Patent Application
20070292916
The present invention relates to a mutant protein having a peptide-synthesizing activity, and more particularly relates to a mutant protein having an excellent peptide-synthesizing activity and a method for producing a peptide using this protein.
Peptides have been used in a variety of fields such as pharmaceuticals and foods. For example, L-alanyl-L-glutamine is widely used as a component for infusions and serum-free media taking advantage of its higher stability and water-solubility than that of L-glutamine.
Peptides have hitherto been produced by chemical synthesis methods. However, the chemical synthesis has not always been satisfactory in terms of simplicity and efficiency.
On the other hand, methods for producing the peptide using an enzyme have been developed (e.g., Patent documents 1 and 2). However, the conventional enzymological method for producing the peptide still had room for improvement such as slow synthesis rate and low yield of the peptide products. In such a context, it has been desired to develop a method for efficiently producing peptides on an industrial scale.
The present inventors have already been found an enzyme derived from Sphingobacterium as an enzyme having an excellent peptide-synthesizing activity (Patent documents 3 to 6).
[Patent document 1]
EP 0278787 A1
[Patent document 2]
EP 359399 A1
[Patent document 3]
WO2004/011653
[Patent document 4]
JP 2005-040037 A
[Patent document 5]
JP 2005-058212 A
[Patent document 6]
JP 2005-168405 A
It is an object of the present invention to provide a more excellent peptide-synthesizing protein and a method for efficiently producing the peptide.
As a result of an extensive study, the present inventors have found that a protein having a more excellent peptide-synthesizing activity is obtainable by modifying a specific position in an amino acid sequence or a nucleotide sequence of a protein derived from a microorganism belonging to genus Sphingobacterium and having a peptide-synthesizing activity, and completed the present invention. That is, the present invention provides the following protein and method for producing a peptide using this protein.
[1] A mutant protein having an amino acid sequence comprising one or more mutations selected from any of the following mutations 1 to 68 in an amino acid sequence of SEQ ID NO:2.
mutation 1 F207V, mutation 2 Q441E, mutation 3 K83A, mutation 4 A301V, mutation 5 V257I, mutation 6 A537G, mutation 7 A324V, mutation 8 N607K, mutation 9 D313E, mutation 10 Q229H, mutation 11 M208A, mutation 12 E551K, mutation 13 F207H, mutation 14 T72A, mutation 15 A137S, mutation 16 L439V, mutation 17 G226S, mutation 18 D619E, mutation 19 Y339H, mutation 20 W327G, mutation 21 V184A, mutation 22 V184C, mutation 23 V184G, mutation 24 V184I, mutation 25 V184L, mutation 26 V184M, mutation 27 V184P, mutation 28 V184S, mutation 29 V184T, mutation 30 Q441K, mutation 31 N442K, mutation 32 D203N, mutation 33 D203S, mutation 34 F207A, mutation 35 F207S, mutation 36 Q441N, mutation 37 F207T, mutation 38 F207I, mutation 39 T210K, mutation 40 W187A, mutation 41 S209A, mutation 42 F211A, mutation 43 F211V, mutation 44 V257A, mutation 45 V257G, mutation 46 V257H, mutation 47 V257M, mutation 48 V257N, mutation 49 V257Q, mutation 50 V257S, mutation 51 V257T, mutation 52 V257W, mutation 53 V257Y, mutation 54 K47G, mutation 55 K47E, mutation 56 N442F, mutation 57 N607R, mutation 58 P214T, mutation 59 Q202E, mutation 60 Y494F, mutation 61 R117A, mutation 62 F207G, mutation 63 S209D, mutation 64 S209G, mutation 65 Q441D, mutation 66 R445D, mutation 67 R445F, mutation 68 N442D.
[2] The mutant protein according to [1] above wherein, in said amino acid sequence comprising one or more mutations selected from any of the mutations 1 to 68, said amino acid sequence further comprises at other than the mutated position(s) one or several amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions, said mutant protein having a peptide-synthesizing activity.
[3] The mutant protein according to [1] or [2] above comprising at least the mutation 2.
[4] The mutant protein according to any one of [1] to
[3] above comprising at least the mutation 14.
[5] A mutant protein having an amino acid sequence comprising one or more mutations selected from any of the following mutations 239 to 290 and 324 to 377 in an amino acid sequence of SEQ ID NO:2:
mutation 239 F207V/Q441E
mutation 240 F207V/K83A
mutation 241 F207V/E551K
mutation 242 K83A/Q441E
mutation 243 M208A/E551K
mutation 244 V257I/Q441E
mutation 245 V257I/A537G
mutation 246 F207V/S209A
mutation 247 K83A/S209A
mutation 248 K83A/F207V/Q441E
mutation 249 L439V/F207V/Q441E
mutation 250 A537G/F207V/Q441E
mutation 251 A301V/F207V/Q441E
mutation 252 G226S/F207V/Q441E
mutation 253 V257I/F207V/Q441E
mutation 254 D619E/F207V/Q441E
mutation 255 Y339H/F207V/Q441E
mutation 256 N607K/F207V/Q441E
mutation 257 A324V/F207V/Q441E
mutation 258 Q229H/F207V/Q441E
mutation 259 W327G/F207V/Q441E
mutation 260 A301V/L439V/A537G/N607K
mutation 261 K83A/Q229H/A301V/D313E/A324V/L439V/A537G/N607K
mutation 262 Q229H/V257I/A301V/A324V/Q441E/A537G/N607K
mutation 263 Q229H/A301V/A324V/Q441E/A537G/N607K
mutation 264 Q229H/V257I/A301V/D313E/A324V/Q441E/A537G/N607K
mutation 265 T72A/A137S/A301V/L439V/Q441E/A537G/N607K
mutation 266 T72A/A137S/A301V/Q441E/A537G/N607K
mutation 267 T72A/A137S/Q229H/A301V/A324V/L439V/A537G/N607K
mutation 268 T72A/A137S/Q229H/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 269 T72A/Q229H/V257I/A301V/D313E/A324V/L439V/Q441E/A537G/N607K
mutation 270 T72A/Q229H/V257I/A301V/D313E/A324V/Q441E/A537G/N607K
mutation 271 T72A/A137S/Q229P/A301V/L439V/Q441E/A537G/N607K
mutation 272 T72A/A137S/Q229L/A301V/L439V/Q441E/A537G/N607K
mutation 273 T72A/A137S/Q229G/A301V/L439V/Q441E/A537G/N607K
mutation 274 T72A/Q229I/V257I/A301V/D313E/A324V/L439V/Q441E/A537G/N607K
mutation 275 T72A/A137S/I228G/Q229P/A301V/L439V/Q441E/A537G/N607K
mutation 276 T72A/A137S/I228L/Q229P/A301V/L439V/Q441E/A537G/N607K
mutation 277 T72A/A137S/I228D/Q229P/A301V/L439V/Q441E/A537G/N607K
mutation 278 T72A/A137S/Q229P/I230D/A301V/L439V/Q441E/A537G/N607K
mutation 279 T72A/A137S/Q229P/I230V/A301V/L439V/Q441E/A537G/N607K
mutation 280 T72A/I228S/Q229H/V257I/A301V/D313E/A324V/L439V/Q441E/A537G/N607K
mutation 281 T72A/Q229H/S256C/V257I/A301V/D313E/A324V/L439V/Q441E/A537G/N607K
mutation 282 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 283 T72A/A137S/Q229P/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 284 T72A/Q229P/V257I/A301G/D313E/A324V/Q441E/A537G/N607K
mutation 285 T72A/Q229P/V257I/A301V/D313E/A324V/Q441E/A537G/N607K
mutation 286 T72A/A137S/V184A/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 287 T72A/A137S/V184G/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 288 T72A/A137S/V184N/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 289 T72A/A137S/V184S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 290 T72A/A137S/V184T/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K
mutation 324 V184A/V257Y
mutation 325 V184A/W187A
mutation 326 V184A/N442D
mutation 327 V184P/N442D
mutation 328 V184A/N442D/L439V
mutation 329 A301V/L439V/A537G/N607K/V184A
mutation 330 A301V/L439V/A537G/N607K/V184P
mutation 331 A301V/L439V/A537G/N607K/V257Y
mutation 332 A301V/L439V/A537G/N607K/W187A
mutation 333 A301V/L439V/A537G/N607K/F211A
mutation 334 A301V/L439V/A537G/N607K/Q441E
mutation 335 A301V/L439V/A537G/N607K/N442D
mutation 336 A301V/L439V/A537G/N607K/V184A/F207V
mutation 337 A301V/L439V/A537G/N607K/V184A/A182G
mutation 338 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/A537G/N607K/V184A/N442D
mutation 339 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/A537G/N607K/V184A/N442D/T185F
mutation 340 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/K83A
mutation 341 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/W187A
mutation 342 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/F211A
mutation 343 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/V178G
mutation 344 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185A
mutation 345 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/A182G
mutation 346 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/K314R
mutation 347 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/A515V
mutation 348 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L66F
mutation 349 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/S315R
mutation 350 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/K484I
mutation 351 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/V213A
mutation 352 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/A245S
mutation 353 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/P214H
mutation 354 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L263M
mutation 355 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/P183A
mutation 356 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185K
mutation 357 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185D
mutation 358 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185C
mutation 359 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185S
mutation 360 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185F
mutation 361 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185P
mutation 362 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185N
mutation 363 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/P183A/A182G
mutation 364 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/P183A/A182S
mutation 365 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/T185F/N442D
mutation 366 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L66F/E80K/I157L/A182G/P214H/L263M
mutation 367 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L66F/E80K/I157L/A182G/P214H/L263M/Y328F
mutation 368 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L66F/Y81A/I157L/A182G/P214H/L263M/Y328F
mutation 369 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/L66F/E80K/I157L/A182G/T210L/L263M/Y328F
mutation 370 A301V/L439V/A537G/N607K/Q441K
mutation 371 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/I157L
mutation 372 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/G161A
mutation 373 T72A/A137S/Q229P/V257I/A301V/A324V/L439V/Q441E/A537G/N607K/V184A/Y328F
mutation 374 F207V/G226S
mutation 375 F207V/W327G
mutation 376 F207V/Y339H
mutation 377 F207V/D619E.
[6] The mutant protein according to [5] above wherein, in said amino acid sequence comprising one or more mutations selected from any of the mutations 239 to 290 and 324 to 377, said amino acid sequence further comprises at other than the mutated position(s) one or more amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions, said mutant protein having a peptide-synthesizing activity.
[7] The mutant protein according to [5] or [6] above comprising at least the mutation 260.
[8] The mutant protein according to any one of [5] to [7] above comprising at least the mutation 286.
[9] A polynucleotide encoding the amino acid sequence of the mutant protein according to any one of [1] to [8] above.
[10] A recombinant polynucleotide comprising the polynucleotide according to [9] above.
[11] A transformed microorganism comprising the recombinant polynucleotide according to [10] above.
[12] A method for producing a mutant protein comprising culturing the transformed microorganism according to [11] above in a medium, to accumulate the mutant protein in the medium and/or the transformed microorganism.
[13] A method for producing a peptide comprising performing a peptide-synthesizing reaction in the presence of the mutant protein according to any one of [1] to [8] above.
[14] A method for producing a peptide comprising culturing the transformed microorganism according to [11] above in a medium to accumulate the mutant protein in the medium and/or the transformed microorganism for performing a peptide-synthesizing reaction.
[15] A method for producing α-L-aspartyl-L-phenylalanine-β-ester comprising reacting L-aspartic acid-α,β-diester and L-phenylalanine in the presence of the mutant protein according to any one of [1] to [8] above.
[16] A method for producing α-L-aspartyl-L-phenylalanine-β-ester comprising culturing the transformed microorganism according to [11] above in a medium to accumulate the mutant protein in the medium and/or the transformed microorganism for performing a reaction of L-aspartic acid-α,β-diester and L-phenylalanine.
[17] A method for designing and producing a mutant protein having a peptide-synthesizing activity comprising:
analyzing a protein having an amino acid sequence of SEQ ID NO:208 by X-ray crystal structure analysis to obtain a tertiary structure thereof;
predicting a substrate binding site of the protein based on said tertiary structure; and
substituting, inserting or deleting an amino acid residue located at said substrate binding site.
[18] A mutant protein having an amino acid sequence comprising one or more amino acid substitutions, insertions or deletions at positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340, and 437 to 447 in an amino acid sequence in a tertiary structure of a protein having an amino acid sequence of SEQ ID NO:208, and having a peptide-synthesizing activity.
[19] A mutant protein of a protein having a peptide-synthesizing activity wherein:
three dimensional structures of the mutant protein and a protein having an amino acid sequence of SEQ ID NO:209 are similar as a result of determination by a threading method;
in alignment obtained upon the determination, at least one or more amino acid residues are substituted, inserted or deleted at positions corresponding to positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340 and 437 to 447 in the amino acid sequence of SEQ ID NO:209; and
said mutant protein has the peptide-synthesizing activity.
[20] A mutant protein of a protein having a peptide-synthesizing activity wherein:
when an alignment of primary sequences of the mutant protein and a protein having an amino acid sequence of SEQ ID NO:209 or an alignment of three dimensional structures of the mutant protein and the protein having the amino acid sequence of SEQ ID NO:209 is performed, homology of the primary sequences is 25% or more, and at least one or more amino acid residues are substituted, inserted or deleted at positions corresponding to positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340 and 437 to 447 in the amino acid sequence of SEQ ID NO:209; and
said mutant protein has the peptide-synthesizing activity.
[21] A mutant protein having one or more changes in a tertiary structure selected from the following (a) to (i) in the tertiary structure of a protein having an amino acid sequence of SEQ ID NO:208, said mutant protein having a peptide-synthesizing activity:
(a) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:208;
(b) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:208;
(c) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:208;
(d) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:208;
(e) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 70, 106, 113, 115, 193, 207, 209 to 212, 216 and 259 in the amino acid sequence of SEQ ID NO:208;
(f) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 200, 202 to 205, 207 and 228 in the amino acid sequence of SEQ ID NO:208;
(g) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:208;
(h) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:208; and
(i) at least one or more amino acid residue substitutions, insertions or deletions at any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:208.
[22] A mutant protein of a protein having a peptide-synthesizing activity wherein:
three dimensional structures of the mutant protein and a protein having an amino acid sequence of SEQ ID NO:209 are similar as a result of determination by a threading method, and in alignment obtained upon the determination, one or more changes selected from the following (a′) to (i′) are present; and
the mutant protein has a peptide-synthesizing activity:
(a′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:209;
(b′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:209;
(c′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:209;
(d′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:209;
(e′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 70, 106, 113, 115, 193, 207, 209 to 212, 216 and 259 in the amino acid sequence of SEQ ID NO:209;
(f′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 200, 202 to 205, 207 and 228 in the amino acid sequence of SEQ ID NO:209;
(g′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:209;
(h′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:209; and
(i′) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:209.
