgttgcat ttgccttaga agatcatctt gatcgttttt ataatagttg tcgcctacta

181
gagatcgatt tccctttaaa tcgcgatgaa cttaaagaaa agctttacgc tgttattgat

241
gctaacgaag ttgatactgg tatcctttat tggcaaactt cacgtggttc tggtttacgt

301
aaccatattt tcccagaaga tagccaacct aatttattaa tttttactgc tccttatggt

361
ttagttccat ttgatactga atataaactt atatctcgcg aagacactcg cttcttacat

421
tgcaatatta aaactttgaa tttacttcca aacgttattg caagtcaaaa ggctaatgaa

481
agtcattgcc aagaagtggt cttccatcgc ggtgacagag ttacagaatg tgcacactct

541
aacatcttaa ttctaaaaga tggcgttctt tgctccccac ctagagataa tttaatcttg

601
ccaggaatta ctttgaaaca tctcttgcaa ttagcaaaag aaaataatat tcctacttcc

661
gaagcaccat tcactatgga tgatcttaga aatgctgatg aagttattgt tagttcttca

721
gcttgtctag gtattcgcgc agtcgagctt gatggtcagc ctgttggtgg aaaagatgga

781
aagactttaa agatcttgca agatgcttat gctaagaaat ataatgctga aactgtaagt

841
cgttaa

Protein Sequence LsDAT (ACCESSION YP_536555 VERSION YP_536555.1 GI: 90962639)

(SEQ ID NO: 1068)

1
MKQVGYYNGT IADLNELKVP ATDRALYFGD GCYDATTFKN NVAFALEDHL DRFYNSCRLL

61
EIDFPLNRDE LKEKLYAVID ANEVDTGILY WQTSRGSGLR NHIFPEDSQP NLLIFTAPYG

121
LVPFDTEYKL ISREDTRFLH CNIKTLNLLP NVIASQKANE SHCQEVVFHR GDRVTECAHS

181
NILILKDGVL CSPPRDNLIL PGITLKHLLQ LAKENNIPTS EAPFTMDDLR NADEVIVSSS

241
ACLGIRAVEL DGQPVGGKDG KTLKILQDAY AKKYNAETVS R

Example 10
Analysis of DATs

HMS174 E. coli containing the DAT nucleic acids having the sequence of SEQ ID NO:865, 867, 869, 871, 873, 875, and 877 in vector pSE420-cHis were obtained and streaked on agar plates containing LB medium with ampicillin. One skilled in the art can synthesize the genes encoding these D-aminotransferases using assembly PCR techniques such as those described in Example 4. Single colonies were used to inoculate 3 mL of LB medium containing ampicillin (100 μg/mL). Five hundred μl of the overnight culture was used to inoculate 50 mL of the same medium in 250 mL baffled flasks. The cells were grown at 30° C. to approximately an OD_600nmof 0.5. IPTG was added to a final concentration of 1 mM. Cells were induced at 30° C. for 4 hours and collected by centrifugation.

Cell extracts were prepared as described in Example 4. Total protein and DAT concentrations were determined as described in Example 4. The DATs all appeared to express well, and most of them showed a high degree of solubility.

A monatin formation assay was done as described in Example 5 except with a DAT concentration of 0.1 mg/mL and the aldolase at a concentration of 10 μg/mL. As a control, 0.1 mg/mL of purified B. sphaericus DAT was assayed. After 6 and 22 hours, an aliquot was taken and formic acid added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin concentrations using the LC/MS/MS methodology described in Example 3. Under the conditions tested, SEQ ID NO:870, 874 and 878 all appeared to have high activity in the 3-step monatin formation assay. DAT polypeptides having the sequences shown in SEQ ID NOs:866, 872, and 876 also had activity in the monatin formation pathway but not to the same extent as did polypeptides having the sequence shown in SEQ ID NOs:870, 874 and 878 under the conditions tested. Table 14 shows the results for monatin formation (in ppm).

TABLE 14

Monatin formation assay

DAT polypeptide (SEQ ID NO)
6 hr
22 hr

866
17.4
76

868
nd
nd

870
132
836

872
13.8
50

874
281.6
798

876
2.4
12

878
223.4
576

B. sphaericus DAT
175.6
616

nd, not detected under conditions tested

Further Analysis of Polypeptides Having the Sequence of SEQ ID NO:870, 874 and 878 in pET30a

Cultures of E. coli BL21 DE3 transformed with pET30a plasmids containing nucleic acids encoding the above-indicated DATs were grown overnight in 50 mL of Overnight Express II (Solution 1-6, Novagen) at 30° C. As a positive control, a strain containing the DAT from ATCC #4978 in pET30a was also grown and induced (described in Example 6). Cells were collected at an OD_600nmof 5-10, harvested by centrifugation and frozen at −80° C. until further processed.

Cell extracts were prepared as described in the Example 4. Total protein and DAT concentrations were determined as described in Example 4.

A monatin formation assay was done as described in Example 5 except with a DAT polypeptide concentration of 0.5 mg/mL for SEQ ID NO:870 and a concentration of 0.275 mg/mL for each of SEQ ID NO:874 and 878. As a control, DAT4978 and purified B. sphaericus DAT were assayed at 0.5 mg/mL concentration. After 0.5, 1, 2, 4, 6.5, 9, 24 and 22 hr, an aliquot was taken and formic acid added to a final concentration of 2% and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. The results are shown in Table 15 (in ppm of monatin formed).

TABLE 15

DAT

polypeptide

(SEQ ID NO)
0.5 hr
1 hr
2 hr
4 hr
6.5 hr
9 hr
24 hr

4978 DAT
18
85.6
283.4
673.2
890
1226
2020

870
14.4
71
279.4
736
1340
1680
3362

874
63.8
182.6
415.6
674
888
938
1154

878
97.8
244.4
607
912.2
1068
1174
1356

B. sphaericus

44.6
142.8
375.2
813
1294
1382
2746

All three of the subcloned DATs (encoding polypeptides having the sequence of SEQ ID NO:870, 874, and 878) expressed well in the pET system and yielded soluble protein. The polypeptide having the sequence shown in SEQ ID NO:870 gave the highest amount of expression in the soluble fraction and exhibited high activity that did not appear to diminish over time in comparison to the DAT polypeptides having the sequence of SEQ ID NO:874 and 878.

Comparison Between Wild Type and Mutant DAT Polypeptides

A mutant polypeptide in which the residue of SEQ ID NO:870 was changed from a T to a N (SEQ ID NO:870 T242N) was constructed as described in Example 4 and expressed and compared to DAT4978, DAT4978 T243N (described in Example 6), B. sphaericus and wildtype SEQ ID NO:870.

Cultures of BL21 DE3 in which the wild type and mutant polypeptides having the sequence of SEQ ID NO:870, 870 T242N, DAT4978 and DAT4978 T243N were expressed from the pET30a vector, were grown in 50 mL of Overnight Express (Novagen) in a 250 mL baffled flask overnight at 30° C. and 250 rpm. The cells were collected by centrifugation when they reached an optical density at 600 nm of over 10. Cell extracts were prepared as described in Example 4, and total protein and DAT concentrations were determined as described in Example 4. All of the DATs tested were highly expressed and soluble, all near 30% as determined using the Experion software. The polypeptide having the sequence of SEQ ID NO:870 T242N had the highest expression, which was predicted to be 36.3% of the total soluble protein.

A monatin formation assay was done as described in Example 5 at a DAT polypeptide concentration of 0.5 mg/mL. As a control, 0.5 mg/mL of purified B. sphaericus DAT was assayed. After 0.5, 1 2, 4, 6.5, 9 and 23.25 hr, an aliquot was taken, formic acid added to the aliquot to a final concentration of 2% and the samples frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin, tryptophan, alanine and 4-hydroxy-4-methyl glutamic acid (HMG) as described in Example 3.

In the last time point, an additional aliquot was taken to determine % R,R monatin by the FDAA-derivatization method described in Example 3.

Monatin formation numbers (ppm) are presented in Table 16 below. The percent R,R is given in the right-hand column, for the 23.25 hr timepoint.

TABLE 16

DAT polypeptide(SEQ ID NO)
0.5 hr
1 hr
2 hr
4 hr
6.5 hr
9 hr
23.25 hr
% R,R

Wild type DAT 4978
11
57
216
472
694
942
1616
95.0

4978 T243N
74
237
542.6
1106
1396
1784
2202
99.0

870
15.6
74.4
269.6
702
1250
1522
2788
97.8

870 T242N
49.4
194
655.2
1496
2212
2666
3670
99.5

B. sphaericus

40.6
144
372
800
1090
1458
2434
97.2

The activity of the T242N mutant of the SEQ ID NO:870 polypeptide was very high, and was better than the positive controls and higher than the wildtype form of DAT polypeptides. The percentage of R,R monatin formed by this mutant was also higher than any of the other benchmark enzymes. The analysis of the amount of HMG (a by-product) formed is qualitative, but it appears that, at the 9 hour and 23.25 hour timepoints, similar amounts of HMG were formed by DAT 4978 T243N polypeptides and SEQ ID NO:870 T242N polypeptides.

The DAT polypeptide having the sequence shown in SEQ ID NO:870 is a novel protein, exhibiting 76% sequence identity to the closest known D-aminotransferase (Bacillus YM-1 D-aminotransferase) and 69% amino acid sequence identity to the B. sphaericus DAT described in Example 6. FIG. 2 shows an alignment of this novel enzyme with other published DATS, and one can see the residues that make this enzyme unique and may account for its superior activity.

The highly active DAT polypeptide having the sequence shown in SEQ ID NO:910 (more similar to B. sphaericus type DATs; see Example 12) is also shown in the alignment. As an example of the uniqueness of the SEQ ID NO:870 polypeptide, in the region surrounding amino acid residue 54-55 (B. sphaericus numbering) in the alignment of FIG. 2, it is clear that the Bacillus-like DATs have a high degree of conservation whereas SEQ ID NO:870 has the residues EC rather than AS. As another example, in the highly conserved region surrounding residue 135 of the alignment shown in FIG. 2, the SEQ ID NO:870 polypeptide has a more hydrophilic residue (T) versus predominantly valine residues. The core sequence that represents the SEQ ID NO:870 enzyme, but excludes previously known broad specificity D-aminotransferases and highly related homologs, is shown as Consensus Sequences A and B. It is expected that any polypeptide containing one of these consensus sequences would exhibit DAT activity and be active in monatin formation pathway steps.

Consensus Sequence A

(SEQ ID NO: 1069)

Y.*LWND.*IV.*EDRGYQFGDG.*YEV.*KVY.*G.*FT.*EH.*DR.*YECAEKI.*PYTK.*H.*L

LH.*L.*E.*N.*TG.*YFQ.*TRGVA.*RVHNFPAGN.*Q.*V.*SGT.*K.*F.*R.*N.*KGVKAT.*

TED.*RWLRCDIKSLNLLGAVLAKQEAIEKGCYEA.*LHR.*G.*TE.*SS.*N.*GIK.*GTLYT

HPA.*N.*ILRGITR.*V.*TCAKEIE.*PV.*Q.*T.*K.*LEMDE.*V.*S.*SE.*TP.*I.*DG.*KI.*N

G.*G.*WTR.*LQ.*F.*K.*P.

Consensus Sequence B

(SEQ ID NO: 1070)

Y[ST]LWND[QK]IV.[DE].{2}[VI].[IV].{2}EDRGYQFGDG[IV]YEV[IV]KVY[ND]G.[ML]F

T.{2}EH[IV]DR.YECAEKI[RK][LIV].[IV]PYTK.{3}H[QK]LLH.L[VI]E.N.[LV].TG[HN][IVL]

YFQ[IV]TRGVA.RVHNFPAGN[VI]Q.V[LI]SGT.K.F.R.{3}N.[EQ]KGVKAT.TED[IV]RWL

RCDIKSLNLLGAVLAKQEAIEKGCYEA[IV]LHR.G.[VI]TE.SS.N[VI][FY]GIK[DN]GTLYT

HPA[ND]N.ILRGITR.V[IV][LI]TCAKEIE[LMI]PV.[EQ]Q.{2}T.K.{2}LEMDE[LIVM].V[ST]

S.[TS]SE[IV]TP[VI]I[DE][IVL]DG.KI.NG.{2}G[ED]WTR[KQ]LQ.{2}F.{2}K[IL]P..

Similar to PERL regular expression convention language, “.*” indicates that any number of amino acid residues may be present from any of the 20 proteinogenic amino acids; [ ] indicates that any one of the amino acids in the brackets can be present; “.{#}” indicates that any of the 20 proteinogenic amino acids can be present as long as the number of residues matches the number {#} indicated in the brackets.

With respect to the use of “.*” in Consensus sequence A, the number of amino acids at any of the “.*” positions can vary, for example, from 0 to about 20 residues (see, for example, Consensus sequence B (SEQ ID NO:1070)) or from about 20 residues up to about 100 residues, or the number of amino acids can be much larger, for example, up to 1000 or more residues. Without limitation, an insertion at one or more of the “.*” positions can correspond to, for example, a domain such as (but not limited to) a chitinase binding domain (e.g., from Pyrococcus furiosus (Accession No. 2CZN_A) or P. burkholderia (Accession No. YP_—331531) or a cellulose binding domain (e.g., from Cellulomonas fimi (Accession No. 1 EXH_A) or Clostridium stercorarium (Accession No. 1UY1_A). In some embodiments (without limitation), five or less of the positions designated “.*” each contain an insertion of, for example, greater than about 20 residues (e.g., greater than about 100 residues). In other embodiments (without limitation), five or more of the positions designated “.*” each contains an insertion of less than about 100 residues (e.g., less than about 20 residues, e.g., 3, 5, 10, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90 or 95 residues)). The activity of a polypeptide having a sequence that corresponds to one or more of the consensus sequences disclosed herein and containing any number of residues inserted at one or more of the “.*” positions can be evaluated using methods that are described herein.

Non-limiting representative polypeptides that contain the consensus sequence shown in SEQ ID NO:1069 include the polypeptide having the sequence shown in SEQ ID NO:870 and Consensus sequence B (SEQ ID NO:1070).

Comparison Between SEQ ID NO:870, 870 T242N, DAT 4978 and DAT 4978 T243N, Tagged and Untagged

E. coli BL21 DE3 cells expressing the polypeptides having the sequence of SEQ ID NO:870, 870 T242N, DAT 4978 and DAT 4978 T243N were grown in 50 mL of Overnight Express (Novagen) in a 250 mL baffled flask overnight at 30° C. and 250 rpm. The cells were collected by centrifugation when the optical density at 600 nm was greater than 10. Cell extracts were prepared as described in Example 4. Total protein and DAT concentrations were determined as described in Example 4.

E. coli BL21 DE3 cultures expressing C-terminal tagged SEQ ID NO:870, 870 T242N, DAT 4978 and DAT 4978 T243N polypeptides were grown in 200 mL of Overnight Express (Novagen) in a 1000 mL baffled flask overnight at 30° C. and 250 rpm. Two cultures of each clone were grown. The cells were pooled and collected by centrifugation when at an optical density at 600 nm of over 10. Cell extracts were created by the addition of 50 mL of Bug Buster Primary Amine Free (Novagen) with 50 μl of Benzonase Nuclease (Novagen), 0.75 μl of rLysozyme (Novagen), and 250 μl of Protease Inhibitor Cocktail II (Calbiochem). The cells were incubated for 15 minutes at room temperature with gentle rocking. The extracts were centrifuged at 45,000×g for 10 minutes.

The His-tagged proteins were purified as described in the methods section using GE Healthcare (Piscataway, N.J.) Chelating Sepharose™ Fast Flow resin. The purified protein was desalted using a PD10 column into 100 mM potassium phosphate, pH 7.8 (for DAT 4978 and DAT 4978 T243N polypeptides) or 100 mM EPPS pH 8.2 (for SEQ ID NO:870 and 870 T242N polypeptides), both buffers contained 50 μM PLP.

An R,R monatin formation assay was performed as described in Example 5 with a DAT concentration of 0.5 mg/mL. Aliquots were taken at 2.25, 4.5, 9 and 24 hours, pH adjusted with formic acid, and frozen. An extra aliquot was taken at the final time point without formic acid addition for determination of stereoisomeric distribution using the FDAA derivatization method described in Example 3. The samples were thawed and centrifuged for 5 minutes and the supernatant filtered with a 0.2 μm nylon membrane filter. Samples were submitted for monatin analysis using the LC/MS/MS method described in Example 3. The results are shown in Table 17, in ppm monatin formed. The far right column is the % R,R monatin formed at the end of the experiment.

TABLE 17

DAT polypeptide (SEQ ID NO)
2.25 hr
4.5 hr
9 hr
24 hr
% R,R

DAT 4978
330
676
1470
2384
92.3

DAT 4978 T243N
1392
2856
4068
3688
98.2

870
395
952
1896
2998
97.8

870 T242N
1416
2936
3868
3976
99.3

DAT 4978 6xHis tagged
362
887
1664
2818
96.5

DAT 4978 T243N 6xHis tagged
1364
2298
3464
4440
98.9

870 6xHis tagged
228
688
1508
3138
98.1

870 T242N 6xHis tagged
746
2020
3962
4552
99.5

The overall activity and stereospecificity of the C-terminally tagged and untagged enzymes are very similar. In addition, it is expected that the presence of activity in a polypeptide encoded from a subcloned nucleic acid is predictive of the presence of activity in the corresponding polypeptide encoded from the full-length or wild type nucleic acid.

Example 11
Analysis of DATs

E. coli HMS174 containing DAT nucleic acids in the pSE420-cHis vector encoding the polypeptides having the sequence of SEQ ID NO:880, 882, and 884 were streaked onto agar plates containing LB medium with ampicillin. One skilled in the art can synthesize the genes encoding these D-aminotransferases using assembly PCR techniques such as those described in Example 4. Single colonies were used to innoculate 3 mL of LB medium containing ampicillin (100 μg/mL). Five hundred μl was used to inoculate 50 mL of the same medium in a 250 baffled flask. The cells were grown at 30° C. to approximately an OD_600nmof 0.4, and IPTG was added to a final concentration of 1 mM. Cells were grown at 30° C. for 4 hours and collected by centrifugation.

Cell extracts were prepared as described in the Example 4. Total protein and DAT polypeptide concentrations were determined as described in Example 4. SEQ ID NO:882 and 884 expressed well and were present at high levels in the soluble fraction.

An R,R monatin formation assay was performed as described in Example 5 using approximately 0.5 mg/mL of each DAT polypeptide (except that 0.35 mg/mL of the SEQ ID NO:880 polypeptide was utilized). After 2, 8, and 23 hours, an aliquot was taken, formic acid was added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. Results are shown in Table 18.

At the last time point, an extra aliquot was taken (without pH adjustment) to determine the stereoisomeric distribution of the monatin produced using the FDAA derivatization methodology described in Example 3. The percentage of R,R produced is shown in the right hand column of Table 18 below, the balance is predominantly S,R monatin.

TABLE 18

Polypeptide
monatin ppm
monatin ppm
monatin ppm
% R,R

(SEQ ID NO)
(2 hr)
(8 hr)
(23 hr)
(23 hr)

880
31.6
140
176
97.5

882
31.6
872
2790
99.3

884
79.4
644
1610
100

B. sphaericus

337
1518
2538
96.7

Polypeptides having the sequence shown in SEQ ID NO:882 and 884 exhibited good activity in the monatin formation reactions from D-tryptophan.

The stereopurity of the monatin produced was higher when using these DATs as compared to the B. sphaericus control enzyme. The DAT nucleic acids encoding DAT polypeptides having the sequence of SEQ ID NO:882 and 884 were subcloned into pET30a vectors as described in Example 4.

Analysis of DAT Polypeptides Having the Sequence of SEQ ID NO:882 and 884 Expressed from the pET30a Vector

Cultures of E. coli BL21 DE3 containing nucleic acids encoding DAT polypeptides having the sequence of SEQ ID NO:882 and 884 in the pET30a vector were grown in 50 mL of Overnight Express (Novagen) in a 250 mL baffled flask overnight at 30° C. and 250 rpm. The cells were collected by centrifugation when the optical density at 600 nm was greater than 10.

Cell extracts were prepared as described in Example 4. Total protein and DAT polypeptide concentrations were determined as described. Total and soluble protein samples were analyzed using a 4-15% gradient acrylamide gel as well as by the Experion system. Expression was predicted to be approximately 30% by the Experion software. Visible bands were seen for both the total protein and soluble protein (cell-free extract) fractions.

A monatin formation assay was performed as described in Example 5 with both 0.5 and 2 mg/mL DAT polypeptide concentrations. Purified B. sphaericus DAT was used as a control. After 2, 4.5, 9, 24, 36 and 48 hrs, an aliquot was taken, formic acid was added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. The samples were qualitatively analyzed for HMG levels. Additional aliquots were taken (without pH adjustment) for stereoisomeric analysis using the FDAA derivatization methodology described in Example 3. The results are shown in Tables 19 and 20.

TABLE 19

DAT
Monatin
Monatin
Monatin
Monatin
Monatin
Monatin

polypeptide
(ppm)
(ppm)
(ppm)
(ppm)
(ppm)
(ppm)

(SEQ ID NO)
2 hrs
4.5 hrs
9 hrs
24 hrs
36 hrs
48 hrs

882
61
274
780
1802
2172
2170

(0.5 mg/mL)

882 (2 mg/mL)
985
2452
3232
3128
3082
3158

884
149
362
656
1394
1756
2158

(0.5 mg/mL)

884 (2 mg/mL)
811
1628
2466
2988
3178
2864

B. sphaericus

362
860
1268
2362
2532
2804

(0.5 mg/mL)

B. sphaericus

1335
2344
3154
3866
3842
4008

(2 mg/mL)

TABLE 20

Stereopurities of monatin produced at selected timepoints

DAT polypeptide
24 hrs
48 hrs

(SEQ ID NO)
(% R,R)
(% R,R)

882 (2 mg/mL)
95.4
94.1

884 (2 mg/mL)
99.6
99.4

Bs DAT (2 mg/mL)
95.8
93.3

Polypeptides having the sequence shown in SEQ ID NO:882 and 884 exhibited good monatin formation activity and stereospecifity, and appeared to produce less HMG than the B. sphaericus control during the initial timepoints. Polypeptides having the sequence of SEQ ID NO:882 exhibited similar initial monatin formation rates but appeared to have plateaued in this experiment at a lower monatin titer.

Example 12
Analysis of DATs in pSE420-cHis, and of a DAT in pET30a

The open reading frames encoding DAT polypeptides having the sequence of SEQ ID NO:898, 900, 902, 904, 906, 910, and 896 were evaluated. One of ordinary skill in the art can synthesize the genes encoding these D-aminotransferases using assembly PCR techniques such as those described in Example 4.

A culture of E. coli BL21 DE3 containing a nucleic acid encoding a DAT polypeptide having the sequence shown in SEQ ID NO:896 in the pET30a vector (subcloned as described in Example 4) was grown in 50 mL of Overnight Express (Novagen) in a 250 mL baffled flask overnight at 30° C. and 250 rpm. The cells were collected by centrifugation when the optical density at 600 nm was greater than 10.

Top10 (Invitrogen, Carlsbad, Calif.) E. coli cells were transformed with the pSE420-cHis plasmid containing the DAT nucleic acids having the sequence shown in SEQ ID NO:897, 899, 901, 903, 905, and 909 and plated on LB medium containing ampicillin (100 μg/mL). Five hundred μl of an overnight culture was used to inoculate 50 mL of the same medium in a 250 baffled flask. The cells were grown at 30° C. to an OD_600nmof approximately 0.4 and IPTG was added to a final concentration of 1 mM. Cells were grown at 30° C. for 4 hours and collected by centrifugation.

Cell extracts were prepared as described in Example 4. Soluble protein and estimated DAT concentrations were determined as described in Example 4.

An R,R monatin formation assay was performed as described in Example 5 with DAT polypeptide concentrations of 0.5 mg/mL, except that 0.3 mg/mL of the polypeptide having the sequence of SEQ ID NO:896 was used; 0.06 mg/mL of the polypeptide having the sequence of SEQ ID NO:898 was used; 0.4 mg/mL of the polypeptide having the sequence shown in SEQ ID NO:900 was used; 0.1 mg/mL of the polypeptide having the sequence of SEQ ID NO:902 was used; and 0.12 mg/mL of the polypeptide having the sequence of SEQ ID NO:904 was used. As positive controls, SEQ ID NO:870, 870 T242N, and purified B. sphaericus were tested at DAT polypeptide concentrations of 0.5 mg/mL. After 2, 6, and 24 hours, an aliquot was taken, formic acid was added to a final concentration of 2% and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. Additional aliquots were taken for stereoisomeric distribution analysis and were not treated with formic acid. The results for the 24 hour time point are shown in Table 21. The DAT nucleic acid encoding the DAT polypeptide having the sequence shown in SEQ ID NO:908 was not subcloned and could not be assayed.

TABLE 21

Polypeptide (SEQ
monatin
monatin
monatin
24 hr

ID NO)
2 hrs (ppm)
6 hrs (ppm)
24 hrs (ppm)
% R,R

B. sphaericus

261
1203
2604
95.6

870
193
1067
2490
96.8

870 T242N
813
2230
3380
98.8

896
30
127
286
99.8

898
nd
3
15
95.7

900
4
16
56
92.9

902
144
411
1209
96.7

904
nd
1
4
92.3

906
14
18
25
98

910
487
1154
2770
94.5

nd = not detectable under conditions tested

DAT polypeptides having the sequence shown in SEQ ID NO:910 and 902 had high levels of activity for the monatin formation reactions, and produced fairly high levels of R,R monatin. Results indicated that the DAT polypeptide having the sequence shown in SEQ ID NO:870 exhibited comparable activity to that of the wildtype polypeptide having the sequence shown in SEQ ID NO:910 under the conditions tested; however, the T242N mutation in the SEQ ID NO:870 polypeptide makes a large improvement in activity and stereospecificity of the enzyme.

Example 13
Analysis of DATs

Plasmids (pSE420-cHis) containing the nucleic acid sequences encoding SEQ ID NO:912, 914, 916, 918, 920, 922, 924, and 926 DATs were obtained. One skilled in the art could clone the genes using any number of gene assembly protocols such as the one described in Example 4.

E. coli Top10 (Invitrogen) cells were transformed with the pSE420-cHis plasmids containing DAT polypeptides having the sequence of SEQ ID NO:912, 914, 916, 918, 920, 922, 924, and 926 and plated on LB medium containing ampicillin (100 μg/mL). Five hundred μl of the overnight culture was used to inoculate 50 mL of the same medium into 250 mL baffled flasks. Cultures were grown at 30° C. to an OD_600nmof approximately 0.4. IPTG was added to a final concentration of 1 mM. Cells were grown at 30° C. for 4 hours and collected by centrifugation.

Cell extracts were prepared as described in Example 4. Total soluble protein and DAT protein concentrations were determined as described in Example 4. Most of the DAT polypeptides that were expressed were soluble except for the SEQ ID NO:916 polypeptide, which was only partially soluble.

An R,R monatin formation assay was performed as described in Example 5, with a DAT polypeptide concentration targeted to about 0.25 mg/mL; except that 0.1 mg/mL of the SEQ ID NO:922 polypeptide was used and 0.2 mg/mL of the SEQ ID NO:926 polypeptide was used. As a positive control, purified B. sphaericus DAT was tested at a 0.25 mg/mL concentration. After 2, 8 and 24 hours, an aliquot was taken and formic acid was added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 3. The results are shown in Table 22.

TABLE 22

Polypeptides
monatin (ppm)
monatin (ppm)
monatin (ppm)

(SEQ ID NO)
2 hours
8 hours
24 hours

B. sphaericus

179
774
1482

912
0.2
2
2

914
4
22
62

916
0.6
2
6

918
158.8
402
496

920
5
40
96

922
0.2
2
2

924
nd
nd
nd

926
1.2
12
30

nd = not detected under conditions assayed

DAT nucleic acids having the sequence shown in SEQ ID NO:169, 171, 167, 173 and 175 (encoding DAT polypeptides having the sequence shown in SEQ ID NO:170, 172, 168, 174 and 176) were obtained as PCR products and were subcloned in pET30a as described in Example 4. One of ordinary skill in the art could reconstruct the genes using any number of gene assembly methods such as the one described in Example 4.

E. coli BL21 DE3 cells containing DAT nucleic acids having the sequence of SEQ ID NO:169, 171, 167, 173 and 175 in the pET30a vector were grown in 50 mL of Overnight Express (Novagen) in a 250 mL baffled flask, overnight at 30° C. and 250 rpm. The cells were collected by centrifugation when the optical density at 600 nm was greater than 10.

Cell extracts were prepared as described in the Example 4. Total soluble protein and DAT protein concentrations were determined as described in Example 4. The polypeptide having the sequence of SEQ ID NO:170 (encoded by the DAT nucleic acid having the sequence of SEQ ID NO:169) did not appear to be soluble, which may have impeded activity assays.

An R,R monatin formation assay was performed as described in Example 5 using a DAT polypeptide concentration of 0.5 mg/mL, except that 0.25 mg/mL of the SEQ ID NO:170 polypeptide was used. As a positive control, purified B. sphaericus DAT was tested at a 0.5 mg/mL concentration. After 2, 8 and 24 hours, an aliquot was taken, formic acid was added to a final concentration of 2%, and the samples were frozen. Samples were then thawed, spun and filtered, and analyzed for monatin using the LC/MS/MS methodology described in Example 3. Results are shown in Table 23.

TABLE 23

Polypeptides
monatin (ppm)
monatin (ppm)
monatin (ppm)

(SEQ ID NO)
2 hr
8 hr
24 hr

B. sphaericus

456
1502
2970

170
2
8
14

172
5
20
60

168
15
68
186

174
1
4
8

176
451
1508
2744

Samples (without pH adjustment) were analyzed to determine % R,R using the FDAA derivatization protocol described in Example 3. The monatin produced by DAT polypeptide having the sequence shown in SEQ ID NO:176 was 99.6% R,R after 24 hrs compared to that produced by B. sphaericus, which was 95.2% R,R at the same timepoint. The activity and stereopurity resulting from the DAT polypeptide having the sequence of SEQ ID NO:176 were both quite high, and the corresponding nucleic acid was subcloned as a C-terminal tagged protein as described in Example 4 for more quantitative studies.

Characterization of SEQ ID NO:176 C-His-Tagged Protein

The nucleic acid having SEQ ID NO:175, which encodes the polypeptide having the sequence of SEQ ID NO:176, was cloned into pET30a without a stop codon so that it could be expressed as a fusion protein with a 6×His-tag on the C-terminus. The protein was purified using the His-bind resin described in Example 4. When the fusion protein was eluted from the PD-10 desalting column, a yellow precipitate formed in the solution. A yellow residue was also observed on the column. The yellow color usually is indicative of the presence of a PLP-binding protein. In an effort to prevent the precipitation of the PLP-binding protein at the desalting step, different buffers (100 mM phosphate and 100 mM EPPS with or without 10% glycerol) at two pH values (7.8 and 8.2) were utilized. None of the buffers tried appeared to completely prevent the precipitation.

The monatin assay was performed using a well-mixed heterogeneous protein solution and a DAT polypeptide concentration of 0.5 mg/mL. The results are shown in Table 24. The purified SEQ ID NO:176 DAT polypeptide (C-tagged) showed comparable activity to the positive control DAT polypeptide from B. sphaericus; however, the activity appeared to be lower than the activity exhibited by the mutant polypeptides having the sequence of SEQ ID NO:870 T242N or SEQ ID NO:870 T242N.

TABLE 24

Monatin Production (ppm)

Polypeptide (SEQ ID NO)
2 hr
4 hr
8 hr
24 hr

B. sphaericus

262
676
1044
2150

870
332
678
1346
2826

870 T242N
942
1938
2834
4004

176
208
392
732
1806

Example 14
Evaluation of DATs

The open reading frames encoding 29 DATs were obtained as PCR products. It is noted that one of ordinary skill in the art can synthesize the genes encoding the DATs using assembly techniques such as those described in Example 4. The DAT nucleic acids were subcloned into the pET30a vector and expressed as untagged proteins as described in Example 4. The desalted cell-free extracts (prepared as described in Example 4) were used in monatin formation assays. A DAT polypeptide concentration of 0.5 mg/mL was used for the monatin assay except for the following polypeptides (amounts used in parentheses): the SEQ ID NO:156 polypeptide (0.4 mg/mL), the SEQ ID NO:182 polypeptide (0.45 mg/mL), the SEQ ID NO:240 polypeptide (0.47 mg/mL), and the SEQ ID NO:204 polypeptide (0.42 mg/mL).

Most of the DAT polypeptides showed undetectable to low monatin production under the conditions assayed as compared to positive control enzymes. Most of the expressed DAT polypeptides were soluble as determined by the Experion; however, the polypeptides having SEQ ID NO:204 and 240 were expressed at very low levels and may not have been very soluble. On the other hand, the polypeptide having SEQ ID NO:220 was predicted to be 68% of the total soluble protein as judged by the Experion software.

The monatin production results are shown in Table 25 and 26. At 24 h, the DAT polypeptide having SEQ ID NO:156 and 214 produced 40-50% of monatin as compared to the positive control enzyme, the DAT from B. sphaericus. The most active DAT polypeptide was the SEQ ID NO:220 polypeptide. Approximately 4 h after the reaction was started, the monatin concentration reached a maximum. It is expected that the mature protein of SEQ ID NO:156 (without the predicted leader sequence) is the active component of the DAT polypeptide and, therefore, the protein can be produced recombinantly with the leader sequence absent.

TABLE 25

Monatin Formed (ppm)

Polypeptide (SEQ ID NO)
2 hr
4 hr
8 hr
24 hr

178
11
24
62
194

180
nd
nd
nd
nd

154
52
103
166
178

182
nd
nd
nd
nd

218
1.6
2.8
274
12

188
2.4
5.2
10
22

190
3.8
9.4
22
42

208
1
1.2
nd
nd

220
2418
3563
3812
3882

196
1
1.8
nd
8

156
64.8
156
296
796

B. sphaericus

422
791
1302
2124

nd = not detectable under conditions assayed

TABLE 26

Monatin Formed (ppm)

Polypeptide (SEQ ID NO)
2
4
8
24

166
nd
nd
1
nd

216
69
91
109
134

200
nd
nd
1
1

198
nd
nd
nd
nd

210
1.6
3.8
6.2
15.2

202
3.4
6.2
12.2
29.8

222
3.6
7
12.8
25.8

236
nd
nd
nd
nd

204
nd
nd
nd
3.6

238
10.4
21.8
46.4
115.6

240
3
6
12.4
32.2

224
39.8
85
171.8
268.8

226
2.6
5.8
12.4
30.6

228
4.2
9.8
21.4
66.8

230
9.2
21.8
42.2
94.4

232
3.6
9.4
21.6
57

246
nd
nd
nd
nd

214
160
327
694
1346

B. sphaericus

393
986
1624
2597

nd = not detectable under conditions assayed

The high activity of the SEQ ID NO:220 polypeptide was confirmed in another monatin formation assay where the SEQ ID NO:220 polypeptide was compared to the SEQ ID NO:870, 870 T242N, and B. sphaericus DAT polypeptides. A DAT polypeptide concentration of 0.1 mg/mL and 0.5 mg was used for each of the DAT polypeptides assayed. The results are shown in Table 27. Due to the high degree of activity of the DAT polypeptides assayed, the monatin samples had to be diluted 100-fold to be within the quantitative range of the instruments used (as opposed to a typical 10- or 20-fold dilution).

TABLE 27

Monatin Formed (ppm)

DAT Polypeptide (SEQ ID NO)
2 hr
4 hr
8 hr
24 hr

B. sphaericus (0.1 mg/mL)
74
170
309
728

B. sphaericus (0.5 mg/mL)
510
921
1068
2704

870 (0.1 mg/mL)
28
81
179
706

870 (0.5 mg/mL)
399
847
1466
2916

870 T242N (0.1 mg/mL)
93.2
245.8
582.4
1270

870 T242N (0.5 mg/mL)
1158.8
2026
3202
4126

220 (0.1 mg/mL)
965.8
1512
2330
3788

220 (0.5 mg/mL)
2950
4302
4618
4488

The percentage of R,R formed by the DAT polypeptide having SEQ ID NO:220 in the above experiments was determined using the FDAA derivatization methodology described in Example 3. The DAT polypeptide having the sequence of SEQ ID NO:220 is highly stereospecific, producing 99.3% R,R monatin at 24 hours as compared to 92.9% R,R for B. sphaericus. In another assay, the SEQ ID NO:220 polypeptide produced 99.8% R,R-monatin.

The DAT polypeptide having the sequence of SEQ ID NO:220 is a novel protein that is 62% identical at the protein level to the C. beijerinckii DAT polypeptide shown in Example 9. The SEQ ID NO:220 polypeptide has 86%-90% primary sequence homology to other highly active DAT polypeptides (e.g., those having the sequence shown in SEQ ID NO:892 and 894 (Example 8), 946 (Example 7) and 176 (Example 13)). These highly active and novel DAT polypeptides were uncharacterized prior to this work, and these enzymes exhibited higher activity and stereospecificity for R,R monatin production reactions than any of the published Bacillus-like D-aminotransferases. FIG. 3 shows an alignment of these related D-aminotransferases and the consensus sequence motifs they have in common are described below.

Consensus Sequence C

(SEQ ID NO: 1071)

M.*GYYNG.*P.*DR.*FGDG.*YDAT.*N.*FAL.*H.*RF.*NS.*LL.*I.*K.*YWQ.*RG.*G.*R.*

H.*F.*N.*I.*P.*KLI.*DTRF.*HCNIKTLNL.*P.*VIA.*Q.*E.*C.*E.*VFHRG.*VTECAHSN.*I.

*NLIL.*G.*HL.*P.*E.*F.*L.*ADE.*V.*SS.*DG.*GGK.*K.*Q.*T

Consensus Sequence D

(SEQ ID NO: 1072)

M.{3}GYYNG.{10}P.{2}DR.{3}FGDG.YDAT.{3}N.{3}FAL.{2}H.{2}RF.NS.{2}LL.I.{9}K.

{17}YWQ.{2}RG.G.R.H.F.{5,7}N.{2}I.{3}P.{10}KLI.{3}DTRF.HCNIKTLNL.P.VIA.Q.{3}E.

{2}C.E.VFHRG.{2}VTECAHSN.{2}I.{11}DNLIL.G.{4}HL.{9}P.{2}E.{2}F.{4}L.{2}ADE.

{2}V.SS.{10}DG.{3}GGK.{5}K.{2}Q.{10}T

Consensus Sequence E

(SEQ ID NO: 1073)

M.*[LV]GYYNG.*[LI].*[ML].*[VI]P.*DR.*[YF]FGDG.*YDAT.*N.*FAL[DE][ED]H[IL][DE]

RF.*NS.*LL*I.*[KR].*[EQ][LMV]K[KE].*[MV].*[DE].*[VL]YWQ.*[TS]RG[TS]G.*R[NS]

H.*F.*N[LI].*I.*P.*[IVL].*[KE].*KLI[TS].*[ED]DTRF.*HCNIKTLNL[IL]P[NS]VIA[SA]Q[R

K].*E.*C.*E.*VFHRG[ED].*VTECAHSN[V1].*I[IL][KR][ND].*[TS].*DNLIL.*G.*HL[LI][Q

K].*[IV]P.*E.*F[TS][LM].*[ED]L.*ADE[VI][LI]V[ST]SS.*[LM1].*[IL]DG.*GGK.[LVI]K.*

[IL]Q.*[EK][FY].*T

Similar to PERL regular expression convention language (perldoc.perl.org), “.*” indicates that any number of amino acid residues may be present from any of the 20 proteinogenic amino acids; [ ] indicates that any one of the amino acids in the brackets can be present; “.{#}” indicates that any of the 20 proteinogenic amino acids can be present as long as the number of residues matches the number (#) indicated in the brackets.

With respect to the use of “.*” in Consensus sequence C, the number of amino acids at any of the “.*” positions can vary, for example, from about 0 to about 20 residues (see, for example, Consensus sequences D (SEQ ID NO:1072) and E (SEQ ID NO:1073)) or from about 20 residues up to about 100 residues, or the number of amino acids can be much larger, for example, up to 1000 or more residues. Without limitation, an insertion at one or more of the “.*” positions can correspond to, for example, a domain such as (but not limited to) a chitinase binding domain (e.g., from Pyrococcus litriosus (Accession No. 2CZN_A) or P. burkholderia (Accession No. YP_—331531) or a cellulose binding domain (e.g., from Cellulomonas fimi (Accession No. 1EXH_A) or Clostridium stercorarium (Accession No. 1UY1_A). In some embodiments (without limitation), five or less of the positions designated “.*” each contain an insertion of, for example, greater than about 20 residues (e.g., greater than about 100 residues). In other embodiments (without limitation), five or more of the positions designated “.*” each contains an insertion of less than about 100 residues (e.g., less than about 20 residues, e.g., 3, 5, 10, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, or 95 residues). The activity of a polypeptide having a sequence that corresponds to one or more of the consensus sequences disclosed herein and containing any number of residues inserted at one or more of the “.*” positions can be evaluated using methods that are described herein.

Non-limiting representative polypeptide that contain the consensus sequence shown in SEQ ID NO:1071 include SEQ ID NO:220, 892, 894, 176 and 946 and Consensus sequences D (SEQ ID NO:1072) and E (SEQ ID NO:1073)). It is expected that any D-aminotransferase exhibiting any of consensus sequences C, D, or E would be active in monatin formation pathway steps.

Characterization of a c-His-Tagged Polypeptide Having the Sequence of SEQ ID NO:220

The DAT nucleic acid having the sequence of SEQ ID NO:219 (encoding the polypeptide of SEQ ID NO:220) was cloned into pET30a without a stop codon such that it was expressed as a fusion protein with a 6×His-tag on the C-terminus (as described in Example 4). The fusion protein was purified using the His-Bind column (Novagen) described in Example 4. The eluate from the PD-10 desalting column formed a yellow precipitate. Yellow residue was also observed on the column. Monatin assays were done using a well-mixed heterogenous protein solution. Amounts of DAT polypeptide used are indicated in parentheses in the far left column. The notation w/Trp indicates that the enzyme was incubated with 10 mM D-tryptophan overnight on ice. Results are shown in Table 28.

TABLE 28

Monatin formed (ppm)

Polypeptide (SEQ ID NO)
2 hr
4 hr
8 hr
24 hr

B. sphaericus (0.5 mg/mL)

382
660
1021
1986

870 T242N (0.1 mg/mL)
69
205
412
1074

870 T242N w/Trp (0.1 mg/mL)
63
163
383
978

870 T242N (0.5 mg/mL)
919
1698
2356
3130

870 T242N w/ Trp (0.5 mg/mL)
772
1519
2294
3023

220 (0.1 mg/mL)
847
1462
2202
3004

220 (0.1 mg/mL)
811
1522
2202
2887

220 w/ Trp (0.1 mg/mL)
537
1080
1590
2401

220 (0.5 mg/mL)
2885
3446
3813
4066

220 w/ Trp (0.5 mg/mL)
1933
3223
3939
3911

The reaction containing 0.1 mg/mL of the SEQ ID NO:220 polypeptide showed a similar monatin formation time course as the reaction containing 0.5 mg/mL of the SEQ ID NO:870 T242N polypeptide. Addition of D-tryptophan (10 mM) to the solution containing the purified protein eliminated the precipitation. Activity loss was observed for the sample in which SEQ ID NO:220 was incubated with D-tryptophan (10 mM) overnight on ice, but no negative effect was observed when the SEQ ID NO:870 T242N polypeptide was treated with D-tryptophan (10 mM). The presence of HMG was also analyzed qualitatively for reactions catalyzed by the SEQ ID NO:220 polypeptide by comparing peak areas. When both DAT polypeptides were utilized at a concentration of 0.5 mg/mL, the reaction catalyzed by the SEQ ID NO:220 polypeptide formed around 40% of the HMG compared to the reaction containing the SEQ ID NO:870 T242N polypeptide. Earlier time points show an even more pronounced difference between the two enzymes.

In an attempt to prevent the protein precipitation during the purification of the SEQ ID NO:220 polypeptide, DTT (5 mM) was included in all the buffers including the Bugbuster reagent, the buffers for His-Bind column and the buffer for PD-10 column. No precipitation was observed after the desalting column, and no negative effect was observed on the activity of the SEQ ID NO:220 polypeptide when DTT was included during purification or added into purified protein solution at a concentration of 2 mM. Data for monatin formation assays are shown in Table 29. The amount of DAT polypeptide used is indicated in the left column in parentheses. “added DTT” indicates that 2 mM DTT was added to resolubilize the protein after purification; and “purified w/DTT” indicates that 5 mM DTT was present throughout the purification.

TABLE 29

Monatin Formed (ppm)

Polypeptide (SEQ ID NO)
2 hr
4 hr
24 hr

B. sphaericus

426
965
2638

(0.5 mg/mL)

870 T242N (0.5 mg/mL)
977
1916
4227

220 (0.1 mg/mL)
1214
2163
3964

220 (0.5 mg/mL)
3534
4246
4415

220 added DTT (0.1 mg/mL)
1287
2202
3566

220 added DTT (0.4 mg/mL)
3495
4833
5082

220 purified w/ DTT (0.1 mg/mL)
1204
2169
3997

220 purified w/ DTT (0.5 mg/mL)
3562
4110
4353

The highly desirable properties of the SEQ ID NO:220 polypeptide make it an excellent candidate for further mutagenesis or directed evolution experiments.

Site-Directed Mutagenesis of the SEQ ID NO:220 Polypeptide

A loop region of the DAT polypeptide related to the Bacillus DAT polypeptide was identified as being important for the substrate specificity and stereospecificity of the enzymes (Ro et al., 1996, FEBS Lett, 398:141-145; Sugio et al., 1995, Biochemistry 34:9661-9669; and EP 1 580 268). One key residue in this region is a T at residue 242 (in the DAT polypeptide from ATCC #4978, this position corresponds to a Tat residue 243). A T242N mutant of the SEQ ID NO:870 polypeptide showed improvement in both activity and stereospecificity, as did the T243N mutant of DAT 4978 (see Example 10). Primary sequence alignment of the SEQ ID NO:220 polypeptide with the SEQ ID NO:870 polypeptide showed only 35% amino acid sequence identity and 65% homology. The T242 residue in SEQ ID NO:870 aligned with a G240 residue in SEQ ID NO:220, which is followed by a T241 residue. Using Accelrys DS Modeler software for both proteins (with Bacillus YM-1 structures as templates), it was difficult to overlap the loop region of the SEQ ID NO:870 polypeptide with the SEQ ID NO:220 polypeptide. Therefore, both amino acids were chosen as targets for site-directed mutagenesis.

A mutant polypeptide designated SEQ ID NO:220 G240N and SEQ ID NO:220 T241N were generated by site-directed mutagenesis of the corresponding nucleic acid (SEQ ID NO:219) as described in Example 4. The two mutant polypeptides were expressed and purified as 6×His-tagged fusion proteins that were used in the monatin formation assay. Yellow precipitation was observed at the desalting step for both of the mutant SEQ ID NO:220 polypeptides. Results are shown in Tables 30 and 31 for monatin formation assays. The amount of D-aminotransferase used is indicated in the left-hand column in parentheses. Different preparations of the SEQ ID NO:220 polypeptide were utilized in the assay. “ferm” indicates that the SEQ ID NO:220 polypeptide used was produced in a fermentor as described in Example 15.

TABLE 30

Monatin Produced (ppm)

Polypeptide (SEQ ID NO)
2 hrs
4 hrs
8 hrs
24 hrs

B. sphaericus (0.5 mg/mL)
440
777
1510
2621

870 T242N (0.5 mg/mL)
961
1913
2793
3904

ferm 220 (0.1 mg/mL)
1396
2379
3217
3770

ferm 220 (0.2 mg/mL)
2301
3277
3789
4328

ferm 220 w/ DTT (0.1 mg/mL)
1434
2384
3109
3730

ferm 220 w/ DTT (0.2 mg/mL)
2423
3568
3859
4755

220 (0.1 mg/mL)
1109
1912
2809
3713

220 T241N (0.1 mg/mL)
554
856
1084
1986

TABLE 31

Monatin Formed (ppm)

Polypeptide (SEQ ID NO)
2 hr
4 hr
8 hr
24 hr

B. sphaericus (0.5 mg/mL)
634
938
1651
2754

870 T242N (0.5 mg/mL)
1422
1922
3211
3793

ferm 220 (0.1 mg/mL)
1976
2505
3442
4211

ferm 220 (0.2 mg/mL)
3198
3430
4452
4639

220 G240N (0.1 mg/mL)
3
5
14
42

220 G240N (0.2 mg/mL)
9
17
46
94

A very small amount of monatin (95.7% R,R monatin) was formed in the reaction catalyzed by the mutant SEQ ID NO:220 G240N polypeptide. The mutant SEQ ID NO:220 T241N polypeptide lost about 50% of the activity, but still maintained the stereospecificity (99.7% R,R monatin produced). These results, together with the homology modeling and alignments, suggest that, in the region surrounding residues 242-243 (and potentially beyond), the structure of the SEQ ID NO:220 polypeptide is not similar to the structure of the SEQ ID NO:870 polypeptide or the structure of the Bacillus-like DAT polypeptide in the literature. Since there is no x-ray crystal structure, random mutagenesis, combinatorial approaches and other directed evolution approaches of the SEQ ID NO:220 polypeptide and related DAT polypeptides are expected to be highly productive in further improving the enzyme's activity.

Example 15
Production of a DAT in a Fermentor

Bacterial growth media components were from Difco, Fisher Scientific, or VWR; other reagents were of analytical grade or the highest grade commercially available. The fermentation was run in a New Brunswick Scientific (Edison, N.J.) BioFlo 3000® fermenter. Centrifugation was carried out using a Beckman (Fullerton, Calif.) Avanti® J-25I centrifuge with a JLA-16.250 or JA-25.50 rotor.

The DAT nucleic acid encoding the polypeptide having the sequence in SEQ ID NO:220 with a C-terminal His-tag was cloned using Nde I/Xho I restriction sites into the pMet1a vector described in Example 16. The antibiotic marker (bla gene) can further be removed using Psi I restriction enzyme digestion, gel purification of the vector band, self-ligation of the vector ends, transformation into the E. coli host, and selection on minimal medium plates that do not contain methionine. Typically, Neidhardt's medium with 15 amino acids is used. The cloning sites were NdeI/XhoI to insert the SEQ ID NO:220 nucleic acid sequence into pMET1a (see Example 16).

The SEQ ID NO:220 DAT polypeptide carrying a C-terminal His-purification tag was produced in a fermentor at the 2.5-L scale, in a fed-batch process that achieves high cell densities and high levels of expression of the desired protein. The protocol and results for growth of E. coli strain B834(DE3)::SEQ ID NO:220cHIS pMET1 are described as follows: Starting from a fresh culture plate (Neidhardt's+15 amino acids, no methionine), the cells were grown in 5 mL of Neidhardt's medium supplemented with 15 amino acids, at 30° C. and 225 rpm for 6-8 h. One mL of the culture was transferred to each of 2 125-mL aliquots of the production medium supplemented with 5 g/L of glucose. The flasks were grown at 30° C. and 225 rpm overnight (16-18 h). A fermentor was charged with 2.5 liters of the production medium, containing (per liter): 2.0 g/L (NH₄)₂SO₄; 8.0 g/L K₂HPO₄; 2.0 g/L NaCl; 1.0 g/L Na₃Citrate.2H₂O; 1.0 g/L MgSO₄. 7H₂O; 0.025 g/L CaCl₂.2H₂O; 0.05 g/L FeSO₄.7H₂O; 0.4 mL/L Neidhardt micronutrients, and 2.0 g/L glucose. The fermenter was inoculated with 10% v/v of the overnight culture. Three hours after inoculation, an exponential glucose feed was set up using a 60% w/v glucose solution. The feed was supplied at the required rate to support microbial growth at an exponential rate of 0.15 h⁻¹. When the carbon dioxide evolution rate (CER) had reached a value of 100 mmoles/L/h (approximately 21 hours after inoculation; corresponding to a cell biomass of 15-16 g DCW/L), gene expression was induced with a bolus addition of 2 g/L lactose (fed as a 20% solution). The feed was changed from 60% w/v glucose to 50% w/v glucose+10% w/v lactose while the feed rate was fixed to the rate at time of induction. The “50% w/v glucose+10% w/v lactose” feed was maintained for 6 hours. At the end of the fermentation, the cells were harvested by centrifugation at 5000-7000×g for 10 min and frozen as a wet cell paste at −80° C. Cell paste (318 grams) was harvested from 2.8 L of cell broth.

To prepare cell free extract containing the SEQ ID NO:220 polypeptide, 50 g of wet cell paste was suspended in 150 mL of 50 mM EPPS buffer (pH 8.4) containing 50 μM pyridoxal phosphate (PLP) and then disrupted using a Microfluidics homogenizer (Microfluidics, Newton, Mass.) (3 passes at 18,000 psi), maintaining the temperature of the suspension at less than 15° C. The cell debris was removed by centrifugation (20,000×g for 30 minutes). Two mM DTT was added to the clarified cell extract.

To prepare purified SEQ ID NO:220, 2×25 mL aliquots of clarified cell extract were loaded each onto a 45 mL Chelating Sepharose™ Fast Flow resin (nickel(II) form) column that had been previously equilibrated with 50 mM EPPS (pH 8.4) containing 0.05 mM PLP and 200 mM sodium chloride. After loading the sample, the column was washed/eluted successively with 3-5 volumes of the equilibration buffer, 3-5 volumes of the equilibration buffer containing 25 mM imidazole, 3-5 volumes of the equilibration buffer containing 100 mM imidazole and 3-5 volumes of the equilibration buffer containing 500 mM imidazole. The 500 mM imidazole eluent was concentrated 10× with an Amicon (Billerica, Mass.) Centricon-70 centrifugal filter device (MWCO 10 kDa). The imidazole and sodium chloride were removed by passage through disposable GE Healthcare PD10 desalting columns previously equilibrated with 50 mM EPPS (pH 8.4) containing 0.05 mM PLP. The protein concentration of the desalted solution was determined using the Pierce BCA assay kit (Rockford, Ill.). The purity of each fraction and the level of expression in the cell free extract fraction were determined by SDS-PAGE with 4-15% gradient gels. Approximately 450 mg of protein that was ˜90% pure was recovered from the 50 mL of clarified cell extract. Two mM DTT was added to 10 mL of the purified protein. The purified protein was dispensed into aliquots (0.5-5 mL) and stored at −80° C.

Bench scale reactions (250 mL) were carried out in 0.7 L Sixfors agitated fermenters (Infors AG, Bottmingen, Switzerland) under a nitrogen headspace. The reaction mix contained 10 mM potassium phosphate, 1 mM MgCl₂, 0.05 mM PLP, 200 mM sodium pyruvate and 100 mM D-tryptophan. The reaction mix was adjusted to the appropriate temperature, and adjusted to the appropriate pH with potassium hydroxide. The aldolase described in Example 6 was added as a clarified cell extract at 0.02 mg/mL of target protein. The SEQ ID NO:220 DAT polypeptide was added (either as purified enzyme or as a clarified cell extract) at 0.25 mg/mL of target protein.

The progress of the reactions was followed by measuring monatin concentration using the LC/MS/MS methodology described in Example 3.

Starting with D-tryptophan and under the conditions tested, the pH optimum of the monatin formation reactions using the SEQ ID NO:220 polypeptide was found to be approximately pH 8.0 and the temperature optimum of the monatin formation reactions utilizing the SEQ ID NO:220 polypeptide was found to be approximately 25° C. These reactions have complex dynamics and the optimum reaction conditions for the full monatin production reaction may not be the same as the optimal conditions for individual reactions catalyzed by the DAT polypeptide.

Example 16
The Co-Expression of Chaperones to Increase the Soluble Expression of a DAT Polypeptide

Because the soluble expression of the SEQ ID NO:894 DAT polypeptide was low using the standard expression protocols (either 1 mM IPTG in LB or Novagen Overnight Express Autoinduction System2, see Example 8), co-expression of the SEQ ID NO:894 polypeptide and a variety of commercially available chaperones was examined.

Chaperones:

The TaKaRa Chaperone Set (TAKARA BIO catalog #3340) consists of five different sets of chaperones developed by HSP Research Institute, Inc. They are designed to enable efficient expression of multiple molecular chaperones known to work in cooperation in the folding process. The set contained the following:

Resistance

Plasmid
Chaperone
Promoter
Inducer
Marker

pG-
dnaK-dnaJ-grpE;
araB;
L-Arabinose;
chloramphenicol

KJE8
groES-groEL
Pzt1
tetracycline

pGro7
groES-groEL
araB
L-Arabinose
chloramphenicol

pKJE7
dnaK-dnaJ-grpE
araB
L-Arabinose
chloramphenicol

pG-Tf2
groES-groEL-tig
Pzt1
Tetracycline
chloramphenicol

pTf16
tig
araB
L-Arabinose
chloramphenicol

Transformation Protocol

Chemically competent BL21 (DE3) cells (EMD Biosciences/Novagen catalog #69450) were transformed with 20 ng of one of the TaKaRa chaperone plasmids and 20 ng of SEQ ID NO:893/pET30a (encoding the SEQ ID NO:894 polypeptide; see Example C2 for the plasmid construction) by heat shock for 30 seconds at 42° C. The transformed cells were recovered in 0.5 mL of SOC medium for 1 hr at 37° C. and plated on LB plates containing 50 mg/L kanamycin and 25 mg/L chloramphenicol. The plates were incubated overnight at 37° C. Colonies were picked from the overnight plates and used to inoculate 5 mL of 2×YT medium containing 50 mg/L kanamycin and 25 mg/L chloramphenicol. After overnight incubation at 37° C., the plasmids were isolated from the cell pellets using a QUIAprep Spin Miniprep Kit (Qiagen catalog #27104). The plasmids were analyzed by restriction digestion with one-cutter enzymes from New England Biolabs (Beverly, Mass.) for both the chaperone plasmid and the SEQ ID NO:893/pET30a plasmid following the manufacture's recommended protocol.

Plasmid
Restriction Enzyme

pG-KJE8
XhoI

pGro7
XbaI

pKJE7
NheI

pG-Tf2
XhoI

pTf16
XbaI

The isolated DNA containing both SEQ ID NO:893/pET30a and pKJE7 was digested with NheI and XbaI.

Expression Studies

Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6, 50 mg/L kanamycin and 25 mg/L chloramphenicol (25 mL in each flask) were inoculated from fresh plates of the cells co-transformed with a chaperone plasmid and SEQ ID NO:893/pET30. At inoculation the inducers required for the chaperone plasmids were also added.

Plasmid
Inducer concentration

pG-KJE8
2 mg/mL L-arabinose; 10 ng/mL tetracycline

pGro7
2 mg/mL L-arabinose

pKJE7
2 mg/mL L-arabinose

pG-Tf2
10 ng/mL tetracycline

pTf16
2 mg/mL L-arabinose

The cells were incubated at 30° C. overnight and harvested by centrifugation when the OD at 600 nm reached 6 or greater. The cells were washed with cold 50 mM EPPS buffer (pH 8.4), centrifuged again, and either used immediately or frozen at −80° C.

Cell extracts were prepared by adding 5 mL per g of cell pellet of BugBuster® (primary amine-free) Extraction Reagent (EMD Biosciences/Novagen catalog #70923) with 5 μL/mL of Protease Inhibitor Cocktail II (EMD Bioscience/Calbiochem catalog #539132), 1 μl/mL of Benzonase® Nuclease (EMD Biosciences/Novagen catalog #70746), and 0.033 μl/mL of r-Lysozyme solution (EMD Biosciences/Novagen catalog #71110) to the cells. The cell suspensions were incubated at room temperature with gentle mixing for 15 min; spun at 14,000 rpm for 20 min (4° C.) and the supernatants carefully removed. Total protein concentrations were determined using the Pierce BCA protein assay kit (Pierce catalog #23225) with bovine serum albumin as the standard and a microtiter plate format. The expression of the D-aminotransferase was analyzed by SDS-PAGE using Bio-Rad Ready Gel® Precast 4-15% polyacrylamide gradient gels (Bio-Rad Laboratories catalog #161-1104). BioRad SDS-PAGE low range standards (catalog #161-0304) were run as standards on each gel. Aliquots of the cell extracts (15 μg protein) were mixed with protein loading buffer containing 2% SDS, 10% glycerol, 12.5% 2-mercaptoethanol, 0.1% bromophenol blue and 62.5 mM Tris-HCl (pH 8), incubated at 95° C. for 5 min, cooled and then loaded on the gel. In addition, the combined soluble and insoluble protein expression (total protein) was analyzed for each transformant. A 10 μl aliquot of each cell suspension before centrifugation was diluted in 90 μL protein loading buffer, incubated at 95° C. for 10 min, and cooled. Ten μl of each cooled solution was loaded on the gel.

The soluble protein gel showed that the best soluble expression of the polypeptide having the sequence of SEQ ID NO:894 occurred when chaperones GroEL-GroES (pGro7) were co-expressed.

The expression of the SEQ ID NO:894 polypeptide using an alternative plasmid in the presence of the GroEL-GroES chaperones was also examined. The SEQ ID NO:893 nucleic acid was subcloned into the pMET1a plasmid using the restriction enzymes NdeI and XhoI from New England Biolabs. This plasmid is a derivative of pET23a (EMD Biosciences/Novagen catalog #69745-3) and carries the metE gene (inserted at the NgoMIV site of the plasmid) and can complement the methionine auxotrophy of E. coli strains B834(DE3) and E. coli BW30384 (DE3) ompTmetE (“EE2D”). The construction of the “EE2D” strain is described in WO 2006/066072. The construction of an analogous plasmid to pMET1a that is a derivative of pET23d is described in the same PCT application.

The SEQ ID NO:893/pMET1a plasmid (25 ng) was transformed into “EE2D” electrocompetent cells singly or was co-transformed with pGro7 (20 ng) using the standard Bio-Rad electroporation protocol for E. coli cells with a Bio-Rad Gene Pulser II system (catalog #165-2111). The transformed cells were recovered in 0.5 mL of SOC medium for 1 h at 37° C. and plated on LB plates containing 100 mg/L ampicillin or on plates containing 100 mg/L ampicillin and 25 mg/L chloramphenicol (double plasmid transformants). The plates were incubated overnight at 37° C. One colony from each plate set was used to inoculate 50 mL of Novagen Overnight Express™ AutoinductionSystem 2 containing solutions 1-6, 100 mg/L ampicillin and 2 mg/mL L-arabinose. The culture inoculated with cells containing the pGro7 plasmid also contained 25 mg/L chloramphenicol. The cells were incubated at 30° C. overnight and harvested by centrifugation when the OD₆₀₀reached 6 or greater. The cell pellets were washed with cold 50 mM EPPS buffer (pH 8.4), centrifuged again, and either used immediately or frozen at −80° C. Cell extracts were prepared as described above using the Novagen BugBuster® (primary amine-free) Extraction Reagent. The expression of soluble and total D-aminotransferase was analyzed by SDS-PAGE as described above.

The gel showed that expression of soluble SEQ ID NO:894 polypeptide was greater when the GroEL-GroES proteins were co-expressed. However, the soluble expression was not as high as with the pET30a construct described above.

The effect of incubation temperature during expression was also examined. A 5 mL culture of LB containing 100 mg/L ampicillin and 25 mg/L chloramphenicol was inoculated from a fresh plate of EE2D::SEQ ID NO:894PMET1a+pGro7. The culture was incubated overnight at 30° C. and then used to inoculate 3 flasks, each containing 50 mL of Novagen Overnight Express™ Autoinduction System 2 containing solutions 1-6, 100 mg/mL ampicillin, 25 mg/L chloramphenicol, and 2 mg/mL L-arabinose. One flask was incubated at 20° C., the second at 25° C. and the third at 30° C. The cells were harvested when the OD₆₀₀reached 6 or greater. The cells were harvested and cell extracts were prepared as described above. Total protein concentrations were determined using the Pierce BCA protein assay kit (Pierce catalog #23225) with bovine serum albumin as the standard and a microtiter plate format. The expression of the D-aminotransferase was analyzed using the Bio-Rad Experion Pro260 Automated Electrophoresis Station following the manufacturer's protocol with the cell extract solutions diluted to 1 mg/mL. The results are shown in Table 32. It appears that the lowest temperature gave the maximum amount of expression of the SEQ ID NO:894 polypeptide.

TABLE 32

Estimated DAT

Lane
Sample
Temp
Expression

1
Pro260 Ladder

2
EE2D::23463pMET1 + pGRO7
20° C.
23%

cell extract

3
EE2D::23463pMET1 + pGRO7
25° C.
21%

cell extract

4
EE2D::23463pMET1 + pGRO7
30° C.
19%

cell extract

Activity Assay Protocol

The enzymatic activity of the SEQ ID NO:894 DAT co-expressed with the GroEL-GroES chaperones was tested following the standard monatin reaction protocol. Briefly, each assay tube contained the following (in a total of 2 mL): 0.050 mg/mL aldolase in cell extract (assuming 20% soluble expression); 1.0 mg/mL D-aminotransferase in cell extract (assuming 20% soluble expression for an extract containing the SEQ ID NO:894 polypeptide) or purified B. sphaericus D-aminotransferase; 0.01% Tween-80; 200 mM sodium pyruvate; 100 mM D-tryptophan; 100 mM EPPS (pH 8.2); 1 mM MgCl₂; 0.05 mM PLP; and 10 mM potassium phosphate.

The results are shown in Table 33. At 22 h, the concentration of monatin was 9.2 mM when the SEQ ID NO:894 polypeptide was present and 12.4 mM when the B. sphaericus enzyme was used. The concentration of the co-product HMG was significantly less when the SEQ ID NO:894 polypeptide was in the assay mixture (<⅓ the concentration when compared to the assay sample containing B. sphaericus enzyme). The HMG concentrations were evaluated by comparing the peak areas of the OPA derivatized samples.

TABLE 33

Monatin Formation (mM)

Polypeptide (SEQ ID NO)
1 h
4 h
8 h
22 h

894 DAT + GroEL-ES
1.3
4.5
6.8
9.2

B. sphaericus DAT
1.6
5.7
8.3
12.4

Example 17
Use of ArcticExpress™ System to Increase the Soluble Expression of a DAT Polypeptide

Because the soluble expression of the SEQ ID NO:894 polypeptide was low using the standard expression protocols (either 1 mM IPTG in LB or Novagen Overnight Express™ AutoinductionSystem 2—see Example 8), expression of the SEQ ID NO:893/pMET1a plasmid in the Stratagene ArcticExpress™ system was examined.

The Stratagene ArcticExpress™ system contains E. coli competent cells that carry the psychrophilic chaperones Cpn10 and Cpn60. These are chaperones isolated from the psychrophilic organism Oleispira antarctica. Cpn10 and Cpn60 show high sequence similarity to the E. coli chaperones GroEL and GroES, respectively, and have high protein folding activities at 4-12° C. The ArcticExpress™ host cells are derived from the E. coli BL21 strain. Not only do these cells lack the Lon protease, but they have been engineered to be deficient in OmpT protease as well.

Transformation Protocol

The plasmid SEQ ID NO:893/pMET1a (described in Example 16) was transformed into chemically competent ArcticExpress™ (DE3) cells (catalog #230192) following the manufacturer's protocol. The transformed cells were recovered in 0.5 mL of SOC medium for 1 h at 37° C. and plated on LB plates containing 100 mg/L ampicillin. The plates were incubated overnight at 37° C. and then stored at 4° C.

Expression Protocol

Colonies from the transformation plates were used to inoculate 5 mL of 2×YT medium containing 100 mg/L ampicillin and 10 mg/L gentamycin and incubated overnight at 30° C. Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6, with 100 mg/L ampicillin and 12 mg/L gentamycin were inoculated using the overnight cultures. After incubation at 30° C. for 6 h and the Overnight Express™ cultures were moved to either 15° C. or 20° C. or 25° C. incubators. The incubations were continued until the OD at 600 nm of the cultures reached 6 or greater. The cells were harvested by centrifugation, washed with cold 50 mM EPPS, pH 8.4, and the cell pellets were frozen at −80° C.

The electrophoresis results show that the ArcticExpress™ system significantly increased the soluble expression of the SEQ ID NO:894 polypeptide when compared to the expression without chaperones or when co-expressed with the E. coli GroEL-GroES chaperones described in Example 16. The soluble expression was higher at lower temperatures, but still very high at 25° C.

Incubation
Estimated

Lane
Sample
Temperature
DAT Expression

1
Pro260 Ladder

2
ArcticExpress(DE3)::894pMET1
15° C.
58%

cell extract

3
ArcticExpress(DE3)::894pMET1
20° C.
46%

cell extract

4
ArcticExpress(DE3)::894pMET1
25° C.
47%

cell extract

Activity Assay Protocol:

The enzymatic activity of the SEQ ID NO:894 polypeptide expressed in the ArcticExpress™ system was tested by following monatin formation in the presence of the aldolase described in Example 6. Each assay tube contained the following (in a total of 2 mL): 0.010 mg/mL aldolase in cell extract (assuming 20% soluble expression); 1.0 or 2.0 mg/mL of the SEQ ID NO:894 polypeptide in cell extract (assuming 50% soluble expression for the extract containing the SEQ ID NO:894 polypeptide) or purified B. sphaericus D-aminotransferase; 0.01% Tween-80; 200 mM sodium pyruvate; 100 mM D-tryptophan; 100 mM EPPS, pH 8.2; 1 mM MgCl₂; 0.05 mM PLP; and 10 mM potassium phosphate.

The reactions were incubated at room temperature in a Coy Laboratory Products, Inc. anaerobic chamber to minimize exposure to oxygen. All components except the enzymes were mixed together (the tryptophan did not completely dissolve until at least 1 h after the addition of the enzymes). The reactions were initiated by the addition of the enzymes. Samples were withdrawn at 1, 4, 7 and 22 h. Control reactions using 1 or 2 mg/mL purified B. sphaericus D-aminotransferase were also run. The concentrations of the substrates and products were measured as described in Example 3. The results are shown in Table 34. At 22 h, the concentration of monatin was 8.2 mM when the SEQ ID NO:894 polypeptide was present at 1 mg/mL and 10.5 mM at 2 mg/mL DAT polypeptide. When the B. sphaericus enzyme was added at 1 mg/mL, the concentration of monatin at 22 h was 10.7 mg/mL; at 2 mg/mL, the monatin concentration was 14.5 mM. The stereopurity (as determined by the FDAA derivatization protocol in Example 3) of the product was >98% R,R with both enzymes and enzyme concentrations. The concentration of the co-product HMG was significantly less when the SEQ ID NO:894 polypeptide was used (˜⅓ the concentration when compared to the assay samples containing B. sphaericus enzyme at either enzyme concentration). The HMG concentrations were evaluated by comparing the peak areas of the OPA derivatized samples.

TABLE 34

Monatin Formation (mM)

Polypeptide (SEQ ID NO)
1 h
4 h
7 h
22 h

894 DAT (1 mg/mL)
0.9
2.3
3.6
8.3

894 DAT (2 mg/mL)
1.4
3.7
6.3
10.5

B. sphaericus DAT (1 mg/lmL)
1.0
4.2
6.1
10.7

B. sphaericus DAT (2 mg/lmL)
1.5
6.7
8.2
14.5

Example 18
Use of Stratagene ArcticExpress™ System to Increase the Soluble Expression of DATs

Transformation Protocol:

The plasmids SEQ ID NO:891/pET30a (encoding the SEQ ID NO:892 polypeptide), SEQ ID NO:873/pET30a (encoding the SEQ ID NO:874 polypeptide) and the Clostridium beijerinckii DAT (CbDAT) in pET30a were transformed into chemically competent Stratagene ArcticExpress™ (DE3) cells (catalog #230192) following the manufacturer's protocol. The cloning of these genes is described in Example 4 and assay results are in Example 9. The transformed cells were recovered in 0.5 mL of SOC medium for 1 h at 37° C. and plated on LB plates containing 100 mg/L ampicillin and 13 mg/L gentamycin. The plates were incubated at room temperature for 2 days and then stored at 4° C.

Expression Protocol:

Colonies from the transformation recovery plates were used to inoculate 5 mL of 2×YT medium containing 50 mg/L kanamycin and 13 mg/L gentamycin; the liquid cultures were incubated for 6 h at 30° C. Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6, with 100 mg/L ampicillin and 13 mg/L gentamycin were inoculated from the 5 mL cultures. After incubation at 30° C. for 5-6 h, the cultures were moved to a 15° C. incubator. The 15° C. incubations were continued until the OD₆₀₀of the cultures reached 6 or greater. The cells were harvested by centrifugation, washed with cold 50 mM EPPS, pH 8.4, and then the cell pellets were frozen at −80° C.

Cell extracts were prepared by adding 5 mL per g of cell pellet of BugBuster (primary amine-free) Extraction Reagent (EMD Biosciences/Novagen catalog #70923) with 5 μL/mL of Protease Inhibitor Cocktail II (EMD Bioscience/Calbiochem catalog #539132), 1 μl/mL of Benzonase Nuclease (EMD Biosciences/Novagen catalog #70746), and 0.033 μl/mL of r-Lysozyme™ solution (EMD Biosciences/Novagen catalog #71110) to the cells. The cell suspensions were incubated at room temperature with gentle mixing for 15 min; spun at 14,000 rpm for 20 min (4° C.) and the supernatants were carefully removed. Total protein concentrations were determined using the Pierce BCA protein assay kit (Pierce catalog #23225) with bovine serum albumin as the standard and a microtiter plate format. The expression of the DAT was analyzed using the Bio-Rad Experion Pro260 Automated Electrophoresis Station following the manufacturer's protocol with the cell extracts solutions diluted to 1 mg/mL. The results are shown in Tables 35 and 36.

The electrophoresis results show that the SEQ ID NO:874 polypeptide expressed in a soluble form slightly better than the SEQ ID NO:892 polypeptide using the ArcticExpress™ system. The soluble expression of the Cb DAT varied depending on the colony picked in the transformation plate. None of these DAT polypeptides expressed in a soluble form using the ArcticExpress™ system as well as the SEQ ID NO:894 polypeptide described in Example 16 was expressed.

TABLE 35

Incubation
Estimated DAT

Lane
Sample
Temperature
Expression

1
Pro260 Ladder

2
ArcticExpress(DE3)::891/pET30a
15° C.
11%

cell extract (colony #1)

3
ArcticExpress(DE3)::891/pET30a
15° C.
9%

cell extract (colony #2)

4
ArcticExpress(DE3)::873/pET30a
15° C.
15%

cell extract (colony #1)

5
ArcticExpress(DE3)::873/pET30a
15° C.
10%

cell extract (colony #2)

6
ArcticExpress(DE3)::891/pET30a
15° C.
9%

cell extract (colony #1)

7
ArcticExpress(DE3)::891/pET30a
15° C.
8%

cell extract (colony #2)

9
ArcticExpress(DE3)::873/pET30a
15° C.
15%

cell extract (colony #1)

10
ArcticExpress(DE3)::873/pET30a
15° C.
11%

cell extract (colony #2)

TABLE 36

Incubation
Estimated DAT

Lane
Sample
Temperature
Expression

1
Pro260 Ladder

2
ArcticExpress(DE3)::CbDAT in
15° C.
9%

pET30a cell extract (colony #1)

3
ArcticExpress(DE3)::CbDAT in
15° C.
19%

pET30a cell extract (colony #2)

4
ArcticExpress(DE3)::CbDAT in
15° C.
13%

pET30a cell extract (colony #3)

5
ArcticExpress(DE3)::CbDAT in
15° C.
4%

pET30a cell extract (colony #4)

Activity Assay Protocol

The enzymatic activity of the DAT polypeptides expressed in the ArcticExpress™ system were tested by following monatin formation in the presence of the aldolase described in Example 6. Each assay tube contained the following (in a total of 3 mL): 0.050 mg/mL aldolase in cell extract (estimating 20% soluble expression); 0.5 mg/mL DAT polypeptide in cell extract (estimating the soluble expression from the Experion data) or purified B. sphaericus DAT; 0.01 Tween-80; 200 mM sodium pyruvate; 100 mM D-tryptophan; 50 mM EPPS, pH 8.2; 1 mM MgCl₂; 0.05 mM PLP; and 10 mM potassium phosphate.

The reactions were incubated at room temperature in a Coy Laboratory Products, Inc. anaerobic chamber to minimize exposure to oxygen All components except the enzymes were mixed together (the tryptophan did not completely dissolve until at least 1 h after the addition of the enzymes). The reactions were initiated by the addition of the enzymes. Samples were withdrawn at 2, 4.5, 9 and 24 h. Control reactions with purified B. sphaericus D-aminotransferase were also run. The concentrations of the substrates and products were measured as described in Example 3. At 24 h, the assays containing the SEQ ID NO:892 or 894 polypeptide had produced approximately the same titer of monatin as the control B. sphaericus DAT reaction. The C. beijerinckii DAT reaction produced less than one-eighth of the monatin product, while the SEQ ID NO:874 polypeptide produced about half. The stereopurity of the product at 24 h (as determined by the FDAA derivatization protocol in Example 3) was 96% R,R monatin or greater for the SEQ ID NO:892 polypeptide. The concentration of the by-product HMG (4-hydroxy-4-methyl glutamic acid) was measured for the reactions with the SEQ ID NO:892, the SEQ ID NO:894 and the B. sphaericus DAT polypeptides. The assay with polypeptides having the sequence shown in SEQ ID NO:894 produced far less of the HMG by-product than the other two (about 20% of that produced by the assay containing the B. sphaericus DAT and about 40% of that produced by the assay with the SEQ ID NO:892 polypeptide). The HMG concentrations were estimated by comparing the peak areas of the OPA post-column derivatized samples.

TABLE 37

Monatin Formation (mM)

Polypeptide (SEQ ID NO)
2 h
4.5 h
9 h
24 h

C. beijerinckii DAT
0.3
0.7
0.8
0.9

874 DAT
1.8
3.2
4.1
4.4

892 DAT
1.6
3.7
5.4
8.4

894 DAT
1.4
2.8
4.5
8.4

B. sphaericus DAT
1.2
2.9
4.3
8.1

These results indicate that when expressed under the appropriate conditions, the polypeptides having the sequence of SEQ ID NO:892 and 894 can be utilized in reactions to produce highly pure R,R monatin at a titer as high as the positive control enzyme.

Example 19
Evaluation of Alternative Expression Hosts to Increase the Soluble Expression of a DAT

Because the soluble expression of the SEQ ID NO:894 polypeptide was low when the nucleic acid was expressed in BL21(DE3) (see Example 8), alternative expression hosts were evaluated for improving soluble expression. The OverExpress™ C41(DE3) and C43(DE3) hosts contain genetic mutations phenotypically selected for conferring toxicity tolerance and express some toxic proteins at higher titers than other E. coli hosts.

Transformation Protocol

The plasmid SEQ ID NO:893/pET30a was transformed into electrocompetent cells of the OverExpress™ C41(DE3) and C43(DE3) (Lucigen catalog #60341 and 60345, respectively) using a Bio-Rad Gene Pulsar II system following the manufacturer's protocol. The transformation mixtures were recovered in 1 mL SOC medium for 1 hr at 37° C. and plated on LB plates containing 50 mg/L kanamycin. The plates were incubated overnight at 37° C. Multiple colonies were patched onto fresh plates and analyzed for the appropriate insert size using colony PCR. A small aliquot of cells was suspended in 0.025 mL H₂O and incubated at 95° C. for 10 min. After cooling, 2 μL of each of the suspensions were used as the template in 0.025 mL reactions, each also containing 0.5 μL T7 promoter primer (0.1 mM), 0.5 μL T7 terminator primer (0.1 mM), 0.5 μL PCR Nucleotide Mix (Roche #12526720; 10 mM each nucleotide), 2.5 μL Roche Expand DNA polymerase buffer #2, and 0.5 μL Expand DNA polymerase (Roche Expand High Fidelity PCR System catalog #1732650). The 3-step thermocycler program was run for 25-30 cycles: 1 min at 94° C.; 1 min at 54° C., 1.3 min at 72° C. with a final polishing step of 7 min at 72° C.

Expression Studies

Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6 and 50 mg/L kanamycin (40 mL in each flask) were inoculated from the patch plates of the transformed C41(DE3) and C43(DE3) cells (2 patches for each of the transformations). The cells were incubated at 30° C. overnight and harvested by centrifugation when the OD₆₀₀reached 6 or greater. The cells were washed with cold buffer, were centrifuged again, and either used immediately or frozen at −80° C.

Cell extracts were prepared by adding 5 mL per g of cell pellet of BugBuster® (primary amine-free) Extraction Reagent (EMD Biosciences/Novagen catalog #70923) with 5 μL/mL of Protease Inhibitor Cocktail II (EMD Bioscience/Calbiochem catalog #539132), 1 μl/mL of Benzonase® Nuclease (EMD Biosciences/Novagen catalog #70746), and 0.033 μl/mL of r-Lysozyme™ solution (EMD Biosciences/Novagen catalog #71110) to the cells. The cell suspensions were incubated at room temperature with gentle mixing for 15 min; spun at 14,000 rpm for 20 min (4° C.) and the supernatants carefully removed. Total protein concentrations were determined using the Pierce BCA protein assay kit (Pierce catalog #23225) with bovine serum albumin as the standard and a microtiter plate format. The expression of the DAT polypeptide was analyzed by SDS-PAGE using Bio-Rad Ready Gel® Precast 4-15% polyacrylamide gradient gels (Bio-Rad Laboratories catalog #161-1104). BioRad SDS-PAGE low range standards (catalog #161-0304) were run as standards on each gel. Aliquots of the cell extracts (15 μg protein) were mixed with protein loading buffer containing 2% SDS, 10% glycerol, 12.5% 2-mercaptoethanol, 0.1% bromophenol blue and 62.5 mM Tris-HCl (pH 8), incubated at 95° C. for 5 min, cooled and then loaded on the gel. In addition, the combined soluble and insoluble protein expression (total protein) was analyzed for the transformants. A 10 μl aliquot of each cell suspension before centrifugation was diluted in 90 μL protein loading buffer, incubated at 95° C. for 10 min, and cooled. Ten μL of each cooled solution was loaded on the gel.

The electrophoresis gel shows that the protein expressed better in the C41(DE3) host than in the C43(DE3) host, however the apparent soluble expression was not higher than when BL21(DE3) cells were used.

Example 20
Evaluation of Low Temperature Expression to Increase the Soluble Expression of DAT

Because the soluble expression of SEQ ID NO:894 D-aminotransferase was low when the gene was expressed in the E. coli strain BL21(DE3) (see Example 8), the gene was inserted in vectors with cold shock Protein A promoters to evaluate low temperature expression.

The Takara pCold Expression Vectors are four different vectors that utilize the cold shock Protein A (cspA) promoter for expression of high purity, high yield recombinant protein in E. coli. These vectors selectively induce target protein synthesis at low temperatures (15° C.) where the synthesis of other proteins is suppressed and protease activity is decreased. In addition to the cspA promoter, all four vectors contain a lac operator (for control of expression), ampicillin resistance gene (amp′), ColE1 origin of replication, M13 IG fragment, and multiple cloning site (MCS). Three of the vectors also contain a translation enhancing element (TEE), a His-Tag sequence, and/or Factor Xa cleavage site.

Cloning Protocol

The SEQ ID NO:893 DAT nucleic acid from plasmid SEQ ID NO:893/pET30a (encoding the polypeptide having the sequence of SEQ ID NO:894) was subcloned into the Takara pCold vectors at the NdeI and XhoI sites of the pCOLDII (contains a TEE and a His-tag sequence), pCOLDIII (contains a TEE) and pCOLDIV vectors. The digested vector and insert bands were gel purified using a QIAquick Gel Extraction Kit (Qiagen catalog #28704) and ligated using a Roche Rapid DNA Ligation Kit (catalog #1635379) following the manufacturer's protocol. The ligation mixtures were transformed into Invitrogen OneShot TOP10 chemically competent cells (catalog #C404003) by heat shock at 42° C. After recovery in 500 μL SOC medium for 1 h at 37° C., the transformation mixtures were plated on LB plates containing 100 mg/L ampicillin and incubated at 37° C. overnight. Colonies were picked from the transformation plates and used to inoculate 5 mL cultures of LB containing 100 mg/mL ampicillin that were incubated overnight at 37° C. Plasmid DNA was purified from the 5 mL cultures using a QIAprep® Spin Miniprep Kit (Qiagen catalog #27104). The inserts were verified restriction digestion with NdeI and XhoI by sequencing (Agencourt Bioscience Corp, Beverly, Mass.).

The SEQ ID NO:894dat pCOLD plasmids were transformed into chemically competent Stratagene ArcticExpress™ (DE3) cells and Novagen BL21(DE3) cells following the manufacturers' protocols. The transformation mixtures were recovered in 0.5-1 mL SOC medium for 1 h at 37° C. and plated on LB plates containing 100 mg/mL ampicillin and 13 mg/L gentamycin (ArcticExpress™ (DE3)) or 100 mg/mL ampicillin (BL21(DE3)). The plates were incubated overnight at 37° C.

Expression Studies

Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6 and 100 mg/L ampicillin and 13 mg/L gentamycin (ArcticExpress™ (DE3)) or 100 mg/mL ampicillin (BL21(DE3) were inoculated from the patch plates of the transformed cells (2 patches for each of the SEQ ID NO:893/pCOLDII, SEQ ID NO:893/pCOLDIII and SEQ ID NO:893/pCOLDIV transformations).

After incubation at 30° C. for 3-5 hr the cultures were moved to a 15° C. incubator. The 15° C. incubations were continued until the OD at 600 nm of the cultures reached 6 or greater. The cells were harvested by centrifugation, washed with cold buffer, and then the cell pellets were frozen at −80° C.

TABLE 38

Estimated % DAT

Lane
Sample
Expression

L
Pro260 Ladder

1
BL21(DE3)::SEQ ID NO: 893/pCOLDII#1
8.7

2
BL21(DE3):: SEQ ID NO: 893/pCOLDII#2
8.5

3
ArcticExpress ™(DE3):: SEQ ID NO: 893/
9.8

pCOLDII#1

4
ArcticExpress ™(DE3):: SEQ ID NO: 893/
6.4

pCOLDII#2

TABLE 39

Estimated %

Lane
Sample
DAT Expression

L
Pro260 Ladder

1
BL21(DE3):: SEQ ID NO: 893/pCOLDIII#1
4.3

2
BL21(DE3):: SEQ ID NO: 893/pCOLDIII#2
2.3

3
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#1
14.6

4
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#2
14.2

5
BL21(DE3):: SEQ ID NO: 893/pCOLDIII#1
4.4

6
BL21(DE3):: SEQ ID NO: 893/pCOLDIII#2
5.2

7
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#1
13.8

8
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#2
16.1

9
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#1
16.2

10
BL21(DE3):: SEQ ID NO: 893/pCOLDIV#2
16.8

The Experion Pro260 results show that the SEQ ID NO:894 DAT protein expressed better when the nucleic acid was incorporated in the pCOLDIV vector than in either the pCOLDII or pCOLDIII vector. From the experiments shown above, the average expression level for SEQ ID NO:893/pCOLDII was about 8%, regardless of expression host used; the average expression level for SEQ ID NO:893/pCOLDIII was about 4%, while the average expression level for SEQ ID NO:893/pCOLDIV was ˜15%. These expression levels are significantly less than those described in Examples 16 when the SEQ ID NO:893 nucleic acid was co-expressed with the GroEL-GroES chaperones and in Example 17 when the nucleic acid was expressed in the Stratagene ArcticExpress™ system.

Example 21
Codon Modification of a DAT

An attempt to improve the solubility of the SEQ ID NO:894 polypeptide expressed in E. coli was undertaken with the presumption that, slowing the rate of translation in E. coli would allow more time for proper folding of the SEQ ID NO:894 polypeptide, thereby giving a higher expression of soluble protein. A BLAST search (NCBI) of the SEQ ID NO:894 polypeptide sequence revealed that some of the most closely related public sequences were from Clostridium species, specifically Clostridium beijerinckii. Example 9 describes the results from cloning, expressing, and assaying the CbDAT and its use in monatin formation reactions. Specifically, expression was high in the total protein fraction but very low in the soluble protein fraction.

The codon usage tables of C. beijerinckii and E. coli K12 were compared. Several rarely used codons in C. beijerinckii were found to be highly abundant in E. coli K12 (Table 40). It is possible that these rare codons cause translational pauses in C. beijerinckii, whereas in an E. coli K12 host, there may not be a pause. In the SEQ ID NO:894 sequence, 4 doublets were identified in which tandem rare codons for C. beijerinckii had become “non-rare” (i.e. abundant) in E. coli K12. The goal was to change these codons into rare codons for expression in E. coli K12 host using the E. coli K12 codon usage table. Primers were designed to change these doublets. SEQ ID NO:893/pET30a (described in Example 4) was used as a template and mutation was carried out according to the Stratagene QuickChange kit instructions. The primers utilized to modify the SEQ ID NO:893 nucleic acid sequence are shown below, along with the native gene (the targeted doublet sequences are underlined).

TABLE 40

Codon Usage

Codon

Original
(per thousand)
Altered
Usage

Codons

C. beijerinckii

E. coli

Codons

E. coli

GCC
3.7
25.6
GCT
15.3

CTG
1.4
52.9
CTA
3.9

ACC
2.5
23.5
ACA
7.0

CGC
0.8
22.0
CGA
3.5

GCG
2.9
33.8
GCT
15.3

CCG
1.1
23.3
CCC
5.4

native sequence

>SEQ ID NO: 893

ATGGACGCACTGGGATATTACAACGGAAAATGGGGGCCTCTGGACGAGATGACCGTGCCGATGAACGACAG

GGGTTGTTTCTTTGGGGACGGAGTGTACGACGCTACCATCGCCGCTAACGGAGTGATCTTTGCCCTGGACGAGCACA

TTGACCGGTTTTTAAACAGCGCAAAGCTCCTGGAAATAGAAATCGGTTTTACAAAAGAGGAATTAAAAAAAACTTTT

TTTGAAATGCACTCCAAAGTGGATAAAGGGGTGTACATGGTTTATTGGCAGGCGACTCGCGGAACAGGCCGTCGAAG

CCATGTATTTCCGGCAGGTCCCTCAAATCTCTGGATTATGATTAAGCCCAATCACGTCGACGATCTTTATAGAAAAA

TCAAGCTCATTACCATGGAAGATACCCGCTTCCTCCACTGCAACATCAAGACCCTTAACCTTATTCCCAATGTCATT

GCCTCCCAGCGGGCGCTGGAAGCGGGCTGCCACGAGGCGGTCTTTCACCGGGGTGAAACAGTAACCGAGTGCGCCCA

CAGCAATGTCCACATCATTAAAAACGGCAGGTTTATCACCCACCAGGCGGACAACCTAATCCTTCGGGGCATAGCCC

GTAGCCATTTATTGCAAGCCTGTATCAGGCTGAACATTCCATTTGACGAACGGGAATTTACCCTTTCGGAATTATTT

GACGCGGATGAGATTCTTGTGTCCAGCAGCGGCACACTCGGCCTTAGCGCCAATACAATTGATGGAAAAAACGTGGG

GGGAAAAGCGCCGGAACTGCTAAAAAAAATTCAGGGCGAAGTGTTGAGGGAATTTATCGAAGCGACAGGCTACACGC

CTGAGTGGAGCACAGTATAG

Primers for Doublet 1 mutant

(SEQ ID NO: 1074)

CTAACGGAGTGATCTTTGCTCTAGACGAGCACATTGAC

(SEQ ID NO: 1075)

GTCAATGTGCTCGTCTAGAGCAAAGATCACTCCGTTAG

Primers for Doublet 2 mutant

(SEQ ID NO: 1076)

CATGGAAGATACACGATTCCTCCACTGCAACATCAAGAC

(SEQ ID NO: 1077)

GTCTTGATGTTGCAGTGGAGGAATCGTGTATCTTCCATG

Primers for Doublet 3 mutant

(SEQ ID NO: 1078)

ATTGCCTCCCAGCGGGCTCTAGAAGCGGGCTGCCACG

(SEQ ID NO: 1079)

CGTGGCAGCCCGCTTCTAGAGCCCGCTGGGAGGCAAT

Primers for Doublet 4 mutant

(SEQ ID NO: 1080)

GGGGGGAAAAGCTCCCGAACTGCTAAAAAAAATTCAGG

(SEQ ID NO: 1081)

CCTGAATTTTTTTTAGCAGGTCGGGAGCTTTTCCCCCC

Clones with the correctly altered sequence were transformed into BL21(DE3) host for enzyme expression assays. Enzyme expression was determined by growing the cells overnight in Overnight Express II and lysing the cells with BugBuster reagent followed by SDS PAGE analyses of crude cell extract and soluble protein.