[23] A mutant protein of a protein having a peptide-synthesizing activity wherein:
when an alignment of primary sequences of the mutant protein and a protein having an amino acid sequence of SEQ ID NO:209 or an alignment of three dimensional structures of the mutant protein and the protein having the amino acid sequence of SEQ ID NO:209 is performed, homology of the primary sequences is 25% or more, and one or more changes selected from the following (a″) to (i″) are present; and
said mutant protein has the peptide-synthesizing activity:
(a″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:209;
(b″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:209;
(c″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:209;
(d″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:209;
(e″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 70, 106, 113, 115, 193, 207, 209 to 212, 216 and 259 in the amino acid sequence of SEQ ID NO:209;
(f″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 200, 202 to 205, 207 and 228 in the amino acid sequence of SEQ ID NO:209;
(g″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:209;
(h″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:209; and
(i″) at least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:209.
[24] A mutant protein having at least one or more amino acid residue substitutions, insertions or deletions at positions 67, 69, 70, 72 to 85, 103, 106, 107, 113 to 116, 165, 182, 183, 185, 187, 188, 190, 200, 202, 204 to 206, 209 to 211, 213 to 235, 301, 328, 338 to 340, 440 to 442 and 446 in a tertiary structure of a protein having an amino acid sequence of SEQ ID NO:208, said mutant protein having a peptide-synthesizing activity.
[25] A mutant protein having at least one or more amino acid residue substitutions, insertions or deletions at positions 67, 69, 70, 72 to 84, 106, 107, 114, 116, 183, 185, 187, 188, 202, 204 to 206, 209, 211, 213 to 233, 235, 328, 338 to 442 and 446 in a tertiary structure of a protein having an amino acid sequence of SEQ ID NO:208, said mutant protein having a peptide-synthesizing activity.
[26] A mutant protein having at least one or more amino acid residue substitutions, insertions or deletions at positions 67, 70, 72 to 75, 77 to 79, 81 to 84, 114, 116, 185, 188, 202, 204, 206, 209, 211, 213 to 215, 218 to 224, 226 to 233, 235, 328, 338 to 441 and 446 in a tertiary structure of a protein having an amino acid sequence of SEQ ID NO:208, said mutant protein having a peptide-synthesizing activity.
[27] A mutant protein having an amino acid sequence comprising one or more mutations selected from any of the following mutations L1 to L335 in an amino acid sequence of SEQ ID NO:208:
mutation L1 N67K
mutation L2 N67L
mutation L3 N67S
mutation L4 T69I
mutation L5 T69M
mutation L6 T69Q
mutation L7 T69R
mutation L8 T69V
mutation L9 P70G
mutation L10 P70N
mutation L11 P70S
mutation L12 P70T
mutation L13 P70V
mutation L14 A72C
mutation L15 A72D
mutation L16 A72E
mutation L17 A72I
mutation L18 A72L
mutation L19 A72M
mutation L20 A72N
mutation L21 A72Q
mutation L22 A72S
mutation L23 A72V
mutation L24 V73A
mutation L25 V73I
mutation L26 V73L
mutation L27 V73M
mutation L28 V73N
mutation L29 V73S
mutation L30 V73T
mutation L31 S74A
mutation L32 S74F
mutation L33 S74K
mutation L34 S74N
mutation L35 S74T
mutation L36 S74V
mutation L37 P75A
mutation L38 P75D
mutation L39 P75L
mutation L40 P75S
mutation L41 Y76F
mutation L42 Y76H
mutation L43 Y76I
mutation L44 Y76V
mutation L45 Y76W
mutation L46 G77A
mutation L47 G77F
mutation L48 G77K
mutation L49 G77M
mutation L50 G77N
mutation L51 G77P
mutation L52 G77S
mutation L53 G77T
mutation L54 Q78F
mutation L55 Q78L
mutation L56 N79D
mutation L57 N79L
mutation L58 N79R
mutation L59 N79S
mutation L60 E80D
mutation L61 E80F
mutation L62 E80L
mutation L63 E80P
mutation L64 E80S
mutation L65 Y81A
mutation L66 Y81C
mutation L67 Y81D
mutation L68 Y81E
mutation L69 Y81F
mutation L70 Y81H
mutation L71 Y81K
mutation L72 Y81L
mutation L73 Y81N
mutation L74 Y81S
mutation L75 Y81T
mutation L76 Y81W
mutation L77 K82D
mutation L78 K82L
mutation L79 K82P
mutation L80 K82S
mutation L81 K83D
mutation L82 K83F
mutation L83 K83L
mutation L84 K83P
mutation L85 K83S
mutation L86 K83V
mutation L87 S84D
mutation L88 S84F
mutation L89 S84K
mutation L90 S84L
mutation L91 S84N
mutation L92 S84Q
mutation L93 L85F
mutation L94 L85I
mutation L95 L85P
mutation L96 L85V
mutation L97 N87E
mutation L98 N87Q
mutation L99 F88E
mutation L100 V103I
mutation L101 V103L
mutation L102 K106A
mutation L103 K106F
mutation L104 K106L
mutation L105 K106Q
mutation L106 K106S
mutation L107 W107A
mutation L108 W107Y
mutation L109 F113A
mutation L110 F113W
mutation L111 F113Y
mutation L112 E114A
mutation L113 E114D
mutation L114 D115E
mutation L115 D115Q
mutation L116 D115S
mutation L117 I116F
mutation L118 I116K
mutation L119 I116L
mutation L120 I116M
mutation L121 I116N
mutation L122 I116T
mutation L123 I116V
mutation L124 I157K
mutation L125 I157L
mutation L126 Y159G
mutation L127 Y159N
mutation L128 Y159S
mutation L129 P160G
mutation L130 G161A
mutation L131 F162L
mutation L132 F162Y
mutation L133 Y163I
mutation L134 T165V
mutation L135 Q181F
mutation L136 A182G
mutation L137 A182S
mutation L138 P183A
mutation L139 P183G
mutation L140 P183S
mutation L141 T185A
mutation L142 T185G
mutation L143 T185V
mutation L144 W187A
mutation L145 W187F
mutation L146 W187H
mutation L147 W187Y
mutation L148 Y188F
mutation L149 Y188L
mutation L150 Y188W
mutation L151 G190A
mutation L152 G190D
mutation L153 F193W
mutation L154 H194D
mutation L155 F200A
mutation L156 F200L
mutation L157 F200S
mutation L158 F200V
mutation L159 L201Q
mutation L160 L201S
mutation L161 Q202A
mutation L162 Q202D
mutation L163 Q202F
mutation L164 Q202S
mutation L165 Q202T
mutation L166 Q202V
mutation L167 D203E
mutation L168 A204G
mutation L169 A204L
mutation L170 A204S
mutation L171 A204T
mutation L172 A204V
mutation L173 F205L
mutation L174 F205Q
mutation L175 F205V
mutation L176 F205W
mutation L177 T206F
mutation L178 T206K
mutation L179 T206L
mutation L180 F207I
mutation L181 F207W
mutation L182 F207Y
mutation L183 M208A
mutation L184 M208L
mutation L185 S209F
mutation L186 S209K
mutation L187 S209L
mutation L188 S209N
mutation L189 S209V
mutation L190 T210A
mutation L191 T210L
mutation L192 T210Q
mutation L193 T210V
mutation L194 F211A
mutation L195 F211I
mutation L196 F211L
mutation L197 F211M
mutation L198 F211V
mutation L199 F211W
mutation L200 F211Y
mutation L201 G212A
mutation L202 V213D
mutation L203 V213F
mutation L204 V213K
mutation L205 V213S
mutation L206 P214D
mutation L207 P214F
mutation L208 P214K
mutation L209 P214S
mutation L210 R215A
mutation L211 R215I
mutation L212 R215K
mutation L213 R215Q
mutation L214 R215S
mutation L215 R215T
mutation L216 R215Y
mutation L217 P216D
mutation L218 P216K
mutation L219 K217D
mutation L220 P218F
mutation L221 P218L
mutation L222 P218Q
mutation L223 P218S
mutation L224 I219D
mutation L225 I219F
mutation L226 I219K
mutation L227 T220A
mutation L228 T220D
mutation L229 T220F
mutation L230 T220K
mutation L231 T220L
mutation L232 T220S
mutation L233 P221A
mutation L234 P221D
mutation L235 P221F
mutation L236 P221K
mutation L237 P221L
mutation L238 P221S
mutation L239 D222A
mutation L240 D222F
mutation L241 D222L
mutation L242 D222R
mutation L243 Q223F
mutation L244 Q223K
mutation L245 Q223L
mutation L246 Q223S
mutation L247 F224A
mutation L248 F224D
mutation L249 F224G
mutation L250 F224K
mutation L251 F224L
mutation L252 K225D
mutation L253 K225G
mutation L254 K225S
mutation L255 G226A
mutation L256 G226F
mutation L257 G226L
mutation L258 G226N
mutation L259 G226S
mutation L260 K227D
mutation L261 K227F
mutation L262 K227S
mutation L263 I228A
mutation L264 I228F
mutation L265 I228K
mutation L266 I228S
mutation L267 P229A
mutation L268 P229D
mutation L269 P229K
mutation L270 P229L
mutation L271 P229S
mutation L272 I230A
mutation L273 I230F
mutation L274 I230K
mutation L275 I230S
mutation L276 K231F
mutation L277 K231L
mutation L278 K231S
mutation L279 E232D
mutation L280 E232F
mutation L281 E232G
mutation L282 E232L
mutation L283 E232S
mutation L284 A233D
mutation L285 A233F
mutation L286 A233H
mutation L287 A233K
mutation L288 A233L
mutation L289 A233N
mutation L290 A233S
mutation L291 D234L
mutation L292 D234S
mutation L293 K235D
mutation L294 K235F
mutation L295 K235L
mutation L296 K235S
mutation L297 F259Y
mutation L298 R276A
mutation L299 R276Q
mutation L300 A298S
mutation L301 D300N
mutation L302 V301M
mutation L303 Y328F
mutation L304 Y328H
mutation L305 Y328M
mutation L306 Y328W
mutation L307 W332H
mutation L308 E336A
mutation L309 N338A
mutation L310 N338F
mutation L311 Y339K
mutation L312 Y339L
mutation L313 Y339T
mutation L314 L340A
mutation L315 L340I
mutation L316 L340V
mutation L317 V439P
mutation L318 I440F
mutation L319 I440V
mutation L320 E441F
mutation L321 E441M
mutation L322 E441N
mutation L323 N442A
mutation L324 N442L
mutation L325 R443S
mutation L326 T444W
mutation L327 R445G
mutation L328 R445K
mutation L329 E446A
mutation L330 E446F
mutation L331 E446Q
mutation L332 E446S
mutation L333 E446T
mutation L334 Y447L
mutation L335 Y447S.
[28] The mutant protein according to [20] above wherein, in said amino acid sequence comprising one or more mutations selected from any of the mutations L1 to L335, said amino acid sequence further comprises at other than the mutated position(s) one or several amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions, said mutant protein having a peptide-synthesizing activity.
[29] The mutant protein according to [27] or [28] above comprising at least the mutation L124 or L125.
[30] The mutant protein according to any one of [27] to [29] above comprising at least the mutation L303.
[31] The mutant protein according to any one of [27] to [30] above comprising at least the mutation L12.
[32] The mutant protein according to any one of [27] to [31] above comprising at least the mutation L127.
[33] The mutant protein according to any one of [27] to [32] above comprising at least the mutation L195 or L199.
[34] The mutant protein according to any one of [27] to [33] above comprising at least the mutation L130.
[35] The mutant protein according to any one of [27] to [34] above comprising at least the mutation L115.
[36] The mutant protein according to any one of [27] to [35] above comprising at least the mutation L316.
[37] The mutant protein according to any one of [27] to [36] above comprising at least the mutation L99.
[38] The mutant protein according to any one of [27] to [37] above comprising at least the mutation L15 or L16.
[39] The mutant protein according to any one of [27] to [38] above comprising at least the mutation L131.
[40] The mutant protein according to any one of [27] to [39] above comprising at least the mutation L284.
[41] The mutant protein according to any one of [27] to [40] above comprising at least the mutation L191.
[42] The mutant protein according to any one of [27] to [41] above comprising at least the mutation L65.
[43] The mutant protein according to any one of [27] to [42] above comprising at least the mutation L265.
[44] The mutant protein according to any one of [27] to [43] above comprising at least the mutation L317.
[45] The mutant protein according to any one of [27] to [44] above comprising at least the mutation L255.
[46] The mutant protein according to any one of [27] to [45] above comprising at least the mutation L52.
[47] The mutant protein according to any one of [27] to [46] above comprising at least the mutation L155.
[48] The mutant protein according to any one of [27] to [47] above comprising at least the mutation L298.
[49] The mutant protein according to any one of [27] to [48] above comprising at least the mutation L201.
[50] The mutant protein according to any one of [27] to [49] above comprising at least the mutation L145.
[51] The mutant protein according to any one of [27] to [50] above comprising at least the mutation L170.
[52] The mutant protein according to any one of [27] to [51] above comprising at least the mutation L87.
[53] The mutant protein according to any one of [27] to [52] above comprising at least the mutation L60.
[54] The mutant protein according to any one of [27] to [53] above comprising at least the mutation L110.
[55] A mutant protein having an amino acid sequence comprising one or more mutations selected from any of the following mutations M1 to M642 in an amino acid sequence of SEQ ID NO:208:
mutation M1 T69N/I157L
mutation M2 T69Q/I157L
mutation M3 T69S/I157L
mutation M4 P70A/I157L
mutation M5 P70G/I157L
mutation M6 P70I/I157L
mutation M7 P70L/I157L
mutation M8 P70N/I157L
mutation M9 P70S/I157L
mutation M10 P70T/I157L
mutation M11 P70T/T210L
mutation M12 P70T/Y328F
mutation M13 P70V/I157L
mutation M14 A72E/G77S
mutation M15 A72E/E80D
mutation M16 A72E/Y81A
mutation M17 A72E/S84D
mutation M18 A72E/F113W
mutation M19 A72E/I157L
mutation M20 A72E/G161A
mutation M21 A72E/F162L
mutation M22 A72E/A184G
mutation M23 A72E/W187F
mutation M24 A72E/F200A
mutation M25 A72E/A204S
mutation M26 A72E/T210L
mutation M27 A72E/F211L
mutation M28 A72E/F211W
mutation M29 A72E/G226A
mutation M30 A72E/I228K
mutation M31 A72E/A233D
mutation M32 A72E/Y328F
mutation M33 A72S/I157L
mutation M34 A72V/Y328F
mutation M35 V73A/I157L
mutation M36 V73I/I157L
mutation M37 S74A/I157L
mutation M38 S74N/I157L
mutation M39 S74T/I157L
mutation M40 S74V/I157L
mutation M41 G77A/I157L
mutation M42 G77F/I157L
mutation M43 G77M/I157L
mutation M44 G77P/I157L
mutation M45 G77S/E80D
mutation M46 G77S/Y81A
mutation M47 G77S/S84D
mutation M48 G77S/F113W
mutation M49 G77S/I157L
mutation M50 G77S/Y159N
mutation M51 G77S/Y159S
mutation M52 G77S/G161A
mutation M53 G77S/F162L
mutation M54 G77S/A184G
mutation M55 G77S/W187F
mutation M56 G77S/F200A
mutation M57 G77S/A204S
mutation M58 G77S/T210L
mutation M59 G77S/F211L
mutation M60 G77S/F211W
mutation M61 G77S/I228K
mutation M62 G77S/A233D
mutation M63 G77S/R276A
mutation M64 G77S/Y328F
mutation M65 E80D/Y81A
mutation M66 E80D/F113W
mutation M67 E80D/I157L
mutation M68 E80D/Y159N
mutation M69 E80D/G161A
mutation M70 E80D/A184G
mutation M71 E80D/F211W
mutation M72 E80D/Y328F
mutation M73 E80S/I157L
mutation M74 Y81A/F113W
mutation M75 Y81A/I157L
mutation M76 Y81A/Y159N
mutation M77 Y81A/Y159S
mutation M78 Y81A/G161A
mutation M79 Y81A/A184G
mutation M80 Y81A/W187F
mutation M81 Y81A/F200A
mutation M82 Y81A/T210L
mutation M83 Y81A/F211W
mutation M84 Y81A/F211Y
mutation M85 Y81A/G226A
mutation M86 Y81A/I228K
mutation M87 Y81A/A233D
mutation M88 Y81A/Y328F
mutation M89 Y81H/I157L
mutation M90 Y81N/I157L
mutation M91 K83P/I157L
mutation M92 S84A/I157L
mutation M93 S84D/F113W
mutation M94 S84D/I157L
mutation M95 S84D/Y159N
mutation M96 S84D/G161A
mutation M97 S84D/A184G
mutation M98 S84D/Y328F
mutation M99 S84E/I157L
mutation M100 S84F/I157L
mutation M101 S84K/I157L
mutation M102 L85F/I157L
mutation M103 L85I/I157L
mutation M104 L85P/I157L
mutation M105 L85V/I157L
mutation M106 N87A/I157L
mutation M107 N87D/I157L
mutation M108 N87E/I157L
mutation M109 N87G/I157L
mutation M110 N87Q/I157L
mutation M111 N87S/I157L
mutation M112 F88A/I157L
mutation M113 F88D/I157L
mutation M114 F88E/I157L
mutation M115 F88E/Y328F
mutation M116 F88L/I157L
mutation M117 F88T/I157L
mutation M118 F88V/I157L
mutation M119 F88Y/I157L
mutation M120 K106H/I157L
mutation M121 K106L/I157L
mutation M122 K106M/I157L
mutation M123 K106Q/I157L
mutation M124 K106R/I157L
mutation M125 K106S/I157L
mutation M126 K106V/I157L
mutation M127 W107A/I157L
mutation M128 W107A/Y328F
mutation M129 W107Y/I157L
mutation M130 W107Y/T206Y
mutation M131 W107Y/K217D
mutation M132 W107Y/P218L
mutation M133 W107Y/T220L
mutation M134 W107Y/P221D
mutation M135 W107Y/Y328F
mutation M136 F113A/I157L
mutation M137 F113H/I157L
mutation M138 F113N/I157L
mutation M139 F113V/I157L
mutation M140 F113W/I157L
mutation M141 F113W/Y159N
mutation M142 F113W/Y159S
mutation M143 F113W/G161A
mutation M144 F113W/F162L
mutation M145 F113W/A184G
mutation M146 F113W/W187F
mutation M147 F113W/F200A
mutation M148 F113W/T206Y
mutation M149 F113W/T210L
mutation M150 F113W/F211L
mutation M151 F113W/F211W
mutation M152 F113W/F211Y
mutation M153 F113W/V213D
mutation M154 F113W/K217D
mutation M155 F113W/T220L
mutation M156 F113W/P221D
mutation M157 F113W/G226A
mutation M158 F113W/I228K
mutation M159 F113W/A233D
mutation M160 F113W/R276A
mutation M161 F113Y/I157L
mutation M162 F113Y/F211W
mutation M163 E114D/I157L
mutation M164 D115A/I157L
mutation M165 D115E/I157L
mutation M166 D115M/I157L
mutation M167 D115N/I157L
mutation M168 D115Q/I157L
mutation M169 D115S/I157L
mutation M170 D115V/I157L
mutation M171 I157L/Y159I
mutation M172 I157L/Y159L
mutation M173 I157L/Y159N
mutation M174 I157L/Y159S
mutation M175 I157L/Y159V
mutation M176 I157L/P160A
mutation M177 I157L/P160S
mutation M178 I157L/G161A
mutation M179 I157L/F162L
mutation M180 I157L/F162M
mutation M181 I157L/F162N
mutation M182 I157L/F162Y
mutation M183 I157L/T165L
mutation M184 I157L/T165V
mutation M185 I157L/Q181A
mutation M186 I157L/Q181F
mutation M187 I157L/Q181N
mutation M188 I157L/A184G
mutation M189 I157L/A184L
mutation M190 I157L/A184M
mutation M191 I157L/A184S
mutation M192 I157L/A184T
mutation M193 I157L/W187F
mutation M194 I157L/W187Y
mutation M195 I157L/F193H
mutation M196 I157L/F193I
mutation M197 I157L/F193W
mutation M198 I157L/F200A
mutation M199 I157L/F200H
mutation M200 I157L/F200L
mutation M201 I157L/F200Y
mutation M202 I157L/A204G
mutation M203 I157L/A204I
mutation M204 I157L/A204L
mutation M205 I157L/A204S
mutation M206 I157L/A204T
mutation M207 I157L/A204V
mutation M208 I157L/F205A
mutation M209 I157L/F207I
mutation M210 I157L/F207M
mutation M211 I157L/F207V
mutation M212 I157L/F207W
mutation M213 I157L/F207Y
mutation M214 I157L/M208A
mutation M215 I157L/M208K
mutation M216 I157L/M208L
mutation M217 I157L/M208T
mutation M218 I157L/M208V
mutation M219 I157L/S209F
mutation M220 I157L/S209N
mutation M221 I157L/T210A
mutation M222 I157L/T210L
mutation M223 I157L/F2111
mutation M224 I157L/F211L
mutation M225 I157L/F211V
mutation M226 I157L/F211W
mutation M227 I157L/G212A
mutation M228 I157L/G212D
mutation M229 I157L/G212S
mutation M230 I157L/R215K
mutation M231 I157L/R215L
mutation M232 I157L/R215T
mutation M233 I157L/R215Y
mutation M234 I157L/T220L
mutation M235 I157L/G226A
mutation M236 I157L/G226F
mutation M237 I157L/I228K
mutation M238 I157L/A233D
mutation M239 I157L/R276A
mutation M240 I157L/Y328A
mutation M241 I157L/Y328F
mutation M242 I157L/Y328H
mutation M243 I157L/Y328I
mutation M244 I157L/Y328L
mutation M245 I157L/Y328P
mutation M246 I157L/Y328V
mutation M247 I157L/Y328W
mutation M248 I157L/L340F
mutation M249 I157L/L340I
mutation M250 I157L/L340V
mutation M251 I157L/V439A
mutation M252 I157L/V439P
mutation M253 I157L/R445A
mutation M254 I157L/R445F
mutation M255 I157L/R445G
mutation M256 I157L/R445K
mutation M257 I157L/R445V
mutation M258 Y159N/G161A
mutation M259 Y159N/A184G
mutation M260 Y159N/A204S
mutation M261 Y159N/T210L
mutation M262 Y159N/F211W
mutation M263 Y159N/F211Y
mutation M264 Y159N/G226A
mutation M265 Y159N/I228K
mutation M266 Y159N/A233D
mutation M267 Y159N/Y328F
mutation M268 Y159S/G161A
mutation M269 Y159S/F211W
mutation M270 G161A/F162L
mutation M271 G161A/A184G
mutation M272 G161A/W187F
mutation M273 G161A/F200A
mutation M274 G161A/A204S
mutation M275 G161A/T210L
mutation M276 G161A/F211L
mutation M277 G161A/F211W
mutation M278 G161A/G226A
mutation M279 G161A/I228K
mutation M280 G161A/A233D
mutation M281 G161A/Y328F
mutation M282 F162L/A184G
mutation M283 F162L/F211W
mutation M284 F162L/A233D
mutation M285 P183A/Y328F
mutation M286 A184G/W187F
mutation M287 A184G/F200A
mutation M288 A184G/A204S
mutation M289 A184G/T210L
mutation M290 A184G/F211L
mutation M291 A184G/F211W
mutation M292 A184G/I228K
mutation M293 A184G/A233D
mutation M294 A184G/R276A
mutation M295 V184G/Y328F
mutation M296 T185A/Y328F
mutation M297 T185N/Y328F
mutation M298 W187F/F211W
mutation M299 W187F/Y328F
mutation M300 F193W/F211W
mutation M301 F200A/F211W
mutation M302 F200A/Y328F
mutation M303 L201Q/Y328F
mutation M304 L201S/Y328F
mutation M305 A204S/F211W
mutation M306 A204S/Y328F
mutation M307 T210L/F211W
mutation M308 T210L/Y328F
mutation M309 F211L/A233D
mutation M310 F211L/Y328F
mutation M311 F211W/I228K
mutation M312 F211W/A233D
mutation M313 F211W/Y328F
mutation M314 R215A/Y328F
mutation M315 R215L/Y328F
mutation M316 T220L/A233D
mutation M317 T220L/D300N
mutation M318 P221L/A233D
mutation M319 P221L/Y328F
mutation M320 F224A/A233D
mutation M321 G226A/Y328F
mutation M322 G226F/A233D
mutation M323 G226F/Y328F
mutation M324 I228K/Y328F
mutation M325 A233D/K235D
mutation M326 A233D/Y328F
mutation M327 R276A/Y328F
mutation M328 Y328F/Y339F
mutation M329 A27T/Y81A/S84D
mutation M330 P70T/A72E/I157L
mutation M331 P70T/G77S/I157L
mutation M332 P70T/E80D/F88E
mutation M333 P70T/Y81A/I157L
mutation M334 P70T/S84D/I157L
mutation M335 P70T/F88E/Y328F
mutation M336 P70T/F113W/I157L
mutation M337 P70T/I157L/A204S
mutation M338 P70T/I157L/T210L
mutation M339 P70T/I157L/A233D
mutation M340 P70T/I157L/Y328F
mutation M341 P70T/I157L/V439P
mutation M342 P70T/I157L/I440F
mutation M343 P70T/G161A/T210L
mutation M344 P70T/G161A/Y328F
mutation M345 P70T/A184G/W187F
mutation M346 P70T/A204S/Y328F
mutation M347 P70T/F211W/Y328F
mutation M348 P70V/A72E/I157L
mutation M349 A72E/S74T/I157L
mutation M350 A72E/G77S/Y328F
mutation M351 A72E/E80D/Y328F
mutation M352 A72E/Y81H/I157L
mutation M353 A72E/K83P/I157L
mutation M354 A72E/S84D/Y328F
mutation M355 A72E/L85P/I157L
mutation M356 A72E/F113W/I157L
mutation M357 A72E/F113W/Y328F
mutation M358 A72E/F113Y/I157L
mutation M359 A72E/D115Q/I157L
mutation M360 A72E/I157L/G161A
mutation M361 A72E/I157L/F162L
mutation M362 A72E/I157L/A184G
mutation M363 A72E/I157L/F200A
mutation M364 A72E/I157L/A204S
mutation M365 A72E/I157L/A204T
mutation M366 A72E/I157L/T210L
mutation M367 A72E/I157L/F211W
mutation M368 A72E/I157L/G226A
mutation M369 A72E/I157L/A233D
mutation M370 A72E/I157L/Y328F
mutation M371 A72E/I157L/L340V
mutation M372 A72E/I157L/V439P
mutation M373 A72E/G161A/Y328F
mutation M374 A72E/F162L/Y328F
mutation M375 A72E/A184G/Y328F
mutation M376 A72E/W187F/Y328F
mutation M377 A72E/F200A/Y328F
mutation M378 A72E/A204S/Y328F
mutation M379 A72E/T210L/Y328F
mutation M380 A72E/I228K/Y328F
mutation M381 A72E/A233D/Y328F
mutation M382 A72E/Y328F/Y159N
mutation M383 A72E/Y328F/F211W
mutation M384 A72E/Y328F/F211Y
mutation M385 A72E/Y328F/G226A
mutation M386 A72V/Y81A/Y328F
mutation M387 A72V/G161A/Y328F
mutation M388 G77M/I157L/T210L
mutation M389 G77P/I157L/F162L
mutation M390 G77P/I157L/A184G
mutation M391 G77P/F211W/Y328F
mutation M392 G77S/Y81A/Y328F
mutation M393 G77S/S84D/I157L
mutation M394 G77S/F88E/I157L
mutation M395 G77S/F113W/I157L
mutation M396 G77S/F113Y/I157L
mutation M397 G77S/D115Q/I157L
mutation M398 G77S/I157L/G161A
mutation M399 G77S/I157L/F200A
mutation M400 G77S/I157L/A204S
mutation M401 G77S/I157L/T210L
mutation M402 G77S/I157L/F211W
mutation M403 G77S/I157L/G226A
mutation M404 G77S/I157L/A233D
mutation M405 G77S/I157L/L340V
mutation M406 G77S/I157L/V439P
mutation M407 G77S/G161A/Y328F
mutation M408 E80D/Y81A/Y328F
mutation M409 Y81A/S84D/Y328F
mutation M410 Y81A/F113W/Y328F
mutation M411 Y81A/I157L/T210L
mutation M412 Y81A/I157L/Y328F
mutation M413 Y81A/G161A/Y328F
mutation M414 Y81A/F162L/Y328F
mutation M415 Y81A/A184G/Y328F
mutation M416 Y81A/W187F/Y328F
mutation M417 Y81A/A204S/Y328F
mutation M418 Y81A/T210L/Y328F
mutation M419 Y81A/I228K/Y328F
mutation M420 Y81A/A233D/Y328F
mutation M421 Y81A/Y328F/Y159N
mutation M422 Y81A/Y328F/Y159S
mutation M423 Y81A/Y328F/F211W
mutation M424 Y81A/Y328F/F211Y
mutation M425 Y81A/Y328F/G226A
mutation M426 Y81A/Y328F/R276A
mutation M427 K83P/I157L/A184G
mutation M428 K83P/I157L/T210L
mutation M429 K83P/F211W/Y328F
mutation M430 S84D/F113W/I157L
mutation M431 S84D/I157L/T210L
mutation M432 F88E/I157L/F162L
mutation M433 F88E/I157L/A184G
mutation M434 F88E/I157L/F200A
mutation M435 F88E/I157L/T210L
mutation M436 F88E/I157L/Y328F
mutation M437 F88E/I157L/Y328Q
mutation M438 F88E/I157L/L340V
mutation M439 F88E/T210L/Y328F
mutation M440 F88E/F211W/Y328F
mutation M441 F113W/I157L/G161A
mutation M442 F113W/I157L/A184G
mutation M443 F113W/I157L/W187F
mutation M444 F113W/I157L/F200A
mutation M445 F113W/I157L/A204S
mutation M446 F113W/I157L/A204T
mutation M447 F113W/I157L/T210L
mutation M448 F113W/I157L/F211W
mutation M449 F113W/I157L/G226A
mutation M450 F113W/I157L/A233D
mutation M451 F113W/I157L/Y328F
mutation M452 F113W/I157L/L340V
mutation M453 F113W/I157L/V439P
mutation M454 F113W/G161A/T210L
mutation M455 F113W/G161A/Y328F