It appeared that there was a slight improvement in soluble protein expression with codon changes to doublets 1, 2 and 3. Codon changes at doublet 4 were not beneficial for soluble protein expression. Codon changes for doublets 1, 2 and 3 were combined in pairs using the Stratagene QuickChange kit and the primers designed for the initial codon changes. Clones with the correctly altered sequence were transformed into BL21(DE3) host for enzyme expression assays. Enzyme expression was determined by growing the cells overnight in Overnight Express II and lysing the cells with BugBuster reagent followed by SDS PAGE analyses of crude cell extract and soluble protein. The combinations of mutations to doublets 1 and 2, 2 and 3 and 1 and 3 yielded soluble protein bands visible on an SDS-PAGE gel. However, there still appeared to be more protein in the total protein fractions.

Example 22
The Evaluation of Periplasmic Expression of a DAT Polypeptide

Because the soluble expression of the SEQ ID NO:894 polypeptide was low when the gene product was expressed as a cytoplasmic protein in the E. coli host BL21(DE3) (see Example 8), the gene was cloned into vectors to generate fusion proteins that should be exported into the periplasmic space. The periplasm provides conditions that promote proper folding and disulfide bond formation and may enhance the solubility and activity of certain target proteins.

Cloning into EMD Biosciences/Novagen pET26b allows production of the target protein with a periplasmic signal sequence. The signal sequence is cleaved by signal peptidase concomitant with export. The EMD Biosciences/Novagen pET39b and pET40b are designed for cloning and expression of target proteins fused with a 208 amino acid DsbA-Tag™ or 236 amino acid DsbC-Tag™. DsbA and DsbC are periplasmic enzymes that catalyze the formation and isomerization of disulfide bonds, respectively. The fusion proteins are typically localized in the periplasm.

Cloning Protocol

The SEQ ID NO:893 nucleic acid from plasmid SEQ ID NO:893/pET30a (described in Example 4) was cloned into the EMD Biosciences/Novagen pET26b (catalog #69862-3), pET39b (catalog #70090-3), and pET40b (catalog #70091-3) vectors at the EcoRI and NotI sites of the vectors. The DATs nucleic acid with a 5′ EcoRI site and a 3′ NotI site was generated using the amplification protocol described in Example 4 and the following primers:

(SEQ ID NO: 1082)

5′-CGCA custom character

GGACGCACTGGGATATTACAAC-3′

(SEQ ID NO: 1083)

5′-GTTA custom character

TATACTGTGCTCCACTCAG-3′

The restriction sites are in italics in the primer sequences. The resulting DNA product and the pET26b, pET39b and pET40b vectors were digested with EcoR1 and Not I (New England Biolabs) following the suggested manufacturer's protocol. The vector reaction mixtures were subsequently treated with Shrimp Alkaline Phosphatase (Roche catalog #1758250). The digested vector and insert bands were gel purified from a 1% agarose gel using a Qiagen QIAquick® Gel Extraction Kit (catalog #28704) and ligated using a Roche Rapid Ligation Kit (catalog #1635379) following the manufacturer's protocol. The ligation mixtures were transformed into Invitrogen OneShot® TOP10 chemically competent cells (catalog #C404003) by heat shock at 42° C. After recovery in 500 μL SOC medium for 1 h at 37° C., the transformation mixtures were plated on LB plates containing 50 mg/L kanamycin and incubated at 37° C. overnight. Colonies were picked from the transformation plates and used to inoculate 5 mL cultures of LB containing 50 mg/mL kanamycin that were incubated overnight at 37° C. Plasmid DNA was purified from the 5 mL cultures using a Qiagen QIAprep spin miniprep kit (catalog #27104). The nucleic acid sequences were verified by sequencing (Agencourt Bioscience Corp, Beverly, Mass.). Plasmids with the correct insert sequences were transformed into EMD Biosciences/Novagen BL21(DE3) chemically competent cells (catalog #69450) by heat shock as described above.

Expression Studies

Flasks of Novagen Overnight Express™ AutoinductionSystem 2 (EMD Biosciences/Novagen catalog #71366) containing solutions 1-6 and 50 mg/L kanamycin (50 mL in each flask) were inoculated from fresh plates of BL21(DE3) cells carrying the SEQ ID NO:893 DAT nucleic acid (encoding the polypeptide of SEQ ID NO:894) in either pET26b, pET39b or pET40b. The cells were incubated at 30° C. overnight and harvested by centrifugation when the OD₆₀₀reached 6 or greater. The cells were washed with cold buffer, were centrifuged again, and used immediately or the cell pellets were frozen at −80° C. Before harvesting, 2 mL culture aliquots were withdrawn from each flask for soluble and total protein (soluble and insoluble) expression analyses. Cell extracts were prepared as described in Example 16. Total protein samples were prepared by suspending a small amount of cell pellet in protein loading buffer containing 2% SDS, 10% glycerol, 12.5% 2-mercaptoethanol, 0.1% bromophenol blue and 62.5 mM Tris-HCl, pH 8, and incubating at 95° C. for 10 min.

The periplasmic cellular fractions were prepared from the remainder of the cells from each culture following the protocol described in the EMD Biosciences/Novagen pET System Manual. The resulting fractions were concentrated 30-fold using Amicon Ultracel 10 k centrifugal filter devices (Millipore catalog #UFC901024). Total protein concentrations of the cell extracts and the periplasmid fractions were determined using the Pierce BCA protein assay kit (Pierce catalog #23225) with Bovine Serum Albumin as the standard and a microtiter plate format. Fifteen μg protein samples of the cell extracts and 10 μg protein samples of the periplasmic fractions were analyzed by SDS-PAGE using Bio-Rad Ready Gel® Precast 4-15% polyacrylamide gradient gels (Bio-Rad Laboratories catalog #161-1104). In addition, the total protein samples were analyzed by SDS-PAGE. BioRad SDS-PAGE low range standards (catalog #161-0304) were run as standards on each gel.

Analysis of the total protein SDS-PAGE gel shows that proteins with the predicted molecular weights expressed using the Overnight Express™ AutoinductionSystem 2. However, analysis of the SDS-PAGE gel loaded with the cell extract fractions or with the periplasmic fractions suggests that these proteins did not express solubly nor were they exported into the periplasm.

Example 23
Production of Monatin from Indole-3-pyruvate

The maximum concentration of monatin obtained when D-tryptophan and pyruvic acid are the starting raw materials in the monatin formation assay described in Example 5 is limited by the solubility of tryptophan. In order to explore the potential of using an aldolase and the SEQ ID NO:220 DAT polypeptide (described in Example 14) in reaching higher monatin concentrations, the reaction starting with indole-3-pyruvatr (I3P) and pyruvate acid as raw materials were analyzed. In this case, it was also necessary to provide an amino donor such as D-alanine or both D-alanine and D-tryptophan.

The test was conducted using purified SEQ ID NO:220 DAT polypeptide (production and purification described in Example 15) and an aldolase (described in Example 6). The reaction was set up as follows (in a total of 1 mL): 200 mM Indole-3-pyruvate (I3P); 200 mM sodium pyruvate; 400 mM D-alanine; 100 mM EPPS, pH 8.0; 1 mM MgCl₂; 0.05 mM PLP; and 10 mM potassium phosphate.

Both enzymes were added in excess to facilitate conversion to monatin to minimize completion from non-enzymatic degradation reactions. The reactions were incubated at room temperature in a Coy Laboratory Products, Inc. anaerobic chamber to minimize exposure to oxygen All components except the enzymes were mixed together and the pH was adjusted to 8.0. The reactions were initiated by the addition of the enzymes (0.04 mg/mL aldolase as cell extract (assuming 20% expression) and 0.40 mg/mL purified SEQ ID NO:220 DAT polypeptide).

In some tests as indicated in the table below, D-tryptophan was also added at either 50 or 100 mM in addition to the D-alanine to act as amino donor and also to limit the amount of indole-3-pyruvate consumed in the formation of D-tryptophan. The monatin formation was measured after 18 hours using the LC/MS/MS methodology described in Example 3, and the results are presented in Table 41 below.

TABLE 41

Monatin Formation from I3P (mM)

Reactant initial concentrations (mM)
Monatin concentration (mM)

200 I3P; 200 pyr: 400 D-ala
44.9

200 I3P; 200 pyr: 400 D-ala, 50 D-trp
47.8

200 I3P; 200 pyr: 400 D-ala, 100 D-trp
61.0

As shown above, the aminotransferase and aldolase enzymes were active at the higher reactant concentrations and a much higher monatin concentration was achieved.

At 18 h, while using 200 mM indole-3-pyruvate, 200 mM sodium pyruvate and 100 mM D-tryptophan, the concentration of monatin was 61 mM. A small increase in monatin production (47.8 mM) was observed under the conditions of the assay, with the addition of 50 mM D-tryptophan vs. just using 400 mM D-alanine.

Example 24
Homology Table

Table 42 shows some of the most active DAT polypeptides and the corresponding closest homologs from the published databases or literature.

TABLE 42

DAT

polypeptide

%

(SEQ

Sequence

ID NO)
Closest Hit from Database
Identity

896

Bacillus sp. YM-1
76

874
Serine glyoxylate transaminase from
51

Acidiphilium cryptum JF-5 (NR Accession No:

148260372)

878
Putative glutamate-1-semialdehyde 2,1-
43

aminomutase from Planctomyces maris DSM

8797 (NR Accession No. 149173540)

882
D-alanine transaminase from Oceanobacter sp.
57

RED65 (NR Accession No: 94500389)

910
DAT from B. macerans
91

176
D-amino acid aminotransferase from
62

Clostridium beijerincki (NCIMB 8052)

220
D-amino acid aminotransferase from
62

Clostridium beijerincki (NCIMB 8052)

156
Aminotransferase class-III (leadered) from
46

Chloroflexus aggregans DSM 9485 (NR

Accession No: 118045454)

214
D-amino acid aminotransferase from
61

Clostridium beijerincki (NCIMB 8052)

918
Aminotransferase class IV from Robiginitalea
57

biformata HTCC2501 (NR Accession No:

88806011)

902
Putative glutamate-1-semialdehyde 2;1-
46

aminomutase from Planctomyces maris DSM

8797 (same protein as above)

884
D-alanine transaminase from Thiobacillus
40

denitrificans ATCC 25259 (NR Accession No:

74316285)

866
D-alanine aminotransferase from Lactobacillus
49

salivarius subsp. salivarius UCC118

946
D-amino acid aminotransferase from
63

Clostridium beijerincki (NCIMB 8052)

As shown in Example 9, homologs of the polypeptides having the sequence shown in SEQ ID NO:866, 946, 220, and 176 were cloned and also had activity in the production of R,R monatin, despite a sequence identity among those polypeptides of between 49% and 63%. Similarly, the predicted D-alanine transaminase from Oceanobacter species and the Robinginitalea biformata aminotransferase are expected to have broad D-amino acid aminotransferase activity like the DAT polypeptides having the sequence of SEQ ID NO:882 and 918.

Appendix I shows a table that describes selected characteristics of exemplary nucleic acids and polypeptides of the invention, including sequence identity comparison of the exemplary sequences to public databases. By way of example and to further aid in understanding Appendix I, the first row, labeled “SEQ ID NO:”, the numbers “1, 2” represent the exemplary polypeptide of the invention having a sequence as set forth in SEQ ID NO:2, encoded by, e.g., SEQ ID NO:1. The sequences described in Appendix I (the exemplary sequences of the invention) have been subject to a BLAST search (as described herein) against two sets of databases. The first database set is available through NCBI (National Center for Biotechnology Information). The results from searches against these databases are found in the columns entitled “NR Description”, “NR Accession Code”, “NR E-value” or “NR Organism”. “NR” refers to the Non-Redundant nucleotide database maintained by NCBI. This database is a composite of GenBank, GenBank updates, and EMBL updates. The entries in the column “NR Description” refer to the definition line in any given NCBI record, which includes a description of the sequence, such as the source organism, gene name/protein name, or some description of the function of the sequence. The entries in the column “NR Accession Code” refer to the unique identifier given to a sequence record. The entries in the column “NR E-value” refer to the Expected value (E-value), which represents the probability that an alignment score as good as the one found between the query sequence (the sequences of the invention) and that particular database sequence would be found in the same number of comparisons between random sequences as was done in the present BLAST search. The entries in the column “NR Organism” refer to the source organism of the sequence identified as the closest BLAST hit.

The second database set is collectively known as the GENESEQ™ database, which is available through Thomson Derwent (Philadelphia, Pa.). The results from searches against this database are found in the columns entitled “GENESEQ Protein Description”, “GENESEQ Protein Accession Code”, “E-value”, “GENESEQ DNA Description”, “GENESEQ DNA Accession Code” or “E-value”. The information found in these columns is comparable to the information found in the NR columns described above, except that it was derived from BLAST searches against the GENESEQ™ database instead of the NCBI databases.

In addition, this table includes the column “Predicted EC No.”. An EC number is the number assigned to a type of enzyme according to a scheme of standardized enzyme nomenclature developed by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). The results in the “Predicted EC No.” column are determined by a BLAST search against the Kegg (Kyoto Encyclopedia of Genes and Genomes) database. If the top BLAST match has an E-value equal to or less than e-6, the EC number assigned to the top match is entered into the table. The columns “Query DNA Length” and “Query Protein Length” refer to the number of nucleotides or the number amino acids, respectively, in the sequence of the invention that was searched or queried against either the NCBI or GENESEQ™ databases. The columns “Subject DNA Length” and “Subject Protein Length” refer to the number of nucleotides or the number amino acids, respectively, in the sequence of the top match from the BLAST searches. The results provided in these columns are from the search that returned the lower E-value, either from the NCBI databases or the GENESEQ™ database. The columns “% ID Protein” and “% ID DNA” refer to the percent sequence identity between the sequence of the invention and the sequence of the top BLAST match. The results provided in these columns are from the search that returned the lower E-value, either from the NCBI databases or the GENESEQ™ database.

Part C
Example 25
Construction and Testing of GSSM^SM Mutants

This example describes the construction of exemplary nucleic acids and polypeptides, and describes their enzymatic activity. The nucleotide sequence (SEQ ID NO:219) was subcloned into pSE420-C-His vector and expressed in E. coli XL1-BLUE host (Stratagene, La Jolla, Calif.) to produce the exemplary D-aminotransferase (DAT) enzyme having the amino acid sequence shown in SEQ ID NO:220. The pSE420-C-His vector was created by adding a C-terminal His-tag to the pSE420 vector from Invitrogen (Carlsbad, Calif.). Construct SEQ ID NO:220 (in E. coli XL1-BLUE), was used as a starting sequence into which modifications were introduced and is referred to herein as the wild type (WT) sequence. A first round of modification (i.e., single-residue mutations) was performed using Gene Site Saturated Mutagenesis^SM (GSSM^SM) technology (see, for example, U.S. Pat. No. 6,171,820). The mutants made using GSSM^SM technology were expressed in the pSE420-C-His vector in E. coli host XL1-BLUE, arrayed into 384-well plates and grown at 37° C. overnight. Samples were subcultured and grown at 30° C. for two nights (36-48 hours). Cultures were frozen at −20° C. until cell lysates could be prepared.

Cells were lysed by addition of 10 μL of BPER II (Thermo Scientific, Rockford, Ill.) to each well. Samples were mixed three times and lysed on ice for one hour. Crude lysates were then assayed in the primary screen. 25 μL of crude lysate was assayed with 1 mM R,R-monatin, 25 mM pyruvic acid sodium salt, 0.08 mM PLP in 50 mM sodium phosphate (pH 8) at room temperature. After three hours, an aliquot was taken and formic acid was added to a final concentration of 2%. Samples were diluted with water to be within the range of the standard curve. Samples were analyzed for monatin consumption and alanine formation using the LC/MS/MS methods described in Example 1 (LC/MS/MS Method for Detecting D-alanine or R,R-monatin). Sample performance was compared to the performance of the wild type control (i.e., SEQ ID NO:220).

Mutants that outperformed the wild type control were selected as hits from the GSSM^SM primary screen. Glycerol stocks of the primary hits were used to inoculate new 384-well plates. The hits were arrayed in quadruplicate, grown and lysed as indicated for the primary screen. The primary hits were then tested in a secondary screen. The secondary screen method was the same as for the primary screen except the mutants were tested with 1 mM and 15 mM R,R-monatin substrate. Samples were analyzed for monatin consumption and alanine formation using LC/MS/MS. Sample performance was compared to the performance of the wild type control.

Sample performance was evaluated using a scoring system based on alanine production and monatin consumption. The maximum score for a single sample was six. A maximum of three points were assigned for alanine production and a maximum of three points were assigned for monatin consumption. The scoring criteria were as follows: 1 point assigned for a value between average and one standard deviation of the positive control; 2 points assigned for a value between one and two standard deviations of the positive control; and 3 points assigned for a value beyond two standard deviations of the positive control.

The highest potential total score for a mutant was 48 (since the samples were screened in quadruplicate at 1 and 15 mM monatin). In general, mutants scoring 20 points or more were selected as secondary hits. However, some exceptions were made for samples scoring less than 20 points. Samples with alanine formation and monatin consumption values on the verge of the threshold requirements were also selected as hits. This prevented the premature elimination of hits and allowed for further testing and characterization in the tertiary screen.

Samples identified as secondary screen hits, using the criteria above, are listed in Table 43. Secondary hits were streaked from glycerol stocks onto LB agar plates containing 100 μg/mL carbenicillin and grown overnight at 37° C. Single colonies were used to inoculate 1 mL LB containing carbenicillin (100 μg/mL). Cultures were grown overnight at 37° C. DNA was isolated from the cultures, and then prepared and sequenced using 3730XL automated sequencers (Applied Biosystems, Foster City, Calif.).

Mutations and the amino acid position of the mutation for secondary hits are listed below in Table 43. Numbering of the amino acid positions starts with the N-terminal methionine. For example, the first mutation listed “Y6L” refers to changing the tyrosine in amino acid position 6 of the wild type enzyme (SEQ ID NO:220) to leucine. At the nucleic acid level, any codon which codes for the desired (mutated) amino acid can be used.

All of the amino acid sequences described in Tables 43, 44 and 50, below, are exemplary polypeptides; also provided are nucleic acid sequences that encode such polypeptides.

Example 26
List of GSSM^SM Mutations

TABLE 43

GSSM^SMMutants Identified as Secondary Screen Hits

Mutant name
Mutation

1
Y6L

2
Y6C; SILENT MUTATION

AT AA31 (GGC → GGT)

3
Y6F

4
Y6L

5
Y6H

6
Y6L

7
Y6M

8
N10S

9
N10W

10
N10T

11
N10R

12
N10T

13
L14V

14
L14L

15
G41G

16
T18W

17
N40N

18
V19T

19
V42V

20
I62C

21
V82A

22
A57M

23
V42M

24
G41Y

25
A45L

26
V93Y

27
V93G

28
L46A

29
L46H

30
G98A

31
P20S

32
V93A

33
V103T

34
P108F

35
V93L

36
S101S

37
A106G

38
S101Q

39
P108T

40
N118G

41
P108C

42
I120L

43
A106W

44
N118R

45
N110A; N118G

46
N118A

47
N118R

48
P117W; N118K

49
D133N

50
K126Q

51
K126R

52
K128S

53
I127M

54
T131T

55
D133L

56
M132A

57
D133E

58
L129V

59
K126K

60
I130M

61
M132Y

62
K128R

63
M132R

64
L129I

65
K128L; D2D (GAC → GAT)

66
F137W

67
I152V

68
N55L

69
N150S

70
L138L

71
P149P

72
G161G

73
A165T

74
H163R

75
H163K

76
H168A

77
E171S

78
E171R

79
E171R

80
T172I

81
C176G

82
A177S

83
A177S

84
S80L; R156W

85
H182G

86
N186S

87
K185R

88
K185T

89
D2H

90
D2T; E260G

91
D2Y

92
D2G

93
D2Q

94
D2F

95
D2A

96
D2T

97
D2N

98
D2R

99
D2I

100
D2V; G9A

101
G12A

102
D47W

103
S56S

104
I64H

105
L66L

106
I64C

107
L66G

108
E69Y

109
T74L

110
K73L

111
T74V

112
T74M

113
T74R

114
T74A

115
N76C

116
E77R

117
R156A

118
K72M

119
S205A

120
Q209S

121
V212E

122
R213W

123
I216T

124
P217H

125
P217V

126
D219F

127
E220V

128
R221E

129
F223C

130
S226P

131
L228F

132
V234A

133
S238S

134
V236T

135
V236T

136
T241R

137
L242F

138
T241R

139
T241C

140
E248F

141
D250E

142
K257V

143
G256K

144
E260G

145
L262R

146
K263M

147
D267G

148
D267R

149
I265L

150
E268S

151
L270S

152
L270G

153
L270W

154
R271S

155
I274W

156
G278S

157
Y279C

158
S284R

159
E282G

160
T280N

161
V286G

162
R285F

163
V286R

164
G240G

165
E61R

166
E61D

167
E61Y

168
G85G

169
G85D

170
S80R

171
Y79R

172
Y79V

173
W283V

174
W283E

175
W283A

176
W283S

177
W283G

178
W283A

179
W283R

180
W283T

181
P281W

182*
V236T; T241R

*Mutant 182 was created using site-directed mutagenesis, using Mutant 136 DNA as a template and then introducing the V236T mutation. One skilled in the art can synthesize this gene using site-directed mutagenesis techniques.

Samples listed in Table 43 were then prepared for the tertiary screen. Glycerol stocks were used to inoculate 5 mL of LB containing 100 μg/mL carbenicillin. Cultures were grown overnight at 37° C. The overnight cultures were then used to inoculate 50 mL cultures of LB containing 100 μg/mL carbenicillin in 250 mL baffled flasks to OD_600nmof 0.05. IPTG was added to a final concentration of 1 mM when the OD_600nmreached 0.4-0.8. Cultures were induced overnight at 30° C. Cell pellets were harvested by centrifugation at 6,000 rpm for 20 minutes. Cell pellets were frozen at −20° C. until cell lysates could be prepared. Cells were lysed with BPER II (Thermo Scientific, Rockford, Ill.) on ice for 1 hour. Clarified lysates were prepared by centrifugation at 12,000 rpm for 30 minutes.

Protein was quantified by Bio-Rad Bradford Protein Assay (Bio-Rad, Hercules, Calif.) per the manufacturer's instructions. SDS-PAGE analysis and densitometry were used to determine the amount of expressed D-aminotransferase. Samples were normalized for expressed D-aminotransferase. 0.02 mg/mL D-aminotransferase was tested in the tertiary screen. The tertiary screening method was the same as the secondary screening method except that samples were taken at 0, 5, 10, 15, 30, 60, 120 and 210 minutes to develop a timecourse. Alanine production and monatin consumption values were measured by LC/MS/MS analysis and compared to a standard curve. Samples were compared to the wild type control.

Samples with higher final titers or faster initial rates than the wild type control were identified as hits and are referred to as upmutants. The GSSM^SM upmutants identified in the tertiary screen are listed in Table 44. These upmutants are further described in Example 27 below.

Example 27
Enzymatic Activity of Polypeptides Upmutants

This example describes data demonstrating the enzymatic activity of exemplary upmutant polypeptides disclosed herein, e.g., the polypeptides having amino acid sequences described in Table 44. Table 44 shows the activity of the upmutants relative to the wild type control at the 15 minute time point in reactions using 1 mM and 15 mM R,R-Monatin substrate. Relative activity is the amount of alanine produced by the sample divided by the amount of alanine produced by the wild type control.

TABLE 44

Activity of GSSM Upmutants in Tertiary Screen

Activity relative to wild type control

(SEQ ID NO: 220)

Reaction with 1 mM
Reaction with 15 mM

Mutant
Mutation
monatin substrate
monatin substrate

23
V42M
1.28
1.04

24
G41Y
1.37
1.31

27
V93G
1.73
1.98

31
P20S
1.29
1.60

35
V93L
1.14
0.96

40
N118G
2.61
1.52

44
N118R
1.55
0.47

45
N110A; N118G
2.50
2.02

46
N118A
2.28
0.69

48
P117W; N118K
2.54
1.12

58
L129V
1.04
0.85

66
F137W
1.25
1.44

67
I152V
1.19
1.24

81
C176G
1.11
1.27

82
A177S
1.24
1.02

104
I64H
1.37
1.07

109
T74L
1.37
1.31

110
K73L
2.83
3.75

111
T74V
1.99
2.19

112
T74M
1.78
2.01

135
V236T
3.44
2.88

136
T241R
2.64
1.79

152
L270G
1.24
0.89

153
L270W
2.00
1.54

174
W283E
1.23
0.84

175
W283A
1.61
1.09

177
W283G
1.71
1.06

6
Y6L
2.52
2.21

88
K185T
1.04
0.95

107
L66G
1.08
1.02

Several samples were identified that outperformed the wild type control under the conditions tested. Potential K_mand V_maxupmutants were identified. These results indicate that the wild type control (SEQ ID NO:220) is further evolvable for increased specific D-aminotransferase activity on monatin.

Example 28
Activity of GSSM^SM Mutants in Monatin Process

Analysis of GSSM DATs in pSE420-C-His

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein. Mutant 27, Mutant 44, Mutant 58, Mutant 119, Mutant 135, Mutant 136, Mutant 152, Mutant 154 and the wild type control (in vector pSE420-C-His in E. coli XL1-Blue, as described in Examples 25 and 26) were streaked onto agar plates containing LB medium with ampicillin (100 μg/mL). Single colonies were used to inoculate 5 mL of LB medium containing ampicillin (100 μg/mL). Five hundred μl were used to inoculate 50 mL of the same medium in a 250 mL baffled flask. The cells were grown at 30° C. to approximately an OD_600nmof 0.4. IPTG was added to a final concentration of 1 mM. Cells were grown at 30° C. for 4 hours and collected by centrifugation. Cells were immediately frozen at −80° C. until cell extracts were prepared.

Cell extracts were prepared as described in Example 4. Protein concentrations were determined using the BCA (Pierce, Rockford, Ill.) microtiter plate assay with BSA (Pierce Rockford, Ill.) as the standard, per the manufacturer's instructions. To estimate the concentration of the D-aminotransferase in the cell-free extracts, SDS-PAGE analysis was done and visual estimation was used to estimate percentage of expression. The DAT proteins were soluble in the range of 10-25% expression as percentage of total protein and this was used to calculate the dosage of the assays.

An R,R monatin formation assay was performed containing 100 mM EPPS buffer pH 7.8, 1 mM MgCl², 0.05 mM PLP, 200 mM sodium pyruvate, 10 mM potassium phosphate, 0.01% Tween-80 with 0.1 mg/mL aldolase and 0.2 mg/mL of DAT in a 4 mL reaction at room temperature. Mutant 27 used 0.15 mg/mL of DAT enzyme instead of 0.2 mg/mL. After 0.5, 1, 2, 4 and 23 hours, an aliquot was taken, formic acid was added to a final concentration of 2%, and the samples spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described in Example 36. Results are shown in Table 45.

TABLE 45

Activity of DATs (cloned into pSE420-C-His)

Monatin

DAT
Monatin (mM)
Monatin (mM)
Monatin (mM)
(mM)

polypeptide
0.5 hr
1 hr
2 hr
4 hr

wild type
2.12
5.26
9.34
13.05

control

Mutant 27
4.74
9.55
14.72
18.06

Mutant 44
3.73
6.61
10.38
13.23

Mutant 58
3.61
7.51
11.85
14.56

Mutant 135
3.50
7.72
12.50
16.17

Mutant 136
1.40
4.63
6.59
—

Mutant 152
4.79
9.19
13.08
14.85

Mutant 154
3.76
7.66
11.85
14.38

As can be seen from the data shown in Table 45, a number of DAT mutants obtained through GSSM^SM evolution showed improved initial rates of monatin formation over the wild type control under the conditions of the assay.

Analysis of GSSM^SM DATs in pMet1a

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein. Mutant 2, Mutant 6, Mutant 11, Mutant 27, Mutant 40, Mutant 44, Mutant 45, Mutant 58, Mutant 110, Mutant 135, and Mutant 136 were recreated by site directed mutagenesis using QuikChange Multi Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) according to the manufacturer's instructions. To generate the mutants, the pMET1a tagged construct described in Example 16 (pMET1a:SEQ ID NO:220(WT)) was used as the template. The mutagenic primers used are listed below in Table 46. The PCR fragments were digested with Dpn1 (Invitrogen, Carlsbad, Calif.) for 1 hour and transformed into E. coli Top 10 cells (Invitrogen, Carlsbad, Calif.). The resultant purified plasmid preparations were sequenced (Agencourt, Beverly, Mass.) to verify that the correct mutations were incorporated. The plasmids were then transformed into E. coli B834(DE3) expression host (Novagen, San Diego, Calif.).

TABLE 46

Primers for Mutagenesis

Mutant

produced
PCR primers
Template

Mutant 2
5′-ATG GAC GCA CTG GGA TGT TAC AAC GGA AAT TGG-3′
SEQ ID

(SEQ ID NO: 1084)
NO: 220

5′-CCA ATT TCC GTT GTA ACA TCC CAG TGC GTC CAT-3′

(SEQ ID NO: 1085)

Mutant 6
5′-ATG GAC GCA CTG GGA CTT TAC AAC GGA AAT TGG
SEQ ID

GGG-3′ (SEQ ID NO: 1086)
NO: 220

5′-CCC CCA ATT TCC GTT GTA AAG TCC CAG TGC GTC

CAT-3′ (SEQ ID NO: 1087)

Mutant
5′-TAC CTG GTT TAT TGG CAG GGT ACT CGC GGA ACA
SEQ ID

27
GGC CGG-3′ (SEQ ID NO: 1088)
NO: 220

5′-CCG GCC TGT TCC GCG AGT ACC CTG CCA ATA AAC

CAG GTA-3′ (SEQ ID NO: 1089)

Mutant
5′-CTC TGG ATT ATA ATT AAG CCC GGC CAC ATC GAC
SEQ ID

40
AAT CTT TAT AG-3′ (SEQ ID NO: 1090)
NO: 220

5′-CTA TAA AGA TTG TCG ATG TGG CCG GGC TTA ATT

ATA ATC CAG AG-3′ (SEQ ID NO: 1091)

Mutant
5′-CTC TGG ATT ATA ATT AAG CCC AGG CAC ATC GAC
SEQ ID

44
AAT CTT TAT AG-3′ (SEQ ID NO: 1092)
NO: 220

5′-CTA TAA AGA TTG TCG ATG TGC CTG GGC TTA ATT

ATA ATC CAG AG-3′ (SEQ ID NO: 1093)

Mutant
5′-GTA TTT CCG GCA GGC CCT TCA GCG CTC TGG ATT ATA
Mutant 40

45
ATT AAG CC-3′ (SEQ ID NO: 1094)

5′-GGC TTA ATT ATA ATC CAG AGC GCT GAA GGG CCT

GCC GGA AAT AC-3′ (SEQ ID NO: 1095)

Mutant
5′-CAA TCT TTA TAG AAA AAT CAA GGT TAT TAC CAT
SEQ ID

58
GGA TGA TAC CCG C 3′ (SEQ ID NO: 1096)
NO: 220

5′-GCG GGT ATG ATC CAT GGT AAT AAC CTT GAT TTT TCT

ATA AAG ATT G-3′ (SEQ ID NO: 1097)

Mutant
5′-CTT AAC AAA AGA GGA ATT GAA ACT GAC TTT AAA
SEQ ID

110
TGA AAT GTA CTC C-3′ (SEQ ID NO: 1098)
NO: 220

5′-GGA GTA CAT TTC ATT TAA AGT CAG TTT CAA TTC CTC

TTT TGT TAA G-3′ (SEQ ID NO: 1099)

Mutant
5′-TTC GAC GCG GAC GAG GTG CTT ACT TCC AGC AGC
SEQ ID

135
GGC ACA CTC G-3′ (SEQ ID NO: 1100)
NO: 220

5′-CGA GTG TGC CGC TGC TGG AAG TAA GCA CCT CGT

CCG CGT CGA A-3′ (SEQ ID NO: 1101)

Mutant
5′-TGC TTG TGT CCA GCA GCG GCC GGC TCG GCC TTA
SEQ ID

136
GCG CCG-3′ (SEQ ID NO: 1102)
NO: 220

5′-CGG CGC TAA GGC CGA GCC GGC CGC TGC TGG ACA

CAA GCA-3′ (SEQ ID NO: 1103)

Mutant 2, Mutant 6, Mutant 27, Mutant 40, Mutant 45, Mutant 58, Mutant 110, Mutant 119, Mutant 131, Mutant 135, Mutant 136, Mutant 152, Mutant 154 were generated in the pMET1a vector and transformed into the compatible E. coli expression host B834(DE3) (Novagen, San Diego, Calif.) described in Example 2. Overnight cultures in LB medium containing carbenicillin (100 μg/mL) were diluted 1:100 in 100 mL of the same medium and grown in a 500 mL baffled flask. The culture was grown at 30° C. overnight to an OD_600nmof 10 in Overnight Express II medium (Solution 1-6, Novagen). Samples for total protein were taken immediately prior to harvesting. Cells were harvested by centrifugation and washed once with 10 mL of potassium phosphate buffer pH 7.8. Cells were immediately frozen at −80° C. until cell extracts were prepared. It is noted that, in addition to site-directed mutagenesis, one skilled in the art can synthesize the genes encoding these D-aminotransferases using multi-change mutagenesis PCR techniques such as those described in Example 25.

Transamination of R,R monatin with pyruvate as the amino acceptor were performed as described in Example 5 except that 15 mM R,R monatin was utilized. Initial analyses of alanine, monatin, and monatin precursor levels identified Mutant 40, Mutant 135 and Mutant 136 as superior mutants resulting in the highest levels of alanine production as shown in Table 47. DAT Mutant 136 appeared to have the highest activity for conversion of R,R monatin to R-MP. The alanine production numbers (in mM) for the various time points are shown in Table 47.

TABLE 47

Alanine formation (mM) from R,R monatin transamination

reactions from DATs cloned into pMET1a

Alanine

Alanine
Alanine

DAT
(mM)
Alanine (mM)
(mM)
(mM)

polypeptide
15 minutes
30 minutes
60 minutes
120 minutes

wild type
3.08
5.47
8.19
10.07

control

Mutant 2
3.38
5.74
8.85
10.52

Mutant 6
3.51
5.97
8.99
10.81

Mutant 27
4.36
8.00
10.72
10.52

Mutant 40
7.89
10.37
11.79
12.50

Mutant 44
2.65
4.58
7.18
—

Mutant 58
3.90
6.95
9.93
10.52

Mutant 110
3.50
6.17
9.53
10.52

Mutant 135
5.35
8.64
10.82
10.91

Mutant 136
6.24
9.46
11.24
11.15

Mutant 152
4.26
7.12
9.83
10.32

Mutant 154
4.16
7.13
10.07
10.76

—: not determined under present conditions

To further assess activity, a monatin formation assay was done as described in Example 1 with a DAT concentration of approximately 0.2 mg/mL. As a control, 0.2 mg/mL concentration of purified wild type DAT was evaluated. After 0.5, 1, 2, and 4 hrs, an aliquot was taken and formic acid was added to a final concentration of 2%, and the samples were spun and filtered. Samples were analyzed for monatin using the LC/MS/MS methodology described herein and for tryptophan and alanine using the LC/OPA post-column fluorescence methodology described in Example 36.

TABLE 48

Activity of DATs in pMET1a

Monatin

DAT
Monatin (mM)
Monatin (mM)
Monatin (mM)
(mM)

polypeptide
0.50 hr
1.00 hr
2.00 hr
4.00 hr

wild type
3.96
7.83
9.70
11.18

control

Mutant 2
1.56
3.78
8.77
12.68

Mutant 27
4.70
9.70
n.d.
13.80

Mutant 44
3.03
5.61
8.50
12.28

Mutant 45
1.40
4.00
7.70
11.50

Mutant 58
3.83
7.23
11.33
14.12

Mutant 110
2.60
5.90
9.90
12.70

Mutant 119
4.12
7.87
11.37
13.50

Mutant 131
3.75
7.41
11.40
13.90

Mutant 135
6.39
10.65
13.49
13.15

Mutant 136
3.36
8.02
12.86
13.16

Mutant 154
3.00
6.06
10.67
13.17

All the DATs shown in Table 48 produced monatin. DAT mutants Mutant 58, Mutant 135 and Mutant 136 had faster initial rates than the wild type control. Mutant 136 was slower for reaction one (conversion of D-Trp to I3P) but had better overall monatin production than the wild type control.

For the final time point, an additional aliquot was taken (without the addition of formic acid) to determine the stereoisomeric distribution of the monatin produced using the FDAA derivatization methodology described in Example 36. For the select mutants tested, there was little to no impact on stereopurity. In all cases, the mutants produced over 98.8% R,R under the assay conditions tested. These results are shown in Table 49.

TABLE 49

Stereopurities of Monatin Produced by Select Mutants at 4 hours

DAT polypeptide
% SS
% RS
% RR
% SR

wild type (pMet1a)
0.00
0.40
99.30
0.20

control

Mutant 6
0.00
0.40
99.50
0.10

Mutant 27
0.00
0.80
98.80
0.30

Mutant 40
0.00
0.20
99.80
0.00

Mutant 45
0.00
0.50
99.40
0.10

Mutant 110
0.10
0.40
99.30
0.10

Mutant 135
0.00
0.40
99.50
0.10

Mutant 136
0.02
1.00
99.00
0.03

Example 29
Construction and Testing of Tailored Multi-Site Combinatorial Assembly (TMCA^SM) Mutants

This example describes the construction of exemplary nucleic acids and polypeptides, and describes their enzymatic activity. A subset of GSSM mutations were selected for combination using Tailored Multi-Site Combinatorial Assembly^SM (TMCA^SM) technology. The top ten performers from the GSSM evolution in either the 1 or 15 mM monatin reactions were selected for TMCA^SM evolution. The wild type sequence (SEQ ID NO:220) was threaded onto a model of 3DAA-D amino acid aminotransferase (FIG. 4). The model in FIG. 4 is shown with pyridoxyl-5′-phosphate D-alanine, with the numbered residues indicating those sites selected for TMCA^SM evolution. Table 50 also lists the mutations that were selected for inclusion in the TMCA^SM library. TMCA^SM evolution was performed on wild type (SEQ ID NO:220) and Mutant 45 using the methods described in PCT Application No. PCT/US08/071,771.

TMCA evolution is described in PCT Application Number PCT/US08/071,771 and comprises a method for producing a plurality of progeny polynucleotides having different combinations of various mutations at multiple sites. The method can be performed, in part, by a combination of at least one or more of the following steps:

Obtaining sequence information of a (“first” or “template”) polynucleotide. For example, the first or template sequence can be a wild type (e.g. SEQ ID NO:220) or mutated (e.g. Mutant 45) sequence. The sequence information can be of the complete polynucleotide (e.g., a gene or an open reading frame) or of partial regions of interest, such as a sequence encoding a site for binding, binding-specificity, catalysis, or substrate-specificity.

Identifying three or more mutations of interest along the first or template polynucleotide sequence. For example, mutations can be at 3, 4, 5, 6, 8, 10, 12, 20 or more positions within the first or template sequence. The positions can be predetermined by absolute position or by the context of surrounding residues or homology. For TMCA of DAT polypeptides, the top 10 codon changes that resulted in improved enzyme performance were included as mutations of interest. The sequences flanking the mutation positions on either side can be known. Each mutation position may contain two or more mutations, such as for different amino acids. Such mutations can be identified by using Gene Site Saturation Mutagenesis^SM (GSSM^SM) technology, as described herein and in U.S. Pat. Nos. 6,171,820; 6,562,594; and 6,764,835.

Providing primers (e.g., synthetic oligonucleotides) comprising the mutations of interest. In one embodiment, a primer is provided for each mutation of interest. Thus, a first or template polynucleotide having 3 mutations of interest can use 3 primers at that position. The primer also can be provided as a pool of primers containing a degenerate position so that the mutation of interest is the range of any nucleotide or naturally occurring amino acid, or a subset of that range. For example, a pool of primers can be provided that favor mutations for aliphatic amino acid residues.

The primers can be prepared as forward or reverse primers, or the primers can be prepared as at least one forward primer and at least one reverse primer. When mutations are positioned closely together, it can be convenient to use primers that contain mutations for more than one position or different combinations of mutations at multiple positions.

Providing a polynucleotide containing the template sequence. The first or template polynucleotide can be circular, or can be supercoiled, such as a plasmid or vector for cloning, sequencing or expression. The polynucleotide may be single-stranded (“ssDNA”), or can be double-stranded (“dsDNA”). For example, the TCMA method subjects the supercoiled (“sc”) dsDNA template to a heating step at 95° C. for 1 min (see Levy, Nucleic Acid Res., 28(12):e57(i-vii) (2000)).

Adding the primers to the template polynucleotide in a reaction mixture. The primers and the template polynucleotide are combined under conditions that allow the primers to anneal to the template polynucleotide. In one embodiment of the TMCA protocol, the primers are added to the polynucleotide in a single reaction mixture, but can be added in multiple reactions.

Performing a polymerase extension reaction. The extension products (e.g., as a “progeny” or “modified extended polynucleotide”) may be amplified by conventional means. The products may be analyzed for length, sequence, desired nucleic acid properties, or expressed as polypeptides. Other analysis methods include in-situ hybridization, sequence screening or expression screening. The analysis can include one or more rounds of screening and selecting for a desired property.

The products can also be transformed into a cell or other expression system, such as a cell-free system. The cell-free system may contain enzymes related to DNA replication, repair, recombination, transcription, or for translation. Exemplary hosts include bacterial, yeast, plant and animal cells and cell lines, and include E. coli, Pseudomonas fluorescens, Pichia pastoris and Aspergillus niger. For example, XL1-Blue or Stb12 strains of E. coli can be used as hosts.

The method of the invention may be used with the same or different primers under different reaction conditions to promote products having different combinations or numbers of mutations.

By performing the exemplary method described above, this protocol also provides one or more polynucleotides produced by this TMCA evolution method, which then can be screened or selected for a desired property. One or more of the progeny polynucleotides can be expressed as polypeptides, and optionally screened or selected for a desired property. Thus, this embodiment of the TMCA evolution protocol provides polynucleotides and the encoded polypeptides, as well as libraries of such polynucleotides encoding such polypeptides. This embodiment of the TMCA evolution protocol further provides for screening the libraries by screening or selecting the library to obtain one or more polynucleotides encoding one or more polypeptides having the desired activity.

Another embodiment of the TMCA evolution protocol described in PCT/US08/071,771 comprises a method of producing a plurality of modified polynucleotides. Such methods generally include (a) adding at least three primers to a double stranded template polynucleotide in a single reaction mixture, wherein the at least three primers are not overlapping, and wherein each of the at least three primers comprise at least one mutation different from the other primers, wherein at least one primer is a forward primer that can anneal to a minus strand of the template and at least one primer is a reverse primer that can anneal to a plus strand of the template, and (b) subjecting the reaction mixture to a polymerase extension reaction to yield a plurality of extended modified polynucleotides from the at least three primers.

Another embodiment of the TMCA evolution protocol described in PCT/US08/071,771 comprises a method wherein a cell is transformed with the plurality of extended products that have not been treated with a ligase. In another embodiment of the invention, the plurality of extended modified polynucleotides is recovered from the cell. In another embodiment, the recovered plurality of extended modified polynucleotides is analyzed, for example, by expressing at least one of the plurality of extended modified polynucleotides and analyzing the polypeptide expressed therefrom. In another embodiment, the plurality of extended modified polynucleotides comprising the mutations of interest is selected.

In another embodiment of the TMCA evolution protocol, sequence information regarding the template polynucleotide is obtained, and three or more mutations of interest along the template polynucleotide can be identified. In another embodiment, products obtained by the polymerase extension can be analyzed before transforming the plurality of extended modified products into a cell.

In one embodiment of the TMCA evolution protocol, products obtained by the polymerase extension are treated with an enzyme, e.g., a restriction enzyme, such as a Dpn1 restriction enzyme, thereby destroying the template polynucleotide sequence. The treated products can be transformed into a cell, e.g., an E. coli cell.

In one embodiment of the TMCA evolution protocol, at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or more primers can be used. In one embodiment, each primer comprises a single point mutation. In another embodiment, two forward or two reverse primers comprise a different change in the same position on the template polynucleotide. In another embodiment, at least one primer comprises at least two changes in different positions on the template polynucleotide. In yet another embodiment, at least one primer comprises at least two changes in different positions and at least two forward or two reverse primers comprise a different change in the same position on the template polynucleotide.

In one embodiment of the TMCA evolution protocol, the forward primers are grouped into a forward group and the reverse primers are grouped into a reverse group, and the primers in the forward group and the primers in the reverse group, independent of one another, are normalized to be equal concentration in the corresponding group regardless of positions on the template polynucleotide, and wherein after the normalization an equal amount of the forward and reverse primers is added to the reaction. In this normalization method, a combination of some positions may be biased. The bias can be due to, for example, a relatively low primer concentration at one position containing a single primer compared to a position containing multiple primers. “Positional bias” refers to resulting polynucleotides which show a strong preference for the incorporation of primers at a single position relative to the other positions within its forward or reverse primer group. This results in a combination of modified polynucleotides which may have a high percentage of mutations within a single primer position but a low percentage of mutations at another position within its forward or reverse primer group. This bias is unfavorable when the goal of the TMCA is to generate progeny polynucleotides comprising all possible combinations of changes to the template. The bias can be corrected, for example, by normalizing the primers as a pool at each position to be equal.

In one embodiment of the TMCA evolution protocol, the primer normalization is performed by organizing the primers into multiple groups depending on their location on the template polynucleotide, wherein the primers covering the same selected region on the template are in one group; normalizing the grouped primers within each group to be equal concentration; pooling the forward primers within one group into a forward group and normalizing concentration between each group of the forward primers to be equal; pooling the reverse primers within one group into a reverse group and normalizing concentration between each group of the reverse primers to be equal; and adding an equal amount of the pooled forward and reversed primers into the reaction. No bias has been observed for position combinations.

In one embodiment of the TMCA evolution protocol, a set of degenerate primers each comprising a degenerate position is provided, wherein the mutation of interest is a range of different nucleotides at the degenerate position. In another embodiment, a set of degenerate primers is provided comprising at least one degenerate codon corresponding to at least one codon of the template polynucleotide and at least one adjacent sequence that is homologous to a sequence adjacent to the codon of the template polynucleotide sequence. In another embodiment, the degenerated codon is N,N,N and encodes any of 20 naturally occurring amino acids. In another embodiment, the degenerated codon encodes less than 20 naturally occurring amino acids.