mutation M456 F113W/A184G/W187F
mutation M457 F113Y/I157L/T210L
mutation M458 F113Y/I157L/Y328F
mutation M459 F113Y/G161A/T210L
mutation M460 D115Q/I157L/T210L
mutation M461 D115Q/I157L/Y328F
mutation M462 I157L/Y159N/T210L
mutation M463 I157L/Y159N/Y328F
mutation M464 I157L/G161A/W187F
mutation M465 I157L/G161A/F200A
mutation M466 I157L/G161A/A204S
mutation M467 I157L/G161A/T210L
mutation M468 I157L/G161A/A233D
mutation M469 I157L/G161A/Y328F
mutation M470 I157L/F162L/A184G
mutation M471 I157L/F162L/T210L
mutation M472 I157L/F162L/L340V
mutation M473 I157L/A184G/W187F
mutation M474 I157L/A184G/F200A
mutation M475 I157L/A184G/A204T
mutation M476 I157L/A184G/T210L
mutation M477 I157L/A184G/F211W
mutation M478 I157L/A184G/L340V
mutation M479 I157L/W187F/T210L
mutation M480 I157L/W187F/Y328F
mutation M481 I157L/F200A/T210L
mutation M482 I157L/F200A/Y328F
mutation M483 I157L/A204S/T210L
mutation M484 I157L/A204S/Y328F
mutation M485 I157L/A204T/T210L
mutation M486 I157L/A204T/Y328F
mutation M487 I157L/T210L/F211W
mutation M488 I157L/T210L/G212A
mutation M489 I157L/T210L/G226A
mutation M490 I157L/T210L/A233D
mutation M491 I157L/T210L/Y328F
mutation M492 I157L/T210L/L340V
mutation M493 I157L/T210L/V439P
mutation M494 I157L/F211W/Y328F
mutation M495 I157L/G226A/Y328F
mutation M496 I157L/A233D/Y328F
mutation M497 I157L/Y328F/L340V
mutation M498 I157L/Y328F/V439P
mutation M499 Y159N/F211W/Y328F
mutation M500 G161A/A184G/W187F
mutation M501 G161A/T210L/Y328F
mutation M502 G161A/F211W/Y328F
mutation M503 A182G/P183A/Y328F
mutation M504 A182S/P183A/Y328F
mutation M505 A184G/W187F/F200A
mutation M506 A184G/W187F/A204S
mutation M507 A184G/W187F/F211W
mutation M508 A184G/W187F/I228K
mutation M509 A184G/W187F/A233D
mutation M510 F200A/F211W/Y328F
mutation M511 A204S/F211W/Y328F
mutation M512 A204T/F211W/Y328F
mutation M513 F211W/Y328F/L340V
mutation M514 P70T/A72E/I157L/Y328F
mutation M515 P70T/A72E/T210L/Y328F
mutation M516 P70T/G77M/I157L/Y328F
mutation M517 P70T/Y81A/I157L/T210L
mutation M518 P70T/Y81A/I157L/Y328F
mutation M519 P70T/S84D/I157L/Y328F
mutation M520 P70T/F88E/I157L/Y328F
mutation M521 P70T/F88E/T210L/Y328F
mutation M522 P70T/F113W/I157L/T210L
mutation M523 P70T/F113W/G161A/Y328F
mutation M524 P70T/F113Y/I157L/Y328F
mutation M525 P70T/D115Q/I157L/T210L
mutation M526 P70T/D115Q/I157L/Y328F
mutation M527 P70T/I157L/G161A/T210L
mutation M528 P70T/I157L/A184G/W187F
mutation M529 P70T/I157L/A184G/T210L
mutation M530 P70T/I157L/W187F/T210L
mutation M531 P70T/I157L/W187F/Y328F
mutation M532 P70T/I157L/A204T/T210L
mutation M533 P70T/I157L/A204T/Y328F
mutation M534 P70T/I157L/A204T/T210L
mutation M535 P70T/I157L/T210L/F211W
mutation M536 P70T/I157L/T210L/G226A
mutation M537 P70T/I157L/T210L/A233D
mutation M538 P70T/I157L/T210L/Y328F
mutation M539 P70T/I157L/T210L/L340V
mutation M540 P70T/I157L/T210L/V439P
mutation M541 P70T/I157L/Y328F/V439P
mutation M542 P70T/G161A/T210L/Y328F
mutation M543 P70T/G161A/A233D/Y328F
mutation M544 A72E/S74T/I157L/Y328F
mutation M545 A72E/G77S/F113W/I157L
mutation M546 A72E/Y81H/I157L/Y328F
mutation M547 A72E/K83P/I157L/Y328F
mutation M548 A72E/F88E/F113W/I157L
mutation M549 A72E/F88E/I157L/Y328F
mutation M550 A72E/F88E/G161A/Y328F
mutation M551 A72E/F113W/I157L/Y328F
mutation M552 A72E/F113W/G161A/Y328F
mutation M553 A72E/F113Y/I157L/Y328F
mutation M554 A72E/F113Y/G161A/Y328F
mutation M555 A72E/F113Y/G226A/Y328F
mutation M556 A72E/I157L/G161A/Y328F
mutation M557 A72E/I157L/F162L/Y328F
mutation M558 A72E/I157L/A184G/Y328F
mutation M559 A72E/I157L/F200A/Y328F
mutation M560 A72E/I157L/A204T/Y328F
mutation M561 A72E/I157L/F211W/Y328F
mutation M562 A72E/I157L/F211Y/Y328F
mutation M563 A72E/I157L/A233D/Y328F
mutation M564 A72E/I157L/Y328F/L340V
mutation M565 A72E/G161A/A204T/Y328F
mutation M566 A72E/G161A/T210L/Y328F
mutation M567 A72E/G161A/F211W/Y328F
mutation M568 A72E/G161A/F211Y/Y328F
mutation M569 A72E/G161A/A233D/Y328F
mutation M570 A72E/G161A/Y328F/L340V
mutation M571 A72E/A184G/W187F/Y328F
mutation M572 A72E/T210L/Y328F/L340V
mutation M573 A72V/I157L/W187F/Y328F
mutation M574 G77P/I157L/T210L/Y328F
mutation M575 Y81A/S84D/I157L/Y328F
mutation M576 Y81A/F88E/I157L/Y328F
mutation M577 Y81A/F113W/I157L/Y328F
mutation M578 Y81A/I157L/G161A/Y328F
mutation M579 Y81A/I157L/W187F/Y328F
mutation M580 Y81A/I157L/A204S/Y328F
mutation M581 Y81A/I157L/T210L/Y328F
mutation M582 Y81A/I157L/A233D/Y328F
mutation M583 Y81A/I157L/Y328F/V439P
mutation M584 Y81A/A184G/W187F/Y328F
mutation M585 F88E/I157L/T210L/Y328F
mutation M586 F88E/I157L/A233D/Y328F
mutation M587 F113W/I157L/A204T/T210L
mutation M588 F113W/I157L/T210L/Y328F
mutation M589 I157L/G161A/A184G/W187F
mutation M590 I157L/G161A/T210L/Y328F
mutation M591 I157L/A184G/W187F/T210L
mutation M592 I157L/A204S/T210L/Y328F
mutation M593 I157L/A204T/T210L/Y328F
mutation M594 I157L/T210L/A233D/Y328F
mutation M595 G161A/A184G/W187F/Y328F
mutation M596 P70T/A72E/S84D/I157L/Y328F
mutation M597 P70T/A72E/A204S/I157L/Y328F
mutation M598 P70T/A72E/T210L/I157L/Y328F
mutation M599 P70T/A72E/G226A/I157L/Y328F
mutation M600 P70T/A72E/A233D/I157L/Y328F
mutation M601 P70T/Y81A/I157L/T210L/Y328F
mutation M602 P70T/Y81A/I157L/A233D/Y328F
mutation M603 P70T/Y81A/I157L/T210L/Y328F
mutation M604 P70T/Y81A/A233D/I157L/Y328F
mutation M605 P70T/S84D/I157L/T210L/Y328F
mutation M606 P70T/F113W/I157L/T210L/Y328F
mutation M607 P70T/I157L/A184G/W187F/A233D
mutation M608 P70T/I157L/W187F/T210L/Y328F
mutation M609 P70T/I157L/A204S/T210L/Y328F
mutation M610 P70T/G161A/A184G/W187F/Y328F
mutation M611 P70V/A72E/F113Y/I157L/Y328F
mutation M612 P70V/A72E/I157L/F211W/Y328F
mutation M613 A72E/S74T/F113Y/I157L/Y328F
mutation M614 A72E/S74T/I157L/F211W/Y328F
mutation M615 A72E/Y81H/I157L/F211W/Y328F
mutation M616 A72E/K83P/F113Y/I157L/Y328F
mutation M617 A72E/W17F/F113Y/I157L/Y328F
mutation M618 A72E/F113Y/D115Q/I157L/Y328F
mutation M619 A72E/F113Y/I157L/Y328F/L340V
mutation M620 A72E/F113Y/I157L/Y328F/V439P
mutation M621 A72E/F113Y/G161A/I157L/Y328F
mutation M622 A72E/F113Y/A204S/I157L/Y328F
mutation M623 A72E/F113Y/A204T/I157L/Y328F
mutation M624 A72E/F113Y/T210L/I157L/Y328F
mutation M625 A72E/F113Y/A233D/I157L/Y328F
mutation M626 A72E/I157L/G161A/F162L/Y328F
mutation M627 A72E/I157L/W187F/F211W/Y328F
mutation M628 A72E/I157L/A204S/F211W/Y328F
mutation M629 A72E/I157L/A204T/F211W/Y328F
mutation M630 A72E/I157L/F211W/Y328F/L340V
mutation M631 A72E/I157L/F211W/Y328F/V439P
mutation M632 A72E/I157L/G226A/F211W/Y328F
mutation M633 A72E/I157L/A233D/F211W/Y328F
mutation M634 Y81A/S84D/I157L/T210L/Y328F
mutation M635 Y81A/I157L/A184G/W187F/Y328F
mutation M636 Y81A/I157L/A184G/W187F/T210L
mutation M637 Y81A/I157L/A233D/T210L/Y328F
mutation M638 F88E/I157L/A184G/W187F/T210L
mutation M639 F113Y/I157L/Y159N/F211W/Y328F
mutation M640 I157L/A184G/W187F/T210L/Y328F
mutation M641 P70T/I157L/A184G/W187F/T210L/Y328F
mutation M642 Y81A/I157L/A184G/W187F/T210L/Y328F.
[56] The mutant protein according to [55] above wherein, in said amino acid sequence comprising one or more mutations selected from any of the mutations M1 to M642, said amino acid sequence further comprises at other than the mutated position(s) one or several amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions, said mutant protein having a peptide-synthesizing activity.
[57] The mutant protein according to any one of [55] to [56] above comprising at least the mutation M241.
[58] The mutant protein according to any one of [55] to [57] above comprising at least the mutation M340.
[59] The mutant protein according to any one of [55] to [58] above comprising at least the mutation M412.
[60] The mutant protein according to any one of [55] to [59] above comprising at least the mutation M491.
[61] The mutant protein according to any one of [55] to [60] above comprising at least the mutation M496.
[62] The mutant protein according to any one of [55] to [61] above comprising at least the mutation M581.
[63] The mutant protein according to any one of [55] to [62] above comprising at least the mutation M582.
[64] The mutant protein according to any one of [55] to [63] above comprising at least the mutation M594.
[65] A polynucleotide encoding an amino acid sequence of the mutant protein according to any one of [18] to [64] above.
[66] A recombinant polynucleotide comprising the polynucleotide according to [65] above.
[67] A transformed microorganism comprising the recombinant polynucleotide according to [66] above.
[68] A method for producing a mutant protein comprising culturing the transformed microorganism according to [67] above in a medium, to accumulate the mutant protein in the medium and/or the transformed microorganism.
[69] A method for producing a peptide comprising performing a peptide-synthesizing reaction in the presence of the mutant protein according to any one of [18] to [64] above.
[70] A method for producing a peptide comprising culturing the transformed microorganism according to [67] above in a medium to accumulate the mutant protein in the medium and/or the transformed microorganism for performing a peptide-synthesizing reaction.
[71] A method for producing α-L-aspartyl-L-phenylalanine-β-ester comprising reacting L-aspartic acid-α,β-diester and L-phenylalanine in the presence of the mutant protein according to any one of [18] to [64] above.
[72] A method for producing α-L-aspartyl-L-phenylalanine-β-ester comprising culturing the transformed microorganism according to [67] above in a medium to accumulate the mutant protein in the medium and/or the transformed microorganism for performing a reaction of L-aspartic acid-α,β-diester and L-phenylalanine.
According to the present invention, a protein having an excellent peptide-synthesizing activity and a method for efficient peptide production are provided.
Embodiments for carrying out the invention will be described below along with the best mode thereof.
Concerning various genetic engineering techniques described below, many standard experimental manuals such as Molecular Cloning, 2nd edition, Cold Spring Harbor Press (1989); Saibo Kogaku Handbook (Cellular Engineering Handbook) edited by Toshio Kuroda et al., Yodosha (1992); and Shin Idenshi Kogaku Handbook (New Genetic Engineering Handbook) revised 3rd version, edited by Muramatsu et al., Yodosha (1999) are available, and the techniques may be carried out by those skilled in the art with reference to these literatures.
Abbreviations as used herein for amino acids, peptides, nucleic acids, nucleotide sequences and the like are in conformity with definitions by IUPAC (International Union of Pure and Applied Chemistry) or IUBMB (International Union of Biochemistry and Molecular Biology), or conventional legends used in “Guideline for the preparation of specification and others containing a base sequence and an amino acid sequence” (edited by Japanese Patent Office) and in this field of art. Sequence numbers used herein indicate the sequence numbers in Sequence Listing unless otherwise specified. With respect to amino acids other than glycine, when a D-amino acid or an L-amino acid is not specified, the amino acid refers to the L-amino acid.
1. Proteins Having a Peptide-Synthesizing Activity of the Present Invention (Mutant Proteins Based on the Amino Acid Sequence of SEQ ID NO:2)
The protein of the present invention is a mutant protein having an amino acid sequence in which one or more mutations from any of the following mutations 1 to 68 have been introduced in the amino acid sequence of SEQ ID NO:2, and has a peptide-synthesizing activity (this protein may be referred to hereinbelow as the “mutant protein (I)”). The mutations 1 to 68 are as shown in Tables 1-1 and 1-2.
As shown in Tables 1-1 and 1-2, each mutation in the present specification is specified by the abbreviation of the amino acid residue and the position in the amino acid sequence in SEQ ID NOS:1 or 2. For example, “F207V” which is designated as the mutation 1 indicates that the amino acid residue, phenylalanine at position 207 in the sequence of SEQ ID NO:2 has been substituted with valine. That is, the mutation is represented by the type of the amino acid residue in a wild type (amino acid specified in SEQ ID NO:2), the position of the amino acid residue in the amino acid sequence of SEQ ID NO:2, and the type of the amino acid residue after introduction of the mutation. Other mutations are represented in the same fashion.
Each of the mutations 1 to 68 may be introduced alone or in combination of two or more. One or more of the mutations 1 to 68 may be introduced in combination with one or more mutations selected from the mutations other than those in Tables 1-1 and 1-2, for example, mutations in V184N, Q229P, Q229L, Q229G, Q229I, I228G, I228L, I228D, I228S, I230D, I230V, I230S, S256C, A301G, L66F, E80K, Y81A, I157L, V178G, A182G, A182S, P183A, V184P, T185F, T185A, T185K, T185D, T185C, T185S, T185P, T185N, T210L, V213A, P214T, P214H, A245S, L263M, K314R, S315R, Y328F, K484I, and A515V. Specifically, the combinations as shown in the following Tables 1-3 and 1-4 are preferable. The mutant protein comprising at least the mutation 2: Q441E and the mutant protein comprising at least the mutation 14: T72A are preferable in terms of enhanced peptide-synthesizing activity. In addition, the mutant proteins comprising the combination of M7-35, and M35-4+V184A (A1) are also preferable in terms of enhanced peptide-synthesizing activity.
M7-35; A301V + L439V + A537G + N607K
M35-4/V184A = A1; T72A + A137S + Q229P + V257I + A301V + A324V + L439V + Q441E + A537G + N607K + V184A
The mutant protein of the present invention has an excellent peptide-synthesizing activity. That is, the mutant protein exert more excellent performance as to capability to catalyze a peptide-synthesizing reaction than the wild type protein having the amino acid sequence of SEQ ID NO:2. More specifically, each mutant protein of the present invention exert more excellent performance as to any of the properties required for the peptide-synthesizing reaction, such as a reaction rate, a yield, a substrate specificity, a pH property and a temperature stability, than the wild type protein when the peptide is synthesized from a specific carboxy component and a specific amine component (specifically, see the following Examples). Thus, the mutant protein of the present invention may be used suitably for production of the peptide on an industrial scale. A preferable embodiment of the mutant protein may be those having the ability to achieve preferably 1.3 times or more, more preferably 1.5 times or more and still more preferably 2 times or more peptide concentration when the peptide concentration achieved by the wild type protein is “1”.
In the present specification, the peptide-synthesizing activity refers to an activity to synthesize a new compound having a peptide bond by forming the peptide bond from two or more substances, and more specifically refers to the activity to synthesize a peptide compound obtained by increasing at least one peptide bond from, e.g., two amino acids or esters thereof.
The mutation shown in the mutations 1 to 68 and the mutations 239 to 290 and 324 to 377 may be introduced by modifying the nucleotide sequence of the gene encoding the protein having the amino acid sequence of SEQ ID NO:2 by, e.g., a site-directed mutagenesis such that the amino acid at specific position is substituted. The nucleotide sequence corresponding to the position to be mutated in the amino acid sequence of SEQ ID NO:2 may easily be identified by referring to SEQ ID NO:1. A polypeptide encoded by the nucleotide sequence modified as the above may be obtained by conventional mutagenesis. Examples of the mutagenesis may include a method of in vitro treatment of a DNA encoding the protein with hydroxylamine, a method of introduction of the mutation by error-prone PCR, and a method of amplification of a DNA in a host which lacks a mutation repair system and subsequent retrieval of the mutated DNA.
According to the present invention, substantially the same protein as the mutant protein comprising one or more mutations selected from the above mutations 1 to 68 and the mutations 239 to 290 and 324 to 377 is also provided. That is, the present invention also provides a mutant protein wherein, in the mutant protein comprising one or more mutations selected from the mutations 1 to 68 and the mutations 239 to 290 and 324 to 377, the amino acid sequence thereof further comprises at other than the mutated position(s) one or more amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions; and wherein the mutant protein has the peptide-synthesizing activity (the protein may be referred to hereinbelow as the “mutant protein (II)”). That is, the mutant protein of the present invention may contain the mutation at the position other than positions of the mutations 1 to 68, 239 to 290 and 324 to 377 of the amino acids shown in SEQ ID NO:2. Therefore, when the mutation such as deletions and insertions has been introduced at the position other than the positions of the mutations 1 to 68, 239 to 290 and 324 to 377, the number of amino acid residues from the position specified by the mutations 1 to 68, 239 to 290 and 324 to 377 to the N terminus or the C terminus may be sometimes different from that before introducing the mutation.
As used herein, “several amino acids” may vary depending on the position and the type in the tertiary structure of the protein of amino acid residues, but may be in a range so as not to significantly impair the tertiary structure and the activity of the protein of amino acid residues. Specifically, “several” may refer to 2 to 50, preferably 2 to 30 and more preferably 2 to 10 amino acids. In the case of the mutant protein comprising the mutated position other than the positions of the mutations 1 to 68, 239 to 290 and 324 to 377, it is desirable to retain the peptide-synthesizing activity at about a half or more, more preferably 80% or more and still more preferably 90% or more of that of the protein comprising one or more mutations from the mutations 1 to 68, 239 to 290 and 324 to 377 (i.e., the mutant protein (I)) under a condition at 50° C. and pH 8.
The mutation other than the mutations 1 to 68, 239 to 290 and 324 to 377 may also be obtained by, e.g., the site-directed mutagenesis method for modifying the nucleotide sequence so that an amino acid at a specific position of the present protein is substituted, deleted, inserted, added or inverted. The polypeptide encoded by the nucleotide sequence modified as the above may also be obtained by the conventional mutagenesis. Examples of the mutagenesis may include the method of in vitro treating the DNA encoding the mutant protein (I) with hydroxylamine, and the method of treating Escherichia bacteria which carries the DNA encoding the mutant protein (I) with ultraviolet ray or with a conventional mutagen for artificial mutagenesis such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and nitrous acid.
The mutations such as substitutions, deletions, insertions, additions and inversions of nucleotides as the above encompass naturally occurring mutations such as those owing to difference of species or microbial strains of the microorganism. A DNA encoding substantially the same protein as the protein of SEQ ID NO:2 may be obtained by expressing the DNA having the mutation as the above in an appropriate cell and examining the enzyme activity of the expressed products.
2. Design and Preparation of Mutant Protein Based on Amino Acid Sequence of SEQ ID NO:208
The present inventor found out that the mutant peptide which is more excellent in peptide-synthesizing activity may be designed and prepared by further adding the mutation to the aforementioned mutant protein. In particular, the inventors found out that the mutant protein which exerts the remarkable peptide-synthesizing activity is obtainable by further adding the mutation to the M35-4/V184A mutant (A1) (mutation 286; see Table 1-3). The present invention also provides the method for designing and producing the mutant protein based on such an M35-4/V184A mutant (A1).
The amino acid sequence corresponding to the M35-4/V184A is as shown in SEQ ID NO:208. That is, in the amino acid sequence of SEQ ID NO:208, the amino acid residues at 11 positions have been substituted with other amino acid residues corresponding to the M35-4/V184A mutation (see Table 1-3) based on the amino acid sequence of SEQ ID NO:2.
The mutant protein may be designed and produced based on tertiary structure determination by X-ray crystal structure analysis and the structural information determined thereby. That is, the mutant protein having the peptide-synthesizing activity may be designed and produced by predicting the substrate binding site based on the tertiary structure obtained by analyzing the X-ray crystal structure of the protein, and changing at least a part of the substrate binding site of the protein.
The determination of the protein tertiary structure by analyzing the X-ray crystal structure may be performed by, for example, the following procedure.
(1) A protein is crystallized. Crystallization is essential for the determination of the tertiary structure, and is industrially useful as the method for purifying the protein at high purity and the method for stably storing the protein with high density and high protease resistance.
(2) The prepared crystal is then irradiated with an X-ray, and diffraction data are collected. The protein crystal is often damaged by X-ray irradiation and lose diffraction quality. In order to avoid such a phenomenon, the low-temperature measurement where the crystal is rapidly cooled to about −173° C. and the diffraction data are collected in that state has become common recently. To finally collect high resolution data used for the structure determination, synchrotron radiation with high luminance may be utilized.
(3) Subsequently, a crystal structure is analyzed. To analyze the crystal structure, phase information is required in addition to the diffraction data. For example, for the protein having the amino acid sequence of SEQ ID NO:209, the structure can be determined by a molecular replacement method because the crystal structure of an analogous protein, the S205A mutant of α-amino acid ester hydrolase (Entry Number of Protein Data Bank: 1NX9), has been known publicly. The model of the protein is then fit to the electron density map calculated using the determined phase. This process is performed on computer graphics using a program such as QUANTA supplied from Accelrys (USA). Subsequently, the structure is refined using the program such as CNX supplied from Accelrys to complete the structural analysis.
The substrate binding site of the protein may be predicted based on the tertiary structure analyzed as a result of the aforementioned processing. As used herein, the “substrate binding site” means the site on the protein surface at which the substrate (e.g., the amino acid or amino acid ester in the case of the protein having the peptide-synthesizing activity) interacts, and is generally present around an active center of the protein.
In the method for design and production of the present invention, the protein having the amino acid sequence of SEQ ID NO:208 is used as the subject of the crystal structure analysis. The protein having the amino acid sequence of SEQ ID NO:208 is the mutant protein M35-4/V184A as already described. That is, the amino acid sequence of SEQ ID NO:208 is the same as the amino acid sequence of SEQ ID NO:2 except that the amino acid residues at 11 positions have been substituted with the specific amino acid residues corresponding to the mutation M35-4/V184A described in Table 1-3.
The amino acid sequence of SEQ ID NO:209 and the amino acid sequence of SEQ ID NO:208 are very highly homologous, and only 4 amino acid residues have been substituted. Therefore, the substrate binding site of the protein having the amino acid sequence of SEQ ID NO:208 may be predicted by analyzing the crystal structure of the protein having the amino acid sequence of SEQ ID NO:209, and referring to the resulting tertiary structure. The substrate binding site of the protein having the amino acid sequence of SEQ ID NO:208 was predicted as a region within 15 angstroms from an active residue serine (position 158 in the amino acid sequence of SEQ ID NO:208, which may be abbreviated hereinbelow as “Ser158”; see an “active site” in
In the method for design and production of the present invention, it is possible to obtain a mutant having a enhanced peptide-synthesizing activity by changing at least a part of the predicted substrate binding site. As used herein, “changing at least a part of the substrate binding site” means modification of one or more residues in the amino acid residues which configure the substrate binding site, particularly substituting, inserting or deleting, and preferably substituting with the other amino acid residues, with a proviso that the mutant protein after changing has the peptide-synthesizing activity. The number of the amino acid residues subjected to the modification may vary depending on the position and the type of the amino acid residues, and may be suitably determined in the range in which the tertiary structure and the activity of the resulting mutant protein are not significantly impaired.
For example, in order to obtain the mutant protein having the peptide-synthesizing activity from the protein having the amino acid sequence of SEQ ID NO:208, at least one or more amino acid residues may be substituted, inserted or deleted at positions in at least a part of the region within 15 angstroms from the active residue Ser158 in the protein, i.e., at positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340, and 437 to 447 in the amino acid sequence of SEQ ID NO:208. Specifically, the desired mutant protein may be obtained by substituting at least one residue among the foregoing amino acid residues with another amino acid residue.
In particular, the mutant protein obtained by substituting, inserting or deleting at least one or more amino acid residues at positions 67, 69, 70, 72 to 85, 103, 106, 107, 113 to 116, 165, 182, 183, 185, 187, 188, 190, 200, 202, 204 to 206, 209 to 211, 213 to 235, 301, 328, 338 to 340, 440 to 442 and 446 in the amino acid sequence of SEQ ID NO:208 may have a high peptide-synthesizing activity and particularly have an enhanced AMP-synthesizing activity. Specifically, AMP yield enhancement probability of these mutant proteins compared with the A1 mutant protein is 20% or more.
Particularly, the mutant protein obtained by substituting, inserting or deleting at least one or more amino acid residues at positions 67, 69, 70, 72 to 84, 106, 107, 114, 116, 183, 185, 187, 188, 202, 204 to 206, 209, 211, 213 to 233, 235, 328, 338 to 442, and 446 in the amino acid sequence of SEQ ID NO:208 and having the peptide-synthesizing activity may have a high peptide-synthesizing activity and a particularly enhanced AMP-synthesizing activity. Specifically, AMP yield enhancement probability of these mutant proteins compared with the A1 mutant protein is 30% or more.
Further, the mutant protein obtained by substituting, inserting or deleting at least one or more amino acid residues at positions 67, 70, 72 to 75, 77 to 79, 81 to 84, 114, 116, 185, 188, 202, 204, 206, 209, 211, 213 to 215, 218 to 224, 226 to 233, 235, 328, 338 to 441 and 446 in the amino acid sequence of SEQ ID NO:208 and having the peptide-synthesizing activity may have a high peptide-synthesizing activity, and a particularly enhanced AMP-synthesizing activity. Specifically, AMP yield enhancement probability of these mutant proteins compared with the A1 mutant protein is 40% or more.
It is preferable that the designed mutant protein has homology in terms of its primary sequence (i.e., amino acid sequences) to some extent with the A1 mutant protein. The homology may be, for example, 25% or more, more preferably 50% or more, still more preferably 80% or more and particularly preferably 90% or more.
It is possible to find out the mutant protein having the enhanced peptide-synthesizing activity by changing at least a part of the amino acid positions, i.e., substituting one or more amino acid residue, in the aforementioned range of the amino acid residues. It is also possible to combine mutations each of which has brought about the enhanced activity, to create a mutant protein having further enhanced peptide-synthesizing activity by their synergistic effect. Meanwhile, in the enhancement of the peptide-synthesizing activity by the mutation, changing of even one atom of a side chain in the amino acid residue may possibly result in a drastic change. Therefore, there are various possibilities for the optimization. For example, if mutation of a certain position reveals that the position is involved in enhancement of the activity, random mutation on several residues neighboring the position in the tertiary structure may result in discovery of a mutant having a further enhanced activity. That is, it is possible to obtain a mutant protein having a peptide-synthesizing activity by modification of at least a part of positions which configure a continuous surface in terms of a tertiary structure with an amino acid residue whose modification brings about enhancement of the peptide-synthesizing activity.
The surface of a protein is an envelop surface of the part exposed to a solvent when constitutive atoms are represented as a sphere with van der Waals radius, and may be figured by a space-filling view as shown in
(a) One or more amino acid residue substitutions, insertions or deletions at any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:208
(b) One or more amino acid residue substitutions, insertions or deletions at any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:208
(c) One or more amino acid residue substitutions, insertions or deletions at any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:208
(d) One or more amino acid residue substitutions, insertions or deletions at any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:208
(e) One or more amino acid residue substitutions, insertions or deletions at any of positions 70, 106, 113, 115, 193, 207, 209-212, 216 and 259 in the amino acid sequence of SEQ ID NO:208
(f) One or more amino acid residue substitutions, insertions or deletions at any of positions 200, 202-205, 207 and 228 in the amino acid sequence of SEQ ID NO:208
(g) One or more amino acid residue substitutions, insertions or deletions at any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:208
(h) One or more amino acid residue substitutions, insertions or deletions at any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:208
(i) One or more amino acid residue substitutions, insertions or deletions at any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:208
3. Design and Preparation of a Mutant Protein on The Basis of Other Proteins than the Mutant Protein of SEQ ID NO:208
The tertiary structure of the protein having the amino acid sequence of SEQ ID NO:209 obtained by the X-ray crystal structure analysis described above may be practically applied to designing and producing a mutant protein on the basis of other proteins than the protein having the amino acid sequence of SEQ ID NO:208. The present invention also provides a mutant protein derived from such other proteins and having the peptide-synthesizing activity equal to or higher than that of the protein having the amino acid sequence of SEQ ID NO:208.