Another embodiment of the TMCA evolution protocol described in PCT/US08/071,771 comprises a method of producing a plurality of modified polynucleotides comprising the mutations of interest. Such methods generally include (a) adding at least two primers to a double stranded template polynucleotide in a single reaction mixture, wherein the at least two primers are not overlapping, and wherein each of the at least two primers comprise at least one mutation different from the other primer(s), wherein at least one primer is a forward primer that can anneal to a minus strand of the template and at least one primer is a reverse primer that can anneal to a plus strand of the template, (b) subjecting the reaction mixture to a polymerase extension reaction to yield a plurality of extended modified polynucleotides from the at least two primers, (c) treating the plurality of extended modified polynucleotides with an enzyme, thereby destroying the template polynucleotide, (d) transforming the treated extended modified polynucleotides that have not been treated with a ligase into a cell, (e) recovering the plurality of extended modified polynucleotides from the cell, and (f) selecting the plurality of extended modified polynucleotides comprising the mutations of interest.

TABLE 50

List of Sites for TMCA evolution

Mutation
New Codon

P20S
AGT

K73L
TTG

T74V
GTG

V93G
GGT

N110A
GCT

P117W
TGG

N118G
GGG

N118A
GCG

V236T
ACT

T241R
CGG

L270W
TGG

TMCA mutants were grown, arrayed, assayed and sequenced using the same method as described for the GSSM evolution in Example 25. Sample performance was compared to the performance of the top candidate from GSSM evolution—Mutant 135—using the same scoring system as described in Example 25. Table 52 lists the TMCA secondary screen hits with unique DNA sequences (TMCA mutants are designated with alphabetic characters to distinguish them from GSSM mutants, which are designated numerically).

TABLE 52

TMCA Mutants Identified as Secondary Screen Hits

Mutant

name
Mutation

A
P20S-N118G

B
T74V-V93G-L270W

C
P20S-T74V-L270W

D
T74V-L270W

E
P20S-K73L-T241R-L270W

F
K73L-V93G-V236T-T241R

G
P20S-T74V-V236T

H
P20S-K73L-V93G

I
K73L-V236T

J
P20S-L270W

K
2N-P20S-K73L-V93G-N118G

L
P20S-T74V-N118A

M
P20S-V236T

N
P20S-T241R-L270W

O
P20S-T241R

P
T74V-V93G-V236T-T241R

Q
P20S-K73L-T74V-L270W

R
P20S-V93G-V236T

S
P20S-K73L-T74V-T241R-L270W

T
P20S-K73L-L270W

U
T74V-V93G-N118G-V236T-T241R

V
P20S-K73L-210A (SILENT-GCC

→ GCT)-V236T

W
N118A-L270W

X
P20S-58K (SILENT AAG →

AAA)-L270W

Y
P20S-V93G-N118G

Z
P20S-V236T-T241R

AA
P20S-P117W-N118A-V236T-

L270W

BB
V93G-V236T

CC
V236T-L270W

DD
P20S-N118G-L270W

EE
P20S-N110A-N118G

FF
N110A-N118G-T241R-L270W

GG
P20S-T74V-V93G-N110A-N118G-

V236T-L270W

HH
V93G-N110A-N118G-V236T

II
P20S-T74V-N110A-N118G

JJ
N110A-N118G

KK
P20S-V93G-N110A-N118G-T241R

LL
N110A-N118A-L270W

MM
P20S-N110A-N118G-L270W

NN
N110A-N118A-V236T-T241R

OO
N110A-N118G-L270W

PP
V93G-N110A-N118G-T241R

QQ
P20S-V93G-N110A-N118G

RR
V93G-N110A

SS
P20S-N110A-N118G-V236T

TT
T74V-N110A-N118A-V236T

UU
P20S-K73L-T74V-N110A-N118G-

V236T-T241R

VV
86E (SILENT GAG → GAA)-

N110A-N118A-V236T

WW
T74V-N118G

XX
P20S-T241R-L270W-277T

(SILENT ACA → ACG)

YY
T74V-N118A-L270W

ZZ
P20S-K73L-N118A-L270W

AAA
P20S-V93G-T241R

BBB
T74V-V93G-N110A-T241R

CCC
V93G-N110A-N118A

DDD
P20S-T74V-V93G-N110A-N118G-

T241R

EEE
T74V-N110A-N118G-L270W

FFF
P20S-231A (SILENT GCG →

GCA)-V236T

GGG
V93G-V236T-T241R

The samples identified in Table 52 were grown, normalized and assayed in the tertiary screen using the same method as described for the GSSM evolution in Example 26. Monatin and alanine values were determined by LC/MS/MS and compared to a standard curve. Sample performance was compared to the activity of Mutant 135 (the top performer from GSSM evolution). TMCA upmutants identified in the tertiary screen are listed in Table 53.

Example 31
Activity of TMCA Hits

This example describes data demonstrating the enzymatic activity of exemplary polypeptides. Table 53 below shows the activity of the upmutants relative to Mutant 135 at the minute time point in reactions using 1 mM and 15 mM R,R-monatin substrate. Relative activity is the amount of alanine produced by the sample divided by the amount of alanine produced by Mutant 135.

TABLE 53

Activity of TMCA Upmutants in Tertiary Screen

Activity relative

to GSSM

Mutant 135

Reactions
Reactions

with 1 mM
with 15 mM

monatin
monatin

Mutant
Mutation
substrate
substrate

C
P20S-T74V-L270W
1.02
0.93

E
P20S-K73L-T241R-L270W
1.32
1.31

F
K73L-V93G-V236T-T241R
1.29
0.64

G
P20S-T74V-V236T
1.28
1.30

I
K73L-V236T
1.24
1.29

J
P20S-L270W
0.79
1.01

L
P20S-T74V-N118A
1.62
0.83

M
P20S-V236T
1.27
1.46

O
P20S-T241R
1.33
1.71

R
P20S-V93G-V236T
1.22
1.02

S
P20S-K73L-T74V-T241R-
1.16
1.18

L270W

V
P20S-K73L-210A
1.03
1.00

(SILENT-GCC → GCT)-

V236T

Z
P20S-V236T-T241R
1.02
0.89

BB
V93G-V236T
1.55
1.98

CC
V236T-L270W
1.24
1.40

DD
P20S-N118G-L270W
1.54
1.78

PP
V93G-N110A-N118G-T241R
1.40
1.53

TT
T74V-N110A-N118A-V236T
1.10
0.42

VV
86E (SILENT GAG →
1.31
0.52

GAA)-N110A-N118A-V236T

WW
T74V-N118G
1.23
1.49

YY
T74V-N118A-L270W
1.97
1.30

ZZ
P20S-K73L-N118A-L270W
1.01
0.44

AAA
P20S-V93G-T241R
1.86
3.49

CCC
V93G-N110A-N118A
1.26
0.56

Several samples were identified that outperformed Mutant 135 under the conditions tested. Potential K_mand V_maxupmutants were identified. The results of the GSSM and TMCA evolutions indicate that wild type SEQ ID NO:220 is further evolvable for increased specific activity on monatin.

Example 32
Evaluation of TMCA Mutant DATs in pMET1a

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein. Mutant E, Mutant G, Mutant I, Mutant M, Mutant O, Mutant P, Mutant BB, Mutant PP, Mutant WW, and Mutant AAA (DATs created using TMCA technology, see Examples 29 and 30) were recreated by site-directed mutagenesis using QuikChange Multi Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) according to the manufacturer's instructions. To generate the mutants, pMET1a tagged constructs described in Example 16 and Example 28 were used as templates. The mutagenic primers used are listed below in Table 54. The PCR fragments were digested with Dpn1 (Invitrogen, Carlsbad, Calif.) for 1 hour and transformed into E. coli XL10-Gold cells (Stratagene, La Jolla, Calif.). The resultant purified plasmid preparations were sequenced (Agencourt, Beverly, Mass.) to verify that the correct mutations were incorporated. The plasmids were then transformed into E. coli B834(DE3) expression host (Novagen, San Diego, Calif.).

TABLE 54

Primers for Mutants in pMET1a Vector

TMCA

mutant

polypeptide

produced
PCR primers
Template

Mutant E
5′-CTG GAC GAG ATG ACT GTG AGT ATG AAC GAC AGG
Mutant

GGC TGC TAC-3′ (SEQ ID NO: 1104)
110

5′-TGC TTG TGT CCA GCA GCG GCC GGC TCG GCC TTA

GCG CCG-3′ (SEQ ID NO: 1105)

5′CTA AAA AAA ATC CAG GAT GAA GTG TGG AGG GAA

TTT ATC GAA GCG ACA GG3′ (SEQ ID NO: 1106)

Mutant G
5′-CAA AAG AGG AAT TGA AAA AAG TGT TAA ATG AAA
Mutant M

TGT ACT CC-3′ (SEQ ID NO: 1107)

5′-GGA GTA CAT TTC ATT TAA CAC TTT TTT CAA TTC

CTC TTT TG-3′ (SEQ ID NO: 1108)

Mutant I
5′-CTT AAC AAA AGA GGA ATT GAA ACT GAC TTT AAA
Mutant

TGA AAT GTA CTC C-3′ (SEQ ID NO: 1109)
135

5′-GGA GTA CAT TTC ATT TAA AGT CAG TTT CAA TTC

CTC TTT TGT TAA G-3′ (SEQ ID NO: 1110)

Mutant M
5′-CTG GAC GAG ATG ACT GTG AGT ATG AAC GAC AGG
Mutant

GGC TGC TAC-3′ (SEQ ID NO: 1111)
135

5′-GTA GCA GCC CCT GTC GTT CAT ACT CAC AGT CAT

CTC GTC CAG-3′ (SEQ ID NO: 1112)

Mutant O
5′-CTG GAC GAG ATG ACT GTG AGT ATG AAC GAC AGG
Mutant

GGC TGC TAC-3′ (SEQ ID NO: 1113)
136

5′-GTA GCA GCC CCT GTC GTT CAT ACT CAC AGT CAT

CTC GTC CAG-3′ (SEQ ID NO: 1114)

Mutant P
5′-CAA AAG AGG AAT TGA AAA AAG TGT TAA ATG AAA
Mutant

TGT ACT CC-3′ (SEQ ID NO: 1115)
27

5′-TTC GAC GCG GAC GAG GTG CTT ACT TCC AGC AGC

GGC ACA CTC G-3′ (SEQ ID NO: 1116)

5′-TGC TTG TGT CCA GCA GCG GCC GGC TCG GCC TTA

GCG CCG-3′ (SEQ ID NO: 1117)

Mutant BB
5′-TAC CTG GTT TAT TGG CAG GGT ACT CGC GGA ACA
Mutant

GGC CGG-3′ (SEQ ID NO: 1118)
135

5′-CCG GCC TGT TCC GCG AGT ACC CTG CCA ATA AAC

CAG GTA-3′ (SEQ ID NO: 1119)

Mutant PP
5′-TAC CTG GTT TAT TGG CAG GGT ACT CGC GGA ACA
Mutant

GGC CGG-3′ (SEQ ID NO: 1120)
45

5′-TGC TTG TGT CCA GCA GCG GCC GGC TCG GCC TTA

GCG CCG-3′ (SEQ ID NO: 1121)

Mutant
5′-CAA AAG AGG AAT TGA AAA AAG TGT TAA ATG AAA
Mutant M

WW
TGT ACT CC-3′ (SEQ ID NO: 1122)

5′-GGA GTA CAT TTC ATT TAA CAC TTT TTT CAA TTC

CTC TTT TG-3′ (SEQ ID NO: 1123)

Mutant
5′-CTG GAC GAG ATG ACT GTG AGT ATG AAC GAC AGG
Mutant

AAA
GGC TGC TAC-3′ (SEQ ID NO: 1124)
27

5′-TGC TTG TGT CCA GCA GCG GCC GGC TCG GCC TTA

GCG CCG-3′ (SEQ ID NO: 1125)

E. coli B834(DE3) (Novagen, San Diego, Calif.) cultures expressing carboxy-terminal His-tagged Mutant 110, Mutant 135, Mutant 136, Mutant E, Mutant G, Mutant I, Mutant M, Mutant O, Mutant P, Mutant BB, Mutant PP, Mutant WW, Mutant AAA and wild type (SEQ ID NO:220) proteins were grown in 200 mL of Overnight Express II medium (Solution 1-6, Novagen) in a 500 mL baffled flask overnight at 30° C. to an OD₆₀₀of 10. Samples for total protein were taken immediately prior to harvesting. Cells were harvested by centrifugation and immediately frozen at −80° C. until cell extracts were prepared as described in Example 4.

Cell extracts were created by the addition of 50 mL of Bug Buster Primary Amine Free (Novagen, San Diego, Calif.) with 50 μl of Benzonase Nuclease (Novagen, San Diego, Calif.), 0.75 μl of rLysozyme (Novagen, San Diego, Calif.), and 250 μl of Protease Inhibitor Cocktail II (Calbiochem, San Diego, Calif.). The cells were incubated for 15 minutes at room temperature with gentle rocking. The extracts were centrifuged at 45,000×g for 10 minutes.

His-tagged proteins were purified as described in Example 4 using GE Healthcare (Piscataway, N.J.) Chelating Sepharose™ Fast Flow resin. The exception was Mutant 182, which was analyzed as CFE as described in Example 4. Purified protein was desalted using a PD10 column into 100 mM potassium phosphate, pH 7.8 with 0.050 mM PLP. Total protein and DAT concentrations were determined as described in Example 4.

A 3-step monatin formation assay was done as described in Example 5 with a DAT concentration of approximately 0.2 mg/mL and the aldolase at a concentration of 0.1 mg/mL. As a control, 0.2 mg/mL concentration of purified wild type DAT (SEQ ID NO:220) was evaluated. After 0.5, 1, 2, 4 and 24 hours, an aliquot was taken, formic acid was added to a final concentration of 2% and the samples were spun and filtered. Samples were analyzed for monatin using LC/MS/MS methodology and for tryptophan and alanine using the LC/OPA post-column fluorescence methodology described in Example 36. At the last time point, an additional aliquot was taken (without pH adjustment) to determine % R,R monatin by the FDAA-derivatization method described in Example 36. The amount of monatin (mM) produced at various time points can be found in Table 55. Stereopurity was also determined and the percent of the R,R stereoisomer can be found in the far right hand column. The stereoisomer R,S made up the majority of the balance.

TABLE 55

Activity of Select DAT Mutants

Monatin
Monatin
Monatin
Monatin

DAT
(mM)
(mM)
(mM)
(mM)

polypeptide
0.25 hr
0.5 hr
1 hr
4 hr
% RR

Wild type
1.60 (±0.42)
2.95 (±0.64)
5.00 (±0.85)
11.40 (±0.42)
99.50 (±0.08)

control (SEQ

ID NO: 220)

Mutant 110
1.70 (±0.00)
3.20 (±0.85)
5.75 (±0.21)
12.60 (±0.14)
99.48 (±0.32)

Mutant 135
3.65 (±0.35)
6.17 (±0.65)
10.33 (±0.32)
13.20 (±0.56)
99.42 (±0.11)

Mutant 136
2.60
5.00
8.10
12.90
98.98

Mutant 182
—
3.20
6.80
14.30
99.50

Mutant E
1.80
3.80
8.60
18.60
99.45

Mutant G
3.10
6.50
9.90
12.90
99.05

Mutant I
2.90
5.30
8.50
12.90
99.46

Mutant M
4.20
8.10
11.20
13.80
98.96

Mutant O
2.60
5.70
9.50
14.00
98.59

Mutant BB
4.20
8.20
11.40
13.70
98.97

Mutant PP
2.40
3.20
6.20
17.40
97.25

Mutant AAA
2.80
6.80
11.80
14.80
97.98

—= not determined under conditions tested

The relative rates of monatin production under the conditions tested indicate the greatest improvement in initial activity from Mutant 135, Mutant 136, Mutant E, Mutant G, Mutant M, Mutant O, Mutant BB, and Mutant AAA as determined by comparing the rate of monatin formation with purified protein over the first hour between the mutants and the wild type control (SEQ ID NO:220) DAT. DATs Mutant E and Mutant AAA had high activity but were not well expressed (less than 5% of the total protein) nor very soluble under the conditions tested.

The assay samples were also analyzed for intermediates such as monatin precursor, I3P, and byproduct 4-hydroxy-4-methyl glutmatic acid (HMG) as described in Example 36. The analysis of the amount of HMG formed was determined for the mutants Mutant E, Mutant G, Mutant 1, Mutant M, Mutant O, Mutant BB, Mutant PP, Mutant AAA and Mutant 110, Mutant 135, and Mutant 136. It appears that at the 4 hour time point, more HMG were formed by the mutants Mutant 135, Mutant G, Mutant 1, Mutant M and Mutant BB. These mutants all contained the change V236T. HMG was also present above the levels of the wild type control (SEQ ID NO:220) with mutants Mutant E, Mutant G, Mutant M and Mutant AAA likely due to the change in residue P20S.

TABLE 56

HMG Formation by DAT Mutants after 4 hours

HMG (mM)

DAT polypeptide
4 hr

Wild type control
nd

(SEQ ID NO: 220)

Mutant 110
nd

Mutant 135
1.0

Mutant 136
nd

Mutant E
0.2

Mutant G
1.6

Mutant I
0.8

Mutant M
1.6

Mutant O
nd

Mutant BB
1.5

Mutant AAA
0.6

nd = not detected

DAT Assay Monitoring I3P Formation

The formation of I3P from tryptophan was detected and monitored at a wavelength of 340 nm. Reactions were carried out in 1 mL reaction volume containing 900 μL, of a 25 mM D-tryptophan, 25 mM pyruvic acid sodium salt, 0.05 mM PLP, 100 mM potassium phosphate (pH 7.8) solution combined with 100 μL dilutions of DAT (total protein) prepared as described above. Enzymes were diluted 1:100 and 1:200 with cold 50 mM potassium phosphate (pH 7.8) and 50 μM PLP prior to addition to the assay. Enzyme was added to the reaction mixture 1:100 and monitored in increments of 15 seconds for 3 minutes. The formation of indole-3-pyruvate (I3P) was monitored at a wavelength of 340 nm for 3 minutes on a BioRad Spectrophotometer (GE Healthscience, Piscataway, N.J.) and rates were measured within the dynamic range of a standard curve. The standard curve was generated with purified wild type (SEQ ID NO:220) DAT protein and the concentration of DAT in cell extract was determined based on the equation of the line for the standard curve. The effective concentration of DAT with respect to the wild type DAT for the first reaction is reported in Table 57.

TABLE 57

Activity of DAT (Conversion of Tryptophan to I3P)

Concentration of

Rate of 13P
DAT

formation
(determined by
Activity relative to

DAT
(Δ Abs340 nm/
activity)
Wild type of first

Polypeptide
minute)
mg/mL
reaction

Wild type
0.058
0.065
1.0

control (SEQ

ID NO: 220)

Mutant 135
0.067
0.075
1.2

Mutant 136
0.017
0.019
0.3

Mutant E
0.000
0.002
0.1

Mutant G
0.027
0.030
0.5

Mutant M
0.050
0.055
0.9

Mutant O
0.031
0.033
0.8

Mutant BB
0.045
0.050
0.8

Mutant AAA
0.002
0.004
0.2

The wild type DAT (SEQ ID NO:220) and mutants 136, E, G, M, O, BB and AAA can facilitate the conversion of both tryptophan to I3P and of monatin precursor to monatin. Table 57 shows that these mutants had lower activity for the conversion of tryptophan to I3P relative to the wild type DAT (SEQ ID NO:220). Yet, according to Table 55, the same mutants produced more total monatin from tryptophan than did the wild type DAT (SEQ ID NO:220). Thus, under the conditions of the assay described herein, there appears to be a beneficial effect on monatin production through controlling the conversion of tryptophan to I3P in the monatin biosynthetic pathway. For example, although Mutant E showed the lowest relative activity for conversion of tryptophan to I3P (see Table 57), it also produced the highest amount of monatin at 4 hours (see Table 55). Without being bound by theory, the beneficial effects of controlling the first step in the reaction could be attributed to a reduction of I3P buildup and subsequent potential I3P degradation to products other than monatin. Generally, it also appears that controlling the rate of one or more of the reactions involved in the production of monatin from tryptophan, using, for example, one or more mutant DATs, can have a beneficial effect on the total amount of monatin produced.

Example 33
Evaluation of Mutant DATs at 35° C.

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein. Starter cultures were grown overnight at 37° C. with shaking at 250 rpm until the OD_600nmreached 0.05. 200 mL of Overnight Express II medium (Novagen, San Diego, Calif.) was inoculated and grown as described in Example 3. Cultures were grown in duplicate and the cell pellets were combined. The pellets were resuspended in 40 mL of 50 mM sodium phosphate buffer (pH 7.8) with 0.05 mM PLP and lysed using a French Press (Sim Aminco, Rochester, N.Y.) per the manufacturer's instructions. The supernatant was collected in a clean tube and stored at −80° C. until used.

A 3-step monatin formation assay was performed as described in the methods with a DAT concentration of approximately 0.2 mg/mL and the aldolase at a concentration of 0.1 mg/mL in glass vials. Duplicate samples were incubated at either 25° C. or 35° C. and after 1, 3, and 4 hours, an aliquot was taken and formic acid was added to a final concentration of 2%, and the samples were spun and filtered. Samples were analyzed for monatin using LC/MS/MS methodology and for tryptophan and alanine using the LC/OPA post-column fluorescence methodology described in Example 36. Samples were also analyzed for intermediates such as monatin precursor, I3P, and 4-hydroxy-4-methyl glutmatic acid (HMG) as described in Example 36. The amount of monatin (mM) produced at various time points is shown in Table 58.

The monatin formation assay was repeated for the wild type control (SEQ ID NO:220), Mutant 135 and Mutant M under similar conditions except the reactions were carried out in plastic vials. Monatin production at various time points can be found in Table 58.

TABLE 58

Monatin Formation at 25° C. and 35° C.

Monatin

Monatin

(mM)
Monatin (mM)
(mM)

DAT polypeptide
1 hr
3 hr
4 hr

25° C.

wild type control (pMet1a)
2.0
6.8
8.4

Mutant 135 (V236T)
10.0
14.4
14.2

Mutant 136 (241R)
4.0
10.8
12.4

Mutant E (20S, 73L, 241R, 270W)
0.8
4.2
5.6

Mutant M (20S, 236T)
10.0
13.4
14.2

Mutant O (20S, 241R)
8.0
13.8
13.6

Mutant BB (93G, 236T)
4.0
11.4
12.4

Mutant AAA (20S, 93G, 241R)
0.2
1.0
1.6

35° C.

wild type control (pMet1a)
2.2
5.4
6.2

Mutant 135 (V236T)
9.4
9.2
9.8

Mutant 136 (241R)
4.8
9.4
10.4

Mutant E (20S, 73L, 241R, 270W)
0.6
3.4
4.2

Mutant M (20S, 236T)
9.2
13.6
14.6

Mutant O (20S, 241R)
9.6
10.6
10.8

Mutant BB (93G, 236T)
4.6
9.0
9.2

Mutant AAA (20S, 93G, 241R)
0.2
1.6
2.2

Lower monatin titers were observed using the DAT enzymes described here at 35° C. under the conditions of the assay. However, select mutants Mutant 135, Mutant 136, Mutant M, Mutant O and Mutant BB showed increased initial monatin production rates and greater 4 hour monatin titers than the wild type control (SEQ ID NO:220) at 35° C. under the assay conditions.

Example 34
Evaluation of Mutant DATs in BioReactors

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein in bioreactors. Glycerol stocks of the wild type control (SEQ ID NO:220), Mutant 135, Mutant 136, Mutant M, Mutant O, and Mutant BB were used to streak plates for single colonies. Single colonies were used to inoculate flasks containing 5 mL of LB medium with the appropriate antibiotic. The starter cultures were grown overnight at 37° C. with shaking at 250 rpm and the OD_600nmwas checked. When the OD_600nmreached 0.05, the 5 mL culture was inoculated into a 200 mL of Overnight Express II medium (Novagen, San Diego, Calif.) and then incubated at 30° C. with shaking at 250 rpm. Each culture was grown in duplicate and the cell pellets were combined. Cultures were harvested by pelleting cells by centrifugation at 4000 rpm for 15 minutes. The supernatant was poured off and the pellet was either frozen for later use or resuspended in 40 mL of 50 mM sodium phosphate buffer (pH 7.8) and lysed using a French Press (Sim Aminco, Rochester, N.Y.) or a microfluidizer (Microfluidics Corporation, Newton, Mass.) per the manufacturer's instructions. The supernatant was collected in a clean tube and stored at −80° C. until used. Approximately 1 mL of the clarified lysate was retained for protein quantitation using the BCA assay (Pierce, Rockford, Ill.) and SDS-PAGE analysis.

Bench scale reactions (250 mL) were carried out in 0.7 L Sixfors agitated fermentors (Infors AG, Bottmingen, Switzerland) under a nitrogen headspace as described in Example 15. The reaction mix contained 10 mM potassium phosphate, 1 mM MgCl₂, 0.05 mM PLP, 200 mM sodium pyruvate and 130 mM D-tryptophan. The reaction mix was adjusted to 25° C. and adjusted to pH 7.8 with potassium hydroxide. The aldolase described in Example 6 was added as a clarified cell extract at 0.02 mg/mL of target protein. Wild type control (SEQ ID NO:220), Mutant 135, Mutant 136, Mutant M, Mutant O, and Mutant BB DATs have soluble protein expressions ranging from 15-35% based on visual estimation. The clarified cell extracts were added at 0.20 mg/mL of target protein.

The progress of the reactions was followed by measuring monatin production at 1, 2, 4 and 24 hours using the LC/MS/MS methodology described in Example 36. The results are shown in Table 59.

TABLE 59

Monatin Production in Fermentors

Monatin
Monatin
Monatin
Monatin

Protein
(mM)
(mM)
(mM)
(mM)

DAT polypeptide
Expression
1 hr
2 hr
4 hr
24 hr

wild type control
25%
0.90
2.80
12.40
12.80

Mutant 135
30%
0.50
8.80
12.40
12.40

Mutant 136
35%
3.80
7.80
11.60
12.80

Mutant M
15%
3.40
6.80
12.10
12.20

Mutant O
15%
5.20
8.60
10.90
9.80

Mutant BB
15%
3.40
6.20
10.50
12.60

The initial rate of monatin production observed with mutants Mutant 136, Mutant M, Mutant O, and Mutant BB was faster than the rate with the wild type control (SEQ ID NO:220). All the mutants showed improved monatin formation at 2 hours under the conditions tested. The lower than expected monatin titer at 1 hour for Mutant 135 was attributed to the inadvertent exposure to oxygen during the first hour. After 4 hours, the monatin titer was comparable between the mutants and the control under the conditions tested.

Example 35
Evaluation of the Impact of Temperature on Mutant DATs in BioReactors

This example describes data demonstrating the enzymatic activity of exemplary polypeptides disclosed herein under different temperature conditions. The wild type control (SEQ ID NO:220), Mutant 135 and Mutant M were produced in a fermentor at the 2.5 L scale as described in Example 15. At the end of fermentation, the cells were harvested by centrifugation at 5000-7000×g for 10 minutes and frozen as a wet cell paste at −80° C.

To prepare cell free extract containing the wild type control, Mutant 135 and Mutant M D-aminotransferases, 50 g of wet cell paste was suspended in 150 mL of 50 mM potassium phosphate buffer (pH 7.8) containing 0.05 mM pyridoxal phosphate (PLP) and then disrupted using a Microfluidics homogenizer (Microfluidics, Newton, Mass.) (3 passes at 18,000 psi), maintaining the temperature of the suspension at less than 15° C. Cellular debris was removed by centrifugation (20,000×g for 30 minutes).

The rate of formation of I3P from tryptophan was monitored at 340 nm for three minutes as described in Example 32. The concentration of the wild type control was determined to be 6.8 mg/mL, the concentration of Mutant 135 was determined to be 7.0 mg/mL and Mutant M was determined to be 5.6 mg/mL based on a standard curve generated with purified DAT wild type control. The DAT concentrations determined by I3P formation were used to dose the Infors to 0.2 mg/mL DAT. The aldolase was added as a cell free extract at 0.02 mg/mL aldolase. The reaction mix contained 10 mM potassium phosphate, 1 mM MgCl₂, 0.05 mM PLP, 200 mM sodium pyruvate and 130 mM D-tryptophan under a nitrogen headspace. Each of the DATs was evaluated for monatin production in a bioreactor at 35° C. and at 25° C.

Samples were taken at 0.5, 1, 3, 4 and 24 hours and analyzed using the LC/MS/MS methodology described in Example 36. The results are shown in Table 60.

TABLE 60

Fermenters at 25° and 35° C.

Monatin
Monatin
Monatin
Monatin
Monatin

DAT
(mM)
(mM)
(mM)
(mM)
(mM)

polypeptide
0.5 hr
1 hr
3 hr
4 hr
24 hr

25° C.

Wild type
0.9
2.4
5.6
7.9
19.1

control (SEQ

ID NO: 220)

Mutant 135
1.6
4.4
10.9
12.1
18.6

Mutant M
2.1
4.5
9.4
12.4
17.4

35° C.

Wild type
2.3
3.9
6.5
7.9
10.7

control (SEQ

ID NO: 220)

Mutant 135
4.1
6.1
9.8
11.5
14.9

Mutant M
4.1
6.3
9.9
11.3
14.9

As seen in Example 34, select mutant DATs yielded higher monatin titers at 35° C. compared to the wild type control DAT (SEQ ID NO:220). The wild type control DAT had a slower initial rate of monatin production but a higher final titer at 25° C. under the conditions tested. Both mutants Mutant 135 and Mutant M showed improved activity over the wild type control at 25° C. and 35° C. Mutants Mutant 135 and Mutant M had both a higher initial rate of monatin production and a higher final titer at 35° C. compared to the control under the conditions tested. The selected mutants were more stable than the wild type control at the higher temperatures. This indicates the advantages of GSSM and TMCA technologies in producing mutants with greater thermostability than the wild type control. One skilled in the arts could screen these GSSM or TMCA libraries for mutants with, for example, increased temperature tolerance.

Example 36
Detection of Monatin, MP, Tryptophan, Alanine, and HMG

This example describes the analytical methodology associated with the further characterization of exemplary D-aminotransferase (DAT) enzymes disclosed herein.

UPLC/UV Analysis of Monatin and Tryptophan

Analyses of mixtures for monatin and tryptophan derived from biochemical reactions were performed using a Waters Acquity UPLC instrument including a Waters Acquity Photo-Diode Array (PDA) absorbance monitor. UPLC separations were made using an Agilent XDB C8 1.8 μm 2.1×100 mm column (part #928700-906) (Milford, Mass.) at 23° C. The UPLC mobile phase consisted of A) water containing 0.1% formic acid B) acetonitrile containing 0.1% formic acid.

The gradient elution was linear from 5% B to 40% B, 0-4 minutes, linear from 40% B, to 90% B, 4-4.2 minutes, isocratic from 90% B to 90% B, 4.2-5.2 minutes, linear from 90% B to 5% B, 5.2-5.3 minutes, with a 1.2 minute re-equilibration period between runs. The flow rate was 0.5 mL/min, and PDA absorbance was monitored at 280 nm.

Sample concentrations are calculated from a linear least squares calibration of peak area at 280 nm to known concentration, with a minimum coefficient of determination of 99.9%.

Derivatization of Monatin Intermediates (Indole-3-Pyruvic Acid (I3P), Hydroxymethyloxyglutaric Acid, Monatin Precursor, and Pyruvate) with O-(4-Nitrobenzyl)hydroxylaminehydrochloride (NBHA)

In the process of monatin production, various intermediate compounds are formed and utilized. These compounds include: Indole-3-Pyruvic Acid (I3P), Hydroxymethyloxyglutaric Acid, Monatin Precursor, and Pyruvate. The ketone functional group on these compounds can be derivatized with O-(4-Nitrobenzyl)hydroxylamine hydrochloride (NBHA).

To 20 μL of sample or standard, 140 μL of NBHA (40 mg/mL in pyridine) was added in an amber vial. Samples were sonicated for 15 min in the presence of heat with occasional mixing. A 1:3 dilution in 35% Acetonitrile in water was performed.

UPLC/UV Analysis of Monatin Intermediates (Indole-3-Pyruvic Acid, Hydroxymethyloxyglutaric Acid, Monatin Precursor, and Pyruvate)

A Waters Acquity UPLC instrument including a Waters Acquity Photo-Diode Array (PDA) absorbance monitor (Waters, Milford, Mass.) was used for the analysis of the intermediate compounds. UPLC separations were made using a Waters Acquity HSS T3 1.8 mm×150 mm column (Waters, Milford, Mass.) at 50° C. The UPLC mobile phase consisted of A) water containing 0.3% formic acid and 10 mM ammonium formate and B) 50/50 acetonitrile/methanol containing 0.3% formic acid and 10 mM ammonium formate.

The gradient elution was linear from 5% B to 40% B, 0-1.5 minutes, linear from 40% B, to 50% B, 1.5-4.5 minutes, linear from 50% B to 90% B, 4.5-7.5 minutes, linear from 90% B to 95% B, 7.5-10.5 minutes, with a 3 minute re-equilibration period between runs. The flow rate was 0.15 mL/min from 0-7.5 minutes, 0.18 mL/min from 7.5-10.5 minutes, 0.19 mL/min from 10.5-11 minutes, and 0.15 mL/min from 11-13.5 minutes. PDA absorbance was monitored at 270 nm.

Sample concentrations were calculated from a linear least squares calibration of peak area at 270 nm to known concentration, with a minimum coefficient of determination of 99.9%.

Chiral LC/MS/MS (MRM) Measurement of Monatin

Determination of the stereoisomer distribution of monatin in biochemical reactions was accomplished by derivatization with 1-fluoro-2-4-dinitrophenyl-5-L-alanine amide 30 (FDAA), followed by reversed-phase LC/MS/MS MRM measurement.

Derivatization of Monatin with FDAA

100 μL of a 1% solution of FDAA in acetone was added to 50 μL of sample or standard. Twenty μL of 1.0 M sodium bicarbonate was added, and the mixture was incubated for 1 hour at 40° C. with occasional mixing. The sample was removed and cooled, and neutralized with 20 μL of 2.0 M HCl (more HCl may be required to effect neutralization of a buffered biological mixture). Samples were analyzed by LC/MS/MS.

LC/MS/MS Multiple Reaction Monitoring for the Determination of the Stereoisomer Distribution of Monatin

Analyses were performed using the Waters/Micromass® liquid chromatography-tandem mass spectrometry (LC/MS/MS) instrument including a Waters 2795 liquid chromatograph with a Waters 996 Photo-Diode Array (PDA) absorbance monitor (Waters, Milford, Mass.) placed in series between the chromatograph and a Micromass® Quattro Ultima® triple quadrupole mass spectrometer. The LC separations capable of separating all four stereoisomers of monatin (specifically FDAA-monatin) were performed on a Phenomenex Luna® 2.0×250 mm (3 μm) C18 reversed phase chromatography column at 40° C. The LC mobile phase consisted of A) water containing 0.05% (mass/volume) ammonium acetate and B) acetonitrile. The elution was isocratic at 13% B, 0-2 minutes, linear from 13% B to 30% B, 2-15 minutes, linear from 30% B to 80% B, 15-16 minutes, isocratic at 80% B 16-21 minutes, and linear from 80% B to 13% B, 21-22 minutes, with a 8 minute re-equilibration period between runs. The flow rate was 0.23 mL/min, and PDA absorbance was monitored from 200 nm to 400 nm. All parameters of the ESI-MS were optimized and selected based on generation of deprotonated 20 molecular ions ([M−H]−) of FDAA-monatin, and production of characteristic fragment ions. The following instrumental parameters were used for LC/MS analysis of monatin in the negative ion ESI/MS mode: Capillary: 3.0 kV; Cone: 40 V; Hex 1: 15 V; Aperture: 0.1 V; Hex 2: 0.1 V; Source temperature: 120° C.; Desolvation temperature: 350° C.; Desolvation gas: 662 L/h; Cone gas: 42 L/h; Low mass resolution (Q1): 14.0; High mass resolution (Q1): 15.0; Ion energy: 0.5; Entrance: 0 V; Collision Energy: 20; Exit: 0 V; Low mass resolution (Q2): 15; High mass resolution (Q2): 14; Ion energy (Q2): 2.0; Multiplier: 650. Three FDAA-monatin-specific parent-to-daughter transitions were used to specifically detect FDAA-monatin in in vitro and in vivo reactions. The transitions monitored for monatin were 542.97 to 267.94, 542.97 to 499.07, and 542.97 to 525.04. Identification of FDAA-monatin stereoisomers was based on chromatographic retention time as compared to purified monatin stereoisomers, and mass spectral data.

Liquid Chromatography-Post Column Derivatization with OPA, Fluorescence Detection of Amino Acids, Including: Hydroxymethyl Glutamate (HMG) and Alanine

Analyses of mixtures for HMG and alanine derived from biochemical reactions were performed using a Waters Alliance 2695 and a Waters 600 configured instrument with a Waters 2487 Dual Wavelengths Absorbance Detector and Waters 2475 Fluorescence Detector as a detection system (Waters, Milford, Mass.). HPLC separations were made using two Phenomenex Aqua C18 125A, 150 mm×2.1 mm, 3μ, Cat #00F-4311B0 columns in series as the analytical columns, and a Phenomenex Aqua C18 125A, 30 mm×2.1 mm, 3μ, Cat #00A-4311B0 as an on-line solid phase extraction (SPE) column. Temperature for the two analytical columns was set at 55° C., and the on-line SPE column was at room temperature. The HPLC mobile phase consisted of A) 0.6% acetic acid with 1% methanol. The flow rate was (100% A) 0.2 mL/min from 0-3.5 minutes, 0.24 mL/min from 3.5-6.5 minutes, 0.26 mL/min from 6.5-10.4 minutes, and 0.2 mL/min from 10.4-11 minutes. UV-VIS absorbance detector was set to monitor at 336 nm wavelength. Fluorescence detector was set at 348 nm and 450 nm to monitor the excitation and emission wavelengths respectively.

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

APPENDIX 1

Geneseq

Geneseq

Predic-

SEQ

NR

Geneseq
Protein

Geneseq
DNA

ted
Query
Query
Subject
Subject

%

ID
NR
Accession
NR
NR
Protein
Accession

DNA
Accession

EC
DNA
Protein
DNA
Protein
% ID
ID

NO:
Description
Code
Evalue
Organism
Description
Code
Evalue
Description
Code
Evalue
Number
Length
Length
Length
Length
Protein
DNA

1, 2
conserved
115385557
1.00E−125
Aspergillus
Amino-
ADS78245
1.00E−168
Amino-
ADS78244
0
2.6.1.42
879
292
954
317

hypothetical

terreus
transferase/

transferase/

protein

NIH2624
mutase/

mutase/

[Aspergillus

deaminase

deaminase

terreus

enzyme #14.

enzyme #14.

NIH2624]

3, 4
amino-
99078146
1.00E−96

Silicibacter

Bacterial
ADF03944
9.00E−69
Plant cDNA
ADJ41018
2.4
2.6.1.21
855
284
0
286
66

transferase;

sp.
polypeptide

#31

.class IV

TM1040
#19.

[Silicibactersp

TM1040]

5, 6
D-amino acid
39935662
8.00E−77

Rhodo-

Bacterial
ADF03944
1.00E−53
S.
ADI39160
0.61
2.6.1.21
855
284
0
285
51

amino-

pseudomonas

polypeptide

hygroscopicus

transferase

palustris

#19.

geldanamycin

[Rhodo-

CGA009

PKS AT1

pseudomonas

mutant

palustris

fragment,

CGA009]

SEQ

ID NO:83.

7, 8
D-alanine
119896473
1.00E−92

Azoarcus
sp.

P. stutzeri 4
AEM18040
7.00E−55

Klebsiella

ABZ69309
0.16
2.6.1.21
870
289
0
285
58

transaminase

BH72
D-HPG AT

multi-

[Azoarcussp.

outer forward

copper

BH72]

N-term PCR

oxidase.

primer 1.

9, 10
amino-
114330773
2.00E−46

Nitrosomonas

Prokaryotic
ABU33175
2.00E−20
Prokaryotic
ACA26397
0.28
2.6.1.21
435
144
0
286
60

transferase

eutropha

essential gene

essential gene

class IV

C91
#34740.

#34740.

[Nitrosomonas

eutropha C91]

11, 12
D-alanine
89360213
5.00E−85

Xanthobacter

Bacterial

aminotransferase

autotrophicus

polypeptide
ADF03944
7.00E−55
Drosophila
ABL17260
2.5
2.6.1.21
879
292
0
285
56

[Xanthobacter

Py2
#19.

melanogaster

autotrophicus

Dolypeptide

Py2]

SEQ ID

gi|89350945|gb|E

NO 24465

AS 16227.11

D-alanine

aminotransferase

[Xanthobacter

autotrophicus

Py2]

13, 14
D-amino acid
82745661
2.00E−99

Clostridium

P. stulzeri 4
AEM18031
2.00E−46
Human gene
AAH32576
0.039
2.6.1.21
855
284
0
282
63

aminotransferase

beijerincki

D-HPG

18-encoded

[Clostridium

NCIMB 8052
AT outer

secreted

beijerincki

forward

protein

NCIMB 8052]

N-term PCR

HCUGC55,

gi|82726488|gb|E

primer 1

SEQ ID

AP61226.1| D-

NO: 185

amino acid

aminotransferase

[Clostridium

Deijerincki

NCIMB 8052]

15, 16
d-alanine
110834821
4.00E−56

Alcanivorax

Bacillus

AAY13560
2.00E−54
Bacterial
ADE99771
0.038
2.6.1.21
837
278
0
294
45

aminotransferase

borkumensis

D-amino acid

polypeptide

[Alcanivorax

SK2
amino-

#19.

borkumensis

transferase.

SK2]

17, 18
PUTATIVE
3122274
6.00E−49

Methano-

Prokaryotic
ABU21638
2.00E−45

0
2.6.1.42
918
305
0
306
34

BRANCHED-

thermobacter

essential gene

CHAIN AMINO

therm-

#34740.

ACID

autotrophicus

AMINOTRANSFE

RASE

(TRANSAMINAS

E B) (BCAT).

19, 20
D-amino acid
82745661
7.00E−97

Clostridium

P. stutzeri 4
AEM18031
1.00E−47
Drosophila
ABL03988
2.4
2.6.1.21
861
286
0
282
61

aminotransferase

beijerincki

D-HPG

melanogaster

[Clostridium

NCIMB
AT outer

polypeptide

beijerincki NCIMB

8052
forward

SEQ ID

8052]

N-term

NO 24465.

gi|82726488|gb|E

PCR

AP61226.1| D-

primer 1.

amino acid

aminotransferase

[Clostridium

beijerincki NCIMB

8052]

21, 22
D-amino acid
82745661
1.00E−100

Clostridium

Mutant
ABB08244
2.00E−47

Photorhabdus

ACF71263
2.4
2.6.1.21
861
286
0
282
63

aminotransferase

beijerincki

Bacillus

luminescens

[Clostridium

NCIMB

sphaericus dat

protein

beijerincki NCIMB

8052
protein.

sequence

8052]

#59.

gi|82726488|gb|E

AP61226.1| D-

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

23, 24
D-amino acid
82745661
6.00E−96

Clostridium

Mutant
ABB08244
5.00E−46
Mouse
ADA66322
0.16
2.6.1.21
861
286
0
282
61

aminotransferase

beijerincki

Bacillus

mCG15938

[Clostridium

NCIMB

sphaericus

gene

beijerincki

8052
dat

coding DNA

NCIMB 8052]

protein.

(cDNA)

gi|82726488|gb|E

sequence.

AP61226.1|D-

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

25, 26
D-amino acid
53802655
3.00E−86

Methylo-

Staphylococcus

ABM71198
2.00E−53
Human
ABN23130
0.6
2.6.1.21
840
279
0
283
55

aminotransferase

coccus

aureus

ORFX

putative

capsulatus

protein #10.

protein

[Methylococcus

str. Bath

sequence

capsulatus str.

SEQ ID

Bath]

NO: 19716.

27, 28
aminotransferase,
119716594
9.00E−33

Nocardioides

Escherichia

AEK20408
3.00E−27
Human
ADL15020
0.57
2.6.1.42
801
266
0
274
37

class IV

sp.

coli

Toll/

[Nocardioidessp.

JS614
amino-

interleukin

JS614].

transferase

receptor-like

gi|119537255|gb|

ilvE

protein for

ABL81872.1|

SEQ ID NO 2.

cancer

aminotransferase,

treatment.

class IV

[Nocardioidessp.

JS614]

29, 30
D-amino acid
15894079
3.00E−81

Clostridium

Prokaryotic
ABU32980
1.00E−45
Human
AAK71577
0.6
2.6.1.21
849
282
843
280
51
51

aminotransferase

aceto-

essential gene

immune/

[Clostridium

butylicum

#34740.

haematopo

acetobutylicum]

ietic entigen

genomic

sequence

SEQ ID

NO: 41436.

31, 32
histidinol-
145644535
1.00E−40

Methano-

Bacterial
ADS43070
2.00E−37
Human
ABA15896
0.003
2.6.19
1062
353
0
371
32

phosphate

coccus

polypeptide

nervous

aminotransferase

maripaludis

#10001.

system related

[Methanococcus

c7

poly-

maripaludis C7]

nucleotide

gi|145278069|gb|

SEQ ID

EDK17867.1|

NO: 115893

histidinol-

phosphate

aminotransferase

[Methanococcus

maripaludis C7]

33, 34
D-ALANINE
118222
1.00E−108

Bacillus sp.
P. stutzeri 4
AEM18018
1.00E−108
Listeria
ABQ69245
4.00E−08
2.6.1.21
852
283
0
283
66

AMINOTRANSFE

YM-1
D-HPGAT

innocua

RASE (D-

outer

DNA

ASPARTATE

forward

sequence

AMINOTRANSFE

N-term

#303.

RASE) (D-AMINO

PCR primer 1.

ACID

AMINOTRANSFE

RASE) (D-AMINO

ACID

TRANSAMINASE)

(DAAT).

35, 36
pyridoxal
126353148
2.00E−53

Caldivirga

Klebsiella

ABO62434
2.00E−31

Pseudomonas

ABD13518
0.21
2.9.1.1
1143
380
0
388
35

phosphate-

maquilin-

pneumoniae

aeruginosa

dependent

gensis

polypeptide

polypeptide

enzyme,

IC-167
seq id 7178.