The mutant protein on the basis of other proteins than the protein having the amino acid sequence of SEQ ID NO:208 may be designed and produced by the alignment of the tertiary structure with the protein having the amino acid sequence of SEQ ID NO:209 by the threading method, and giving the same amino acid mutations as the protein having the amino acid sequence of SEQ ID NO:208. As already described, the amino acid residues at only 3 positions are different between the protein having the amino acid sequence of SEQ ID NO:208 and the protein having the amino acid sequence of SEQ ID NO:209. Thus, their three dimensional structures may be regarded to be almost the same.
The protein to which mutation is introduced with the threading method is a protein other than the protein having the amino acid sequence of SEQ ID NO:208, and preferably a protein having the peptide-synthesizing activity. Furthermore, it is preferable to use the protein whose amino acid sequence has been already known. It is preferable that the protein to be mutated has a tertiary structure similar to that of the mutant protein having the amino acid sequence of SEQ ID NO:209. As used herein, “having a similar tertiary structure” means that secondary structures or three dimensional structures are similar, and specifically means the similarity in distances between the amino acid residues and angles of backbones and side chains which configure the peptides.
The threading method may be used for determining whether the protein other than the protein having the amino acid sequence of SEQ ID NO:208 has the similar tertiary structure to that of the protein having the amino acid sequence of SEQ ID NO:209 or not. The threading method is a method in which what tertiary structure the amino acid sequence has is assessed and predicted on the basis of the similarity with known tertiary structures in the database (Science 253:164-170, 1991).
The similarity of the tertiary structures is determined and assessed in the threading method by aligning the amino acid sequence of the subject protein with the tertiary structure of the protein having the amino acid sequence of SEQ ID NO:209, calculating an objective function which quantifies fitness of these structures as to, e.g. easiness to make the secondary structure, and comparing/examining the results. The data described in
The threading method may be carried out by the use of the program such as INSIGHT II and LIBRA. INSIGHT II is available from Accelrys in USA. To carry out the threading method using INSIGHT II, SeqFold module in the program may be utilized. Meanwhile, LIBRA may be used by using the Internet and accessing the address of a homepage of DDBJ (http://www.ddbj.nig.ac.jp/search/libra_i-j.html).
As a standard to determine whether the certain protein has the similarity in the tertiary structure with the protein having the amino acid sequence of SEQ ID NO:209 or not, it is preferable to use a total assessment value (SeqFold total score (bits)) calculated by gathering up all assessment functions by the threading method when using INSIGHT II-SeqFold. It is possible to determine by calculating SeqFold total score (bits) whether the tertiary structures of the proteins are generally similar. When the threading method is carried out using the program SeqFold, various assessment values such as SeqFold (LIB) P value, SeqFold (LIB) P-value, SeqFold (LEN) P-value, SeqFold (LOW) P-value, SeqFold (High) P-value, SeqFold Total Score (raw), and SeqFold Alignment Score (raw) are calculated, and SeqFold Total Score (bits) is the total assessment value calculated by gathering up all these assessment values. The larger the value of SeqFold Total Score (bits) means that the higher the similarity between the tertiary structures of compared two proteins is. For example, when the threading method is carried out using INSIGHT II, it seems to be reasonable that a threshold for determining whether or not the protein has the similar tertiary structure to that of the protein having the amino acid sequence of SEQ ID NO:209 is about 90 as the value of SeqFold Total Score (bits). That is, if the value of SeqFold Total Score (bits) is 90 or more, it may be appropriate to determine that the tertiary structure of the protein having the amino acid sequence of SEQ ID NO:209 and the tertiary structure of the protein in question have the similarity. The more preferable threshold is 110 or more, still more preferably 130 or more and particularly preferably 150 or more as the value of SeqFold Total Score.
When it is determined that the protein in question has the similar tertiary structure to that of the protein having the amino acid sequence of SEQ ID NO:209, the amino acid residues in the sequence of the determined protein corresponding to the amino acid residues present within 15 angstroms from the active residue Ser158 of the protein having the amino acid sequence of SEQ ID NO:209 are specified. The objective amino acid residues may be specified by the alignment of the three dimensional structure of the objective protein with the protein having the amino acid sequence of SEQ ID NO:209, which is obtained in the process of determining the similarity of the three dimensional structure by the threading method.
In the method for the design and production of the present invention, the peptide other than the peptide having the amino acid sequence of SEQ ID NO:208 may also be subjected to the changing of at least a part of the predicted substrate binding site, to find out the mutant protein having the enhanced peptide-synthesizing activity. It is possible combine mutations each of which has brought about the enhanced activity, to create a mutant having a further enhanced activity by their synergistic effect. As used herein, “changing of at least a part of the substrate binding site” means modification of one or more residues in the amino acid residues which configure the substrate binding site, particularly substituting, inserting or deleting, and preferably substituting with the other amino acid residues, with a proviso that the mutant protein after changing has the peptide-synthesizing activity. The number of the amino acid residues subjected to the modification varies depending on the position and the type of the amino acid residues, and may be suitably determined in the range in which the tertiary structure and the activity of the resulting mutant protein are not significantly impaired.
For example, one or more amino acid residues in the amino acid sequence of the protein in question may be substituted, inserted or deleted at the position(s) corresponding to the positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340 and 437 to 447 in the amino acid sequence of SEQ ID NO:209, the correspondence being made in the three-dimensional alignment of the protein in question with the protein having the amino acid sequence of SEQ ID NO:209 upon the determination by the threading method. Specifically, the desired mutant protein may be obtained by substituting one or more amino acid residues among the amino acid residues at the aforementioned corresponding (overlapping) positions as a result of the alignment, with another amino acid residue.
It is preferable that the mutant protein to be designed has the homology to some extent with the protein having the amino acid sequence of SEQ ID NO:207 in terms of their primary sequences. The homology may be, for example, 25% or more, more preferably 50% or more, still more preferably 80% or more and particularly preferably 90% or more.
It is possible to find out the mutant protein having the enhanced peptide-synthesizing activity by changing at least a part of the amino acid positions, i.e., substituting one or more amino acid residue, in the aforementioned range of the amino acid residues. It is also possible to combine mutations each of which has brought about the enhanced activity, to create a mutant protein having further enhanced peptide-synthesizing activity by their synergistic effect. Meanwhile, in the enhancement of the peptide-synthesizing activity by the mutation, changing of even one atom of a side chain in the amino acid residue may possibly result in a drastic change. Therefore, there are various possibilities for the optimization. For example, if mutation of a certain position reveals that the position is involved in enhancement of the activity, random mutation on several residues neighboring the position in the tertiary structure may result in discovery of a mutant having a further enhanced activity. That is, it is possible to obtain a mutant protein having a peptide-synthesizing activity by modification of at least a part of positions which configure a continuous surface in terms of a tertiary structure with an amino acid residue whose modification brings about enhancement of the peptide-synthesizing activity.
In the protein other than the protein having the amino acid sequence of SEQ ID NO:208, “the position which configures a continuous surface in terms of the tertiary structure with an amino acid residue whose modification brings about enhancement of the peptide-synthesizing activity” is a position which configures a surface (plane) facing the substrate binding site (Ser158) with base positions that are the positions of the amino acid residues which correspond to the positions 67 to 70, 72 to 88, 100, 102, 103, 106, 107, 113 to 117, 130, 155 to 163, 165, 166, 180 to 188, 190 to 195, 200 to 235, 259, 273, 276, 278, 292 to 294, 296, 298, 299, 300 to 304, 325 to 328, 330 to 340 and 437 to 447 in the amino acid sequence of SEQ ID NO:209, the correspondence being made in the three-dimensional threading alignment of the protein in question with the protein having the amino acid sequence of SEQ ID NO:209. Specifically, it is possible to obtain the mutant protein having the peptide-synthesizing activity by causing one or more changes selected from the following (a′) to (i′).
(a′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:209
(b′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:209
(c′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:209
(d′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:209
(e′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 70, 106, 113, 115, 193, 207, 209 to 212, 216 and 259 in the amino acid sequence of SEQ ID NO:209
(f′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 200, 202 to 205, 207 and 228 in the amino acid sequence of SEQ ID NO:209
(g′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:209
(h′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:209
(i′) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:209
It is also possible to obtain a mutant protein having a peptide-synthesizing activity by causing one or more changes selected from the following (a″) to (i″) in those having the homology of 25% or more in the primary sequence when the primary sequence alignment or the tertiary structure alignment of the protein in question with the protein having the amino acid sequence of SEQ ID NO:209 is performed.
(a″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 79 to 82 in the amino acid sequence of SEQ ID NO:209
(b″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 84, 88, 89 and 92 in the amino acid sequence of SEQ ID NO:209
(c″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 72, 75 and 77 in the amino acid sequence of SEQ ID NO:209
(d″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 159, 161, 162, 184, 187 and 276 in the amino acid sequence of SEQ ID NO:209
(e″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 70, 106, 113, 115, 193, 207, 209 to 212, 216 and 259 in the amino acid sequence of SEQ ID NO:209
(f″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 200, 202 to 205, 207 and 228 in the amino acid sequence of SEQ ID NO:209
(g″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 233, 234 and 439 in the amino acid sequence of SEQ ID NO:209
(h″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 328, 339, 340, 445 and 446 in the amino acid sequence of SEQ ID NO:209
(i″) At least one or more amino acid residue substitutions, insertions or deletions in the tertiary structure corresponding to any of positions 87, 155, 157 and 160 in the amino acid sequence of SEQ ID NO:209
4. Proteins Having Peptide-Synthesizing Activity of the Present Invention (Mutant Proteins Based on Amino Acid Sequence of SEQ ID NO:208)
The protein of the present invention is the mutant protein designed and produced by the methods for the design and production described in the sections 2 and 3 above, and specifically is the mutant protein having the amino acid sequence where one or more mutations from any of the following mutations L1 to L335 or the following mutations M1 to M642 have been introduced into the amino acid sequence of SEQ ID NO:208 and having the peptide-synthesizing activity (these proteins may be referred to hereinbelow as the “mutant protein (I′) of the protein having the amino acid sequence of SEQ ID NO:208”). The mutations L1 to L335, and the mutations M1 to M642 are as shown in Tables 2-1 to 2-19.
Each mutation in the present specification is specified, as is the case with the mutant protein based on the amino acid sequence of SEQ ID NO:2 described above, by the abbreviations of the amino acid residues and the position in the amino acid sequence in SEQ ID NO:208, as shown in Tables 2-1 to 2-19. For example, the mutation L1, “N67K” represents that the amino acid residue, asparagine at position 67 in the sequence of SEQ ID NO:208 has been substituted with lysine. That is, the mutation is represented by the type of amino acid residue in M35-4/V184A mutant (amino acid specified by SEQ ID NO:208); the position of the amino acid residue in the amino acid sequence of SEQ ID NO:208; and the type of the amino acid residue after the introduction of the mutation. Other mutations are represented in the same fashion.
Each of the mutations L1 to L335 may be introduced alone or in combination of two or more. One or more of the mutations L1 to L335 may be introduced in combination with one or more selected from the mutations other than the mutations in Tables 2-1 to 2-7, for example, the mutations shown in Table 33 which will be described later. Specifically, the combinations M1 to M642 as shown in Tables 2-8 to 2-19 described above are suitable. Particularly, mutant proteins having any of the following mutations are preferable in terms of improving peptide-synthesizing activity: mutation L125:I157L, mutation L124:I157K, mutation L303:Y328F, mutation L12:P70T, mutation L127:Y159N, mutation L199:F211W, mutation L195:F211I, mutation L130:G161A, mutation L115:D115Q, mutation L316:L340V, mutation L99:F88E, mutation L16:A72E, mutation L15:A72D, mutation L131:F162L, mutation L284:A233D, mutation L191:T210L, mutation L65:Y81A, mutation L265:I228K, mutation L317:V439P, mutation L255:G226A, mutation L52:G77S, mutation L155:F200A, mutation L298:R276A, mutation L201:G212A, mutation L145:W187F, mutation L170:A204S, mutation L87:S84D, mutation L60:E80D, mutation L110:F113W, mutation M241:I157L/Y328F, mutation M340:P70T/I157L/Y328F, mutation M412:Y81A/I157L/Y328F, mutation M491:I157L/T210L/Y328F, mutation M496:I157L/A233D/Y328F, mutation M581:Y81A/I157L/T210L/Y328F, mutation M582:Y81A/I157L/A233D/Y328F, and mutation M594:I157L/T210L/A233D/Y328F.
The present mutant protein has the excellent peptide-synthesizing activity. That is, these mutant protein exert a more excellent performance as to an ability to catalyze a peptide-synthesizing reaction than the protein (M35-4/V184A mutant protein) having the amino acid sequence of SEQ ID NO:208. More specifically, each mutant protein of the present invention exert more excellent performance for any of properties required for the peptide-synthesizing reaction, such as a reaction rate, a yield, a substrate specificity, a pH property and a temperature stability, than the protein shown in SEQ ID NO:208 when the peptide is synthesized from a specific carboxy component and amine component(specifically, see the following Examples). Thus, the mutant protein of the present invention may be used suitably for production of the peptide on an industrial scale.
The mutation shown in the mutations L1 to L335 and the mutations M1 to M642 may be introduced by modifying the nucleotide sequence of the gene encoding the protein having the amino acid sequence of SEQ ID NO:208 by site-directed mutagenesis such that the amino acid at the specific position is substituted. The nucleotide sequence corresponding to the positions to be mutated in the amino acid sequence of SEQ ID NO:208 may easily be identified with reference to SEQ ID NO:207.
The present invention also provides substantially the same protein as the mutant protein comprising one or more mutations shown in the above mutations L1 to L335 or the mutations M1 to M642. That is, the present invention also provides the mutant protein wherein, in the mutant protein comprising one or more of the mutations selected from the mutations L1 to L335 and M1 to M624, the amino acid sequence thereof further comprises, at other than the mutated position(s) in accordance with one or more of the mutations L1 to L335 and M1 to M624, one or more amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions; and wherein the mutant protein has the peptide-synthesizing activity (this protein may be referred to hereinbelow as the “mutant protein (II′) of the protein having the amino acid sequence of SEQ ID NO:208). That is, the mutant protein of the present invention may contain the mutation at position other than the positions of the mutations L1 to L335 and M1 to M624 in the amino acid sequence shown in SEQ ID NO:208. Therefore, when the mutation such as deletions and insertions has been introduced at the position other than the positions of the mutations L1 to L335 and M1 to M624, the number of amino acid residues from the position specified by the mutations L1 to L335 and M1 to M624 to the N terminus or the C terminus may be sometimes different from that before introducing the mutation.