#3.

putative

[Caldivirga

maquilingensis

IC-167]

gi|126311802|gb|

EAZ64256.1|

pyridoxal

phosphate-

dependent

enzyme,

putative

[Caldivirga

maquilingensis

IC-167)

37, 38
glutamate-1-
149173540
1.00E−104

Planctomyces

Bacterial
ADN26446
2.00E−94
Human
ABN18447
0.017
5.4.3.8
1389
462
0
455
43

semialdehyde 2;1-

maris DSM
polypeptide

ORFX

aminomutase;

8797
#10001.

protein

putative

sequence

[Planctomyces

SEQ ID

maris DSM 8797]

NO: 19716.

39, 40
Serine-glyoxylate
148260372
1.00E−94

Acidiphilium

Prokaryotic
ABU21492
1.00E−68
Plant full
ADO84697
0.05
2.6.1.45
1080
359
0
397
48

transaminase

cryptum JF-5
essential gene

length insert

[Acidiphilium

#34740.

poly-

cryptum JF-5]

nucleotide

seqid 4980.

41, 42
Chain A,
1127164
1.00E−126

Bacillus sp.
P. stutzeri 4
AEM18037
1.00E−126
D-amino
AAN81507
1.00E−20
2.6.1.21
852
283
0
282
76

Crystallographic

YM-1
D-HPG

acid

Structure Of

AT outer

transaminase.

D-Amino Acid

forward

Aminotransferase

N-term PCR

Complexed With

primer 1.

Pyridoxal-5

Phosphate.

43, 44
glutamate-1-
149173540
1.00E−115

Planctomyces

Bacterial
ADN26446
1.00E−95
Drosophila
ABL08182
0.99
5.4.3.8
1350
449
0
455
48

semialdehyde 2;1-

maris DSM
polypeptide

melanogaster

aminomutase;

8797
#10001.

Polypeptide

putative

SEQ ID

[Planctomyces

NO 24465.

maris DSM 8797]

45, 46
Serine--glyoxylate
148260372
1.00E−111

Acidiphilium

Prokaryotic
ABU21492
1.00E−82
Prokaryotic
ACA25362
6.00E−08
2.6.1.45
1170
389
0
397
51

transaminase

cryptum JF-5
essential gene

essential gene

[Acidiphilium

#34740.

#34740.

cryptum JF-5]

47, 48
glutamate-1-
149173540
1.00E−103

Planctomyces

Bacterial
ADN26446
1.00E−94
Human
ACA62990
0.066
5.4.3.8
1401
466
0
455
42

semialdehyde 2:1-

maris DSM
polypeptide

metal ion

aminomuatse;

8797
#10001.

transporter,

putative

85080.

[Planctomyces

maris DSM 8797]

49, 50
aminotransferase
118061613
1.00E−108

Roseiflexus

Bacterial
ADN26446
4.00E−93
Bacterial
ADS63519
7.00E−08
5.4.3.8
1353
450
0
454
49

class-III

castenholzii

Polypeptide

Polypeptide

[Roseiflexus

DSM 13941
#10001.

#10001.

castenholzii DSM

13941]

gi|118014341|gb|

EAV28318.1|

aminotransferase

class-III

[Roseiflexus

castenholzii DSM

13941]

51, 52
aminotransferase
118061613
1.00E−107

Roseiflexus

Bacterial
ADN26446
8.00E−98
Clone
ADH48029
1.00E−09
5.4.3.8
1344
447
0
454.
47

class-III

castenholzii

Polypeptide

FS3-135

[Roseiflexus

DSM 13941
#10001.

DNA

castenholzii DSM

sequence

13941]

SEQ ID

gi|118014341|gb|

NO: 2.

EAV28318.1|

aminotransferase

class-III

[Roseiflexus

castenholzii DSM

13941]

53, 54
D-alanine
90962639
3.00E−70

Lactobacillus

Staphylococcus

ABM71198
2.00E−36
Prokaryotic
ACA53304
2.4
2.6.1.21
861
286
0
281
49

aminotransferase

salivarius

aereus

essential gene

[Lactobacillus

subsp.
protein #10.

#34740.

salivarius
subsp.

salivarius

salivarius

UCC118

UCC118]

55, 56
aminotransferase;
148547264
2.00E−66

Pseudomonas

Pseudomonas

ABO84364
2.00E−55

Pseudomonas

ABD17818
4.00E−34
2.6.1.1
399
132
0
396
94

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

57, 58
aminotransferase;
148547264
5.00E−66

Pseudomonas

Pseudomonas

ABO84364
6.00E−55

Pseudomonas

ABD17818
6.00E−36
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

59, 60
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
2.00E−54

Pseudomonas

ABD17818
9.00E−29
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

61, 62
aminotransferase;
148547264
2.00E−66

Pseudomonas

Pseudomonas

ABO84364
2.00E−55

Pseudomonas

ABD17818
1.00E−34
2.6.1.1
399
132
0
396
94

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

63, 64
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
7.00E−56

Pseudomonas

ABD17818
7.00E−48
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

65, 66
COG0436:
84317581
6.00E−59

Pseudomonas

Pseudomonas

ABO84364
2.00E−59

Pseudomonas

ABD17818
5.00E−52
2.6.1.1
399
132
615
410

Aspartate/

aeruginosa

aeruginosa

aeruginosa

tyrosine/

C3719
polypeptide #3.

polypeptide

aromatic

#3.

aminotransferase

[Pseudomonas

aeruginosa

C3719]

gi|126170242|gb|

EAZ55753.1|

aspartate

transaminase

[Pseudomonas

aeruginosa

C3719]

67, 68
COG0436:
84317581
1.00E−57

Pseudomonas

Pseudomonas

ABO84364
3.00E−58

Pseudomonas

ABD17818
4.00E−46
2.6.1.1
399
132
615
410

Aspartate/

aeruginosa

aeruginosa

aeruginosa

tyrosine/

C3719
polypeptide #3.

polypeptide

aromatic

#3.

aminotransferase

[Pseudomonas

aeruginosa

C3719]

gi|126170242|gb|

EAZ55753.1|

aspartate

transaminase

[Pseudomonas

aeruginosa

C3719]

69, 70
COG0436:
84317581
2.00E−58

Pseudomonas

Pseudomonas

ABO84364
5.00E−59

Pseudomonas

ABD17818
1.00E−43
2.6.1.1
399
132
615
410

Aspartate/

aeruginosa

aeruginosa

aeruginosa

tyrosine/

C3719
polypeptide #3.

polypeptide

aromatic

#3.

aminotransferase

[Pseudomonas

aeruginosa

C3719]

gi|126170242|gb|

EAZ55753.1|

71, 72
aspartate
26990429
5.00E−68

Pseudomonas

Pseudomonas

ABO84364
1.00E−57

Pseudomonas

ABD17818
5.00E−52
2.6.1.1
399
132
0
396
96

transaminase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

aeruginosa

#3.

C3719]

aspartate

aminotransferase

[Pseudomonas

putida KT2440]

73, 74
aspartate
26990429
3.00E−68

Pseudomonas

Pseudomonas

ABO84364
1.00E−57

Pseudomonas

ABD17818
5.00E−52
2.6.1.1
399
132
0
396
96

aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide

polypeptide

putida KT2440]

#3.

#3.

75, 76
D-alanine
94500389
1.00E−101

Oceanobacter

L.
AEB37927
2.00E−50

Pseudomonas

ABD03911
2.5
2.6.1.21
873
290
0
265
57

transaminase

sp. RED65
pneumophila

aeruginosa

[Oceanobacter sp.

protein

polypeptide

RED65]

SEQ ID

#3.

gi|94427424|gb|E

NO 3367.

AT12402.1| D-

alanine

transaminase

[Oceanobacter sp.

RED65]

77, 78
D-alanine
94500389
1.00E−101

Oceanobacter

L.
AEB37927
2.00E−50

Pseudomonas

ABD03911
2.5
2.6.1.21
873
290
0
265
57

transaminase

sp. RED65
pneumophila

aeruginosa

[Oceanobacter sp.

protein SEQ

polypeptide

RED65]

ID NO 3367.

#3.

gi|94427424|gb|E

AT12402.1| D-

alanine

transaminase

[Oceanobacter sp.

RED65]

79, 80
aspartate
26990429
3.00E−64

Pseudomonas

Pseudomonas

ABO84364
8.00E−54

Pseudomonas

ABD17818
7.00E−42
2.6.1.1
396
131
0
396
93

aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide

polypeptide

putida KT2440]

#3.

#3.

81, 82
aspartate
26990429
4.00E−66

Pseudomonas

Pseudomonas

ABO84364
1.00E−55

Pseudomonas

ABD17818
1.00E−40
2.6.1.1
396
131
0
396
94

aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide

polypeptide

putida KT2440]

#3.

#3.

83, 84
glutamate-1-
149173540
1.00E−101

Planctomyces

Bacterial
ADN26446
2.00E−93
Bacterial
ADS58845
0.017
5.4.3.8
1398
465
0
455
41

semialdehyde 2;1-

maris DSM
polypeptide

polypeptide

aminomutase;

8797
#10001.

#10001.

putative

[Planctomyces

maris DSM

8797]

85, 86
aminotransferase;
114319339
1.00E−69

Alkalilim-

L. pneumophila
AEB37927
1.00E−46

Myco-

AAI99682
0.62
2.6.1.21
873
290
0
286
46

class IV

nicola

protein SEQ

bacterium

[Alkalilimnicola

ehrlichei

ID NO 3367.

tuberculosis

ehrlichei

MLHE-1

strain H37Rv

MLHE-1]

genome

SEQ ID

NO 2.

87, 88
D-alanine
74316285
3.00E−55

Thiobacillus

P. stutzeri 4
AEM18040
2.00E−49
DNA done
ACL13803
9.8
2.6.1.21
879
292
0
282
40

transminase

denitrificans

D-HPG

originating

[Thiobacillus

ATCC 25259
AT outer

in barley

denitrificans

forward N-term

containing

ATCC 25259]

SNP

PCR primer 1.

sequence #14.

89, 90
aminotransferase;
148547264
5.00E−66

Pseudomonas

Mycobacterium
ABO84364
1.00E−54

Pseudomonas

ABD17818
4.00E−34
2.6.1.1
399
132
0
396
93

class I and II

putida F1
tuberculosis

aeruginosa

[Pseudomonas

strain

polypeptide

putida F1]

Mycobacterium

#3.

91, 92
aminotransferase;
148547264
4.00E−65

Pseudomonas

Pseudomonas

ABO84364
4.00E−56

Pseudomonas

ABD17818
3.00E−53
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

93, 94
aminotransferase;
148547264
4.00E−65

Pseudomonas

Pseudomonas

ABO84364
4.00E−56

Pseudomonas

ABD17818
8.00E−54
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

95, 96
aminotransferase;
148547264
4.00E−65

Pseudomonas

Pseudomonas

ABO84364
4.00E−56

Pseudomonas

ABD17818
8.00E−54
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

97, 98
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
1.00E−56

Pseudomonas

ABD17818
5.00E−55
2.6.1.1
399
132
0
396
93

class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

99,
aspartate
26990429
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
3.00E−56

Pseudomonas

ABD17818
3.00E−44
2.6.1.1
393
130
0
396
96

100
aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

putida KT2440]

#3.

101,
aspartate
26990429
7.00E−68

Pseudomonas

Pseudomonas

ABO84364
3.00E−57

Pseudomonas

ABD17818
8.00E−54
2.6.1.1
396
131
0
396
97

102
aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

putida KT2440]

#3.

103,
aspartate
26990429
5.00E−66

Pseudomonas

Pseudomonas

ABO84364
3.00E−57

Pseudomonas

ABD17818
8.00E−60
2.6.1.1
399
132
0
396
95

104
aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

putida KT2440]

#3.

105,
aspartate
26990429
2.00E−66

Pseudomonas

Pseudomonas

ABO84364
1.00E−57

Pseudomonas

ABD17818
5.00E−55
2.6.1.1
399
132
0
396
94

106
aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

putida KT2440]

#3.

107,
aminotransferase;
148547264
7.00E−65

Pseudomonas

Pseudomonas

ABO84364
3.00E−55

Pseudomonas

ABD17818
8.00E−54
2.6.1.1
399
132
0
396
93

108
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

109,
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
7.00E−56

Pseudomonas

ABD17818
5.00E−49
2.6.1.1
399
132
0
396
93

110
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

111,
aminotransferase;
148547264
3.00E−66

Pseudomonas

Pseudomonas

ABO84364
1.00E−56

Pseudomonas

ABD17818
5.00E−52
2.6.1.1
393
132
0
396
94

112
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

113,
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
1.00E−56

Pseudomonas

ABD17818
3.00E−50
2.6.1.1
396
132
0
396
93

114
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

115,
aspartate
26990429
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
2.00E−56

Pseudomonas

ABD17818
5.00E−52
2.6.1.1
399
130
0
396
96

116
aminotransferase

putida

aeruginosa

aeruginosa

[Pseudomonas

KT2440
polypeptide #3.

polypeptide

putida KT2440]

#3.

117,
aminotransferase;
148547264
4.00E−65

Pseudomonas

Pseudomonas

ABO84364
4.00E−56

Pseudomonas

ABD17818
5.00E−55
2.6.1.1
399
132
0
396
93

118
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

119,
aminotransferase;
148547264
1.00E−65

Pseudomonas

Pseudomonas

ABO84364
1.00E−56

Pseudomonas

ABD17818
5.00E−55
2.6.1.1
399
132
0
396
93

120
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

121,
aminotransferase;
148547264
4.00E−65

Pseudomonas

Pseudomonas

ABO84364
4.00E−56

Pseudomonas

ABD17818
3.00E−56
2.6.1.1
399
132
0
396
93

122
class I and II

putida F1

aeruginosa

aeruginosa

[Pseudomonas

polypeptide #3.

polypeptide

putida F1]

#3.

aspartate

123,
aminotransferase
26990429
8.00E−66

Pseudomonas

Pseudomonas

ABO84364
2.00E−56

Pseudomonas

ABD17818
3.00E−38
2.6.1.1
399
132
0
396
93

124
[Pseudomonas

putida

aeruginosa

aeruginosa

putida KT2440]

KT2440
polypeptide #3.

polypeptide

D-alanine

#3.

125,
aminotransferase
29833346
4.00E−77

Streptomyces

Escherichia

AEK20408
2.00E−33
Bacterial
ADS45796
0.038
2.6.1.42
831
132
0
273
57

126
[Streptomyces

avermitilis

coli

polypeptide

avermitilis

MA-4680
amino-

#10001.

MA-4680]

transferase

ilvE SEQ

ID NO 2.

127,
glutamate-1-
149173540
1.00E−143

Planctomyces

Bacterial
ADN26446
1.00E−100
Clone FS-135
ADH48029
1.00E−09
5.4.3.8
1362
132
0
455
55

128
semialdehyde 2;1-

maris DSM
polypeptide

DNA

aminomutase;

8797
#10001.

sequence

putative

SEQ ID

[Planctomyces

NO: 2.

maris DSM

8797]

129,
D-alanine
77465457
1.00E−87

Rhodobacter

Bacterial
ADF03944
3.00E−68
Drosophila
ABL03211
2.4
2.6.1.21
864
132
0
285
57

130
aminotransferase

sphaeroides

polypeptide

melanogaster

[Rhodobacter

2.4.1
#19.

polypeptide

sphaeroides

SEQ ID

2.4.1]

NO 24465.

131,
D-Amino Acid
126651304
1.00E−158

Bacillus
sp.
P. taetrolens
ADW43694
1.00E−159

B.
sphaericus

ADP27941
0
2.6.1.21
855
284
1709
284

132
Aminotransferase

B14905
aldolase 2.

D-amino-

[Bacillus sp.

transferase

B14905]

BSDAT SEQ

gi|126591833|gb|

ID NO: 4.

EAZ85916.1| D-

Amino Acid

Aminotransferase

[Bacillus sp.

B14905]

133,
aminotransferase
56477154
4.00E−67

Azoarcus
sp.
Prokayotic
ABU33175
4.00E−45

M.
xanthus

ACL64145
0.16
2.6.1.21
876
291
0
285
45

134
class-IV

EbN1
essential gene

protein

[Azoarcussp.

#34740.

sequence,

EbN1]

seq id

9726.

135,
D-alanine
77465457
1.00E−87

Rhodobacter

Bacterial
ADF03944
3.00E−68
Drosophila
ABL03211
2.4
2.6.1.21
864
287
0
285
57

136
aminotransferase

sphaeroides

polypeptide

melanogaster

[Rhodobacter

2.4.1
#19.

polypeptide

sphaeroides

SEQ ID

2.4.1]

NO 24465.

137,
glutamate-1-
149173540
1.00E−111

Planctomyces

Bacterial
ADN26446
1.00E−104
P. cellulosum
AEC75821
0.001
5.4.3.8
1386
461
0
455
46

138
semialdehyde 2;1-

maris

polypeptide

ambruticin

aminomutase;

DSM 8797
#10001.

ambA

putative

protein.

[Planctomyces

maris DSM 8797]

139,
glutamate-1-
149173540
1.00E−108

Planctomyces

Bacterial
ADN26446
7.00E−99
Bacterial
ADS57580
0.065
5.4.3.8
1383
460
0
455
43

140
semialdehyde 2;1-

maris DSM
polypeptide

polypeptide

aminomutase;

8797
#10001.

#10001.

putative

[Planctomyces

maris DSM

8797]

141,
Putative D-alanine
146342961
2.00E−71

Bradyr-

Bacterial
ADF03944
1.00E−61
N.
ABZ41029
0.15
2.6.1.21
855
284
0
286
51

142
aminotransferase

hizobium

polypeptide

gonorrhoeae

[Bradyrhizobium

sp. ORS278
#19.

nucleotide

sp. ORS278]

sequence SEQ

ID 4691.

143,
Aminotransferase,
88806011
1.00E−101

Robiginitalea

Bacillus

AAY13560
2.00E−48
DNA
AAS82939
0.66
2.6.1.21
915
304
0
255
57

144
class IV

biformata

D-amino acid

encoding

[Robiginitalea

HTCC2501
amino-

novel human

biformata

transferase

diagnostic

HTCC2501]

protein

gi|88783620|gb|E

#20574.

AR14791.1|

Aminotransferase,

class IV

[Robiginitalea

biformata

HTCC2501]

145,
glutamate-1-
149173540
1.00E−114

Planctomyces

Bacterial
ADN26446
1.00E−93

M.
xanthus

ACL64704
0.99
5.4.3.8
1350
449
0
455
48

146
semialdehyde 2;1-

maris DSM
polypeptide

protein

aminomutase;

8797
#10001.

sequence,

putative

seq id

[Planctomyces

9726.

maris DSM 8797]

147,
aminotransferase
118061613
1.00E−104

Roseiflexus

Bacterial
ADN26446
2.00E−87
Glutamate-1-
AAQ63611
2.00E−05
5.4.3.8
1383
460
0
454
44

148
class-III

castenholzii

polypeptide

semialdehyde

[Roseiflexus

DSM 13941
#10001.

amino-

castenholzii DSM

transferase

13941]

gi|118014341 |gb|

EAV28318.1|

aminotransferase

class-III

[Roseiflexus

castenholzii DSM

13941]

149,
glutamate-1-
149173540
1.00E−114

Planctomyces

Bacterial
ADN26446
1.00E−90
Bacterial
ADS57112
0.004
5.4.3.8
1377
458
0
455
46

150
semialdehyde 2;1-

maris

polypeptide

polypeptide

aminomutase;

DSM 8797
#10001.

#10001.

putative

[Planctomyces

maris DSM 8797]

151,
D-alanine
52079452
1.00E−56

Bacillus

P. stutzeri 4
AEM18039
2.00E−56
Human
ADE53957
2.4
2.6.1.21
852
283
0
283
40

152
aminotransferase

licheniformis

D-HPG

prostate

[Bacillus

ATCC 14580
AT outer

cancer cDNA

licheniformis

forward

#473.

ATCC 14580]

N-term

PCR

primer 1.

153,
glutamate-1-
149173540
1.00E−97

Planctomyces

Bacterial
ADN26446
2.00E−74

M.
xanthus

ACL64518
0.24
5.4.3.8
1269
422
0
455
46

154
semialdehyde 2;1-

maris DSM
polypeptide

protein

aminomutase;

8797
#10001.

sequence,

putative

seq id

[Planctomyces

9726

maris DSM

8797]

155,
aminotransferase
118045454
1.00E−107

Chloroflexus

Bacterial
ADN26446
1.00E−104
Bacterial
ADT43944
3.00E−04
5.4.3.8
1362
453
0
443
46

156
class-III

aggregans

polypeptide

polypeptide

[Chloroflexus

DSM 9485
#10001.

#10001.

aggregans DSM

9485]

gi|117997930|gb|

EAV12112.1|

aminotransferase

class-III

[Chloroflexus

aggregans

DSM 9485]

157,
aminotransferase,
12675091
2.00E−78

Rhodo-

Bacterial
ADF03944
9.00E−53
Oligonudeo-
ABQ42663
2.5
2.6.1.21
879
292
0
283
48

158
class IV

bacterales

polypeptide

tide for

[Rhodobacterales

bacterium

#19.

detecting

bacterium

HTCC2150

cytosine

HTCC2150]

methylation

gi|126706255|gb|

SEQ ID NO

EBA05345.1|

20311.

aminotransferase,

class IV

[Rhodobacterales

bacterium

HTCC2150]

159,
hypothetical
126646718
6.00E−43

Algoriphagus

prokaryotic
ABU18963
7.00E−26
prokaryotic
ACA38856
0.58
2.6.1.42
822
273
0
277
36

160
protein

sp.
essential

essential

ALPR1J8298

PR1
gene

gene

[Algoriphagus

#34740.

#34740.

sp. PR1]

gi|126576766|gb|

EAZ81014.1|

hypothetical

protein

ALPR1J8298

[Algoriphagus

sp. PR1]

161,
D-amino acid
86140221
1.00E−139

Roseobacter

Bacterial
ADF03944
5.00E−75
Bacterial
ADS56887
2.4
2.6.1.21
861
286
0
287
87

162
aminotransferase,

sp.
polypeptide

polypeptide

putative

MED193
#19.

#19.

[Roseobactersp.

MED193]

gi|85823158|gb|E

AQ43371.1| D-

amino acid

aminotransferase,

putative

[Roseobactersp.

MED193]

163,
glutamate-1-
149173540
1.00E−105

Planctomyces

Bacterial
ADN26446
6.00E−96

M.
xanthus

ACL64750
0065
5.4.3.8
1377
458
0
455
44

164
semialdehyde

maris DSM
polypeptide

protein

2;1-

8797
#10001.

sequence,

aminomutase;

seq id 9726.

putative

[Planctomyces

maris DSM 8797]

165,
aminotransferase
148656729
1.00E−105

Roseiflexus

Bacterial
ADN26446
1.00E−95
Bacterial
ADS63519
7.00E−11
5.4.3.8
1314
437
0
455
46

166
class-III

sp. RS-1
polypeptide

polypeptide

[Roseiflexussp.

#10001.

#10001.

RS-1]

167,
D-amino acid
82745661
8.00E−96

Clostridium

P. stutzeri 4
AEM18031
2.00E−47
Drosophila
ABL03988
2.4
2.6.1.21
861
286
0
282
60

168
aminotransferase

beijerincki

D-HPG

melanogaster

[Clostridium

NCIMB
AT outer

polypeptide

beijerincki

8052
forward

SEQ ID NO

NCIMB 8052]

N-term

24465.

gi|82726488|gb|E

PCR

AP61226.1| D-

primer 1.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

169,
putative amino
120406056
1.00E−144

Myco-

Prokaryolic
ABU33708
1.00E−124
Prokaryolic
ACA37578
2.00E−53
4.1.3.38
882
293
0
293
65

170
acid

bacterium

essential

essential

aminotransferase

vanbaalenii

gene

gene

[Mycobacterium

PYR-1
#34740.

#34740.

vanbaalenii

PYR-

gi|119958874|gb|

ABM 15879.11

putative amino

acid

aminotransferase

[Mycobacterium

vanbaalenii

PYR-1]

171,
D-amino acid
82745661
3.00E−99

Clostridium

P. stutzeri 4
AEM18031
1.00E−47
Drosophila
ABL03988
2.4
2.6.1.21
864
267
0
262
62

172
aminotransferase

beijerincki

D-HPG

melanogaster

[Clostridium

NCIMB
AT outer

polypeptide

beijerincki

8052
forward

SEQ ID

NCIMB

N-term

NO 24465.

8052]

PCR

gi|82726488|gb|E

primer 1.

AP61226.1]

D-amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB

8052]

173,
D-amino acid
82745661
1.00E−98

Clostridium

Mutant
ABB08244
2.00E−47
Fibrotic
AED18099
0.039
2.6.1.21
861
286
0
282
62

174
aminotransferase

beijerincki

Bacillus

disorder

[Clostridium

NCIMB

sphaericus

associated

beijerincki

8052
dat protein.

poly-

NCIMB

nudeotide

8052]

SEQ ID

gi|82726488|gb|E

NO 9.

AP61226.1|

D-amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB

8052]

175,
D-amino acid
82745661
7.00E−98

Clostridium

Mutant
ABB08244
1.00E−46
Human
AAF81809
0.61
2.6.1.21
861
266
0
282
62

176
aminotransferase

beijerincki

Bacillus

secreted

[Clostridium

NCIMB

sphaericus

protein

beijerincki

8052
dat protein.

sequence

NCIMB 8052]

encoded by

gi|82726488|gb|E

gene 11

AP61226.1) D-

SEQ ID

amino acid

NO: 76.

aminotransferase

[Clostridium

beijerincki NCIMB

8052]

177,
aminotransferase
118061613
1.00E−110

Roseiflexus

Bacterial
ADN26446
9.00E−89
Hyper-
ADM27081
0.004
5.4.3.8
1374
457
0
454
47

178
class-III

castenholzii

polypeptide

thermophile

[Roseiflexus

DSM 13941
#10001.

Methanopyrus

castenholzii

kandleri

DSM 13941]

protein #26.

gi|118014341 |gb|

EAV28318.1|

aminotransferase

class-III

[Roseiflexus

castenholzii

DSM 13941]

179,
D-amino acid
124520974
4.00E−54

Bacillus

Staphyloco-

ABM71198
5.00E−54
Plant full
ADX27642
2.4
2.6.1.21
855
264
0
288
41

180
aminotransferase

coagulans

ccus

length

[Bacillus

36D1

aureus

insert

coagulans 36D1]

protein #10.

polynudeotide

gi|124497181|gb|

seqid 4980.

EAY44748.1|

D-amino acid

aminotransferase

[Bacillus

coagulans 36D1]

181,
branched-chain
22299586
7.00E−53

Thermo-

Prokaryolic
ABU18055
1.00E−47
Prostate
ABL61996
0.62
2.6.1.42
876
291
861
286
39
51

182
amino acid

synecho-

essential

cancer

aminotransferase

coccus

gene

related gene

[Thermo-

elongatus

#34740.

sequence

synechococcus

BP-1

SEQ ID

elongatus

NO: 8120.

BP-1].

183,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

184
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence

primer 1.

SEQ

ID NO: 26.

185,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

186
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence

primer 1.

SEQ

ID NO: 26.

187,
D-amino acid
82745661
1.00E−96

Clostridium

P. stutzeri 4
AEM18031
3.00E−46
Human
AAL04589
2.4
2.6.1.21
861
286
0
282
61

188
aminotransferase

beijerincki

D-HPG

repdroductive

[Clostridium

NCIMB
AT outer

system

beijerincki

8052
forward

related

NCIMB 8052]

N-term

antigen

gi|82726488|gb|E

PCR

DNA SEQ

AP61226.1] D-

primer 1.

ID NO: 8114.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

189,
D-amino acid
82745661
9.00E−98

Clostridium

Mutant
ABB08244
2.00E−49
Drosophila
ABL25490
0.62
2.6.1.21
864
287
0
282
62

190
aminotransferase

beijerincki

Bacillus

melanogaster

[Clostridium

NCIMB

sphaericus

polypeptide

beijerincki

8052
dat protein.

SEQ ID

NCIMB 8052]

NO 24465.

gi|82726488|gb|E

AP61226.1] D-

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

191,
D-amino acid
82745661
1.00E−96

Clostridium

P. stutzeri 4
AEM18031
3.00E−46
Human
AAL04589
2.4
2.6.1.21
861
286
0
262
61

192
aminotransferase

beijerincki

D-HPG

repdroductive

[Clostridium

NCIMB
AT outer

system

beijerincki

8052
forward

related

NCIMB 8052]

N-term

antigen

gi|82726488|gb|E

PCR

DNA SEQ

AP61226.1] D-

primer 1.

ID NO: 8114.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

193,
D-amino acid
82745661
1.00E−96

Clostridium

P. stutzeri 4
AEM18031
3.00E−46
Human
AAL04589
2.4
2.6.1.21
861
286
0
282
61

194
aminotransferase

beijerincki

D-HPG

repdroductive

[Clostridium

NCIMB
AT outer

system

beijerincki

8052
forward

related antigen

NCIMB 8052]

N-term

DNA SEQ

gi|82726488|gb|E

PCR

ID NO: 8114.

AP61226.1] D-

primer 1.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

195,
putative
149182609
1.00E−59

Bacillus
sp.

Bacillus

AAY13560
1.00E−57
Human
ADL41705
0.61
2.6.1.21
858
265
0
282
42

196
D-alanine

SG-1
D-amino acid

ovarian

aminotransferase

amino-

cancer DNA

[Bacillussp.

transferase.

marker #5.

SG-1]

197,
putative
149182609
3.00E−57

Bacillus
sp.
P. stutzeri 4
AEM18039
6.00E−56
P. stutzeri 4
AEM18017
0.003
2.6.1.21
858
285
0
282
40

198
D-alanine

SG-1
D-HPG

D-HPG

aminotransferase

AT outer

AT outer

[Bacillussp.

forward

forward

SG-1]

N-term

N-term

putative

PCR

PCR

primer 1.

primer 1.

199,
D-alanine
149182609
5.00E−59

Bacillus
sp.

Bacillus

AAY13560
1.00E−57

Bacillus

ABK78375
2.4
2.6.1.21
858
285
0
282
42

200
aminotransferase

SG-1
D-amino acid

licheniformis

[Bacillussp.

amino-

genomic

SG-1]

transferase.

sequence tag

(GST) #933.

201,
D-alanine
51892468
6.00E−57

Symbio-

Bacillus

AAY13560
2.00E−51

Photorhabdus

ACF67498
0.15
2.6.1.21
855
284
0
281
40

202
aminotransferase

bacterium

D-amino acid

luminescens

[Symbiobacterium

thermophilum

amino-

protein

thermophilum

IAM 14863
transferase.

sequence #59.

IAM 14863]

203,
PUTATIVE
3122274
2.00E−46
Methano
Prokaryotic
ABU23351
6.00E−42
Prokaryotic
ACA40289
0.17
2.6.1.42
921
306
0
306
34

204
BRANCHED-

thermobacter
essential

essential gene

CHAIN AMINO

thermauto-
gene

#34740.

ACID

trophicus
#34740.

AMINO-

TRANSFERASE

(TRANSAMINAS

E B) (BCAT).

205,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

206
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence

primer 1.

SEQ ID

NO: 26.

207,
D-alanine
23098538
7.00E−51

Oceano-

P. stutzeri 4
AEM18040
4.00E−50
Human
ABO99281
0.15
2.6.1.21
825
274
867
288
40
48

208
aminotransferase

bacillus

D-HPG

protein

[Oceanobacillus

iheyensis

AT outer

SEQ ID 537.

iheyensis].

forward

N-term

PCR

primer 1.

209,
aminotransferase
118061613
1.00E−105

Roseiflexus

Bacterial
ADN26446
3.00E−88
Clone
ADH48029
0.001
5.4.3.8
1374
457
0
454
44

210
class-III

castenholzii

polypeptide

FS3-135

[Roseiflexus

DSM 13941
#10001.

DNA

castenholzii

sequence

DSM 13941]

SEQ ID

gi|118014341 |gb|

NO: 2

EAV28318.1|

aminotransferase

class-III

[Roseiflexus

castenholzii

DSM

13941]

211,
hypothetical
145952948
6.00E−42

Clostridium

Bacterial
ADS43070
4.00E−25
Human
AAI92131
0.053
2.6.1.9
1137
378
0
367
29

212
protein

difficile

polypeptide

polynucleoide

CdifQ_04002916

QCD-
#10001.

SEQ ID NO

[Clostridium

32g58

13646.

difficile QCD-

32g58]

213,
D-amino acid
82745661
3.00E−95

Clostridium

P. stutzeri 4
AEM18018
2.00E−52
Plant full
ADX37088
0.6
2.6.1.21
849
262
0
282
61

214
aminotransferase

beijerincki

D-HPG

length

[Clostridium

NCIMB
AT outer

insert

beijerincki

8052
forward

poly-

NCIMB 8052]

N-term

nudeotide

gi|82726488|gb|E

PCR

seqid 4980.

AP61226.1] D-

primer 1.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

215,
aminotransferase
118061613
1.00E−116

Roseiflexus

Bacterial
ADN26446
1.00E−102
Bacterial
ADS57580
0.004
5.4.3.8
1386
461
0
454
49

216
class-III

castenholzii

polypeptide

polypeptide

[Roseiflexus

DSM 13941
#10001.

#10001.

castenholzii

DSM 13941]

gi|118014341 |gb|

EAV28318.1]

aminotransferase

class-III

[Roseiflexus

castenholzii

DSM 13941]

217,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

218
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence SEQ

primer 1.

ID NO: 26.

219,
D-amino acid
82745661
3.00E−98

Clostridium

Mutant
ABB08244
4.00E−48
Human
ABZ36033
0.16
2.6.1.21
861
286
0
282
62

220
aminotransferase

beijerincki

Bacillus

secretory

[Clostridium

NCIMB

sphaericus

poly-

beijerincki

8052
dat protein.

nucleotide

NCIMB 8052]

SPTM

gi|82726488|gb|E

SEQ ID NO

AP61226.1] D-

534.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

221,
D-alanine
51892468
1.00E−57

Symbio-

Bacillus

AAY13560
3.00E−54
Human
ACN44196
2.3
2.6.1.21
840
279
0
281
43

222
aminotransferase

bacterium

D-amino acid

protein

[Symbiobacterium

thermophilum

amino-

sequence

thermophilum

IAM 14863
transferase.

hCP39072.

IAM 14863]

223,
D-alanine
23098538
3.00E−97

Oceano-

Heat
ABB06297
7.00E−90
L. salivarius
AFB66287
0.62
2.6.1.21
867
288
867
288
60
63

224
aminotransferase

bacillus

resistant D-

SIA

[Oceanobacillus

iheyensis

amino acid

protein gene

iheyensis].

amino-

LSL1401b

transferase

(partial).

encoding

DNA.

225,
D-amino acid
82745661
7.00E−97

Clostridium

Mutant
ABB08244
6.00E−47
Fibrotic
AED18099
0.039
2.6.1.21
861
266
0
282
61

226
aminotransferase

beijerincki

Bacillus

disorder

[Clostridium

NCIMB

sphaericus

associated

beijerincki

8052
dat protein.

poly-

NCIMB 8052]

nucleotide

gi|82726488|gb|E

SEQ ID

AP61226.1] D-

NO 9.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

227,
D-amino acid
82745661
4.00E−98

Clostridium

P. stutzeri 4
AEM18031
9.00E−47
Fibrotic
AED18099
0.61
2.6.1.21
861
286
0
282
62

228
aminotransferase

beijerincki

D-HPG

disorder

[Clostridium

NCIMB 8052
AT outer

associated

beijerincki

forward

poly-

NCIMB 8052]

N-term

nucleotide

gi|82726488|gb|E

PCR

SEQ ID

AP61226.1| D-

primer 1.

NO 9.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

229,
D-amino acid
82745661
3.00E−94

Clostridium

Mutant
ABB08244
9.00E−45
Fibrotic
AED18099
0.62
2.6.1.21
873
290
0
282
60

230
aminotransferase

beijerincki

Bacillus

disorder

[Clostridium

NCIMB 8052

sphaericus

associated

beijerincki

dat protein.

poly-

NCIMB 8052]

nucleotide

gi|82726400|gb|E

SEQ ID

AP61226.1| D-

NO 9.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

231,
D-amino acid
82745661
2.00E−97

Clostridium

P. stutzeri 4
AEM18031
5.00E−48
Fibrotic
AED18099
0.62
2.6.1.21
864
287
0
282
61

232
aminotransferase

beijerincki

D-HPG

disorder

[Clostridium

NCIMB
AT outer

associated

beijerincki

8052
forward

poly-

NCIMB 8052]

N-term

nucleotide

gi|82726488|gb|E

PCR

SEQ ID

AP61226.1] D-

primer 1.

NO 9.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

233,
hypothetical
126646718
2.00E−43

Algoriphagus

B.
AEJ13860
1.00E−26
Drosophila
ABL22310
0.58
2.6.142
822
273
0
277
35

234
protein

sp. PR1
licheniformis

melanogaster

ALPR1_18298

butyryl-CoA

polypeptide

[Algoriphagus

dehy-

SEQ ID

sp. PR1]

drogenase/acy

NO 24465.

gi|126576766|gb|

I-CoA

EAZ81014.1|

dehy-

hypo-

drogenase

theticalprotein

pro. 1.

ALPR1_18298

[Algoriphagus

sp. PR1]

235,
branched-chain
18313971
1.00E−43

Pyrobaculum

Aquifex
ABU57358
4.00E−44
Bacterial
ADT43796
0.65
2.6.1.42
906
301
1992
303

236
amino acid

aerophilum

aspartate

polypeptide

aminotransferase

amino-

#10001.

(ilvE)

transferase B

[Pyrobaculum

DNA.

aerophilum].

237,
d-alanine
110834821
1.00E−55

Alcanivorax

Bacillus

AAY13560
4.00E−55
Wheat
AAI70509
2.3
2.6.1.21
837
278
0
294
44

238
aminotransferase

borkumensis

D-amino

tryptophan

[Alcanivorax

SK2
acid amino-

decarboxylase.

borkumensis

transferase.

SK2]

239,
d-alanine
110834821
2.00E−54

Alcanivorax

Bacillus

AAY13560
4.00E−44
P. stutzeri 4
AEM18017
0.038
2.6.1.21
843
280
870
282

240
aminotransferase

borkumensis

D-amino

D-HPG

[Alcanivorax

SK2
acid amino-

AT outer

borkumensis

transferase.

forward

SK2]

N-term

PCR

primer 1.

241,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

242
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence

primer 1.

SEQ

ID NO: 26.

243,
D-alanine
23098538
2.00E−53

Oceano-

P. stutzeri 4
AEM18040
1.00E−51
Plasmid
ADY80523
2.3
2.6.1.21
825
274
867
288
41
51

244
aminotransferase

bacillus

D-HPG

pMRKAd5

[Oceanobacillus

iheyensis

AT outer

HIV-1 gag

iheyensis].

forward

DNA

N-term

noncoding

PCR

sequence

primer 1.

SEQ

ID NO: 26.

245,
aromatic amino
104781758
1.00E−153

Pseudomonas

Klebsiella

ABO61955
1.00E−130
Bacterial
ADS56672
2.00E−28
2.6.1.57
909
302
0
398
90

246
acid

entomophila

pneumoniae

polypeptide

aminotransferase

L48
polypeptide

#10001.

[Pseudomonas

seqid 7178.

entomophila

L48]

247,
D-amino acid
82745661
6.00E−99

Clostridium

Mutant
ABB08244
5.00E−46
Mouse
ABA93421
0.61
2.6.1.21
861
286
0
282
62

248
aminotransferase

beijerincki

Bacillus

arylacetamide

[Clostridium

NCIMB

sphaericus

deacetylase

beijerincki

8052
dat protein.

related

NCIMB 8052]

protein

gi|82726488|gb|E

SEQ

AP61226.1| D-

ID NO: 5.

amino acid

aminotransferase

[Clostridium

beijerincki

NCIMB 8052]

249,
putative
72162511
8.00E−29

Thermobifida

Escherichia

AEK20408
4.00E−23

M.
xanthus

ACL64761
0.15
2.6.1.42
837
278
0
280
34

250
aminotransferase

fusca YX

coli

protein

[Thermobifida

amino-

sequence, seq

fusca YX]

transferase

id 9726.

ilvE

SEQ ID NO 2

251,
D-amino-acid
91775144
6.00E−17

Methylo-

Enterobacter
AEH60497
5.00E−14

P.

ADQ03059
8.00E−04
1.4.99.1
138
45
0
417
93

252
dehydrogenase

bacillus

cloacae

aeruginosa

[Methylobacillus

flagellatus

protein

virulence

flagellatus KT]

KT
amino acid

gene,

sequence -

VIR14,

SEQ ID 5666.

protein.

253,
D-amino acid
32473614
1.00E−152

Rhodo-

N.
ABP80542
6.00E−46
Arabidopsis
ADA71348
0.92
1.4.99.1
1260
419
0
456
61

254
dehydrogenase;

pirellula

gonorrhoeae

thaliana

small chain

baltica SH 1
nucleotide

protein,

[Rhodopirellula

sequence SEQ

SEQ ID 1971.

baltica SH 1]

ID 4691.

255,
D-amino-acid
91779297
0

Burkholderia

Glyphosate
AAR22262
3.00E−48
Prokaryotic
ACA26961
0.004
1.4.99.1
1233
410
0
410
84

256
dehydrogenase

xenovorans

oxido-

essential

[Burkholderia

LB400
reductase

gene

xenovorans

gene

#34740.

LB400]

downstream

flanking

region.

257,
putative D-
146341475
1.00E−174

Bradyrhizo-

Glyphosate
AAR22262
3.00E−42

M.
xanthus

ACL70702
0.058
1.4.99.1
1233
410
0
412
70

258
amino-acid

bium
sp.
oxido-

protein

dehydrogenase

ORS278
reductase

sequence,

(DadA-like)

gene

seq id 9726.

[Bradyrhizobium

downstream

sp. ORS278]

flanking

region.

259,
D-amino acid
27377333
1.00E−163

Bradyrhizo-

P.
ADQ03060
1.00E−152
Human
ABN17150
4.00E−12
1.4.99.1
1254
417
0
421
66

260
dehydrogenase

bium

aeruginosa

ORFX

small subunit

japonicum

virulence gene

protein

[Bradyrhizobium

USDA 110
VIR14, protein.

sequence

japonicum

SEQ ID

USDA 110]

NO:19716.

261,
D-amino-acid
11871743
1.00E−166

Sinorhizo-

Glyphosate
AAR22262
2.00E−42
SigA2
AEB45551
3.6
1. . .
1248
415
0
417
65

262
dehydrogenase

bium

oxido-

without

[Sinorhizobium

medicae

reductase

bla gene

medicae

WSM419
gene

amplifying

WSM419]

downstream

PCR primer,

gi|113726415|gb|

flanking

SigA2-

EAU07507.1|

region.

NotD-P,

D-amino-acid

SEQ ID

dehydrogenase

NO: 52.

[Sinorhizobium

medicae

WSM419]

263,
D-amino acid
13473406
1.00E−164

Mesorhizo-

P.
ADQ03060
1.00E−142

Rhizobium

AAV30459
1.00E−12
1.4.99.1
1254
417
1257
418
66
67

264
dehydrogenase,

bium

aeruginosa

species

small subunit

loti

virulence gene

symbiotic

[Mesorhizobium

VIR14, protein.

plasmid

loti].

pNGR234.

265,
Methylenetetrahy
92114170
1.00E−112

Chromo-
Bacterial
ADS25020
2.00E−97
Bacterial
ADS63414
7.00E−22
1.5.1.5
747
248
0
287
79

266
drofolate

halobacter

polypeptide

polypeptide

dehydrogenase

salexigens

#10001.

#10001.

(NADP+)

DSM 3043

[Chromo-

halobacter

salexigens

DSM 3043]

267,
D-amino acid
33596520
1.00E−172

Bordetella

P.
ADQ03060
7.00E−95
Enterobacter
AEH3102
0.001
1.4.99.1
1254
417
0
418
71

268
dehydrogenase

parapertussis

aeruginosa

cloacae

small subunit

12822
virulence gene

protein

[Bordetella

VIR14,

amino acid

parapertussis

protein.

sequence -

12822]

SEQ ID

5666.

269,
D-amino acid
146280878
0

Pseudomonas

P.
ADQ03060
0

Pseudomonas

ABD08815
3.00E−90
1.4.99.1
1299
432
0
432
78

270
dehydrogenase;

stutzeri

aeruginosa

aeruginosa

small subunit

A1501
virulence gene

polypeptide

[Pseudomonas

VIR14,

#3.

stutzeri A1501]

protein.

271,
D-amino-acid
73541345
1.00E−144

Ralstonia

Glyphosate
AAR22262
6.00E−46
Ramoplanin
AAL40781
0.23
1.4.99.1
1239
412
0
414
59

272
dehydrogenase

eutropha

oxido-

biosynthetic

[Ralstonia

JMP134
reductase

ORF

eutropha

gene

20 protein.

JMP134]

downstream

flanking

region.

273,
D-amino acid
21243478
1.00E−106

Xanthomonas

P.
ADQ03060
3.00E−47
A. orientalis
ADY72597
0.23
1.4.99.1
1257
418
1251
416
48
60

274
dehydrogenase

axonopodis

aeruginosa

polyene

subunit

pv.
virulence

polyketide

[Xanthomonas

citri str. 306
gene VIR14,

ORF 14

axonopodis
pv.

protein.

protein.

citri str. 306].

275,
D-amino-acid
92118208
1.00E−174

Nitrobacter

Glyphosate
AAR22262
8.00E−54

M.
xanthus

ACL64753
0.92
1.4.99.1
1254
417
0
433
70

276
dehydrogenase

hamburgensis

oxido-

protein

[Nitrobacter

X14
reductase

sequence,

hamburgensis

gene

seq id 9726.

X14]

downstream

flanking

region.

277,
D-amino-acid
92118208
1.00E−170

Nitrobacter

Glyphosate
AAR22262
2.00E−56
Drosophila
ABL23528
0.92
1.4.99.1
1254
417
0
433
69

278
dehydrogenase

hamburgensis

oxido-

melanogaster

[Nitrobacter

X14
reductase

polypeptide

hamburgensis

gene

SEQ ID

X14]

downstream

NO 24465.

flanking

region.