As used herein, “several amino acids” vary depending on the position and the type of the tertiary structure of the protein of amino acid residues, but may be in a range so as not to significantly impair the tertiary structure and the activity. Specifically, “several” may refer to 2 to 50, preferably 2 to 30 and more preferably 2 to 10 amino acids. It is desirable that the mutated protein retains the peptide-synthesizing activity at about a half or more, more preferably 80% or more, still more preferably 90% or more and particularly preferably 95% or more of the protein comprising one or more mutations selected from the mutations L1 to L335 and M1 to M624 (i.e., the mutant protein (I′) of the protein having the amino acid sequence of SEQ ID NO:208).
The mutation other than those in the mutations L1 to L335 and M1 to M624 may be obtained by, e.g., site-directed mutagenesis for modifying the nucleotide sequence so that an amino acid at a specific position of the present protein is substituted, deleted, inserted, added or inverted. The polypeptide encoded by the nucleotide sequence modified as the above may also be obtained by conventional mutagenesis. The mutagenesis treatment and the meanings of the substitution, deletion, insertion, addition and inversion of the nucleotide are the same as defined in the foregoing section 1. The DNA encoding substantially the same protein as the protein described in SEQ ID NO:208 is obtainable by expressing the DNA having the above mutation in an appropriate cell and examining the present enzyme activity among the expressed products.
4. Polynucleotides of the Present Invention
The present invention provides a polynucleotide encoding the amino acid sequence of the above mutant protein of the present invention. Owing to codon degeneracy, the multiple nucleotide sequences may be present for defining one amino acid sequence. That is, the polynucleotides of the present invention encompass the following polynucleotides.
(i) The polynucleotide encoding the mutant protein having the amino acid sequence comprising one or more mutations from any of the mutations 1 to 68, and the mutations 239 to 290 and 324 to 377 in the amino acid sequence of SEQ ID NO:2.
(ii) The polynucleotide encoding the mutant protein having the amino acid sequence wherein, in the amino acid sequence comprising one or more mutations from any of the mutations 1 to 68, and the mutations 239 to 290 and 324 to 377 of the mutant protein (I), the amino acid sequence further comprises at other than the mutated positions one or several amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions; and having the peptide-synthesizing activity.
The amino acid sequence of SEQ ID NO:2 is encoded by, e.g., the nucleotide sequence of SEQ ID NO:1.
The present invention also provides a polynucleotide encoding the amino acid sequence of the mutant protein based on the protein having the amino acid sequence of SEQ ID NO:208 of the present invention. Owing to codon degeneracy, the multiple nucleotide sequences may be present for defining one amino acid sequence. That is, the polynucleotides of the present invention encompass the following polynucleotides.
(i′) The polynucleotide encoding the mutant protein having the amino acid sequence comprising one or more mutations from any of the mutations L1 to L335 and the mutations M1 to M624 in the amino acid sequence of SEQ ID NO:208.
(ii′) The polynucleotide encoding the mutant protein having the amino acid sequence further comprising one or more amino acid mutations selected from the group consisting of substitutions, deletions, insertions, additions and inversions at positions other than the mutated positions in the amino acid sequence comprising one or more mutations from any of the mutations 1 to L335 and the mutations M1 to M624 in the amino acid sequence in the mutant protein described in the above (I′), and having the peptide-synthesizing activity.
The amino acid sequence of SEQ ID NO:208 is encoded by, e.g., the nucleotide sequence of SEQ ID NO:207.
Substantially the same polynucleotide as the DNA having the nucleotide sequence shown in SEQ ID NO:1 may include the following polynucleotides. The specific polynucleotide to be separated may be a polynucleotide composed of a nucleotide sequence which hybridizes under a stringent condition with a polynucleotide complementary to the nucleotide sequence described in SEQ ID NO:1, or a probe prepared from the nucleotide sequence; and encodes a protein having the peptide-synthesizing activity. The specific polynucleotide may be isolated from the polynucleotide encoding the protein having the amino acid sequence described in SEQ ID NO:2 or from cells keeping the same. The polynucleotide which is substantially the same as the polynucleotide having the nucleotide sequence described in SEQ ID NO:1 may thus be obtained.
Meanwhile, the substantially the same polynucleotide as the DNA having the nucleotide sequence of SEQ ID NO:207 may also be obtained in the similar way to the aforementioned case with DNA of SEQ ID NO:1, i.e., may be obtained by isolating the polynucleotide from the polynucleotide encoding the protein having the amino acid sequence of SEQ ID NO:208 or from the cell having the same.
Likewise, the present invention provides the following polynucleotide (iii) or (iv) which is substantially the same as the polynucleotide encoding the mutant protein of the present invention.
(iii) The polynucleotide which hybridizes with the polynucleotide having the nucleotide sequence complementary to the nucleotide sequence of the aforementioned polynucleotide (i) under the stringent condition, and encodes the protein keeping one or more mutations selected from the mutations 1 to 68, 239 to 290 and 324 to 377 and having the peptide-synthesizing activity.
(iv) The polynucleotide which hybridizes with the polynucleotide having the nucleotide sequence complementary to the nucleotide sequence of the aforementioned polynucleotide (ii) under the stringent condition, and encodes the protein keeping one or more mutations selected from the mutations 1 to 68, 239 to 290 and 324 to 377 and having the peptide-synthesizing activity.
Likewise, the present invention provides the following polynucleotide (iii′) or (iv′) which is substantially the same as the polynucleotide encoding the mutant protein of the present invention.
(iii′) The polynucleotide which hybridizes with the polynucleotide having the nucleotide sequence complementary to the nucleotide sequence of the aforementioned polynucleotide (i′) under the stringent condition, and encodes the protein keeping one or more mutations selected from the mutations L1 to L335 and M1 to M642 and having the peptide-synthesizing activity.
(iv′) The polynucleotide which hybridizes with the polynucleotide having the nucleotide sequence complementary to the nucleotide sequence of the aforementioned polynucleotide (ii′) under the stringent condition, and encodes the protein keeping one or more mutations selected from the mutations L1 to L335 and M1 to M642 and having the peptide-synthesizing activity.
The probe for obtaining substantially the same polynucleotide may be prepared by standard methods based on the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:207 or the nucleotide sequence encoding the mutant protein. The method of isolating the objective polynucleotide by using the probe and taking the polynucleotide which hybridizes therewith may be performed in accordance with the standard method. For example, the DNA probe may be prepared by amplifying the nucleotide sequence cloned in a plasmid or phage vector, cutting out the nucleotide sequence to be used as the probe with restriction enzymes, and extracting it. The cut out site may be controlled depending on the objective DNA.
As used herein, the “stringent condition” refers to the condition where a so-called specific hybrid is formed whereas non-specific hybrid is not formed. Although it is difficult to clearly quantify this condition, examples thereof may include the condition where a pair of DNA sequences with high homology, e.g., DNA sequences having the homology of 50% or more, more preferably 80% or more, still more preferably 90% or more and particularly preferably 95% or more are hybridized whereas DNA with lower homology than that are not hybridized, and a washing condition of an ordinary Southern hybridization, i.e., hybridization at salt concentrations equivalent to 1×SSC and 0.1% SDS, and preferably 0.1×SSC and 0.1% SDS at 60° C. Among the genes which hybridize under such a condition, those having a stop codon in the middle of the sequence and which has lost the activity because of the mutation of the active center may be included. However, those may be easily removed by ligating them to the commercially available vector, expressing in an appropriate host, and measuring the enzyme activity of the expressed product by the method described below.
In the case of the polynucleotide in the above (ii), (iii) or (iv), it is desirable that the protein encoded by the polynucleotide retains the peptide-synthesizing activity at about a half or more, more preferably 80% or more and still more preferably 90% or more of the mutant protein in the above (I) under the condition at 50° C. and pH 8. Meanwhile, in the case of the polynucleotide in the above (ii′), (iii′) or (iv′), it is desirable that the protein encoded by the polynucleotide retains the peptide-synthesizing activity at about a half or more, more preferably 80% or more and still more preferably 90% or more of the mutant protein in the above (I) under the condition at 22° C. and pH 8.5.
5. Protein Having Amino Acid Sequence of SEQ ID NO:2, and Protein Having Amino Acid Sequence of SEQ ID NO:208
As described above, the mutant protein (I) and the mutant protein of the protein (II) having amino acid sequence of SEQ ID NO:208 may be obtained by modifying the proteins having amino acid sequences of SEQ ID NO:2 and SEQ ID NO:208. The protein which was used as a source of the protein of the invention will be described below. However, the mutant protein of the present invention is not limited to the source of the protein.
The DNA described in SEQ ID NO:1 and the protein having the amino acid sequence described in SEQ ID NO:2, as well as the DNA described in SEQ ID NO:207 and the protein having the amino acid sequence described in SEQ ID NO:208 are derived from Sphingobacterium multivorum FERM BP-10163 strain (indication given by the depositor for identification: Sphingobacterium multivorum AJ 2458). Microbial strains having an FERM number have been deposited to International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology, (Central No. 6, 1-1-1 Higashi, Tsukuba, Ibaraki Prefecture, Japan), and can be furnished with reference to the accession number.
A homogeneous protein to the protein having the amino acid sequence described in SEQ ID NO:2 or SEQ ID NO:208 may be isolated from Sphingobacterium sp. FERM BP-8124 strain. The protein where leucine, the amino acid residue at position 439 in the protein having the amino acid sequence described in SEQ ID NO:2 has been substituted with valine is isolated from Sphingobacterium sp. FERM BP-8124 strain. Sphingobacterium sp. FERM BP-8124 strain (indication given by the depositor for identification: Sphingobacterium sp. AJ 110003) was deposited on Jul. 22, 2002 to International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology, and the accession number was given. Microbial strains having the FERM number have been deposited to International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology, (Central No. 6, 1-1-1 Higashi, Tsukuba, Ibaraki Prefecture, Japan), and can be furnished with reference to the accession number.
The aforementioned microbial strain of Sphingobacterium multivorum was identified to be of Sphingobacterium multivorum by the following classification experiments. The aforementioned microbial strain had the following natures: bacillus (0.6 to 0.7×1.2 to 1.5 μm), gram negative, no sporogenesis, no mobility, circular colony form, smooth entire fringe, low convex, lustrous shining, yellow color, grown at 30° C., catalase positive, oxidase positive and OF test (glucose) negative, and was thereby identified to be of genus Sphingobacterium. Furthermore, the microbial strain was proven to be similar to Sphingobacterium multivorum in characterization by the following natures: nitrate reduction negative, indole production negative, negative for acid generation from glucose, arginine dihydrase negative, urease positive, aesculin hydrolysis positive, gelatin hydrolysis negative, β-galactosidase positive, glucose utilization positive, L-arabinose utilization positive, D-mannose utilization positive, D-mannitol utilization negative, N-acetyl-D-glucosamine utilization positive, maltose utilization positive, potassium gluconate utilization negative, n-capric acid utilization negative, adipic acid utilization negative, dl-malic acid utilization negative, sodium citrate utilization negative, phenyl acetate utilization negative and cytochrome oxidase positive. In addition, as a result of a homology analysis of a nucleotide sequence of 16S rRNA gene, the highest homology (98.5%) to Sphingobacterium multivorum was exhibited, and thus, the present microbial strain was identified as Sphingobacterium multivorum.
A DNA consisting of a nucleotide sequence of the base numbers 61 to 1917 in SEQ ID NO:1 is a code sequence portion. The nucleotide sequence of the base numbers 61 to 1917 includes a signal sequence region and a mature protein region. The signal sequence region is the region of the base numbers 61 to 120, and the mature protein region is the region of the base numbers 121 to 1917. That is, the present invention provides both a peptide enzyme protein gene containing the signal sequence and a peptide enzyme protein gene as the mature protein. The signal sequence containing the sequence described in SEQ ID NO:1 is a class of a leader sequence, and a major function of a leader peptide encoded in the leader sequence region is presumed to be secretion thereof from a cell membrane inside to a cell membrane outside. The protein encoded by the nucleotide sequence of the base numbers 121 to 1917, i.e., the region except the leader peptide sequence corresponds to the mature protein, and is presumed to have the high peptide-synthesizing activity.
The DNA having the nucleotide sequence of SEQ ID NO:1 may be obtained from a chromosomal DNA of Sphingobacterium multivorum or a DNA library by PCR (polymerase chain reaction, see White, T. J. et al; Trends Genet., 5, 185(1989)) or hybridization. Primers for PCR may be designed based on an internal amino acid sequence determined on the basis of the purified protein having the peptide-synthesizing activity. The primer or a probe for the hybridization may be designed based on the nucleotide sequence described in SEQ ID NO:1, or may also be isolated using a probe. When the primers having the sequences corresponding to a 5′-untranslated region and a 3′-untranslated region as the PCR primers, a full length coding region of the present protein may be amplified. Explaining as an example the primers for amplifying the region including the region encoding both the leader sequence and the mature protein described in SEQ ID NO:1, a primer having the nucleotide sequence of the upstream of the base number 61 in SEQ ID NO:1 may be used as the 5′-primer, and a primer having a sequence complementary to the nucleotide sequence of the downstream of the base number 1917 may be used as the 3′-primer.
The primers may be synthesized in accordance with standard methods, for example, by a phosphoamidite method (see Tetrahedron Letters, 22:1859, 1981) using a DNA synthesizer model 380B supplied from Applied Biosystems. The PCR reaction may be performed, for example, using Gene Amp PCR System 9600 (supplied from Perkin Elmer) and TaKaRa LA PCR in vitro Cloning Lit (supplied from Takara Shuzo Co., Ltd.) in accordance with instructions from the supplier such as manufacturer.
6. Method for Producing Mutant Protein of the Present Invention
The method for producing the protein of the present invention and the methods for producing recombinants and transformants used therefor will be subsequently described.
A transformant which expresses the aforementioned mutant protein can produce the mutant protein having the peptide-synthesizing activity. For example, the mutant protein having the activity may be produced by introducing the mutation corresponding to any of the mutations 1 to 38, 239 to 290 and 324 to 377 into a recombinant DNA such as an expression vector having the nucleotide sequence shown in SEQ ID NO:1, and introducing the expression vector into an appropriate host to express the mutant protein. A transformant which expresses the mutant protein of SEQ ID NO:208 can also produce the mutant protein having the peptide-synthesizing activity. For example, the mutant protein having the activity may be produced by introducing the mutation corresponding to any of the mutations L1 to L335, and M1 to M642 into a recombinant DNA such as an expression vector having the nucleotide sequence shown in SEQ ID NO:207, and introducing the expression vector into an appropriate host to express the mutant protein. As the host for expressing the mutant protein specified by the DNA having the nucleotide sequence of SEQ ID NO:1 or No:207, it is possible to use various prokaryotic cells such as microorganisms belonging genera Escherichia (e.g., Escherichia coli), Empedobacter, Sphingobacterium and Flavobacterium, and Bacillus subtilis as well as various eukaryotic cells such as Saccharomryces cerevisiae, Pichia stipitis, and Aspergillus oryzae.