279,
D-amino-acid
86750758
1.00E−116

Rhodo-

Glyphosate
AAR22262
1.00E−53
Bacterial
ADS56371
3.6
1.4.99.1
1251
416
0
417
50

280
dehydrogenase

pseudomonas

oxido-

polypeptide

[Rhodo-

palustris

reductase

#10001.

pseudomonas

HaA2
gene

palustris

downstream

HaA2]

flanking

region.

281,
D-amino-acid
121530396
1.00E−151

Ralstonia

Glyphosate
AAR22262
1.00E−45

Streptococcus

AEC16041
0.058
1.4.99.1
1242
413
0
416
63

282
dehydrogenase

pickettii 12J
oxido-

pyogenes

[Ralstonia

reductase

protein

pickettii 12J]

gene

G, SEQ

gi|121302471|gb|

downstream

ID NO: 28.

EAX43440.1|

flanking

region.

283,
D-amino-acid
27377333
1.00E−158

Bradyrhizo-

P.
ADQ03060
1.00E−147
P.
ADQ03059
4.00E−12
1.4.99.1
1263
420
0
421
62

284
dehydrogenase

bium

aeruginosa

aeruginosa

[Ralstonia

japonicum

virulence

virulence

pickettii 12J]

USDA 110
gene VIR14,

gene VIR14,

D-amino acid

protein.

protein.

dehydrogenase

small subunit

[Bradyrhizobium

japonicum

USDA 110]

285,
D-amino acid
86141912
2.00E−87

Flavo-

M.
ADL05210
9.00E−53
Human ORF
ABQ98347
3.7
1.4.99.1
1263
420
0
416
40

286
dehydrogenase

bacterium

catarrhalis

DNA

[Flavobacterium

sp. MED217
protein #1.

sequence #4.

sp. MED217]

287,
D-amino acid
87309573
1.00E−128

Blasto-

Glyphosate
AAR22262
3.00E−47
Drosophila
ABL11756
0.92
1.4.99.1
1257
418
0
416
52

288
dehydrogenase,

pirellula

oxido-

melanogaster

small chain

marina DSM
reductase

polypeptide

[Blastopirellula

3645
gene

SEQ ID

marina DSM

downstream

NO 24465.

3645]

flanking

gi|87287337|gb|E

region.

AQ79237.1|

D-amino acid

dehydrogenase,

small chain

[Blastopirellula

marina DSM

3645]

289,
possible
39936835
1.00E−120

Rhodo-

Glyphosate
AAR22262
2.00E−52

M.
xanthus

ACL64803
0.06
1.4.99.1
1284
427
0
417
52

290
D-amino-acid

pseudomonas

oxido-

protein

dehydrogenase

palustris

reductase

sequence,

[Rhodopseudomo

CGA009
gene

seq id 9726.

nas
palustris

downstream

CGA009]

flanking

region.

291,
D-amino acid
87309573
1.00E−136

Blasto-

P.
ADQ03060
3.00E−42
Enterobacter
AEH54372
0.92
1.4.99.1
1263
420
0
416
56

292
dehydrogenase,

pirellula

aeruginosa

cloacae

small chain

marina DSM
virulence

protein

[Blastopirellula

3645
gene VIR14,

amino acid

marina DSM

protein.

sequence -

3645]

SEQ ID

gi|87287337|gb|E

5666.

AQ79237.1| D-

amino acid

dehydrogenase,

small chain

[Blastopirellula

marina DSM

3645]

293,
D-amino acid
104781752
0

Pseudomonas

Glyphosate
AAR22262
1.00E−47
Arabidopsis
ADT06724
0.23
1.4.99.1
1245
414
0
414
91

294
dehydrogenase;

entomophila

oxido-

thaliana

small subunit

L48
reductase

axidative

family protein

gene

stress-

[Pseudomonas

downstream

associated

entomophila

flanking

protein #12.

L48]

region.

295,
D-amino acid
124009931
4.00E−86

Microscilla

Glyphosate
AAR22262
5.00E−38
Microscilla
AAV06555
0.24
1.4.99.1
1296
431
0
427
42

296
dehydrogenase

marina ATCC
oxido-

furvescens

small subunit,

23134
reductase

catalase-

putative

gene

53CA1

[Microscilla

downstream

gene.

marina ATCC

flanking

23134]

region.

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

297,
D-amino acid
146284421
1.00E−177

Pseudomonas

Acinetobacter

ADA36279
1.00E−124

Acinetobacter

ADA32153
3.6
1.4.99.1
1242
413
0
419
74

298
dehydrogenase;

stutzeri

baumannii

baumannii

small subunit

A1501
protein

protein

[Pseudomonas

#19.

#19.

stutzeri A1501]

299,
D-amino acid
146284421
1.00E−176

Pseudomonas

Acinetobacter

ADA36279
1.00E−123

Acinetobacter

ADA32153
3.6
1.4.99.1
1242
413
0
419
74

300
dehydrogenase;

stutzeri

baumannii

baumannii

small subunit

A1501
protein

protein

[Pseudomonas

#19.

#19.

stutzeri A1501]

301,
putative d-amino
116250556
1.00E−168

Rhizobium

Glyphosate
AAR22262
3.00E−48

Pseudomonas

ABD16228
0.92
1. . .
1254
417
0
415
66

302
acid

legumino-

oxidoreductase

aeruginosa

dehydrogenase

sarum

gene

polypeptide

small subunit

bv. viciae
downstream

#3.

[Rhizobium

3841
flanking

leguminosarum

region.

bv. viciae 3841]

303,
D-amino-acid
148553731
4.00E−90

Sphingomonas

P.
ADQ03060
3.00E−87
Enterobacter
AEH53102
0.059
1.4.99.1
1269
422
0
416
42

304
dehydrogenase

wittichii

aeruginosa

cloacae

[Sphingomonas

RW1
virulence

protein

wittichii RW1]

gene VIR14,

amino acid

protein.

sequence -

SEQ ID 5666.

305,
D-amino acid
26247503
0

Escherichia

Enterobacter
AEH60497
0
Enterobacter
AEH53102
0
1.4.99.1
1299
432
0
434
93

306
dehydrogenase

coli CFT073
cloacae

cloacae

small subunit

protein

protein

[Escherichiacoli

amino acid

amino acid

CFT073]

sequence -

sequence -

SEQ ID 5666.

SEQ ID 5666.

307,
putative d-amino
116250556
1.00E−129

Rhizobium

Glyphosate
AAR22262
9.00E−40
Aspergillus
ADR84929
0.24
1. . .
1320
439
0
415
51

308
acid

legumino-

oxidoreductase

fumigatus

dehydrogenase

sarum

gene

essential

small subunit

bv. viciae
downstream

gene

[Rhizobium

3841
flanking

protein #10.

leguminosarum

region.

bv. viciae 3841]

309,
D-amino acid
124009931
5.00E−98

Microscilla

H. pylori
AAW98270
9.00E−48
Human
ADC87621
0.001
1.4.99.1
1242
413
0
427
44

310
dehydrogenase

marina

GHPO

GPCR

small subunit,

ATCC
1099 gene.

protein

putative

23134

SEQ ID

[Microscilla

NO: 68.

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1| D-

amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

311,
D-amino acid
27377333
0

Bradyrhizo-

P.
ADQ03060
1.00E−150

Klebsiella

ADB01189
3.00E−13
1.4.99.1
1266
421
0
421
95

312
dehydrogenase

bium

aeruginosa

pneumoniae

small subunit

japonicum

virulence

polypeptide

[Bradyrhizobium

USDA 110
gene VIR14,

seqid 7178.

japonicum

protein.

USDA 110]

313,
D-amino-acid
86750758
1.00E−119

Rhodo-

Glyphosate
AAR22262
3.00E−55
Bacterial
ADS56475
3.6
1.4.99.1
1245
414
0
417
52

314
dehydrogenase

pseudomonas
oxidoreductase

polypeptide

[Rhodo-

palustris

gene

#10001.

pseudomonas

HaA2
downstream

palustris

flanking

HaA2]

region.

315,
D-amino-acid
73541345
1.00E−145

Ralstonia

Glyphosate
AAR22262
1.00E−45
Myco-
AAI99682
0.058
1.4.99.1
1236
411
0
414
60

316
dehydrogenase

eutropha

oxidoreductase

bacterium

[Ralstonia

JMP134
gene

tuberculosis

eutropha

downstream

strain

JMP134]

flanking

H37Rv

region.

genome

SEQ ID

NO 2.

317,
D-aminoacid
88712395
5.00E−96

Flavo-

M. catarrhalis
ADL05210
1.00E−43

Salmonella

ADZ00150
0.91
1.4.99.1
1245
414
0
416
43

318
dehydrogenase

bacteriales

protein #1.

typhi VexC

[Flavobacteriales

bacterium

gene, reverse

bacterium

HTCC2170

PCR primer.

HTCC2170]

gi|88708933|gb|E

AR01167.1] D-

amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

319,
Enoyl-CoA
126727316
2.00E−96

Rhodo-

Bacterial
ADN25932
2.00E−77
Prokaryotic
ACA26563
0.052
1.1.1.35
1110
369
0
646
47

320
hydra tase/

bacterales

polypeptide

essential gene

isomerase:3-

bacterium

#10001.

#34740.

hydroxyacyl-CoA

HTCC2150

dehydrogenase,

3-hydroxyacyl-

CoA

dehydrogenase,

NAD-binding

protein

[Rhodobacterales

bacterium

HTCC2150]

gi|126703311|gb|

EBA02409.1|

Enoyl-CoA

hydratase/isomer

ase:3-

hydroxyacyl-CoA

dehydrogenase,

3-hydroxyac

321,
D-amino-acid
121530396
1.00E−170

Ralstonia

Glyphosate
AAR22262
1.00E−42
Prokaryotic
ACA26625
0.004
1.4.99.1
1248
415
0
416
68

322
dehydrogenase

pickettii 12J
oxidoreductase

essential gene

[Ralstonia

gene

#34740.

pickettii 12J]

downstream

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

323,
D-amino-acid
126355875
0

Pseudomonas

Glyphosate
AAR22262
2.00E−46
Bacterial
ADS56305
0.015
1.4.99.1
1245
414
0
414
97

324
dehydrogenase

putida GB-1
oxidoreductase

polypeptide

[Pseudomonas

gene

#10001.

putida GB-1]

downstream

gi|126320385|gb|

flanking

EAZ71237.1| D-

region.

amino-acid

dehydrogenase

[Pseudomonas

putida GB-1]

325,
D-amino-acid
126356306
0

Pseudomonas

P.
ADQ03060
0

Pseudomonas

ABD08815
########
1.4.99.1
1302
433
0
434
98

326
dehydrogenase

putida GB-1
aeruginosa

aeruginosa

[Pseudomonas

virulence

polypeptide

putida GB-1]

gene VIR14,

#3.

gi|126319114|gb|

protein.

EAZ69967.1|

D-amino-acid

dehydrogenase

[Pseudomonas

putida GB-11

327,
D-amino acid
21243478
1.00E−112

Xanthomonas

P.
ADQ03060
4.00E−47
Bacterial
ADT47109
0.059
1.4.99.1
1254
417
1251
416
49
61

328
dehydrogenase

axonopodis

aeruginosa

polypeptide

subunit

pv.
virulence

#10001.

[Xanthomonas

citri
str. 306
gene VIR14,

axonopodis
pv.

protein.

citri
str. 306].

329,
D-amino acid
88712395
4.00E−95

Flavo-

H. pylori
AAW98270
5.00E−46
Prokaryotic
ACA32282
0.91
1.4.99.1
1251
416
0
416
43

330
dehydrogenase

bacteriales

GHPO

essential gene

[Flavobacteriales

bacterium

1099 gene.

#34740.

bacterium

HTCC2170

HTCC2170]

gi|88708933|gb|E

AR01167.1]

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

331,
HTCC2170]
27377333
0

Bradyrhizo-

P.
ADQ03060
1.00E−144

Klebsiella

ABD01189
1.00E−09
1.4.99.1
1256
421
0
421
79

332
D-amino acid

bium

aeruginosa

pneumoniae

dehydrogenase

japonicum

virulence

polypeptide

small subunit

USDA 110
gene VIR14,

seqid 7178.

[Bradyrhizobium

protein.

japonicum

USDA 110]

333,
Enoyl-CoA
126727316
2.00E−96

Rhodo-

Bacterial
ADN25932
2.00E−77
Prokaryotic
ACA26563
0.052
1.1.1.35
1110
369
0
648
47

334
hydratase/isomer

bacterales

polypeptide

essential gene

ase:3-

bacterium

#10001.

#34740.

hydroxyacyl-CoA

HTCC2150

dehydrogenase,

3-hydroxyacyl-

CoA

dehydrogenase,

NAD-binding

protein

[Rhodobacterales

bacterium

HTCC2150]

gi|126703311|gb|

EBA02409.1|

Enoyl-CoA

hydratase/isomer

ase:3-

hydroxyacyl-CoA

dehydrogenase,

3-hydroxyac

335,
D-amino-acid
121530396
1.00E−170

Ralstonia

Glyphosate
AAR22262
1.00E−42
Prokaryotic
ACA26625
0.004
1.4.99.1
1248
415
0
416
68

336
dehydrogenase

pickettii 12J
oxidoreductase

essential gene

[Ralstonia

gene

#34740.

pickettii 12J]

downstream

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

337,
D-amino-acid
86750758
1.00E−114

Rhodo-

Glyphosate
AAR22262
1.00E−50
Thale cress
AEI59268
0.91
1.4.99.1
1248
415
0
417
49

338
dehydrogenase

pseudomonas
oxidoreductase

polypeptide,

[Rhodo-

palustris

gene

SEQ ID

pseudomonas

HaA2
downstream

NO: 32.

palustris

flanking

HaA2]

region.

339,
D-amino acid
124009931
1.00E−100

Microscilla

M. catarrhalis
ADL05210
7.00E−47
Mouse
ADC85461
0.91
1.4.99.1
1245
414
0
427
42

340
dehydrogenase

marina ATCC
protein #1.

Tnfrsf6

small subunit,

23134

genomic

putative

sequence.

[Microscilla

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

341,
D-amino-acid
121530396
1.00E−170

Ralstonia

Glyphosate
AAR22262
2.00E−42
Prokaryotic
ACA26625
0.91
1.4.99.1
1248
415
0
416
68

342
dehydrogenase

pickettii 12J
oxidoreductase

essential gene

[Ralstonia

gene

#34740.

pickettii 12J]

downstream

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

343,
short-chain
146275754
2.00E−51

Novos-
Bacterial
ADS24609
5.00E−26
Bacterial
ADS58499
0.008
1.1.1.184
693
230
0
228
48

344
dehydrogenase/

phingobium

polypeptide

polypeptide

reductase SDR

aromatici-

#10001.

#10001.

[Novos-

vorans

phingobium

DSM 12444

aromaticivorans

DSM 12444]

345,
D-amino-acid
114570652
2.00E−91

Maricaulis

P.
ADQ03060
4.00E−78
Human
ABN17150
4.00E−09
1.4.99.1
1260
419
0
427
43

346
dehydrogenase

maris MCS10
aeruginosa

ORFX

[Maricaulis

virulence

protein

maris MCS10]

gene VIR14,

sequence

gi|114341114|gb|

protein.

SEQ ID

ABI66394.1| D-

NO: 19716.

amino-acid

dehydrogenase

[Maricaulis

maris MCS1Q]

347,
D-amino-acid
113871743
1.00E−152

Sinorhizobium

Glyphosate
AAR22262
1.00E−48

M.
xanthus

ACL64399
0.23
1. . .
1245
414
0
417
63

348
dehydrogenase

medicae

oxidoreductase

protein

[Sinorhizobium

WSM419
gene

sequence,

medicae

downstream

seq id 9726.

WSM419]

flanking

gi|113726415|gb|

region.

EAU07507.1| D-

amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

349,
D-amino-acid
86750758
1.00E−117

Rhodo-

Glyphosate
AAR22262
3.00E−55

M.
xanthus

ACL64798
0.91
1.4.99.1
1251
416
0
417
51

350
dehydrogenase

pseudomonas

oxidoreductase

protein

[Rhodo-

palustris

gene

sequence,

pseudomonas

HaA2
downstream

seq id 9726.

palustris

flanking

HaA2]

region.

351,
D-amino acid
32473614
1.00E−155

Rhodo-

N.
ABP80542
2.00E−48
Plant
ADT17628
0.92
1.4.99.1
1260
419
0
456
61

352
dehydrogenase;

pirellula

gonorrhoeae

polypeptide,

small chain

baltica SH 1
nucleotide

SEQ ID

[Rhodopirellula

sequence SEQ

5546.

baltica SH 1]

ID 4691.

353,
D-amino acid
88712395
1.00E−88

Flavo-

Bacterial
ADF07894
9.00E−53
Sorangium
AED50859
0.059
1.4.99.1
1263
420
0
416
40

354
dehydrogenase

bacteriales

polypeptide

cellulosum

[Flavobacteriales

bacterium

#19.

jerangolid

bacterium

HTCC2170

biosynthetic

HTCC2170]

cluster

gi|88708933|gb|E

jerB protein.

AR01167.1] D-

amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC21701

355,
aldehyde
108761092
2.00E−97

Myxococcus

Bacterial
ADN25785
1.00E−87
Bacterial
ADS56451
8.00E−07
1.2.1.39
1020
339
0
524
55

356
dehydrogenase

xanthus DK
polypeptide

polypeptide

family protein

1622
#10001.

#10001.

[Myxococcus

xanthus DK

1622]

357,
D-amino acid
124009931
1.00E−96

Microscilla

M.
ADL05210
1.00E−42
Human
ABD32968
0.91
1.4.99.1
1251
416
0
427
40

358
dehydrogenase

marina ATCC
catarrthalis

cancer-

small subunit,

23134
protein #1.

associated

putative

protein

[Microscilla

HP13-036.1.

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

359,
D-amino-acid
111019145
1.00E−163

Rhodococcus

C
AAG93079
1.00E−103

Klebsiella

ABD00632
0.23
1.4.99.1
1251
416
0
415
68

360
dehydrogenase

sp. RHA1
glutamicum

pneumoniae

small subunit

coding

polypeptide

[Rhodococcus

sequence

seqid 7178.

sp. RHA1]

fragment

SEQ ID

NO: 1935.

361,
D-amino-acid
111019145
1.00E−163

Rhodococcus

C
AAG93079
1.00E−103

Klebsiella

ABD00632
0.23
1.4.99.1
1251
416
0
415
68

362
dehydrogenase

sp. RHA1
glutamicum

pneumoniae

small subunit

coding

polypeptide

[Rhodococcus

sequence

seqid 7178.

sp. RHA1]

fragment

SEQ ID

NO: 1935.

363,
D-amino-acid
111019145
1.00E−163

Rhodococcus

C
AAG93079
1.00E−103

Klebsiella

ABD00632
0.23
1.4.99.1
1251
416
0
415
68

364
dehydrogenase

sp. RHA1
glutamicum

pneumoniate

small subunit

coding

polypeptide

[Rhodococcus

sequence

seqid 7178.

sp. RHA1]

fragment

SEQ ID

NO: 1935.

365,
D-amino acid
27377333
0

Bradyrhizo-

P.
ADQ03060
1.00E−149

Klebsiella

ABD01189
2.00E−11
1.4.99.1
1266
421
0
421
93

366
dehydrogenase

bium

aeruginosa

pneumoniate

small subunit

japonicum

virulence

polypeptide

[Bradyrhizobium

USDA 110
gene VIR14,

seqid 7178.

japonicum

protein.

USDA 110]

367,
D-amino acid
134093986
0

Herminii-

P.
ADQ03060
1.00E−101

Klebsiella

ABD01189
3.00E−07
1.4.99.1
1317
438
0
443
80

368
dehydrogenase

monas

aeruginosa

pneumoniae

small subunit

arsenico-

virulence

polypeptide

[Herminiimonas

xydans

gene VIR14,

seqid 7178.

arsenicoxydans]

protein.

gi|133737889|em

b|CAL60934.1|

D-amino acid

dehydrogenase

small subunit

[Herminiimonas

arsenicoxydans]

369,
D-amino acid
124009931
1.00E−101

Microscilla

H. pylori
AAW98270
1.00E−148
Soybean
AEI27664
0.23
1.4.99.1
1245
414
0
427
44

370
dehydrogenase

marina ATCC
GHPO

polymorphic

small subunit,

23134
1099 gene.

locus,

putative

SEQ ID 6.

[Microscilla

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

371,
D-amino acid
27377333
0

Bradyrhizo-

P.
ADQ03060
1.00E−148
Rhizobium
AAV30459
1.00E−15
1.4.99.1
1266
421
0
421
94

372
dehydrogenase

bium

aeruginosa

species

small subunil

japonicum

virulence

symbiotic

[Bradyrhizobium

USDA 110
gene VIR14,

plasmid

japonicum

protein.

pNGR234.

USDA 110]

373,
D-amino-acid
73541345
1.00E−136

Ralstonia

Glyphosate
AAR22262
3.00E−47
Bacterial
ADS56859
0.23
1.4.99.1
1260
419
0
414
57

374
dehydrogenase

eutropha

oxidoreductase

polypeptide

[Ralstonia

JMP134
gene

#10001.

eutropha

downstream

JMP134]

flanking

region.

375,
D-amino acid
91217360
3.00E−98

Psychroflexus

Acinetobacter
ADA33588
2.00E−47
Cyclin-
ADX06332
3.6
1.4.99.1
1257
418
0
415
43

376
dehydrogenase

torquis ATCC
baumannii

dependent

[Psychroflexus

700755
protein

kinase

torquis ATCC

#19.

modulation

700755]

biomarker

gi|91184468|gb|E

SEQ ID

AS70851.1| D-

NO 24.

amino acid

dehydrogenase

[Psychroflexus

torquis ATCC

700755]

377,
D-amino acid
88712395
1.00E−122

Flavo-

M.
ADL05210
4.00E−40
Human
AAK69489
0.23
1.4.99.1
1245
414
0
416
51

378
dehydrogenase

bacteriales

catarrthalis

immune/

[Flavobacteriales

bacterium

protein #1.

haemato-

bacterium

HTCC2170

poietic

HTCC2170]

antigen

gi|88708933|gb|E

genomic

AR01167.1| D-

sequence

amino acid

SEQ ID

dehydrogenase

NO: 41436.

[Flavobacteriales

bacterium

HTCC2170]

379,
D-amino-acid
114570652
8.00E−91

Maricaulis

P.
ADQ03060
6.00E−78
B.
AED48875
0.015
1.4.99.1
1257
418
0
427
43

380
dehydrogenase

maris MCS10
aeruginosa

circulans

[Maricaulis

virulence

putative

maris MCS10]

gene VIR14,

CapJ

gi|114341114|gb|

protein.

protein.

ABI66394.1| D-

amino-acid

dehydrogenase

[Maricaulis

maris MCS1Q]

381,
D-amino-acid
111019145
1.00E−163

Rhodococcus

C
AAG93079
1.00E−103

Klebsiella

ABD00632
0.23
1.4.99.1
1251
416
0
415
68

382
dehydrogenase

sp. RHA1
glutamicum

pneumoniae

small subunit

coding

polypeptide

[Rhodococcus

sequence

seqid 7178.

sp. RHA1]

fragment

SEQ ID

NO: 1935.

383,
D-amino acid
13473406
0

Mesorhizo-

P.
ADQ03060
1.00E−140
P.
ADQ03059
7.00E−11
1.4.99.1
1260
419
1257
418
88
87

384
dehydrogenase,

bium

aeruginosa

aeruginosa

small subunit

loti

virulence

virulence

[Mesorhizobium

gene VIR14,

gene VIR14,

loti].

protein.

protein.

385,
D-amino acid
124009931
5.00E−99

Microscilla

H. pylori
AAW98270
1.00E−47
Human
ABA19863
0.91
1.4.99.1
1245
414
0
427
42

386
dehydrogenase

marina ATCC
GHPO

nervous

small subunit,

23134
1099 gene.

system

putative

related

[Microscilla

poly-

marina ATCC

nucleotide

23134]

SEQ ID NO

gi|123984082|gb|

11589.

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

387,
D-amino acid
13474742
0

Mesorhizo-

Pseudomonas

ABO75104
2.00E−90
M.
AAZ19073
0.91
1.4.99.1
1251
416
1251
416
75
74

388
dehydrogenase,

bium

aeruginosa

tuberculosis

small subunit

loti

polypeptide

recombinant

[Mesorhizobium

#3.

antigen DNA

loti].

encoding

3′ XP32

389,
D-amino acid
134093986
0

Herminii-

Klebsiella

ABO67618
2.00E−95

Klebsiella

ABD01189
2.00E−08
1.4.99.1
1317
438
0
443
80

390
dehydrogenase

monas

pneumoniae

pneumoniae

small subunit

arsenico-

polypeptide

polypeptide

[Herminiimonas

xydans

seqid 7178.

seqid 7178.

arsenicoxydans]

gi|133737889|em

b|CAL60934.1|

D-amino acid

dehydrogenase

small subunit

[Herminiimonas

arsenicoxydans]
87309573
1.00E−139

Blasto-

N.
ABP80542
1.00E−44
Myco-
ADB80216
0.92
1.4.99.1
1257
418
0
416
55

391,
D-amino acid

pirellula

gonorrhoeae

bacterium

392
dehydrogenase,

marina DSM
nucleotide

tuberculosis

small chain

3645
sequence SEQ

nitrient

[Blastopirellula

ID 4691.

starvation-

marina DSM

inducible

3645]

protein #8.

gi|87287337|gb|E

AQ79237.1|

D-amino acid

dehydrogenase,

small chain

[Blastopirellula

marina DSM

3645]

393,
probable D-
119897258
1.00E−111

Azoarcus
sp.

Pseudomonas

ABO84309
1.00E−74
Enterobacter
AEH53102
0.001
1.4.99.1
1257
418
0
416
51

394
amino acid

BH72

aeruginosa

cloacae

dehydrogenase

polypeptide

protein

small subunit

#3.

amino acid

[Azoarcussp.

sequence -

BH72]

SEQ ID 5666.

395,
D-amino-acid
73541345
0

Ralstonia

Glyphosate
AAR22262
1.00E−45
Plant full
ADX30055
0.058
1.4.99.1
1242
413
0
414
88

396
dehydrogenase

eutropha

oxidoreductase

length

[Ralstonia

JMP134
gene

insert

eutropha

downstream

polynuceotide

JMP134]

flanking

seqid 4980.

region.

397,
D-aminoacid
86750758
1.00E−121

Rhodo-

Glyphosate
AAR22262
1.00E−56
Bacterial
ADT43936
0.015
1.4.99.1
1245
414
0
417
52

398
dehydrogenase

pseudomonas
oxidoreductase

polypeptide

[Rhodo-

palustris

gene

#10001.

pseudomonas

HaA2
downstream

palustris

flanking

HaA2]

region.

399,
D-amino acid
124009931
2.00E−97

Microscilla

H. pylori
AAW98270
1.00E−45
Human
ADL62778
0.23
1.4.99.1
1242
413
0
427
44

400
dehydrogenase

marina ATCC
GHPO

ovarian

small subunit,

23134
1099 gene.

cancer DNA

putative

marker #5.

[Microscilla

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1]

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

401,
D-amino-acid
114570652
3.00E−66

Maricaulis

M.
ADL05210
9.00E−56
A. thaliana
AAD06652
3.6
1.4.99.1
1250
419
0
427
33

402
dehydrogenase

maris

catarrthalis

transcription

[Maricaulis

MCS1Q
protein #1.

factor

maris MCS10]

G207

gi|114341114|gb|

homolog,

ABI66394.1|

G227 cDNA.

D-amino-acid

dehydrogenase

[Maricaulis

maris MCS1Q]

403,
D-amino acid
124009931
1.00E−111

Microscilla

H. pylori
AAW98270
3.00E−46
A.
ABQ80343
3.6
1.4.99.1
1257
418
0
427
47

404
dehydrogenase

marina ATCC
GHPO

fumigatus

small subunit,

23134
1099 gene.

AfGOX3.

putative

[Microscilla

marina ATCC

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

405,
D-amino acid
88806240
2.00E−95

Robiginitalea

Glyphosate
AAR22262
3.00E−45
Human 7a5
ADW91994
0.91
1.4.99.1
1239
412
0
417
42

406
dehydrogenase

biformata

oxidoreductase

prognostin

[Robiginitalea

HTCC2501
gene

protein

biformata

downstream

sequence

HTCC2501]

flanking

SeqID2.

gi|88783849|gb|E

region.

AR15020.1|

407,
D-amino acid
27377333
0

Bradyrhizo-

P.
ADQ03060
1.00E−149

Klebsiella

ABD01189
2.00E−11
1.4.99.1
1266
421
0
421
94

408
dehydrogenase

bium

aeruginosa

pneumoniae

[Robiginitalea

japonicum

virulence

polypeptide

biformata

USDA 110
gene VIR14,

seqid 7178.

HTCC2501]

protein.

D-amino acid

dehydrogenase

small subunit

[Bradyrhizobium

japonicum

USDA 110]

409,
D-amino acid
124009931
2.00E−98

Microscilla

P.
ADQ03060
4.00E−52
Human soft
ADQ18897
0.92
1.4.99.1
1260
419
0
427
45

410
dehydrogenase

marina ATCC
aeruginosa

tissue

small subunit,

23134
virulence

sarcoma-

putative

gene VIR14,

upregulated

[Microscilla

protein.

protein -

marina ATCC

SEQ ID 40.

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

411,
ketoglutarate
104783034
1.00E−103

Pseudomonas

Bacterial
ADN25785
1.00E−103
Bacterial
ADS55665
4.00E−09
1.2.1.4
1242
413
0
526
50

412
semialdehyde

entomophila

polypeptide

polypeptide

dehydrogenase

L48
#10001.

#10001.

[Pseudomonas

entomophila

L48]

413,
D-amino-acid
86750758
1.00E−119

Rhodo-
Glyphosate
AAR22262
3.00E−57
Prokaryotic
ACA25332
0.23
1.4.99.1
1248
415
0
417
52

414
dehydrogenase

pseudomonas

oxidoreductase

essential gene

[Rhodo-

palustris

gene

#34740.

pseudomonas

HaA2
downstream

palustris

flanking

HaA2]

region.

415,
D-amino-acid
86750758
1.00E−125

Rhodo-
Glyphosate
AAR22262
1.00E−47
Drosophila
ABL20166
0.015
1.4.99.1
1242
413
0
417
53

416
dehydrogenase

pseudomonas

oxidoreductase

melanogaster

[Rhodo-

palustris

gene

polypeptide

pseudomonas

HaA2
downstream

SEQ ID

palustris

flanking

NO 24465.

HaA2]

region.

417,
AGR_L_3050p
15891640
1.00E−179

Agro-

P.
ADQ03060
1.00E−150

E. coli

ACD81455
3.00E−10
1.4.99.1
1248
415
1257
418
73
73

418
[Agrobacterium

bacterium

aeruginosa

K12 MG1655

tumefaciens].

tumefaciens

virulence

biochip

gene VIR14,

probe

protein.

SEQ ID 1.

419,
D-amino-acid
91786059
0

Polaromonas

Photorhabdus
ABM69115
1.00E−84
P.
ADQ03059
2.00E−05
1.4.99.1
1326
441
0
445
76

420
dehydrogenase

sp. JS666
luminescens

aeruginosa

[Polaromonas

protein

virulence

sp. JS666]

sequence

gene VIR14,

#59.

protein.

421,
D-amino-acid
108804652
1.00E−108

Rubrobacter

C
AAG93079
8.00E−81
Prokaryotic
ACA37735
0.24
1.4.99.1
1293
430
0
419
49

422
dehydrogenase

xylanophilus

glutamicum

essential gene

[Rubrobacter

DSM 9941
coding

#34740.

xylanophilus

sequence

DSM 9941]

fragment

SEQ ID

NO: 1935.

423,
D-amino acid
124009931
4.00E−94

Microscilla

H. pylori
AAW98270
4.00E−44
Chemically
ABL70446
0.91
1.4.99.1
1245
414
0
427
43

424
dehydrogenase

marina ATCC
GHPO

treated

small subunit,

23134
1099 gene.

cell

putative

signalling

[Microscilla

DNA

marina ATCC

sequence#234.

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

425,
D-amino-acid
121530396
1.00E−122

Ralstonia

Glyphosate
AAR22262
2.00E−44
Plant
ADJ44795
0.92
1.4.99.1
1260
419
0
416
53

426
dehydrogenase

pickettii 12J
oxidoreductase

cDNA #31.

[Ralstonia

gene

pickettii 12J]

downstream

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

427,
D-amino-acid
92118208
0

Nitrobacter

Glyphosate
AAR22262
2.00E−49
Bacterial
ADS57588
0.92
1.4.99.1
1254
417
0
433
72

428
dehydrogenase

hamburgensis

oxidoreductase

polypeptide

[Nitrobacter

X14
gene

#10001.

hamburgensis

downstream

X14]

flanking

region.

429,
D-amino acid
124009931
2.00E−97

Microscilla

Glyphosate
AAR22262
4.00E−48
Haemophilus
AAT42063
0.059
1.4.99.1
1263
420
0
427
44

430
dehydrogenase

marina ATCC
oxidoreductase

influenzae

small subunit,

23134
gene

complete

putative

downstream

genome

[Microscilla

flanking

sequence.

marina ATCC

region.

23134]

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

431,
D-amino acid
124009931
1.00E−119

Microscilla

Glyphosate
AAR22262
2.00E−49
Lactic
ADF77343
0.91
1.4.99.1
1242
413
0
427
49

432
dehydrogenase

marina ATCC
oxidoreductase

acid

small subunit,

23134
gene

bacteria

putative

downstream

Lactobacillus

[Microscilla

flanking

johnsonii

marina ATCC

region.

La1

23134]

genomic

gi|123984082|gb|

DNA

EAY24455.1|

SEQ ID

D-amino acid

NO: 1.

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

433,
D-amino-acid
86750758
1.00E−123

Rhodo

Glyphosate
AAR22262
4.00E−45
Drosophila
AEF68383
0.23
1.4.99.1
1245
414
0
417
52

434
dehydrogenase

pseudomonas

oxidoreductase

melanogaster

[Rhodo

paluslris
gene

modified

pseudomonas

HaA2
downstream

translational

paluslris

flanking

start

HaA2]

region.

site DNA.

435,
D-amino-acid
86750758
1.00E−121

Rhodo-
Glyphosate
AAR22262
3.00E−41
Human
ADB80390
0.92
1.4.99.1
1254
417
0
417
51

436
dehydrogenase

pseudomonas

oxidoreductase

MDDT

[Rhodo-

palustris

gene

protein SEQ

pseudomonas

HaA2
downstream

ID NO: 2.

palustris

flanking

HaA2]

region.

437,
carbon monoxide
56697247
1.00E−66

Silicibacter

Bacterial
ADS27598
0.12
Rice abiotic
ACL28407
1.2
1.2.99.2
453
150
0
150
84

438
dehydrogenase

pomeroyi

polypeptide

stress

G protein;

DSS-3
#10001.

responsive

putative

polypeptide

[Silicibacter

SEQ ID

pomeroyi

NO: 4152.

DSS-3]

439,
carbon monoxide
56697248
1.00E−87

Silicibacter

DNA
ABG25235
9.00E−09
Bacterial
ADS63732
2.2

780
259
0
260
64

440
dehydrogenase

pomeroyi

encoding

polypeptide

F protein

DSS-3
novel

#10001.

[Silicibacter

human

pomeroyi

diagnostic

DSS-3]

protein

#20574.

441,
carbon monoxide
56697249
1.00E−171

Silicibacter

Human
AAU75888
3.00E−25
Neisseria
AEB49411
0.22

1182
393
0
393
76

442
dehydrogenase

pomeroyi

adhesion

PCR

E protein

DSS-3
molecule

primer SEQ

[Silicibacter

protein

ID NO 1078.

pomeroyi

AD6/

DSS-3]

CAA17374.11

443,
D-amino-acid
113871743
1.00E−150

Sinorhizo-

Glyphosate
AAR22262
4.00E−55
Prokaryotic
ACA26463
0.06
1. . .
1272
423
0
417
61

444
dehydrogenase

bium

oxidoreductase

essential gene

[Sinorhizobium

medicae

gene

#34740.

medicae

WSM419
downstream

WSM419]

flanking

gi|113726415|gb|

region.

EAU07507.1|

445,
D-amino-acid
126646463
1.00E−175

Algoriphagus

H. pylon
AAW98270
1.00E−45
Tp1 peptide
AEK18770
0.015
1.4.99.1
1245
414
0
415
69

446
dehydrogenase

sp. PR1
GHPO

fragment

[Sinorhizobium

1099 gene.

SEQ ID

medicae

NO: 78.

WSM419]

D-amino acid

dehydrogenase

[Algoriphagus

sp. PR1]

gi|126578095|gb|

EAZ82315.1|

D-amino acid

dehydrogenase

[Algoriphagus

sp. PR1]

447,
D-amino-acid
119877440
0

Steno-
P.
ADQ03060
0

Pseudomonas

ABD08815
4.00E−37
1.4.99.1
1308
435
0
434
84

448
dehydrogenase

trophomonas

aeruginosa

aeruginosa

[Steno-

maltophilia

virulence

polypeptide

trophomonas

R551-3
gene VIR14,

#3.

maltophilia

protein.

R551-3]

gi|119820020|gb|

EAX22641.1|

D-amino-acid

dehydrogenase

[Steno-

trophomonas

maltophilia

R551-3]

449,
D-amino-acid
121530396
1.00E−104

Ralstonia

Glyphosate
AAR22262
9.00E−37

Pseudomonas

ABD03414
0.015
1.4.99.1
1248
415
0
416
48

450
dehydrogenase

pickettii 12J
oxidoreductase

aeruginosa

[Ralstonia

gene

polypeptide

pickettii 12J]

downstream

#3.

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

451,
D-amino-acid
121530396
1.00E−143

Ralstonia

Glyphosate
AAR22262
2.00E−49
Prokaryotic
ACA23380
0.23
1. . .
1245
414
0
416
62

452
dehydrogenase

pickettii 12J
oxidoreductase

essential gene

[Ralstonia

gene

#34740.

pickettii 12J]

downstream

gi|121302471 |gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

453,
D-amino-acid
113871743
1.00E−125

Sinorhizo-

Glyphosate
AAR22262
9.00E−37
Human
ABN24675
0.92
1. . .
1254
417
0
417
53

454
dehydrogenase

bium

oxidoreductase

ORFX

[Sinorhizobium

medicae

gene

protein

medicae

WSM419
downstream

sequence

WSM419]

flanking

SEQ ID

gi|113726415|gb|

region.

NO: 19716.

EAU07507.1|

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

455,
D-amino acid
124009931
1.00E−104

Microscilla

H. pylori
AAW98270
2.00E−50
Human
ACA64961
0.91
1.4.99.1
1242
413
0
427
45

456
dehydrogenase

marina ATCC
GHPO

IMAGE

small subunit,

23134
1099 gene.

249058

putative

DNA

[Microscilla

corresponding

marina ATCC

to

23134]

AW006742.

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

457,
D-amino acid
88712395
1.00E−173

Flavo-

M.
ADL05210
2.00E−48
Drosophila
ABL10568
0.23
1.4.99.1
1251
416
0
416
68

458
dehydrogenase

bacteriales

catarrhalis

melanogaster

[Flavobacteriales

bacterium

protein #1.

polypeptide

bacterium

HTCC2170

SEQ ID

HTCC2170)

NO 24465.

gi|88708933|gb|E

AR01167.11

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

459,
D-amino acid
126666221
0

Marinobacter

Acinetobacter
ADA36279
1.00E−129
Drosophila
ABL12550
3.7
1.4.99.1
1266
421
0
410
78

460
dehydrogenase

sp. ELB17
baumannii

melanogaster

small subunit

protein

polypeptide

[Marinobacter

#19.

SEQ ID

sp. ELB17]

NO 24465.

gi|126629543|gb|

EBA00161.1|

D-amino acid

dehydrogenase

small subunit

[Marinobacter

sp. ELB17]

461,
Short-chain
67154056
1.00E−109

Azotobacter

Klebsiella

ABO66363
1.00E−104

Klebsiella

ACH99914
6.00E−04
1. . .
762
253
0
254
76

462
dehydrogenase/

vinelandii

pneumoniae

pneumoniae

reductase SDR

AvOP
polypeptide

polypeptide

[Azotobacter

seqid 7178.

seqid 7178.

vinelandii

AvOP]

463,
D-amino acid
91217360
1.00E−167

Psychroflexus

H. pylori
AAW98270
2.00E−52
Novel
ADQ64455
0.23
1.4.99.1
1248
415
0
415
69

464
dehydrogenase

torquis ATCC
GHPO

human

[Psychroflexus

700755
1099 gene.

protein

torquis ATCC

sequence #4.

700755]

gi|91184468|gb|E

AS70851.1]

D-amino acid

465,
dehydrogenase
56420489
4.00E−18

Geobacillus

Hyper-
ADM25691
6.00E−11
AB005287
AAC90078
8.00E−05
1.1.1.95
447
148
0
334
34

466
[Psychroflexus

kaustophilus

thermophile

cDNA

torquis ATCC

HTA426
Methano-

clone.

700755]

pyrus

dehydrogenase

kandleri

[Geobacillus

protein #28.

kaustophilus

HTA426]

467,
D-amino-acid
73541345
1.00E−133

Ralstonia

Glyphosate
AAR22262
1.00E−38
Thale cress
AEI59858
0.23
1.4.99.1
1242
413
0
414
55

468
dehydrogenase

eutropha

oxidoreductase

polypeptide,

[Ralstonia

JMP134
gene

SEQ ID

eutropha

downstream

NO: 32.

JMP134]

flanking

region.

469,
putative
116250556
1.00E−166

Rhizobium

Glyphosate
AAR22262
5.00E−46
Murine
ADZ13449
0.91
1. . .
1245
414
0
415
66

470
d-amino acid

legurnino-

oxidoreductase

cancer-

dehydrogenase

sarum

gene

associated

small subunit

bv. viciae

downstream

genomic

[Rhizobium

3841
flanking

DNA #5.

legurninosarum

region.

bv. viciae 3841]

471,
D-amino acid
26247503
0

Escherichia

Enterobacter
AEH60497
0
DNA
AAS77111
0
1.4.99.1
1299
432
0
434
100

472
dehydrogenase

coli

cloacae

encoding

small subunit

CFT073
protein

novel

[Escherichia coli

amino acid

human

CFT073]

sequence -

diagnostic

SEQ ID 5666.

protein

#20574.

473,
D-amino-acid
113871743
1.00E−159

Sinorhizo-

Glyphosate
AAR22262
3.00E−47
G sorghi
ACF04822
0.91
1. . .
1248
415
0
417
64

474
dehydrogenase

bium

oxidoreductase

nitrilase

[Sinorhizobium

medicae

gene

protein

medicae

WSM419
downstream

fragment #2.

WSM419)

flanking

gi|113726415|gb|

region.

EAU07507.1|

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

475,
D-amino-acid
114570652
1.00E−155

Maricaulis

P.
ADQ03060
4.00E−75
S
ADN97550
0.25
1.4.99.1
1341
446
0
427
62

476
dehydrogenase

maris

aeruginosa

ambofaciens

[Maricaulis

MCS10
virulence

spiramycin

maris MCS10]

gene VIR14,

biosynthetic

gi|114341114|gb|

protein.

enzyme

ABI66394.1|

encoded

D-amino-acid

by ORF10*.

dehydrogenase

[Maricaulis

maris MCS10]

477,
D-amino acid
88712395
4.00E−85

Flavo-

P.
ADQ03060
3.00E−51
Human
ACN44608
0.001
1.4.99.1
1239
412
0
416
38

478
dehydrogenase

bacteriales

aeruginosa

protein

[Flavobacteriales

bacterium

virulence

sequence

bacterium

HTCC2170
gene VIR14,

hCP39072.

HTCC2170]

protein.

gi|88708933|gb|E

AR01167.11

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

479,
D-amino acid
88712395
4.00E−85

Flavo-

P.
ADQ03060
3.00E−51
Human
ACN44608
0.001
1.4.99.1
1239
412
0
416
38

480
dehydrogenase

bacteriales

aeruginosa

protein

[Flavobacteriales

bacterium

virulence

sequence

bacterium

HTCC2170
gene VIR14,

hCP39072.

HTCC2170]

protein.

gi|88708933|gb|E

AR01167.11

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

481,
D-amino acid
88712395
1.00E−175

Flavo-

M.
ADL05210
3.00E−50
Human
ADF69167
0.059
1.4.99.1
1251
416
0
416
69

482
dehydrogenase

bacteriales

catarrhalis

MP53

[Flavobacteriales

bacterium

protein #1.

protein

bacterium

HTCC2170

sequence

HTCC2170]

SEQ ID

gi|88708933|gb|E

NO: 69.

AR01167.1]

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

483,
D-amino acid
134093986
0

Herminii-

P.
ADQ03060
4.00E−94

Pseudomonas

ABD08815
0.001
1.4.99.1
1311
436
0
443
82

484
dehydrogenase

monas

aeruginosa

aeruginosa

small subunit

arsenicoxy-

virulence

polypeptide

[Herminiimonas

dans

gene VIR14,

#3.

arsenicoxydans]

protein.

gi|133737889|em

b|CAL60934.1|

485,
D-amino acid
27377333
1.00E−167

Bradyrhizo-

P.
ADQ03060
1.00E−154
Human
ABN17150
2.00E−11
1.4.99.1
1269
422
0
421
67

486
dehydrogenase

bium

aeruginosa

ORFX

small subunit

japonicum

virulence

protein

[Herminiimonas

USDA 110
gene VIR14,

sequence

arsenicoxydans]

protein.

SEQ ID

D-amino acid

NO: 19716.

dehydrogenase

small subunit

[Bradyrhizobium

japonicum

USDA 110]

487
D-amino-acid
113871743
1.00E−129

Sinorhizo-

Glyphosate
AAR22262
1.00E−35
M.
ADI37347
3.7
1. . .
1263
420
0
417
53

488
dehydrogenase

bium

oxidoreductase

tuberculosis

[Sinorhizobium

medicae

gene

low oxygen

medicae

WSM419
downstream

induced

WSM419]

flanking

antigen

gi|113726415|gb|

region.

Rv0363c

EAU07507.1|

SEQ ID

D-amino-acid

NO: 4.

dehydrogenase

[Sinorhizobium

medicae

WSM419]

489,
D-amino-acid
115523700
1.00E−123

Rhodo-

Glyphosate
AAR22262
5.00E−49
Bacterial
ADS57628
0.91
1.4.99.1
1242
413
0
417
54

490
dehydrogenase

pseudomonas

oxidoreductase

polypeptide

[Rhodo-

paluslris
gene

#10001.

pseudomonas

BisA53
downstream

paluslris

flanking

BisA53]

region.

491,
D-amino-acid
114570652
1.00E−78

Maricaulis

P.
ADQ03060
5.00E−59
Prokaryotic
ACA26589
0.015
1.4.99.1
1290
429
0
427
41

492
dehydrogenase

maris

aeruginosa

essential gene

[Maricaulis

MCS10
virulence

#34740.

maris MCS10]

gene VIR14,

gi|114341114|gb|

protein.

ABI66394.1|

D-amino-acid

dehydrogenase

[Maricaulis

maris MCS10]

493,
D-amino acid
124009931
6.00E−90

Microscilla

C
AAG93079
2.00E−37
Plan full
ADO81756
0.063
1.4.99.1
1344
447
0
427
41

494
dehydrogenase

marina ATCC
glutamicum

length

small subunit,

23134
coding

insert

putative

sequence

polynucleotide

[Microscilla

fragment

seqid 4980.

marina ATCC

SEQ ID

23134]

NO: 1935.

gi|123984082|gb|

EAY24455.1|

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

495,
D-amino-acid
115523700
1.00E−112

Rhodo-
Glyphosate
AAR22262
2.00E−54
Plan full
ADO81304
0.92
1.4.99.1
1254
417
0
417
49

496
dehydrogenase

pseudomonas

oxidoreductase

length

[Rhodo-

palustris

gene

insert

pseudomonas

BisA53
downstream

polynucleotide

palustris

flanking

seqid 4980.

BisA53]

region.

497,
D-amino-acid
113871743
1.00E−129

Sinorhizo-

Glyphosate
AAR22262
1.00E−35
Drosophila
ABL27820
3.7
1. . .
1263
420
0
417
53

498
dehydrogenase

bium

oxidoreductase

melanogaster

[Sinorhizobium

medicae

gene

polypeptide

medicae

WSM419
downstream

SEQ ID

WSM419]

flanking

NO 24465.

gi|113726415|gb|

region.

EAU07507.1|

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

499,
D-amino-acid
115523700
1.00E−112

Rhodo-
Glyphosate
AAR22262
2.00E−36
Human
AAL04340
0.91
1.4.99.1
1245
414
0
417
49

500
dehydrogenase

pseudomonas

oxidoreductase

reproductive

[Rhodo-

palustris

gene

system related

pseudomonas

BisA53
downstream

antigen DNA

palustris

flanking

SEQ ID

BisA53]

region.

NO: 8114.

501,
delta-1-pyrroline-
68535524
1.00E−174

Coryne-

Coryne-

AAB79787
1.00E−170

Coryne-

AAF71906
0.11
1.5.1.12
2334
777
0
1158
48

502
5-carboxylate

bacterium

bacterium

bacterium

dehydrogenase

jeikeium

glutamicum

glutamicum

[Corynebacterium

K411]
MP

MP

jeikeium K411]

protein

protein

sequence

sequence

SEQ ID

SEQ ID

NO: 1148.

NO: 1148.

503,
D-amino acid
87309573
1.00E−129

Blasto-

C
AAG93079
8.00E−44
Bacterial
ADS59567
0.015
1.4.99.1
1263
420
0
416
49

504
dehydrogenase,

pirellula

glutamicum

polypeptide

small chain

marina DSM
coding

#10001.

[Blastopirellula

3645
sequence

marina DSM

fragment

3645]

SEQ ID

gi|87287337|gb|E

NO: 1935.

AQ79237.1|

D-amino acid

dehydrogenase,

small chain

[Blastopirellula

marina DSM

3645]

505,
D-amino acid
87309573
1.00E−127

Blasto-

P.
ADQ03060
2.00E−43

Propioni-

ACF64502
0.93
1.4.99.1
1266
421
0
416
50

506
dehydrogenase,

pirellula

aeruginosa

bacterium

small chain

marina DSM
virulence

acnes

[Blastopirellula

3645
gene VIR14,

predicted

marina DSM

protein.

ORF-encoded

3645]

polypeptide

gi|87287337|gb|E

#300.

AQ79237.1|

D-amino acid

dehydrogenase,

small chain

[Blastopirellula

marina DSM

3645]

507,
D-amino-acid
92118208
1.00E−174

Nitrobacter

Glyphosate
AAR22262
6.00E−55

M.

ACL63896
0.059
1.4.99.1
1254
417
0
433
71

508
dehydrogenase

hamburgensis

oxidoreductase

xanthus

[Nitrobacter

X14
gene

protein

hamburgensis

downstream

sequence,

X14]

flanking

seq id 9726.

region.

509,
D-amino-acid
86750758
1.00E−115

Rhodo-
Glyphosate
AAR22262
3.00E−53
Maize
ADP48960
3.6
1.4.99.1
1245
414
0
417
49

510
dehydrogenase

pseudomonas

oxidoreductase

carotenoid

[Rhodo-

palustris

gene

cleavage

pseudomonas

HaA2
downstream

dioxygenase

palustris

flanking

(CCD1)

HaA2]

region.

protein

SEQ ID

NO: 4.

511,
D-amino-acid
73541345
1.00E−166

Ralstonia

Glyphosate
AAR22262
1.00E−42

Klebsiella

ACH97397
0.015
1.4.99.1
1266
421
0
414
65

512
dehydrogenase

eutropha

oxidoreductase

pneumoniae

[Ralstonia

JMP134
gene

polypeptide

eutropha

downstream

seqid 7178.

JMP134]

flanking

region.

513
D-amino acid
134093986
0

Herminii-

P.
ADQ03060
4.00E−94
Prokaryotic
ACA35076
2.00E−04
1.4.99.1
1269
422
0
443
77

dehydrogenase

monas

aeruginosa

essential gene

small subunit

arsenico-

virulence

#34740.

[Herminiimonas

xydans

gene VIR14,

arsenicoxydans]

protein.

gi|133737889|em

b|CAL60934.1|

D-amino acid

dehydrogenase

small subunit

[Herminiimonas

arsenicoxydans]

515,
D-amino acid
146284421
1.00E−177

Pseudomonas

Acinetobacter
ADA36279
1.00E−124
Alpha1-
AEF51726
0.91
1.4.99.1
1242
413
0
419
74

516
dehydrogenase;

stutzeri

baumannii

antitrypsin

small subunit

A1501
protein

specific

[Pseudomonas

#19.

probe,

stutzeri A1501]

AATpro.

517,
D-amino acid
126646463
1.00E−110

Algoriphagus

Acinetobacter
ADA33588
5.00E−46
Human
ACA63029
0.058
1.4.99.1
1239
412
0
415
48

518
dehydrogenase

sp. PR1
baumannii

DICE-1-like

[Algoriphagus

protein

RNA

sp. PR1]

#19.

helicase.

gi|126578095|gb|

EA282315.1|

D-amino acid

dehydrogenase

[Algoriphagus

sp. PR1]

519,
D-amino acid
88712395
3.00E−98

Flavo-

N.
ABP80542
4.00E−45
PCR primer
AAX91990
0.015
1.4.99.1
1251
416
0
416
43

520
dehydrogenase

bacteriales

gonorrhoeae

used to

[Flavobacteriales

bacterium

nucleotide

amplify an

bacterium

HTCC2170
sequence SEQ

ORF of

HTCC2170]

ID 4691.

Chlamydia

gi|88708933|gb|E

pneumoniae.

AR01167.1]

D-amino acid

dehydrogenase

[Flavo-

bacteriales

bacterium

HTCC2170]

521,
D-amino-acid
111019145
0

Rhodococcus

C
AAG93079
1.00E−102
Ryegrass
ABK13581
0.015
1.4.99.1
1254
417
0
415
79

522
dehydrogenase

sp. RHA1
glutamicum

caffeic acid

small subunit

coding

O-methyl

[Rhodococcus

sequence

transferase

sp. RHA1]

fragment

(OMT)

SEQ ID

genomic

NO: 1935.

sequence #2.

523,
D-amino acid
126646463
7.00E−87

Algoriphagus

H. pylori
AAW98270
7.00E−48
Human
ACN44966
0.23
1.4.99.1
1245
414
0
415
40

524
dehydrogenase

sp. PR1
GHPO

protein

[Algoriphagus

1099 gene.

sequence

sp. PR1]

hCP39072.

gi|126578095|gb|

EAZ82315.1]

D-amino acid

dehydrogenase

[Algoriphagus

sp. PR1]

525,
D-amino-acid
121530396
1.00E−146

Ralstonia

Glyphosate
AAR22262
2.00E−45
PCR primer
AAA58472
0.91
1. . .
1242
413
0
416
61

526
dehydrogenase

pickettii 12J
oxidoreductase

used to

[Ralstonia

gene

amplify

pickettii 12J]

downstream

bleomycin

gi|121302471 |gb|

flanking

(BLM) gene

EAX43440.1|

region.

cluster ORF15.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

527,
putative
116250556
0

Rhizobium

Glyphosate
AAR22262
4.00E−47
Bacterial
ADS59863
0.058
1 . . .
1248
415
0
415
78

528
d-amino acid

legumino-

oxidoreductase

polypeptide

dehydrogenase

sarum

gene

#10001.

small subunit

bv. viciae

downstream

[Rhizobium

3841
flanking

leguminosarum

region.

bv. viciae 3841]

529,
D-amino-acid
92118208
1.00E−116

Nitrobacter

Glyphosate
AAR22262
7.00E−48
RT-PCR
ADZ14743
0.058
1.4.99.1
1245
414
0
433
53

530
dehydrogenase

hamburgensis

oxidoreductase

primer to

[Nitrobacter

X14
gene

amplify human

hamburgensis

downstream

tumor

X14]

flanking

associated

region.

antigen RNA

Seq 28.

531,
probable
149824671
1.00E−150

Limnobacter

P.
ADQ03060
1.00E−93

Pseudomonas

ABD17880
0.001
1.4.99.1
1257
418
0
429
59

532
D-amino acid

sp. MED105
aeruginosa

aeruginosa

dehydrogenase

virulence

polypeptide

subunit

gene VIR14,

#3.

[Limnobacter

protein.

sp. MED105]

533,
D-amino acid
88712395
3.00E−88

Flavo-

M.
ADL05210
5.00E−46
Prokaryotic
ACA35414
0.93
1.4.99.1
1269
422
0
416
40

534
dehydrogenase

bacteriales

catarrhalis

essential gene

[Flavobacteriales

bacterium

protein #1.

#34740.

bacterium

HTCC2170

HTCC2170]

gi|88708933|gb|E

AR01167.1]

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

535,
Aldehyde
73537548
1.00E−143

Ralstonia

Bacterial
ADN25785
1.00E−140
Bacterial
ADS55665
1.00E−12
1.2.1.
1581
526
0
525
52

536
dehydrogenase

eutropha

polypeptide

polypeptide

[Ralstonia

JMP134
#10001.

#10001.

eutropha

JMP134]

537,
D-amino-acid
73541345
1.00E−136

Ralstonia

Glyphosate
AAR22262
1.00E−47

Streptomyces

ABN88913
3.6
1.4.99.1
1260
419
0
414
57

538
dehydrogenase

eutropha

oxidoreductase

sp.

[Ralstonia

JMP134
gene

cytochrome

eutropha

downstream

P450

JMP134]

flanking

related PCR

region.

primer SEQ

ID NO: 18.

539,
D-amino-acid
115359189
0

Burkholderia

Glyphosate
AAR22262
3.00E−47

Pseudomonas

ABD17784
0.058
1.4.99.1
1242
413
0
413
96

540
dehydrogenase

cepacia

oxidoreductase

aeruginosa

[Burkholderia

AMMD
gene

polypeptide

cepacia

downstream

#3.

AMMD]

flanking

region.

541,
D-amino acid
21243478
1.00E−139

Xanthomonas

P.
ADQ03060
3.00E−40
M.
ABQ90794
0.059
1.4.99.1
1266
421
1251
416
57

542
dehydrogenase

axonopodis

aeruginosa

capsulatus

subunit

pv. citri str.
virulence

gene #766

[Xanthomonas

306
gene VIR14,

for DNA

axonopodis pv.

protein.

array.

citri str. 306].

543,
D-amino acid
124009931
1.00E−107

Microscilla

H. pylori
AAW98270
3.00E−50
lactic acid
ADF77343
3.6
1.4.99.1
1248
415
0
427
45

544
dehydrogenase

marina ATCC
GHPO

bacteria

small subunit,

23134
1099 gene.

lactobacillus

putative

johnsonii

[Microscilla

La1

marina ATCC

genomic

23134]

DNA

gi|123984082|gb|

SEQ ID

EAY24455.1|

NO: 1.

D-amino acid

dehydrogenase

small subunit,

putative

[Microscilla

marina ATCC

23134]

545,
D-amino-acid
86750758
1.00E−117

Rhodo-
Glyphosate
AAR22262
7.00E−51

Arabidopsis

AAC41739
0.24
1.4.99.1
1296
431
0
417
50

546
dehydrogenase

pseudomonas

oxidoreductase

thaliana

[Rhodo-

palustris
gene

protein

pseudomonas

HaA2
downstream

fragment

palustris

flanking

SEQ ID

HaA2]

region.

NO: 76191.

547,
D-amino acid
88712395
3.00E−86

Flavo-

Photor-
ABM69115
5.00E−53
Bacterial
ADS50144
0.93
1.4.99.1
1266
421
0
416
39

548
dehydrogenase

bacteriales

habdus

polypeptide

[Flavobacteriales

bacterium

luminescens

#10001.

bacterium

HTCC2170
protein

HTCC2170]

sequence

gi|88708933|gb|E

#59.

AR01167.1]

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

549,
probable
149824671
1.00E−146

Limnobacter

P.
ADQ03060
9.00E−96
Human
AAL13181
2.00E−04
1.4.99.1
1254
417
0
429
59

550
D-aminoacid

sp. MED105
aeruginosa

breast

dehydrogenase

virulence

cancer

subunit

gene VIR14,

expressed

[Limnobacter

protein.

polynucleotide

sp. MED105]

8440.

551,
delta-1-pyrroline-
68535524
0

Coryne-

Coryne-

AAB79787
0

Propioni-

ACF64460
0.003
1.5.1.12
3306
1101
0
1158
49

552
5-carboxylate

bacterium

bacterium

bacterium

dehydrogenase

jeikeium

glutamicum

acnes

[Coryne-

K411
MP

predicted

bacterium

protein

ORF-encoded

jeikeium K411]

sequence

polypeptide

SEQ ID

#300.

NO: 1148.

553,
D-amino-acid
115523700
1.00E−112

Rhodo-
Glyphosate
AAR22262
1.00E−53
Plan full
ADO81304
0.92
1.4.99.1
1254
417
0
417
49

554
dehydrogenase

pseudomonas

oxidoreductase

length

[Rhodo-

palustris

gene

insert

pseudomonas

BisA53
downstream

polynucleotide

palustris

flanking

seqid 4980.

BisA53]

region.

555,
D-amino-acid
92118208
1.00E−118

Nitrobacter

Glyphosate
AAR22262
2.00E−49
RT-PCR
ADZ14743
0.058
1.4.99.1
1242
413
0
433
53

556
dehydrogenase

hamburgensis

oxidoreductase

primer to

[Nitrobacter

X14
gene

amplify

hamburgensis

downstream

human tumor

X14]

flanking

associated

region.

antigen RNA

Seq 28.

557,
D-amino-acid
113871743
1.00E−132

Sinorhizo-

Glyphosate
AAR22262
5.00E−41
Human
ACN44650
0.23
1. . .
1260
419
0
417
55

558
dehydrogenase

bium

oxidoreductase

protein

[Sinorhizobium

medicae

gene

sequence

medicae

WSM419
downstream

hCP39072.

WSM419]

flanking

gi|113726415|gb|

region.

EAU07507.1|

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

559,
D-amino-acid
113871743
1.00E−132

Sinorhizo-

Glyphosate
AAR22262
5.00E−41
Human
ACN44650
0.23
1. . .
1260
419
0
417
55

560
dehydrogenase

bium

oxidoreductase

protein

[Sinorhizobium

medicae

gene

sequence

medicae

WSM419
downstream

hCP39072.

WSM419]

flanking

gi|113726415|gb|

region.

EAU07507.1|

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

561,
NADH
21244546
1.00E−143

Xanthomonas

M.

ABM91806
1.00E−115

M.

ACL64800
2.00E−05
1.6.99.3
1230
409
1293
430
62
69

562
dehydrogenase

axonopodis

xanthus

xanthus

[Xanthomonas

pv.
protein

protein

axonopodis pv.

citri str. 306
sequence,

sequence,

citri str. 306].

seq id

seq id 9726.

9726.

563,
short chain
73541108
3.00E−66

Ralstonia

M.

ABM96904
1.00E−53
Cenar-
AAA55186
5.00E−04
1.1.1.100
720
239
0
270
56

564
dehydrogenase

eutropha

xanthus

chaeum

[Ralstonia

JMP134
protein

symbiosum

eutropha

sequence,

open

JMP134]

seq id

reading

9726.

frame protein

sequence

SEQ

ID NO: 80.

565,
D-amino-acid
115523700
1.00E−112

Rhodo-
Glyphosate
AAR22262
2.00E−54
Plan full
ADO81304
0.92
1.4.99.1
1254
417
0
417
49

566
dehydrogenase

pseudomonas

oxidoreductase

length

[Rhodo-

palustris

gene

insert

pseudomonas

BisA53
downstream

polynucleotide

palustris

flanking

seqid 4980.

BisA53]

region.

567,
D-amino-acid
120608839
0

Acidovorax

P.
ADQ03060
2.00E−91

Klebsiella

ACH97385
0.016
1.4.99.1
1344
447
0
444
69

568
dehydrogenase

avenae subsp.
aeruginosa

pneumoniae

[Acidovorax

citrulli

virulence

polypeptide

avenae subsp.

AAC00-1
gene VIR14,

seqid 7178.

citrulli AAC00-1]

protein.

gi|120587303|gb|

ABM30743.1|

D-amino-acid

dehydrogenase

[Acidovorax

avenae subsp.

citrulli

AAC00-1]

569,
D-amino-acid
114570652
8.00E−91

Maricaulis

P.
ADQ03060
9.00E−80
Lung
ABX92073
0.92
1.4.99.1
1260
419
0
427
42

570
dehydrogenase

maris

aeruginosa

specific

[Maricaulis

MCS10
virulence

protein (LSP)

maris MCS10]

gene VIR14,

#21.

gi|114341114|gb|

protein.

ABI66394.1|

D-amino-acid

dehydrogenase

[Maricaulis

maris MCS10]

571,
AGR_L_3050p
15891640
1.00E−180

Agro-

P.
ADQ03060
1.00E−141

Klebsiella

ABD01189
3.00E−13
1.4.99.1
1248
415
1257
418
76
74

572
[Agrobacterium

bacterium

aeruginosa

pneumoniae

tumefaciens].

tumefaciens

virulence

polypeptide

gene VIR14,

seqid 7178.

protein.

573,
D-amino acid
88806240
5.00E−85

Robiginitalea

Enterobacter
AEH60497
2.00E−47
Prokaryotic
ACA26568
0.059
1.4.99.1
1263
420
0
417
39

574
dehydrogenase

biformala

cloacae

essential gene

[Robiginitalea

HTCC2501
protein

#34740.

biformala

amino acid

HTCC2501]

sequence -

gi|88783849|gb|E

SEQ ID 5666.

AR15020.1|

D-amino acid

dehydrogenase

[Robiginitalea

biformata

HTCC2501]

575,
Aldehyde
72384235
1.00E−141

Ralstonia

Bacterial
ADN22241
1.00E−133
Bacterial
ADS56451
2.00E−08
1.2.1
1584
527
0
530
53

576
dehydrogenase

eutropha

polypeptide

polypeptide

[Ralstonia

JMP134
#10001.

#10001.

eutropha

JMP134]

577,
putative
116250556
1.00E−166

Rhizobium

Glyphosate
AAR22262
8.00E−44

M.

ACL64632
0.91
1. . .
1242
413
0
415
67

578
d-amino acid

legumino-

oxidoreductase

xanthus

dehydrogenase

sarum

gene

protein

small subunit

bv. viciae

downstream

sequence,

[Rhizobium

3841
flanking

seq id

leguminosarum

region.

9726.

bv. viciae 3841]

579,
D-amino-acid
86361166
0

Rhizobium

P.
ADQ03060
1.00E−143

Rhizobium

AAV30459
7.00E−51
1.4.99.1
1254
417
0
422
83

580
dehydrogenase;

etli

aeruginosa

species

small subunit

CFN 42
virulence

symbolic

protein

gene VIR14,

plasmid

[Rhizobiumetli

protein.

pNGR234.

CFN 42]

581,
D-amino-acid
73541345
1.00E−136

Ralstonia

Glyphosate
AAR22262
4.00E−47
Thalecress
AEG64174
0.92
1.4.99.1
1260
419
0
414
57

582
dehydrogenase

autropha

oxidoreductase

stress

[Ralstonia

JMP134
gene

related

autropha

downstream

protein SEQ

JMP134]

flanking

ID NO: 80.

region.

583,
D-amino-acid
91779297
0

Burkholderia

Glyphosate
AAR22262
9.00E−48

Pseudomonas

ABD13052
3.6
1.4.99.1
1233
410
0
410
83

584
dehydrogenase

xenovorans

oxidoreductase

aeruginosa

[Burkholderia

LB400
gene

polypeptide

xenovorans

downstream

#3.

LB400]

flanking

region.

585,
D-amino-acid
121603011
0

Polaromonas

Photor-
ABM69115
3.00E−85

Klebsiella

ABD01189
3.00E−04
1.4.99.1
1338
445
0
455
81

586
dehydrogenase

naphthalen-
habdus

pneumoniae

[Polaromonas

ivorans CJ2
luminescens

polypeptide

naphthalen-

protein

seqid 7178.

ivorans CJ2]

sequence #59

587,
D-amino acid
104781752
1.00E−139

Pseudomonas

Glyphosate
AAR22262
3.00E−50
Drosophila
ABL10910
0.24
1.4.99.1
1290
429
0
414
57

588
dehydrogenase;

entomophila

oxidoreductase

melanogaster

small subunit

L48
gene

polypeptide

family protein

downstream

SEQ ID

[Pseudomonas

flanking

NO 24465.

entomophila

region.

L48]

589,
D-amino-acid
111019145
1.00E−166

Rhodococcus

C
AAG93079
1.00E−103

M.

ACL64760
0.92
1.4.99.1
1254
417
0
415
78

590
dehydrogenase

sp. RHA1
glutamicum

xanthus

small subunit

coding

protein

[Rhodococcus

sequence

sequence,

sp. RHA1]

fragment

seq id 9726.

SEQ ID

NO: 1935.

591,
D-amino-acid
113871743
1.00E−145

Sinorhizo-

Glyphosate
AAR22262
9.00E−50
Plan full
ADX35599
0.015
1. . .
1245
414
0
417
59

592
dehydrogenase

bium

oxidoreductase

length

[Sinorhizobium

medicae

gene

insert

medicae

WSM419
downstream

polynucleotide

WSM419]

flanking

seqid 4980.

gi|113726415|gb|

region.

EAU07507.1]

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

593,
D-amino-acid
86750758
1.00E−118

Rhodo-
Glyphosate
AAR22262
4.00E−56
Prokaryotic
ACA26173
0.015
1.4.99.1
1272
423
0
417
50

594
dehydrogenase

pseudomonas

oxidoreductase

essential gene

[Rhodo-

palustris

gene

#34740.

pseudomonas

HaA2
downstream

palustris

flanking

HaA2]

region.

595,
D-amino-acid
92118208
0

Nitrobacter

Glyphosate
AAR22262
5.00E−56
Bacterial
ADS55748
0.015
1.4.99.1
1257
418
0
433
73

596
dehydrogenase

hamburgensis

oxidoreductase

polypeptide

[Nitrobacter

X14
gene

#10001.

hamburgensis

downstream

X14]

flanking

region.

597,
D-amino acid
34497369
0

Chromo-
P.
ADQ03060
1.00E−166
Enterobacter
AEH53102
3.00E−19
1.4.99.1
1317
438
0
435
71

598
dehydrogenase

bacterium

aeruginosa

cloacae

small subunit

violaceum

virulence

protein

[Chromo-

ATCC
gene VIR14,

amino acid

bacterium

12472
protein.

sequence -

violaceum

SEQ ID 5666.

ATCC 12472]

599,
D-amino-acid
86361166
0

Rhizobium

P.
ADQ03060
1.00E−145

Rhizobium

AAV30459
1.00E−61
1.4.99.1
1251
416
0
422
84

600
dehydrogenase;

etli

aeruginosa

species

small subunit

CFN 42
virulence

symbiotic

protein

gene VIR14,

plasmid

[Rhizobium etli

protein.

pNGR234.

CFN 42]

601,
D-amino-acid
86361166
0

Rhizobium

P.
ADQ03060
1.00E−145

Rhizobium

AAV30459
2.00E−60
1.4.99.1
1254
417
0
422
81

602
dehydrogenase;

etli CFN 42
aeruginosa

species

small subunit

virulence

symbiotic

protein

gene VIR14,

plasmid

[Rhizobium

protein.

pNGR234.

etl
iCFN 42]

603,
D-amino acid
88712395
2.00E−93

Flavo-

M.
ADL05210
2.00E−54
Corn ear-
ABX86147
0.23
1.4.99.1
1254
417
0
416
42

604
dehydrogenase

bacteriales

catarrhalis

derived

[Flavobacteriales

bacterium

protein #1.

polynucleotide

bacterium

HTCC2170

(cpd)

HTCC2170]

#5394.

gi|88708933|gb|E

AR01167.1|

D-amino acid

dehydrogenase

[Flavobacteriales

bacterium

HTCC2170]

605,
D-amino-acid
113871743
1.00E−170

Sinorhizo-

Glyphosate
AAR22262
2.00E−48
Bacterial
ADS56578
0.92
1. . .
1254
417
0
417
67

606
dehydrogenase

bium

oxidoreductase

polypeptide

[Sinorhizobium

medicae

gene

#10001.

medicae

WSM419
downstream

WSM419]

flanking

gi|113726415|gb|

region.

EAU07507.1]

D-amino-acid

dehydrogenase

[Sinorhizobium

medicae

WSM419]

607,
probable
149824671
1.00E−125

Limnobacter

P.
ADQ03060
1.00E−94
Insulin
ADZ49334
0.91
1.4.99.1
1251
416
0
429
51

608
D-amino acid

sp. MED105
aeruginosa

signaling

dehydrogenase

virulence

pathway

subunit

gene VIR14,

related

[Limnobacter

protein.

PCR primer,

sp. MED105]

SEQ ID 22.

609,
D-amino-acid
121530396
1.00E−146

Ralstonia

Glyphosate
AAR22262
1.00E−45
Plant
ADT18820
0.004
1. . .
1233
410
0
416
61

610
dehydrogenase

pickettii 12J
oxidoreductase

polypeptide,

[Ralstonia

gene

SEQ ID 5546.

pickettii 12J]

downstream

gi|121302471|gb|

flanking

EAX43440.1|

region.

D-amino-acid

dehydrogenase

[Ralstonia

pickettii 12J]

611,
D-amino-acid
86361166
0

Rhizobium

P.
ADQ03060
1.00E−143

Rhizobium

AAV30459
7.00E−51
1.4.99.1
1254
417
0
422
83

612
dehydrogenase;

etli

aeruginosa

species

small subunit

CFN 42
virulence

symbiotic

protein

gene VIR14,

plasmid

[Rhizobium etli

protein.

pNGR234.

CFN 42]

613,
D-amino acid
149377918
3.00E−98

Marinobacter

N.
ABP80542
3.00E−77

Arabidopsis

ABQ66079
0.24
1.4.99.1
1287
428
0
423
43

614
dehydrogenase

algicola

gonorrhoeae

thaliana

small subunit

DG893
nucleotide

protein

[Marinobacter

sequence SEQ

fragment

algicola

ID 4691.

SEQ ID

DG893]

NO: 76191.

615,
putative
116250556
0

Rhizobium

Glyphosate
AAR22262
3.00E−47

M.

ACL64301
0.91
1. . .
1248
415
0
415
79

616
d-amino acid

legumino-

oxidoreductase

xanthus

dehydrogenase

sarum

gene

protein

small subunit

bv. viciae

downstream

sequence,

[Rhizobium

3841
flanking

seq id 9726.

leguminosarum

region.

bv. viciae 3841]

617,
D-amino-acid
86750758
1.00E−113

Rhodo-
Glyphosate
AAR22262
1.00E−49
Plan full
ADX64511
0.015
1.4.99.1
1245
414
0
417
49

618
dehydrogenase

pseudomonas

oxidoreductase

length

[Rhodo-

palustris

gene

insert

pseudomonas

HaA2
downstream

polynucleotide

palustris

flanking

seqid 4980.

HaA2]

region.

619,
aldehyde
118027543
1.00E−144

Burkholderia

Bacterial
ADN25785
1.00E−131
Bacterial
ADS55665
1.00E−12
1.2.1.39
1593
530
0
526
51

620
dehydrogenase

phymatum

polypeptide

polypeptide

[Burkholderia

STM815
#10001.

#10001.

phymatum

STM815]

gi|117986837|gb|

EAV01212.1|

aldehyde

dehydrogenase

[Burkholderia

phymatum

STM815]

621,
D-amino acid
88712395
1.00E−92

Flavo-

Pseudomonas

ABO75104
1.00E−48

Bifido-

ABQ81842
0.059
1.4.99.1
1266
421
0
416
42

622
dehydrogenase

bacteriales

aeruginosa

bacterium

[Flavobacteriales

bacterium

polypeptide

longum

bacterium

HTCC2170
#3.

NCC2705

HTCC2170]

ORF amino

gi|88708933|gb|E

acid

AR01167.1|

sequence

D-amino acid

SEQ ID

dehydrogenase

NO: 408.

[Flavobacteriales

bacterium

HTCC2170]

623,
D-amino acid
77465126
1.00E−121

Rhodobacter

Photorhabdus

ABM69115
1.00E−111

Pseudomonas

ABD08815
3.00E−07
1.4.99.1
1260
419
0
436
55

624
dehydrogenase

sphaeroides

luminescens

aeruginosa

small subunit

2.4.1
protein

polypeptide

[Rhodobacter

sequence #59

#3.

sphaeroides

2.4.1]

625,
D-amino-acid
148553731
0

Sphingomonas

P.
ADQ03060
1.00E−143
P.
ADQ03059
4.00E−09
1.4.99.1
1254
417
0
416
79

626
dehydrogenase

wittichii

aeruginosa

aeruginosa

[Sphingomonas

RW1
virulence

virulence

wittichii RW1]

gene VIR14,

gene VIR14,

protein.

protein.

627,
probable
149824671
1.00E−151

Limnobacter

P.
ADQ03060
2.00E−93
P.
ADQ03059
0.059
1257
418
0
429
60

628
D-amino acid

sp.
aeruginosa

aeruginosa

dehydrogenase

MED105
virulence

virulence

subunit

gene VIR14,

gene VIR14,

[Limnobacter

protein.

protein.

sp. MED105]

629,
putative
39725441
5.00E−63

Streptomyces

Streptomyces

ADQ74690
1.00E−63

Streptomyces

ADQ74672
0.17
1. . .
921
306
74787
305

630
dehydrogenase

parvulus

parvulus

parvulus

[Streptomyces

borrelidin

borrelidin

parvulus]

polyketide

polyketide

synthase

synthase

orfB8

orfB8

protein.

protein.

631,
FAD dependent
118037424
0

Burkholderia

Glyphosate
AAR22262
3.00E−49
Rice
ACL30152
0.015
1.4.99.1
1233
410
0
465
86

632
oxidoreductase

phytofirmans

oxidoreductase

abiotic

[Burkholderia

PsJN]
gene

stress

phytofirmans

downstream

responsive

PsJN]

flanking

polypeptide

gi|117992233|gb|

region.

SEQ ID

EAV06525.1|

NO: 4152.

FAD

dependent

oxidoreductase

[Burkholderia

phytofirmans

PsJN]

633,
FAD dependent
118734342
0

Delftia

Acinetobacter

ADA33588
1.00E−174

Pseudomonas

ABD08815
8.00E−23
1.4.99.1
1293
430
0
432
74

634
oxidoreductase

acidovorans

baumannii

aeruginosa

[Delftia

SPH-1
protein

polypeptide

acidovorans

#19.

#3.

SPH-1]

gi|118665742|gb|

EAV72348.1|

FAD

dependent

oxidoreductase

[Delftia

acidovorans

SPH-1]

635,
FAD dependent
118734342
0

Delftia

Acinetobacter

ADA33588
1.00E−175

Pseudomonas

ABD08815
2.00E−32
1.4.99.1
1296
431
0
432
76

636
oxidoreductase

acidovorans

baumannii

aeruginosa

[Delftia

SPH-1
protein

polypeptide

acidovorans

#19.

#3.

SPH-1]

gi|118665742|gb|

EAV72348.1|

FAD dependent

oxidoreductase

[Delftia

acidovorans

SPH-1]
77457196
0

Pseudomonas

Pseudomonas

ABO71517
1.00E−151

Pseudomonas

ABD05088
2.00E−66
1.1.99.
1128
375
0
375
87

637,
FAD dependent

fluorescens

aeruginosa

aeruginosa

638
oxidoreductase

PfO-1
polypeptide

polypeptide

[Pseudomonas

#3.

#3.

fluorescens

PfO-1]

639,
oxidoreductase-
118061388
4.00E−72

Roseiflexus

Hyper-
ADM25642
2.00E−38
Prokaryotic
ACA27410
0.18
1.1.1.
1002
333
0
345
44

640
like

castenholzii

thermophile

essential gene

[Roseiflexus

DSM 13941
Methano-

#34740.

castenholzii

pyrus

DSM 13941]

kandleri

gi|118014488|gb|

protein #28.

EAV28464.1|

oxidoreductase-

like

[Roseiflexus

castenholzii

DSM 13941]

641,
FAD dependent
77457196
0

Pseudomonas

Pseudomonas

ABO71517
1.00E−151

Pseudomonas

ADB05088
2.00E−66
1.1.99.1
1128
375
0
375
87

642
oxidoreductase

fluorescens

aeruginosa

aeruginosa

[Pseudomonas

PfO-1
polypeptide

polypeptide

fluorescens

#3.

#3.

PfO-1]

643,
Glycine/D-amino
83311898
4.00E−86

Magneto-

Pseudomonas

ABO75104
8.00E−78
Human
ABN17150
0.059
1.4.99.1
1266
421
0
422
42

644
acid oxidase

spirillum

aeruginosa

ORFX

[Magneto-

magneticum

polypeptide

protein

spirillum

AMB-1
#3.

sequence

magneticum

SEQ ID

AMB-1]

NO: 19716.

645,
FAD dependent
92113847
1.00E−151

Chromo-
Glyphosate
AAR22262
2.00E−40

Silibacter

AEM45684
0.23
1. . .
1245
414
0
414
62

646
oxidoreductase

halobacter

oxidoreductase

sp. TM1040

[Chromo-

salexigens

gene

gene SEQ

halobacter

DSM 3043
downstream

ID NO: 3.

salexigens DSM

flanking

3043]

region.

647,
FAD dependent
118029195
1.00E−165

Burkholderia

Enterobacter
AEH60497
1.00E−150

Pseudomonas

ABD08815
2.00E−06
1.4.99.1
1296
431
0
428
65

648
oxidoreductase

phymatum

cloacae

aeruginosa

[Burkholderia

STM815
protein

polypeptide

phymatum

amino acid

#3.

STM815]

sequence -

gi|117985258|gb|

SEQ ID 5666.

EAU99635.1|

FAD dependent

oxidoreductase

[Burkholderia

phymatum

STM815]

649,
FAD dependent
92113847
1.00E−146

Chromo-
Glyphosate
AAR22262
4.00E−43

Pseudomonas

ABD05284
0.058
1.4.99.1
1245
414
0
414
61

650
oxidoreductase

halobacter

oxidoreductase

aeruginosa

[Chromo-

salexigens

gene

polypeptide

halobacter

DSM 3043
downstream

#3.

salexigens DSM

flanking

3043]

region.

651,
putative
27379412
1.00E−122

Bradyrhizo-

Glyphosate
AAR22262
1.00E−42
Prokaryotic
ACA27392
0.058
1.4.99.1
1236
411
0
410
53

652
oxidoreductase

bium

oxidoreductase

essential gene

protein

japonicum

gene

#34740.

[Bradyrhizobium

USDA 110
downstream

japonicum

flanking

USDA 110]

region.

653,
reductase
66767863
1.00E−128

Xanthomonas

Prokaryotic
ABU14721
1.00E−119
Prokaryotic
ACA36215
1.00E−15
1.8.1.7
1344
447
0
456
55

654
[Xanthomonas

campestris

essential gene

essential gene

campestris pv.

pv.
#34740.

#34740.

campestris str.

campestris

8004]

str.

8004

655,
FAD dependent
75676467
1.00E−118

Nitrobacter

Glyphosate
AAR22262
5.00E−53
G sorghi
ACF04822
0.94
1.4.99.1
1284
427
0
417
48

656
oxidoreductase

winogradskyi

oxidoreductase

nitrilase

[Nitrobacter

Nb-255
gene

protein

winogradskyi

downstream

fragment #2.

Nb-255]

flanking

region.

657,
D-aspartate
115376852
3.00E−85

Stigmatella

Human
AED18771
6.00E−59
M.
AAD55815
2.9
1.4.3.3
1008
335
0
314
45

658
oxidase

aurantiaca

D-aspartate

carbonacea

[Stigmatella

DW4/3-1
oxidase

polyketide

aurantiaca

active site.

synthase

DW4/3-1]

(PKS)

gi|115366155|gb|

domain

EAU65167.1|

peptide #3.

D-aspartate

oxidase

[Stigmatella

aurantiaca

DW4/3-1]

659,
FAD dependent
71909453
1.00E−142

Dechloro-

P.
ADQ03060
6.00E−97
Human
AAL13181
0.001
1.4.99.1
1245
414
0
418
62

660
oxidoreductase

monas

aeruginosa

brest cancer

[Dechloromonas

aromatica

virulence

expressed

aromatica RCB]

RCB
gene VIR14,

polynucleotide

protein.

8440.

661,
putative secreted
78049397
1.00E−102

Xanthomonas

Human
AED18771
4.00E−07
Plant
ADJ40271
0.056

1188
395
0
404
50

662
protein

campestris

D-aspartate

cDNA #31.

[Xanthomonas

pv.
oxidase

campestris pv.

vesicatoria

active site.

vesicatoria str.

str.

85-10]

85-10

663,
FAD dependent
75676467
1.00E−120

Nitrobacter

Glyphosate
AAR22262
6.00E−52
Plant full
ADX45957
0.058
1.4.99.1
1245
414
0
417
52

664
oxidoreductase

winogradskyi

oxidoreductase

length insert

[Nitrobacter

Nb-255
gene

polynucleotide

winogradskyi

downstream

seqid 4980.

Nb-255]

flanking

region.

665,
Glycine/D-amino
88810939
5.00E−83

Nitrococcus

M.
ADL05210
6.00E−71
Aspergillus
ABT17713
0.92
1.4.99.1
1263
420
0
423
41

666
acid oxidase

mobilis

catarrhalis

fumigatus

[Nitrococcus

Nb-231
protein #1.

essential

mobilis Nb-231]

gene

gi|88791478|gb|E

protein #821.

AR22589.1|

Glycine/D-amino

acid oxidase

[Nitrococcus

mobilis Nb-231]

667,
FAD dependent
116624522
5.00E−82

Solibacter

Human
AED18771
5.00E−17
DNA
AAS83512
0.81
1.4.3.1
1113
370
0
377
45

668
oxidoreductase

usitatus

D-aspartate

encoding

[Solibacter

Ellin6076
oxidase

nove human

usitatus

active site.

diagnostic

Ellin6076]

protein

gi|116227684|gb|

#20574.

ABJ86393.1|

FAD dependent

oxidoreductase

[Solibacter

usitatus

Ellin6076]

669,
FAD dependent
75676467
1.00E−122

Nitrobacter

Glyphosate
AAR22262
2.00E−46
A.
AAV21187
0.92
1.4.99.1
1260
419
0
417
52

670
oxidoreductase

winogradskyi

oxidoreductase

mediterranei-

[Nitrobacter

Nb-255
gene

rifamycin

winogradskyi

downstream

synthesis

Nb-255]

flanking

gene cluster

region.

fragment

protein F.

671,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46
Oligo-
ABQ19293
3.6
1.4.99.1
1242
413
0
413
82

672
oxidoreductase

phytofirmans

oxidoreductase

nucleotide for

[Burkholderia

PsJN
gene

detecting

phytofirmans

downstream

cytosine

PsJN]

flanking

methylation

gi|117991720|gb|

region.

SEQ ID

EAV06013.1|

NO 20311.

FAD dependent

oxidoreductase

[Burkholderia

phytofirmans

PsJN]

673,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
1.00E−45
Oligo-
ABQ19293
3.6
1.4.99.1
1242
413
0
413
82

674
oxidoreductase

phytofirmans

oxidoreductase

nucleotide for

[Burkholderia

PsJN
gene

detecting

phytofirmans

downstream

cytosine

PsJN]

flanking

methylation

gi|117991720|gb|

region.

SEQ ID

EAV06013.1| FAD

NO 20311.

dependent

oxidoreductase

[Burkholderia

phytofirmans

PsJN]

675,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
1.00E−45
Oligo-
ABQ19293
3.6
1.4.99.1
1242
413
0
413
82

676
oxidoreductase

phytofirmans

oxidoreductase

nucleotide for

[Burkholderia

PsJN
gene

detecting

phytofirmans

downstream

cytosine

PsJN]

flanking

methylation

gi|117991720|gb|

region.

SEQ ID

EAV06013.1|

NO 20311.

FAD dependent

oxidoreductase

[Burkholderia

phytofirmans

PsJN]

677,
D-amino-acid
119716015
2.00E−51

Nocardioides

Human
AED18771
4.00E−36
Prokaryotic
ACA45556
3.6
1.4.3.3
909
302
0
310
42

678
oxidase

sp. JS614
D-aspartate

essential gene

[Nocardioides

oxidase

#34740.

sp. JS614]

active site.

gi|119536676|gb|

ABL81293.11

D-amino-acid

oxidase

[Nocardioides

sp. JS614]

679,
FAD dependent
118731339
0

Delftia

Pseudomonas

ABO71517
1.00E−102

Pseudomonas

ABD04986
4.00E−09
1.1.99.
1161
386
0
385
83

680
oxidoreductase

acidovorans

aeruginosa

aeruginosa

[Delftia

SPH-1
polypeptide

polypeptide

acidovorans

#3.

#3.

SPH-1]

gi|118668198|gb|

EAV74793.11

FAD dependent

oxidoreductase

[Delftia

acidovorans

SPH-1]

681,
Glycine/D-amino
88810939
5.00E−94

Nitrococcus

Pseudomonas

ADQ03060
5.00E−85
N
ADC76718
0.93
1.4.99.1
1266
421
0
423
43

682
acid oxidase

mobilis

aeruginosa

benthamiana

[Nitrococcus

Nb-231
polypeptide

phytopathogen

mobilis Nb-231]

#3.

resistance-

gi|88791478|gb|E

related

AR22589.1|

contig

Glycine/D-amin

cDNA -

acid oxidase

SEQ ID 5.

[Nitrococcus

mobilis Nb-231]

683,
FAD dependent
114319576
2.00E−86

Alkalilimni-

Pseudomonas

ABO75104
2.00E−77
C.
AAF71130
0.059
1.4.99.1
1251
416
0
421
42

684
oxidoreductase

cola

aeruginosa

glutamicum

[Alkalilimnicola

ehrlichei

polypeptide

SRT protein

ehrlichei

MLHE-1
#3.

sequence

MLHE-1]

SEQ ID

NO: 264.

685,
FAD dependent
114319576
5.00E−86

Alkalilimni-

M.
ADL05210
3.00E−63
Human
ABT07579
0.06
1.4.99.1
1281
426
0
421
40

686
oxidoreductase

cola

catarrhalis

breast cancer

[Alkalilimnicola

ehrlichei

protein #1.

associated

ehrlichei

MLHE-1

coding

MLHE-1]

sequence

SEQ ID

NO: 79.

687,
D-aspartate
115376852
2.00E−71

Stigmatella

Human
AED18771
2.00E−51
Bacterial
ADS56436
0.044
1.4.3.3
957
318
0
314
44

688
oxidase

aurantiaca

D-aspartate

polypeptide

[Stigmatella

DW4/3-1
oxidase

#10001.

aurantiaca

active site.

DW4/3-1]

gi|115366155|gb|

EAU65167.1|

D-aspartate

oxidase

[Stigmatella

aurantiaca

DW4/3-1]

699,
FAD dependent
118716641
1.00E−154

Burkholderia

Glyphosate
AAR22262
5.00E−53
Plant full
ADX50476
0.23
1.4.99.1
1248
415
0
548
64

690
oxidoreductase

multivorans

oxidoreductase

length insert

[Burkholderia

ATCC
gene

poly-

multivorans

17616
downstream

nucleotide

ATCC 17616]

flanking

seqid 4980.

gi|118660081 |gb|

region.

EAV66824.1|

FAD dependent

oxidoreductase

[Burkholderia

multivorans

ATCC 17616]

691,
FAD dependent
94314499
1.00E−159

Ralstonia

Acinetobacter

ADA36279
1.00E−128
N.
AAA81470
0.058
1.4.99.1
1239
412
0
422
66

692
oxidoreductase

metallidurans

baumannii

meningitides

[Ralstonia

CH34
protein

partial DNA

metallidurans

#19.

sequence

CH34]

gnm_640

SEQ ID

NO: 640.

693,
NADH:
110634071
9.00E−58

Mesorhizo-

Drosophila
ABB59730
3.00E−09
Prokaryotic
ACA34135
3.9
1.6.99.3
396
131
0
132
73

694
ubiquinone

bium
sp.
melanogaster

essential gene

oxidoreductase

BNC1
polypeptide

#34740.

17.2 kD subunit

SEQ ID

[Mesorhizobium

NO 24465.

sp. BNC1]

695,
FAD dependent
116695075
1.00E−141

Ralstonia

Pseudomonas

ABO71517
1.00E−121

Pseudomonas

ABD05088
1.00E−12
1.1.99.
1164
387
0
388
63

696
oxidoreductase

eutropha

aeruginosa

aeruginosa

[Ralstonia

H16
polypeptide

polypeptide

eutropha H16]

#3.

#3.

697,
Glycine/D-amino
83311898
1.00E−103

Magnet-

P.
ADQ03060
2.00E−50
Bacterial
ADT43170
0.001
1.4.99.1
1257
418
0
422
47

698
acid oxidase

ospirillum

aeruginosa

polypeptide

[Magnet-

magneticum

virulence

#10001.

ospirillum

AMB-1
gene VIR14,

magneticum

protein.

AMB-1]

699,
FAD dependent
75676467
1.00E−119

Nitrobacter

Glyphosate
AAR22262
1.00E−41
Prokaryotic
ACA26065
0.015
1.4.99.1
1245
414
0
417
52

700
oxidoreductase

winogradskyi

oxidoreductase

essential gene

[Nitrobacter

Nb-255
gene

#34740.

winogradskyi

downstream

Nb-255]

flanking

region.

701,
D-aspartate
115376852
8.00E−51

Stigmatella

Human
AED18771
6.00E−44
Drosophila
ABL13112
0.18
1.4.3.3
981
326
0
314
39

702
oxidase

aurantiaca

D-aspartate

melanogaster

[Stigmatella

DW4/3-1
oxidase

polypeptide

aurantiaca

active site.

SEQ ID

DW4/3-1]

NO 24465.

gi|115366155|gb|

EAU65167.1|

D-aspartate

oxidase

[Stigmatella

aurantiaca

DW4/3-1]

703,
FAD dependent
91976294
1.00E−118

Rhodo-
Glyphosate
AAR22262
6.00E−44
Hyper-
ADM27081
0.23
1.4.99.1
1248
415
0
417
50

704
oxidoreductase

pseudomo

oxidoreductase

thermophile

[Rhodo-

nas palustris

gene

Methanopyrus

pseudomo

BisB5
downstream

kandleri

nas palustris

flanking

protein #28.

BisB5]

region.

705,
putative
27379412
1.00E−133

Bradyrhizo-

Glyphosate
AAR22262
1.00E−42

Pseudomonas

ABD08105
0.23
1.4.99.1
1233
410
0
410
56

706
oxidoreductase

bium

oxidoreductase

aeruginosa

protein

japonicum

gene

polypeptide

[Bradyrhizobium

USDA 110
downstream

#3.

japonicum

flanking

USDA 110]

region.

707,
FAD dependent
75676467
1.00E−121

Nitrobacter

Glyphosate
AAR22262
6.00E−52
S.
ADY66589
0.06
1.4.99.1
1275
424
0
417
52

708
oxidoreductase

winogradskyi

oxidoreductase

mansoni

[Nitrobacter

Nb-255
gene

protein

winogradskyi

downstream

SEQ ID 18.

Nb-255]

flanking

region.

709,
FAD dependent
118034565
0

Burkholderia

Glyphosate
AAR22262
2.00E−49
Bacterial
ADT43021
0.23
1.4.99.1
1233
410
0
410
75

710
oxidoreductase

phymatum

oxidoreductase

polypeptide

[Burkholderia

STM815
gene

#10001.

phymatum

downstream

STM815]

flanking

gi|117979745|gb|

region.

EAU94152.1|

711,
FAD dependent
114319576
1.00E−88

Alkalilim-

P.
ADQ03060
2.00E−81
Rice protein
ADA48957
0.23
1.4.99.1
1266
421
0
421
43

712
oxidoreductase

nicola

aeruginosa

conferring

[Burkholderia

ehrlichei

virulence

disease

phymatum

MLHE-1
gene VIR14,

resistance

STM815]

protein.

in plants/

FAD dependent

oxidoreductase

[Alkalilimnicola

ehrlichei

MLHE-1]

713,
FAD dependent
118034565
0

Burkholderia

Glyphosate
AAR22262
2.00E−49
Bacterial
ADT43021
0.23
1.4.99.1
1233
410
0
410
75

714
oxidoreductase

phymatum

oxidoreductase

polypeptide

[Burkholderia

STM815
gene

#10001.

phymatum

downstream

STM815]

flanking

gi|117979745|gb|

region.

EAU94152.1|

715,
FAD dependent
144897812
4.00E−87

Magneto-

Glyphosate
ABO75104
4.00E−80
Human
AET00128
0.91
1.4.99.1
1251
416
0
420
43

716
oxidoreductase

spirillum

oxidoreductase

acute

[Burkholderia

gryphiswal-

gene

myeloid

phymatum

dense

downstream

leukemia

STM815]

MSR-1
flanking

prognosis

FAD dependent

region.

target gene

oxidoreductase

PCR primer

[Magnetospirillum

#247.

gryphiswaldense

MSR-1]

717,
FAD dependent
124006998
1.00E−29

Microscilla

H.
AAW98270
0.87

0

912
303
0
358
29

718
oxidoreductase,

marina ATCC
pylori

putative

23134
GHPO

[Microscilla

1099 gene.

marina ATCC

23134]

gi|123987451|gb|

EAY27171.1|

719,
FAD dependent
15676467
1.00E−137

Nitrobacter

Glyphosate
AAR22262
6.00E−51

Pseudomonas

ABD10326
3.6
1.4.99.1
1251
416
0
417
57

720
oxidoreductase,

winogradskyi

oxidoreductase

aeruginosa

putative

Nb-255
gene

polypeptide

[Microscilla

downstream

#3.

marina ATCC

flanking

23134]

region.

FAD dependent

oxidoreductase

[Nitrobacter

winogradskyi

Nb-255]

721,
D-amino-acid
119716015
1.00E−53

Nocardioides

Human
AED18771
6.00E−40
Bacterial
ADT44787
0.042
1.4.3.3
918
305
0
310
42

722
oxidase

sp. JS614
D-aspartate

polypeptide

[Nocardioides

oxidase

#10001.

sp. JS614]

active stie.

gi|119536676|gb|

ABL81293.1|

D-amino-acid

oxidase

[Nocardioides

sp. JS614]

723,
Glycine/D-amino
88810939
2.00E−84

Nitrococcus

Pseudomonas

ABO75104
2.00E−77
Human breast
AAL13181
0.001
1.4.99.1
1251
416
0
423
41

724
acid oxidase

mobilis

aeruginosa

cancer

[Nitrococcus

Nb-231
polypeptide

expressed

mobilis Nb-231]

#3.

polynucleotide

gi|88791478|gb|E

8440.

AR22589.1]

Glycine/D-amino

acid oxidase

[Nitrococcus

mobilis Nb-231]

725,
FAD dependent
71909453
1.00E−133

Dechloro-

Enterobacter
AEH60497
4.00E−95
Human ORFX
ABN17150
1.00E−12
1.4.99.1
1260
419
0
418
56

726
oxidoreductase

monas

cloacae

protein

[Dechloromonas

aromatica

protein

sequence

aromatica RCB]

RCB
amino acid

SEQ ID

sequence -

NO: 19716.

SEQ ID 5666.

727,
D-amino acid
149377918
1.00E−136

Marinobacter

Photorhabdus

ABM69115
7.00E−85
Drosophila
ABL15242
3.9
1.4.99.1
1329
442
0
423
56

728
dehydrogenase

algicola

luminescens

melanogaster

small subunit

DG893
protein

polypeptide

[Marinobacter

sequence #59.

SEQ ID

algicola

NO 24465.

DG893]

729,
pyruvate
114319858
1.00E−135

Alkalilim-

Staphy-

ABM73103
1.00E−57

Pseudomonas

ABD01828
0.051
1.2.7.3
1098
365
0
576
65

730
flavodoxin/

nicola

lococcus

aeruginosa

ferredoxin

ehrlichei

aureus

polypeptide

oxidoreductase

MLHE-1
protein #10.

#3.

domain protein

[Alkalilimnicola

ehrlichei

MLHE-1]

731,
FAD dependent
144897812
4.00E−80

Magneto-

Klebsiella

ABO67618
4.00E−62
Human breast
AAL13181
1.00E−06
1.4.99.1
1260
419
0
420
41

732
oxidoreductase

spirillum

pneumoniae

cancer

[Magnetospirillum

gryphiswal-

polypeptide

expressed

gryphiswaldense

dense

seqid 7178.

polynucleotide

MSR-1]

MSR-1

8440.

733,
FAD dependent
144897812
1.00E−89

Magneto-

Pseudomonas

ABO75104
8.00E−76
Bacterial
ADS63429
0.23
1.4.99.1
1257
418
0
420
44

734
oxidoreductase

spirillum

aeruginosa

polypeptide

[Magnetospirillum

gryphiswal-

polypeptide

#10001.

gryphiswaldense

dense

#3.

MSR-1]

MSR-1

735,
FAD linked
149124512
3.00E−61

Methylo-

FAD-
ADM97925
2.00E−57

M.

ACL64584
2.00E−06
1.1.2.4
807
268
0
477
48

736
oxidase domain

bacterium

dependent-

xanthus

protein

sp. 4-46
D-erythronate

protein

[Methylobacte-

4-phosphate

sequence,

rium sp. 4-46]

dehydro-

seq id 9726.

genase.

737,
FAD dependent
92113847
1.00E−150

Chromo-
Glyphosate
AAR20642
2.00E−43

Pseudomonas

ABD10634
0.058
1.4.99.1
1242
413
0
414
62

738
oxidoreductase

halobacter

oxidoreductase

aeruginosa

[Chromohalo-

salexigens

gene

polypeptide

bacter salexigens

DSM 3043
downstream

#3.

DSM 3043]

flanking

region.

739,
FAD dependent
92113847
1.00E−153

Chromo-
Glyphosate
AAR22262
6.00E−41
Human
AAD07816
0.91
1. . .
1245
414
0
414
63

740
oxidoreductase

halobacter

oxidoreductase

secreted

[Chromohalo-

salexigens

gene

protein-

bacter salexigens

DSM 3043
downstream

encoding gene

DSM 3043]

flanking

29 cDNA

region.

clone

HCEFI77,

SEQ ID

NO: 103.

741,
FAD dependent
92113847
1.00E−153

Chromo-
Glyphosate
AAR22262
6.00E−41
Human
AAD07816
0.91
1. . .
1245
414
0
414
63

742
oxidoreductase

halobacter

oxidoreductase

secreted

[Chromohalo-

salexigens

gene

protein-

bacter salexigens

DSM 3043
downstream

encoding gene

DSM 3043]

flanking

29 cDNA

region.

clone

HCEFI77,

SEQ ID

NO: 103.

743,
FAD dependent
92113847
1.00E−150

Chromo-
Glyphosate
AAR20642
6.00E−43

Pseudomonas

ABD10634
0.058
1.4.99.1
1242
413
0
414
62

744
oxidoreductase

halobacter

oxidoreductase

aeruginosa

[Chromohalo-

salexigens

gene

polypeptide

bacter salexigens

DSM 3043
downstream

#3.

DSM 3043]

flanking

region.

745,
FAD dependent
94314005
1.00E−101

Ralstonia

Pseudomonas

ABO71517
6.00E−85

E. coli

AER28868
0.83
1.1.99.
1146
381
0
385
49

746
oxidoreductase

metallidurans

aeruginosa

NCg12640

[Ralstonia

CH34
polypeptide

DNA.

metallidurans

#3.

CH34]

747,
glycine/D-amino
121525574
1.00E−125

Parvibaculum

P.
ADQ03060
6.00E−76

Pseudomonas

ABD08815
0.015
1.4.99.1
1278
425
0
462
53

748
acid oxidase

lavamenti-

aeruginosa

aeruginosa

[Parvibaculum

vorans

virulence

polypeptide

lavamentivorans

DS-1
gene VIR14,

#3.

DS-1]

protein.

gi|121298521|gb|

EAX39710.1|

glycine/D-amino

acid oxidase

[Parvibaculum

lavamentivorans

DS-1]

749,
FAD dependent
71909453
1.00E−139

Dechloro-

P.
ADQ03060
2.00E−96
Human breast
AAL13181
2.00E−07
1.4.99.1
1245
414
0
418
60

750
oxidoreductase

monas

aeruginosa

cancer

[Dechloromonas

aromatica

virulence

expressed

aromatica RCB]

RCB
gene VIR14,

polynucleotide

protein.

8440.

751,
monooxygenase,
118050299
8.00E−81

Comamonas

Farnesyl
ADR01274
6.00E−18
Prokaryotic
ACA23297
0.65
1.14.13.
915
304
0
543
49

752
FAD-binding

testosteroni

dibenzo-

essential gene

[Comamonas

KF-1
diazepinone

#34740.

testosteroni KF-1]

biosynthetic

gi|118002385|gb|

ORF9 protein

EAV16539.1|

HMGA,

monooxygenase,

SEQ ID 18.

FAD-binding

[Comamonas

testosteroni

KF-1]

753,
FAD dependent
75676467
1.00E−120

Nitrobacter

Glyphosate
AAR22262
3.00E−53
Human
ADD01267
0.23
1.4.99.1
1248
415
0
417
52

754
oxidoreductase

winogradskyi

oxidoreductase

nucleic acid-

[Nitrobacter

Nb-255
gene

associated

winogradskyi

downstream

protein

Nb-255]

flanking

NAAP-13

region.

SEQ ID

NO: 13.

755,
FAD dependent
91976294
1.00E−121

Rhodo-
Glyphosate
AAR22262
1.00E−54

0
1.4.99.1
1245
414
0
417
51

756
oxidoreductase

pseudomo

oxidoreductase

[Rhodo-

nas palustris

gene

pseudomonas

BisB5
downstream

palustris

flanking

BisB5]

region.

757,
putative
126732124
1.00E−131

Sagittula

Glyphosate
AAR22262
1.00E−31
Human
ADJ09909
3.6
1.4.99.1
1251
416
0
410
55

758
oxidoreductase

stellate E-37
oxidoreductase

prostate

protein [Sagittula

gene

cancer

stellate E-37]

downstream

associated

gi|126707413|gb|

flanking

polypeptide

EBA06477.1|

region.

SeqID273.

putative

oxidoreductase

protein [Sagittula

stellate E-37]

759,
FAD dependent
75676467
1.00E−113

Nitrobacter

Glyphosate
AAR22262
2.00E−51
Human PRO
AEH18256
0.23
1.4.99.1
1254
417
0
417
49

760
oxidoreductase

winogradskyi

oxidoreductase

protein amino

[Nitrobacter

Nb-255
gene

acid

winogradskyi

downstream

sequence -

Nb-255]

flanking

SEQ ID 59.

region.

761,
FAD dependent
92113847
1.00E−149

Chromohalo-
Glyphosate
AAR20642
2.00E−42
Nocardiopsis
ADR47152
0.23
1.4.99.1
1242
413
0
414
62

762
oxidoreductase

bacter

oxidoreductase

alba copper

[Chromohalo-

salexigens

gene

stable

bacter salexigens

DSM 3043
downstream

protease 08.

DSM 3043]

flanking

region.

763,
FAD dependent
114319576
4.00E−84

Alkalilim-

Pseudomonas

ABO75104
9.00E−80
Human breast
AAL13181
0.001
1.4.99.1
1251
416
0
421
41

764
oxidoreductase

nicola

aeruginosa

cancer

[Alkalilimnicola

ehrlichei

polypeptide

expressed

ehrlichei

MLHE-1
#3.

polynucleotide

MLHE-1]

8440.

765,
FAD linked
149124512
1.00E−106

Methylo-

FAD-
ADM97925
1.00E−94
Bacterial
ADS59768
9.00E−07
1.1.2.4
1182
393
0
477
51

766
oxidase domain

bacterium

dependent-D-

polypeptide

protein

sp. 4-46
erythronate 4-

#10001.

[Methylobacte-

phosphate

rium
sp. 4-46]

dehydrogenase.

767,
FAD dependent
114319576
3.00E−84

Alkalilim-

Pseudomonas

ABO75104
2.00E−75
Human breast
AAL13181
0.015
1.4.99.1
1257
418
0
421
41

768
oxidoreductase

nicola

aeruginosa

cancer

[Alkalilimnicola

ehrlichei

polypeptide

expressed

ehrlichei

MLHE-1
#3.

polynucleotide

MLHE-1]

8440.

769,
FAD dependent
92113847
1.00E−149

Chromohalo-
Glyphosate
AAR20642
2.00E−42
Prokaryotic
ACA37735
0.015
1.4.99.1
1242
413
0
414
62

770
oxidoreductase

bacter

oxidoreductase

essential gene

[Chromohalo-

salexigens

gene

#34740.

bacter
salexigens

DSM 3043
downstream

DSM 3043]

flanking

region.

771,
FAD dependent
75676467
1.00E−121

Nitrobacter

Glyphosate
AAR22262
6.00E−54

Pseudomonas

ABD1413
0.91
1.4.99.1
1245
414
0
417
53

772
oxidoreductase

winogradskyi

oxidoreductase

aeruginosa

[Nitrobacter

Nb-255
gene

polypeptide

winogradskyi

downstream

#3.

Nb-255]

flanking

region.

773,
FAD dependent
92113847
1.00E−149

Chromohalo-
Glyphosate
AAR22262
3.00E−42
Nocardiopsis
ADR47152
0.23
1.4.99.1
1242
413
0
414
62

774
oxidoreductase

bacter

oxidoreductase

alba

[Chromohalo-

salexigens

gene

copper stable

bacter salexigens

DSM 3043
downstream

protease 08.

DSM 3043]

flanking

region.

775,
Glycine/D-amino
88810939
5.00E−77

Nitrococcus

N.
ABP30542
7.00E−64
Aspergillus
ABT17832
3.7
1.4.99.1
1272
423
0
423
38

776
acid oxidase

mobilis

gonorrhoeae

fumigatus

[Nitrococcus

Nb-231
nucleotide

essential

mobilis Nb-231]

sequence SEQ

gene protein

gi|88791478|gb|E

ID 4691.

#821.

AR22589.1]

Glycine/D-amino

acid oxidase

[Nitrococcus

mobilis Nb-231]

777,
putative
27379412
0

Bradyrhizo-

Glyphosate
AAR22262
3.00E−42
Prokaryotic
ACA26366
0.9
1.4.99.1
1233
410
0
410
92

778
oxidoreductase

bium

oxidoreductase

essential gene

protein

japonicum

gene

#34740.

[Bradyrhizobium

USDA 110
downstream

japonicum

flanking

USDA 110]

region.

779,
FAD dependent
118037424
0

Burkholderia

Glyphosate
AAR22262
5.00E−49
Rice abiotic
ACL30152
0.23
1.4.99.1
1233
410
0
465
86

780
oxidoreductase

phytofirmans

oxidoreductase

stress

[Burkholderia

PsJN
gene

responsive

phytofirmans

downstream

polypeptide

PsJN]

flanking

SEQ ID

gi|117992233|gb|

region.

NO: 4152.

EAV06525.1|

FAD dependent

oxidoreductase

[Burkholderia

phytofirmans

PsJN]

781,
FAD dependent
118593299
1.00E−122

Stappia

Glyphosate
AAR22262
2.00E−47
Stress tolerant
AEA26962
0.06
1.4.99.1
1272
423
0
422
52

782
oxidoreductase

aggregata

oxidoreductase

plant-related

[Stappia

IAM 12614
gene

transcription

aggregata IAM

downstream

factor protein

12614]

flanking

SeqID10.

gi|118434190|gb|

region.

EAV40846.1]

FAD dependent

oxidoreductase

[Stappia

aggregata

IAM 12614]

783,
FAD linked
149124512
7.00E−99

Methylo-

FAD-
ADM97925
9.00E−89
Bacterial
ADT42301
9.00E−10
1.1.2.4
1137
378
0
477
51

784
oxidase domain

bacterium

dependent-D-

polypeptide

protein

sp. 4-46
erythronate 4-

#10001.

[Methylobacte-

phosphate

rium
sp. 4-46]

dehydrogenase.

785,
FAD dependent
114319576
1.00E−84

Alkalilim-

Pseudomonas

ABO75104
3.00E−76

Pseudomonas

ABD08815
0.001
1.4.99.1
1251
416
0
421
41

786
oxidoreductase

nicola

aeruginosa

aeruginosa

[Alkalilimnicola

ehrlichei

polypeptide

polypeptide

ehrlichei

MLHE-1
#3.

#3.

MLHE-1]

787,
FAD dependent
144897812
9.00E−85

Magneto-

Pseudomonas

ABO75104
2.00E−81
Human breast
AAL13181
0.001
1.4.99.1
1251
416
0
420
42

788
oxidoreductase

spirillum

aeruginosa

cancer

[Magnetospirillum

gryphiswal-

polypeptide

expressed

gryphiswaldense

dense

#3.

polynucleotide

MSR-1]

MSR-1

8440.

789,
putative
126732124
1.00E−107

Sagittula

Glyphosate
AAR22262
1.00E−40
Prokaryotic
ACA39870
0.23
1.4.99.1
1248
415
0
410
46

790
oxidoreductase

stellata E-37
oxidoreductase

essential gene

protein [Sagittula

gene

#34740.

stellata E-37]

downstream

gi|126707413|gb|

flanking

EBA06477.1|

region.

putative

oxidoreductase

protein [Sagittula

stellata E-37]

791,
Oxidoreductase,
89211549
2.00E−98

Halo-

Propioni-
ABM37055
9.00E−80
Human soft
ADQ24247
3
1.3.1.26
1044
347
0
333
50

792
N-terminal:

thermothrix

bacterium

tissue

Dihydrodi

orenii

acnes predicted

sarcoma-

picolinate

H 168
ORF-encoded

upregulated

reductase

polypeptide

protein -

[Halothermothrix

#300.

SEQ ID 40.

orenii H 168]

gi|89158855|gb|E

AR78543.1|

Oxidoreductase,

N-terminal:

Dihydrodi

picolinate

reductase

[Halothermothrix

orenii H 168]

793,
PUTATIVE
15964495
1.00E−149

Sinorhizo-

Glyphosate
AAR22262
8.00E−46
Plant
ADT18820
0.004
1. . .
1233
410
1254
417
63
65

794
OXIDO-

bium

oxidoreductase

polypeptide,

REDUCTASE

meliloti

gene

SEQ ID

PROTEIN

downstream

5546.

[Sinorhizobium

flanking

meliloti].

region.

795,
indolepyruvate
118593297
0

Stappia

Acinetobacter

ADA35170
0

Silicibacter sp.

AEM45684
0.007
1.2.7.8
2313
770
0
1173
61

796
ferredoxin

aggregata

baumannii

TM1040 gene

oxidoreductase

IAM 12614
protein

SEQ ID

[Stappia

#19.

NO: 3.

aggregata

IAM 12614]

gi|118434188|gb|

EAV40844.1|

indolepyruvate

ferredoxin

oxidoreductase

[Stappia

aggregata

IAM 12614]

797,
FAD linked
149124512
1.00E−128

Methylo-

FAD-
ADM97925
1.00E−113
Bacterial
ADT47055
1.00E−06
1.1.2.4
1437
478
0
477
53

798
oxidase domain

bacterium

dependent-D-

polypeptide

protein

sp. 4-46
erythronate 4-

#10001.

[Methylobacte-

phosphate

rium
sp. 4-46]

dehydrogenase.

799,
FAD dependent
114319576
9.00E−90

Alkalilim-

M.
ADL05210
4.00E−63
Human
ACH13524
0.015
1.4.99.1
1281
426
0
421
42

800
oxidoreductase

nicola

catarrhalis

endothelial

[Alkalilimnicola

ehrlichei

protein #1.

cell cDNA

ehrlichei

MLHE-1

#2412.

MLHE-1]

801,
FAD dependent
144897812
1.00E−89

Magneto-

Pseudomonas

ABO75104
8.00E−76
Bacterial
ADS63429
0.23
1.4.99.1
1257
418
0
420
44

802
oxidoreductase

spirillum

aeruginosa

polypeptide

[Magneto-

gryphiswal-

polypeptide

#10001.

spirillum

dense

#3.

gryphiswaldense

MSR-1

MSR-1]

803,
FAD dependent
114319576
1.00E−86

Alkalilim-

P.
ADQ03060
4.00E−78
Plant
ADJ41976
0.92
1.4.99.1
1257
418
0
421
42

804
oxidoreductase

nicola

aeruginosa

cDNA

[Alkalilimnicola

ehrlichei

virulence

#31.

ehrlichei

MLHE-1
gene VIR14,

MLHE-1]

protein.

805,
FAD linked
149124512
1.00E−121

Methylo-

FAD-
ADM97925
1.00E−104

N.
ABZ40619
4.00E−09
1.1.2.4
1323
440
0
477
53

806
oxidase domain

bacterium

dependent-D-

gonorrhoeae

protein

sp. 4-46
erythronate 4-

nucleotide

[Methylobacte-

phosphate

sequence

rium
sp. 4-46]

dehydrogenase.

SEQ

ID 4691.

807,
D-amino acid
149377918
1.00E−135

Marinobacter

Photorhabdus
ABM69115
5.00E−84
Novel human
AAF66669
0.25
1.4.99.1
1329
442
0
423
55

808
dehydrogenase

algicola

luminescens

polynucleotide,

small subunit

DG893
protein

SEQ ID

[Marinobacter

sequence #59.

NO: 1975.

algicola DG893]

809,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46

Bifido-

ABQ81849
0.91
1.4.99.1
1242
413
0
413
81

810
oxidoreductase

phytofirmans

oxidoreductase

bacterium

[Burkholderia

PsJN
gene

longum

phytofirmans

downstream

NCC2705

PsJN]

flanking

ORF

gi|117991720|gb|

region.

amino acid

EAV06013.1|

sequence

FAD dependent

SEQ ID

oxidoreductase

NO: 408.

[Burkholderia

phytofirmans

PsJN]

811,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46

Bifido-

ABQ81849
0.91
1.4.99.1
1242
413
0
413
81

812
oxidoreductase

phytofirmans

oxidoreductase

bacterium

[Burkholderia

PsJN
gene

longum

phytofirmans

downstream

NCC2705

PsJN]

flanking

ORF

gi|117991720|gb|

region.

amino acid

EAV06013.1|

sequence

FAD dependent

SEQ ID

oxidoreductase

NO: 408.

[Burkholderia

phytofirmans

PsJN]

813,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46

Bifido-

ABQ81849
0.91
1.4.99.1
1242
413
0
413
81

814
oxidoreductase

phytofirmans

oxidoreductase

bacterium

[Burkholderia

PsJN
gene

longum

phytofirmans

downstream

NCC2705

PsJN]

flanking

ORF

gi|117991720|gb|

region.

amino acid

EAV06013.1|

sequence

FAD dependent

SEQ ID

oxidoreductase

NO: 408.

[Burkholderia

phytofirmans

PsJN]

815,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46

Bifido-

ABQ81849
0.91
1.4.99.1
1242
413
0
413
81

816
oxidoreductase

phytofirmans

oxidoreductase

bacterium

[Burkholderia

PsJN
gene

longum

phytofirmans

downstream

NCC2705

PsJN]

flanking

ORF

gi|117991720|gb|

region.

amino acid

EAV06013.1|

sequence

FAD dependent

SEQ ID

oxidoreductase

NO: 408.

[Burkholderia

phytofirmans

PsJN]

817,
FAD dependent
114319576
5.00E−93

Alkalilim-

P.
ADQ03060
1.00E−79
Enterobacter
AEH53102
0.004
1.4.99.1
1269
422
0
421
43

818
oxidoreductase

nicola

aeruginosa

cloacae

[Alkalilimnicola

ehrlichei

virulence

protein

ehrlichei

MLHE-1
gene VIR14,

amino acid

MLHE-1]

protein.

sequence -

SEQ ID 5666.

819,
FAD dependent
144897812
1.00E−124

Magneto-

P.
ADQ03060
2.00E−99
Human
ABN17150
0.015
1.4.99.1
1263
420
0
420
54

820
oxidoreductase

spirillum

aeruginosa

ORFX

[Magneto-

gryphiswal-

virulence

protein

spirillum

dense

gene VIR14,

sequence

gryphiswaldense

MSR-1
protein.

SEQ ID

MSR-1]

NO: 19716.

821,
FAD dependent
92113847
1.00E−150

Chromohalo-
Glyphosate
AAR20642
2.00E−43

Pseudomonas

ABD10634
0.058
1.4.99.1
1242
413
0
414
62

822
oxidoreductase

bacter

oxidoreductase

aeruginosa

[Chromohalo-

salexigens

gene

polypeptide

bacter salexigens

DSM 3043
downstream

#3.

DSM 3043]

flanking

region.

823,
hypothetical
13473721
1.00E−176

Mesorhizo-

Human
AAE00797
2.00E−76
Human
AAV72125
2.00E−04
1.5.3.1
1170
389
1167
388
77

824
protein, contains

bium

Her-2/neu

catalyc

weak similarity to

loti

over

telomerase

sarcosine oxidase

expression

sub-unit

[Mesorhizobium

modulated

PCR primer

loti].

protein

HTR2BAM.

(HOMPS)

H14 cDNA.

825,
FAD dependent
118731339
0

Delftia

Pseudomonas

ABO71517
1.00E−100

Pseudomonas

ABD04986
1.00E−12
1.1.99.
1146
381
0
385
90

826
oxidoreductase

acidovorans

aeruginosa

aeruginosa

[Delftia

SPH-1
polypeptide

polypeptide

acidovorans

#3.

#3.

SPH-1]

gi|118668198|gb|

EAV74793.1|

FAD dependent

oxidoreductase

[Delftia

acidovorans

SPH-1]

827,
FAD dependent
118593299
1.00E−122

Stappia

Glyphosate
AAR22262
2.00E−47
Stress tolerant
AEA26962
0.06
1.4.99.1
1272
423
0
422
52

828
oxidoreductase

aggregata

oxidoreductase

plant-related

[Stappia

IAM
gene

transcription

aggregata IAM

12614
downstream

factor protein

12614]

flanking

SeqID10.

gi|118434190|gb|

region.

EAV40846.1|

FAD dependent

oxidoreductase

[Stappia

aggregata IAM

12614]

829,
FAD dependent
114319576
2.00E−87

Alkalilim-

Pseudomonas

ABO75104
1.00E−66

Pseudomonas

ABD08815
6.00E−05
1.4.99.1
1281
426
0
421
40

830
oxidoreductase

nicola

aeruginosa

aeruginosa

[Alkalilimnicola

ehrlichei

polypeptide

polypeptide

ehrlichei

MLHE-1
#3.

#3.

MLHE-1]

831,
hypothetical
13475565
7.00E−99

Mesorhizo-

Pseudomonas

ABO71517
1.00E−78

Pseudomonas

ADB04986
2.00E−11
1.1.99.
1137
378
1152
383
49
59

832
protein

bium

aeruginosa

aeruginosa

[Mesorhizobium

loti

polypeptide

polypeptide

loti].

#3.

#3.

833,
FAD dependent
144897812
2.00E−89

Magneto-

Pseudomonas

ABO75104
8.00E−76
Bacterial
ADS63429
0.23
1.4.99.1
1257
418
0
420
44

834
oxidoreductase

spirillum

aeruginosa

polypeptide

[Magneto-

gryphiswal-

polypeptide

#10001.

spirillum

dense

#3.

gryphiswaldense

MSR-1

MSR-1]

835,
FAD linked
149124512
1.00E−123

Methylo-

FAD-
ADM97925
1.00E−110
Bacterial
ADS56646
8.00E−14
1.1.2.4
1395
464
0
477
52

836
oxidase domain

bacterium

dependent-D-

polypeptide

protein

sp. 4-46
erythronate 4-

#10001.

[Methylobacte-

phosphate

rium
sp. 4-46]

dehydrogenase.

837,
D-aspartate
115376852
1.00E−56

Stigmatella

Human
AED18771
8.00E−45

Acinetobacter

AEK59509
0.68
1.4.3.1
942
313
0
314
39

838
oxidase

aurantiaca

D-aspartate

species rpoB

[Stigmatella

DW4/3-1
oxidase

gene SEQ

aurantiaca

active site.

ID NO: 19.

DW4/3-1]

gi|115366155|gb|

EAU65167.1|

D-aspartate

oxidase

[Stigmatella

aurantiaca

DW4/3-1]

839,
FAD dependent
118038076
0

Burkholderia

Glyphosate
AAR22262
6.00E−46

Bifido-

ABQ81849
0.91
1.4.99.1
1242
413
0
413
81

840
oxidoreductase

phytofirmans

oxidoreductase

bacterium

[Burkholderia

PsJN
gene

longum

phytofirmans

downstream

NCC2705

PsJN]

flanking

ORF

gi|117991720|gb|

region.

amino acid

EAV06013.1|

sequence

FAD dependent

SEQ ID

oxidoreductase

NO: 408.

[Burkholderia

phytofirmans

PsJN]

841,
FAD dependent
71909453
1.00E−126

Dechloro-

P.
ADQ03060
9.00E−93
Human
ABN17150
2.00E−05
1.4.99.1
1269
422
0
418
52

842
oxidoreductase

monas

aeruginosa

ORFX

[Dechloromonas

aromatica

virulence

protein

aromatica RCB]

RCB
gene VIR14,

sequence

protein.

SEQ ID NO:.

19716

843,
FAD dependent
118029195
1.00E−180

Burkholderia

Enterobacter
AEH60497
1.00E−171

Pseudomonas

ABD08815
1.00E−43
1.4.99.1
1290
429
0
428
72

844
oxidoreductase

phymatum

cloacae

aeruginosa

[Burkholderia

STM815
protein

polypeptide

phymatum

amino acid

#3.

STM815]

sequence -

gi|117985258|gb|

SEQ ID 5666.

EAU99635.1|

FAD dependent

oxidoreductase

[Burkholderia

phymatum

STM815]

845,
putative
27379412
0

Bradyrhizo-

Glyphosate
AAR22262
1.00E−42
Peptide #3
AAD56788
0.23
1.4.99.1
1233
410
0
410
93

846
oxidoreductase

bium

oxidoreduc-

used for

protein

japonicum

tase gene

purifying

[Bradyrhizobium

USDA 110
downstream

peptidyl-tRNA

japonicum

flanking

hydrolase

USDA 110]

region.

(PTH) protein.

847,
FAD dependent
77457196
1.00E−171

Pseudomonas

Pseudomonas

ADQ03060
7.00E−80

Pseudomonas

ABD05088
2.00E−51
1.1.99.
1131
376
0
375
77

848
oxidoreductase

fluorescens

aeruginosa

aeruginosa

[Pseudomonas

PfO-1
polypeptide

polypeptide

fluorescens

#3.

#3.

PfO-1]

849,
FAD dependent
114319576
7.00E−93

Alkalilim-

P.

Enterobacter
AEH53102
0.004
1.4.99.1
1269
422
0
421
43

850
oxidoreductase

nicola

aeruginosa

cloacae

[Alkalilimnicola

ehrlichei

virulence

protein

ehrlichei

MLHE-1
gene VIR14,

amino acid

MLHE-1]

protein.

sequence -

SEQ ID

5666.

851,
D-amino acid
32140775
1.00E−62

Arthrobacter

Primer
ADF68144
4.00E−63
Myco-
AAI99682
0.18
1.4.3.3
975
324
4E+06
326

852
oxidase

protophor-

Aprev4

bacterium

[Arthrobacter

miae

#SEQ ID 8.

tuberculosis

protophormiae].

strain H37Rv

genome SEQ

ID NO 2.

853,
FAD dependent
77457196
1.00E−171

Pseudomonas

Pseudomonas

ABO71517
1.00E−151

Pseudomonas

ABD05088
2.00E−51
1.1.99.
1131
376
0
375
77

854
oxidoreductase

fluorescens

aeruginosa

aeruginosa

[Pseudomonas

PfO-1
polypeptide

polypeptide

fluorescens

#3.

#3.

PfO-1]

855,
FAD dependent
118051673
0

Comamonas

Pseudomonas

ABO71517
1.00E−99

Pseudomonas

ABD04986
1.00E−05
1.1.99.
1173
390
0
390
99

856
oxidoreductase

testosteroni

aeruginosa

aeruginosa

[Comamonas

KF-1
polypeptide

polypeptide

testosteroni

#3.

#3.

KF-1]

gi|118001016|gb|

EAV15172.1|

FAD dependent

oxidoreductase

[Comamonas

testosteroni

KF-1]

857,
FAD dependent
118051673
0

Comamonas

Pseudomonas

ABO71517
1.00E−99

Pseudomonas

ABD04986
1.00E−05
1.1.99.
1173
390
0
390
99

858
oxidoreductase

testosteroni

aeruginosa

aeruginosa

[Comamonas

KF-1
polypeptide

polypeptide

testosteroni

#3.

#3.

KF-1]

gi|118001016|gb|

EAV15172.1|

FAD dependent

oxidoreductase

[Comamonas

testosteroni

KF-1]

859,
FAD dependent
118051673
0

Comamonas

Pseudomonas

ABO71517
1.00E−99

Pseudomonas

ABD04986
1.00E−05
1.1.99.
1173
390
0
390
99

860
oxidoreductase

testosteroni

aeruginosa

aeruginosa

[Comamonas

KF-1
polypeptide

polypeptide

testosteroni

#3.

#3.

KF-1]

gi|118001016|gb|

EAV15172.1|

FAD dependent

oxidoreductase

[Comamonas

testosteroni

KF-1]

861,
D-amino acid
108803375
3.00E−70

Rubrobacter

Human
AED18771
8.00E−62
Yeast
AED11687
5.00E−08
1.4.3.3
987
328
0
326
46

862
oxidase

xylanophilus

D-aspartate

D-amino

[Rubrobacter

DSM 9941
oxidase

acid oxidase.

xylanophilus

active site.

DSM 9941]

863,
D-amino acid
66043505
0

Pseudomonas

P.
ADQ03060
0

Pseudomonas

ABD08815
0
1.4.99.1
1299
432
0
433
88

864
dehydrogenase

syringae pv.
aeruginosa

aeruginosa

small subunit

syringae

virulence

polypeptide

[Pseudomonas

B728a
gene VIR14,

#3.

syringae pv.

protein.

syringae B728a]

867,

868

Methano-

ADS43070
3.00E−37

0.003
2.6.1.9
1062
353
12392
373
30
96

coccus

maripaludis

869,

C7

AEM18037
1.00E−126

2.00E−25
2.6.1.21
852
283
1140
283
78
80

870

871,

Planctomyces

ADN26446
1.00E−95

1.1
5.4.3.8
1350
449
3784
417
46
96

872

maris DSM

8797

873,

Planctomyces

ADN26446
7.00E−94

0.071
5.4.3.8
1401
466
1358
417
44
96

874

maris DSM

8797

875,

Roseiflexus

ADN26446
8.00E−98

1.00E−09
5.4.3.8
1344
447
37500
417
48
88

876

castenholzii

DSM 13941

877,

Planctomyces

ADN26446
2.00E−94

0.018
5.4.3.8
1389
462
231
417
43
100

878

maris DSM

8797

879,

Planctomyces

ADN26446
2.00E−93

0.018
5.4.3.8
1398
465
1356
417
43
96

880

maris DSM

8797

881,

Oceanobacter

AEB37927
3.00E−50

2.7
2.6.1.21
873
290
1653
282
39
100

882

sp. RED65

883,

Thiobacillus

AEM18040
2.00E−49

2.6.1.21

292

283
42

884

denitrificans

ATCC 25259

885,

Clostridium

EEM18031
2.00E−47

2.7
2.6.1.21
861
286
19976
283
40
100

886

beijerinckii

NCIMB 8052

887,

Nocardioides

AEK20408
3.00E−27

0.63
2.6.1.42
801
266
799
284
37
96

888

sp. JS614

889,

Methylococcus

ABM71198
2.00E−53

0.66
2.6.1.21
840
279
264
282
41
100

890

capsulatus str.

Bath

891,

Clostridium

ABB08244
2.00E−47

0.67
2.6.1.21
861
286
599
283
39
100

892

beijerinckii

NCIMB 8052

893,

Clostridium

ABB08244
5.00E−46

0.17
2.6.1.21
861
286
44577
283
37
100

894

beijerinckii

NCIMB 8052

895,

Clostridium

ABU32980
1.00E−45

0.66
2.6.1.21
849
282
16714
289
39
100

896

aceto-

butylicum

ATCC 824

897,

Roseiflexus

ADN26446
5.00E−93

7.00E−08
5.4.3.8
1353
450
1287
417
47
82

898

castenholzii

DSM 13941

899,

Planctomyces

ADN26446
1.00E−100

1.00E−09
5.4.3.8
1362
453
37500
417
47
91

900

maris DSM

8797

901,

Planctomyces

ADN26446
1.00E−104

0.001
5.4.3.8
1386
461
1341
417
49
96

902

maris DSM

8797

903,

Planctomyces

ADN26446
7.00E−99

0.07
5.4.3.8
1383
460
870
417
47
84

904

maris DSM

8797

905,

Rhodobacter

ADF03944
3.00E−68

2.7
2.6.1.21
864
287
5766
298
46
100

906

sphaeroides

2.4.1

907,

Streptomyces

AEK20408
2.00E−33

0.042
2.6.1.42
831
276
591
284
36
100

908

avermitilis

MA-4680

909,

Bacillus sp.

ADW43694
1.00E−159

0
2.6.1.21
855
284
1709
284
97
88

910

B14905

911,

Azoarcus sp.

ABU33175
4.00E−45

0.17
2.6.1.21
876
291
4862
278
36
100

912

EbN1

913,

Bacillus

AEM18039
2.00E−56

2.6
2.6.1.21
852
283
7166
282
43
100

914

licheniformis

ATCC 14580

915,

Roseiflexus

ADN26446
2.00E−87

2.00E−05
5.4.3.8
1383
460
1701
417
41
81

916

castenholzii

DSM 13941

917,

Robiginitalea

AAY13560
3.00E−48

0.72
2.6.1.21
915
304
652
282
39
100

918

biformata

HTCC2501

919,

Planctomyces

ADN26446
1.00E−93

1.1
5.4.3.8
1350
449
18471
417
46
96

920

maris DSM

8797

921,

Planctomyces

ADN26446
6.00E−96

0.07
5.4.3.8
1377
458
20250
417
48
100

922

maris DSM

8797

923,

Roseobacter

ADF03944
5.00E−75

2.7
2.6.1.21
861
286
864
298
50
100

924

sp. MED193

925,

Planctomyces

ADN26446
1.00E−90

0.004
5.4.3.8
1377
458
1251
417
44
96

926

maris DSM

8797

927,

Aquifex

ADN17496
0

0
2.6.1.1
1185
394
1185
394
100
100

928

aeolicus

VF5

929,

Aspergillus

ADS78245
0

2.6.1.42

322

317
100

930

terreus

NIH2624

931,

Oceanicola

ADS78325
0

2.6.1.62

519

461
100

932

granulosus

HTCC2516

933,

Pyrococcus

ADS41897
5.00E−53

3.8
2.6.1.1
1206
401
9502
387
33
100

934

horikoshii

OT3

935,

Aeromonas

ADS78291
0

0
2.6.1.62
1383
460
1383
460
100
100

936

hydrophila

subsp.

hydrophila

ATCC7966

937,

Silibacter sp.

ADF03944
9.00E−69

2.6
2.6.1.21
855
284
2000
298
48
95

938

TM1040

939,

Rhodo-

ADF03944
1.00E−53

0.67
2.6.1.21
855
284
86941
298
39
100

940

pseudomonas

palutris

CGA009

941,

Xanthobacter

ADF03944
8.00E−55

2.7
2.6.1.21
879
292
2840
298
41
100

942

autotrophicus

Py2

943,

Azoarcus sp.

AEM18040
8.00E−53

0.17
2.6.1.21
870
289
1899
283
40
100

944

BH72

945,

Clostridium

AEM18031
2.00E−46

0.011
2.6.1.21
855
284
636
283
39
100

946

beijerinckii

NCIMB 8052

947,

Alcnivorax

AAY13560
2.00E−54

0.042
2.6.1.21
837
278
897
282
40
91

948

borkumensis

SK2

951,
aspartate
14590640
2.00E−52

Pyrococcus

Bacterial
ADS41897
5.00E−53
Tumour
AAS46730
3.6
2.6.1.1
1206
401
9502
387

952
aminotransferase

horikoshii

polypeptide

suppressor

[Pyrococcus

#10001.

gene derived

horikoshii].

chemiclly

modified

sequence

#530.

953,
aspartate
15606968
0

Aquifex

Bacterial
ADN17496
0
Bacterial
ADS45406
0
2.6.1.1
1185
394
0
394
100

954
aminotransferase

aeolicus

polypeptide

polypeptide

[Aquifex aeolicus].

#10001.

#10001.

955,
conserved
115385557
1.00E−126

Aspergillus

Amino-
ADS78245
1.00E−170
Amino-
ADS78244
0
2.6.1.42
879
292
954
317

956
hypothetical

terreus

transferase/

transferase/

protein

NIH2624
mutase/

mutase/

[Aspergillus

deaminase

deaminase

terreus

enzyme #14.

enzyme #14.

NIH2624]

957,
hypothetical
89070918
0

Oceanicola

Amino-
ADS78325
0
Amino-
ADS78324
0
2.6.1.62
1366
461
0
460
72

958
protein

granulosus

transferase/

transferase/

OG2516J 5919

HTCC2516
mutase/

mutase/

[Oceanicola

deaminase

deaminase

granulosus

enzyme #14.

enzyme #14.

HTCC2516]

gi|89043511|gb|E

AR49723.1|

hypothetical

protein

OG2516J5919

[Oceanicola

granulosus

HTCC2516]

959,
aminotrans-
117619456
1.00E−158

Aeromonas

Amino-
ADS78291
0
Amino-
ADS78290
0
2.6.1.62
1383
460
1383
460

960
ferase; class III

hydrophila

transferase/

transferase/

[Aeromonas

subsp.

mutase/

mutase/

hydrophila

hydrophila

deaminase

deaminase

subsp.

ATCC 7966
enzyme #14.

enzyme #14.

hydrophila

ATCC 7966]

Aminotransferase and oxidoreductase nucleic acids and polypeptides and methods of using

Information

Patent Number

Date Filed

Date Issued

Inventors

Original Assignees

Examiners

CPC

US Classifications

Field of Search

US

International Classifications

Term Extension

Abstract

Description

Claims

CROSS-REFERENCE TO RELATED APPLICATIONS

PCT Information

US Referenced Citations (1)

Non-Patent Literature Citations (22)

Related Publications (1)

Provisional Applications (1)