The recombinant DNA for introducing a foreign DNA into the host may be prepared by inserting a predetermined DNA into the vector selected depending on the type of the host in a manner whereby a protein encoded by the DNA can be expressed. When a promoter inherent for a gene encoding the protein produced by Empedobacter brevis works in the host cell, that promoter may be used as the promoter for expressing the protein. If necessary, another promoter which works in the host cell may be ligated to the DNA encoding the mutant protein, which may be then expressed under the control of that promoter.
Examples of a transformation method for introducing the recombinant DNA into the host cell may include D. M. Morrison's method (Methods in Enzymology 68, 326 (1979)) or a method of enhancing permeability of the DNA by treating recipient microorganisms with calcium chloride (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)).
In the case of producing a protein on a large scale using the recombinant DNA technology, one of the preferable embodiments therefor may be formation of an inclusion body of the protein. The inclusion body is configured by aggregation of the protein in the protein-producing transformant. The advantages of this expression production method may be protection of the objective protein from digestion by protease which is present in the microbial cells, and ready purification of the objective protein that may be performed by disruption of the microbial cells and following centrifugation.
The protein inclusion body obtained in this way may be solubilized by a protein denaturing agent, which is then subjected to activation regeneration mainly by removing the denaturing agent, to be converted into correctly refolded and physiologically active protein. There are many examples of such procedures, such as activity regeneration of human interleukin 2 (JP-S61-257931 A).
To obtain the active protein from the protein inclusion body, a series of the manipulations such as solubilization and activity regeneration is required, and thus, the manipulations are more complicate than those in the case of directly producing the active protein. However, when a protein which affects microbial cell growth is produced on a large scale in the microbial cells, effects thereof may be inhibited by accumulating the protein as the inactive inclusion body in the microbial cells.
Examples of the methods for producing the objective protein on a large scale as the inclusion body may include methods of expressing the protein alone under control of a strong promoter, as well as methods of expressing the objective protein as a fusion protein with a protein known to be expressed in a large amount.
As an example, a method for preparing transformed Escherichia coli and producing a mutant protein using this will be described more specifically hereinbelow. When the mutant protein is produced by microorganisms such as E. coli, a DNA encoding a precursor protein including the leader sequence may be incorporated or a DNA for a mature protein region without including the leader sequence may be incorporated as a code sequence of the protein. Either one may be appropriately selected depending on the production condition, the form and the use condition of the enzyme to be produced.
As the promoter for expressing the DNA encoding the mutant protein, the promoter typically used for producing xenogenic proteins in E. coli may be used, and examples thereof may include strong promoters such as T7 promoter, lac promoter, trp promoter, trc promoter, tac promoter, and PR promoter and PL promoter of lambda phage. As the vector, pUC19, pUC18, pBR322, pHSG299, pHSG298, pHSG399, pHSG398, RSF1010, pMW119, pMW118, pMW219, and pMW218 may be used. Other vectors of phage DNA may also be used. In addition, expression vectors which contains a promoter and can express the inserted DNA sequence may also be used.
In order to produce the mutant protein as a fusion protein inclusion body, a fusion protein gene is made by linking a gene encoding another protein, preferably a hydrophilic peptide to upstream or downstream of the mutant protein gene. Such a gene encoding the other protein may be those which increase an amount of the accumulated fusion protein and enhance solubility of the fusion protein after denaturation and regeneration steps. Examples of candidates thereof may include T7 gene 10, β-galactosidase gene, dehydrofolic acid reductase gene, interferon γ gene, interleukin-2 gene and prochymosin gene.
Such a gene may be ligated to the gene encoding the mutant protein so that reading frames of codons are matched. This may be effected by ligating at an appropriate restriction enzyme site or using a synthetic DNA having an appropriate sequence.
In some cases, it is preferable to ligate a terminator, i.e. the transcription termination sequence, to downstream of the fusion protein in order to increase the production amount. Examples of this terminator may include T7 terminator, fd phage terminator, T4 terminator, tetracycline resistant gene terminator and E. coli trpA gene terminator.
The vector for introducing the gene encoding the mutant protein or the fusion protein of the mutant protein with the other protein into E. coli may preferably be of a so-called multicopy type. Examples thereof may include plasmids having a replication origin derived from ColE1, such as pUC based plasmids, pBR322 based plasmids or derivatives thereof. As used herein, the “derivative” means the plasmid modified by the substitution, deletion, insertion, addition and/or inversion of a base(s). “Modified” referred to herein includes the modification by mutagenesis with the mutagen or UV irradiation and natural mutation.
In order to select the transformants, it is preferable that the vector has a marker such as an ampicillin resistant gene. As such a plasmid, expression vectors having the strong promoter are commercially available (pUC series: Takara Shuzo Co., Ltd., pPROK series and pKK233-2: Clontech, etc.).
A DNA fragment where the promoter, the gene encoding the protein having the peptide-synthesizing activity or the fusion protein of the protein having the peptide-synthesizing activity with the other protein, and in some cases the terminator are ligeted sequentially is then ligeted to the vector DNA to obtain a recombinant DNA.
The mutated protein or the fusion protein of the mutated protein with the other protein is expressed and produced by transforming E. coli with the resulting recombinant DNA and culturing this E. coli. Strains commonly used for the expression of the xenogenic gene may be used as the host to be transformed. E. coli JM 109 strain which is a subspecies of E. coli K12 strain is preferable. The methods for transformation and for selecting transformants are described in Molecular Cloning, 2nd edition, Cold Spring Harbor press, 1989.
In the case of expressing as the fusion protein, the fusion protein may be composed so as to be able to cleave the peptide-synthesizing enzyme therefrom using a restriction protease which recognizes a sequence of blood coagulation factor Xa, kallikrein or the like which is not present in the peptide-synthesizing enzyme.
As production media, the media such as M9-casamino acid medium and LB medium typically used for cultivation of E. coli may be used. The conditions for cultivation and a production induction may be appropriately selected depending on types of the marker and the promoter of the vector and the host used.
The following methods are available for recovering the mutant protein or the fusion protein of the mutant protein with the other protein. If the mutant protein or the fusion protein thereof is solubilized in the microbial cells, the cells may be collected and then disrupted or lysed to thereby obtain a crude enzyme solution. If necessary, the crude solution may be purified using techniques such as ordinary precipitation, filtration and column chromatography, to obtain purified mutant protein or the fusion protein. In this case, the purification may be performed using an antibody against the mutant protein or the fusion protein.
In the case where the protein inclusion body is formed, this may be solubilized with a denaturing agent. The inclusion body may be solubilized together with the microbial cells. However, considering the following purification process, it is preferable to take up the inclusion body before solubilization. Collection of the inclusion body from the microbial cells may be performed in accordance with conventionally and publicly known methods. For example, the microbial cells are disrupted, and the inclusion body is then collected by centrifugation and the like. Examples of the denaturing agent which solubilizes the protein inclusion body may include guanidine-hydrochloric acid (e.g., 6 M, pH 5 to 8), urea (e.g., 8 M), and the like.
As a result of removal of the denaturing agent by dialysis and the like, the protein may be regenerated as the protein having the activity. Dialysis solutions used for the dialysis may include Tris hydrochloric acid buffer, phosphate buffer and the like. The concentration thereof may be 20 mM to 0.5 M, and pH thereof may be 5 to 8.
It is preferred that the protein concentration at a regeneration step is kept at about 500 μg/ml or less. In order to inhibit self-crosslinking of the regenerated peptide-synthesizing enzyme, it is preferred that dialysis temperature is kept at 5° C. or below. Methods for removing the denaturing agent other than the dialysis method may include a dilution method and an ultrafiltration method. The regeneration of the activity is anticipated by using any of these methods.
7. Method for Producing Peptide
In the method for producing the peptide of the present invention, the peptide is synthesized using the foregoing mutant protein. That is, in the method for producing the peptide of the present invention, the peptide is synthesized by reacting an amine component and a carboxy component in the presence of at least one of the following proteins (I) and (II).
(I) The mutant protein having the amino acid sequence comprising one or more mutations selected from any of the mutations 1 to 68, and the mutations 239 to 290 and 324 to 377 in the amino acid sequence of SEQ ID NO:2.
(II) The mutant protein having the amino acid sequence further comprising one or several amino acid mutations selected from substitutions, deletions, insertions, additions and inversions at positions other than the mutated positions of one or more mutations selected from any of the mutations 1 to 68, and the mutations 239 to 290 and 324 to 377 in the mutant protein (I); and having the peptide-synthesizing activity.
In the method for producing the peptide of the present invention, the peptide may also be synthesized using the mutant protein based on the protein having the amino acid sequence of SEQ ID NO:208. That is, in the method for producing the peptide of the present invention, the peptide may be synthesized by reacting the amine component and the carboxy component in the presence of at least one of the following proteins (I′) and (III).
(I′) The mutant protein having the amino acid sequence comprising one or more mutations selected from any of the mutations L1 to L335, and the mutations M1 to M642 in the amino acid sequence of SEQ ID NO:208.
(II′) The mutant protein having the amino acid sequence further comprising one or several amino acid mutations selected from substitutions, deletions, insertions, additions and inversions at positions other than the mutated positions of one or more mutations selected from any of the mutations L1 to L335, and the mutations M1 to M642 in the mutant protein described in the above (I′); and having the peptide-synthesizing activity.
In the method for producing the peptide of the present invention, the mutant protein is placed in the peptide-synthesizing reaction system. The mutant protein may be supplied as a mixture containing the protein (I) and/or (II), or (I′) and/or (III) in a biochemically acceptable solvent (the mixture will be referred to hereinbelow as “mutant protein-containing material”). More specifically, the peptide may be synthesized from the amine component and the carboxy component using one or more selected from the group consisting of a cultured product of a microorganism that has been transformed so as to express the mutant protein of the present invention, a microbial cell separated from the cultured product and the treated microbial cells of the microorganism.
As used herein, the “mutant protein-containing material” may be any material containing the mutant protein of the present invention, and specifically includes a cultured product of microorganisms which produce the mutant protein, microbial cells separated from the cultured product, and the treated microbial cells. The cultured product of microorganisms refers to one obtained by cultivation of the microorganisms, and more specifically refers to, e.g., a mixture of microbial cells, the medium used for culturing the microorganisms and substances produced by the cultured microorganisms. Alternatively, the microbial cells may be washed, and used as the washed microbial cells. The treated microbial cells may include ones obtained by disrupting, lysing and lyophilizing the microbial cells, as well as crude purified proteins recovered by further treating the microbial cells, and purified proteins obtained by further purification. As the purified proteins, partially purified proteins obtained by various purification methods may be used, and immobilized proteins obtained by immobilizing by a covalent bond method, an absorption method or an entrapment method may also be used. Depending on the microorganism to be used, bacteriolysis may partially occurs during the cultivation. In this case, a cultured supernatant may also be used as the mutant protein-containing material.
As the microorganism containing the mutant protein of the present invention, a gene recombinant strain which expresses the mutant protein may be used. Alternatively, treated microbial cells such as microbial cells treated with acetone and lyophilized microbial cells may be used. These may further be immobilized by a variety of methods such as the covalent bond method, the absorption method or the entrapment method, to produce immobilized microbial cells or immobilized treated microbial cells for use.
When the cultured product, the cultured microbial cells, the washed microbial cells and the treated microbial cells such as disrupted or lysed microbial cells are used, these materials tend to contain enzymes which are not involved in peptide production and degrade produced peptides. In this case, it is sometimes preferable to add a metal protease inhibitor such as ethylenediamine tetraacetatic acid (EDTA). The amount of such an inhibitor to be added may be in the range of 0.1 mM to 300 mM, and preferably from 1 mM to 100 mM.
The mutant protein or the mutant protein-containing material may be allowed to act upon a carboxy component and an amine component merely by mixing the mutant protein or the mutant protein-containing material, the carboxy component and the amine component. More specifically, the mutant protein or the mutant protein-containing material may be added to a solution containing the carboxy component and the amine component to react. Alternatively, in the case of using microorganisms which produce the mutant protein, the microorganisms which produce the mutant protein may be cultured to generate and accumulate the enzyme in the microorganisms or a cultured medium of the microorganisms, and the carboxy component and the amine component may then be added into the cultured medium. The produced peptide may be recovered in accordance with standard methods, and purified as needed.
To obtain microbial cells (cells of the microorganisms), the microorganisms may be cultured and grown in an appropriate cultivation medium which may be selected depending on the type of the microorganisms. The medium therefor is not particularly limited as long as the microorganisms can be grown in the medium, and may be an ordinary medium containing carbon sources, nitrogen sources, phosphorus sources, sulfur sources, inorganic ions, and, if necessary, organic nutrient sources.
Any carbon sources may be used as long as the microorganism can utilize. Examples of the carbon sources may include sugars such as glucose, fructose, maltose and amylose, alcohols such as sorbitol, ethanol and glycerol, organic acids such as fumaric acid, citric acid, acetic acid and propionic acid and salts thereof, carbohydrates such as paraffin, and mixtures thereof.
As the nitrogen sources, ammonium salts of inorganic acids such as ammonium sulfate and ammonium chloride, ammonium salts of organic acids such as ammonium fumarate and ammonium citrate, nitrate salts such as sodium nitrate and potassium nitrate, organic nitrogen compounds such as peptone, yeast extract, meat extract and corn steep liquor, or mixtures thereof may be used.
If necessary, nutrient sources such as inorganic salts, trace metal salts and vitamins commonly used in the medium may be admixed for use.
A cultivation condition is not particularly limited, and the cultivation may be performed under an aerobic condition at pH 5 to 9 and at a temperature ranging from about 15 to 55° C. for about 12 to 48 hours while appropriately controlling pH and the temperature.
A preferable embodiment of the method for producing the peptide of the present invention may be a method in which the transformed microorganisms are cultured in the medium to accumulate the mutated protein in the medium and/or the transformed microorganisms. Employment of the transformants enables production of the mutant protein readily on a large scale, and thus the peptide may thereby be rapidly synthesized in a large amount.
The amount of the mutant protein or the mutant protein-containing material to be used may be the amount by which an objective effect is exerted (i.e., effective amount). Those skilled in the art can easily determine this effective amount by a simple preliminary experiment. For example, the effective amount is about 0.01 to 100 units (U) or about 0.1 to 500 g/L in the case of using the enzyme or the washed microbial cells, respectively.
Any carboxy component may be used as long as it can be condensed with the amine component, the other substrate, to generate the peptide. Examples of the carboxy component may include L-amino acid ester, D-amino acid ester, L-amino acid amide, D-amino acid amide, and organic acid ester having no amino group. As amino acid ester, not only amino acid esters corresponding to natural amino acids but also amino acid esters corresponding to non-natural amino acids and derivatives thereof are also exemplified. In addition, as amino acid esters, β-, γ-, and ω-amino acid esters in addition to α-amino acid ester having different binding sites of amino groups are also exemplified. Representative examples of amino acid esters may include methyl ester, ethyl ester, n-propyl ester, iso-propyl ester, n-butyl ester, iso-butyl ester and tert-butyl ester of amino acids.
Any amine component may be used as long as it can be condensed with the carboxy component, the other substrate, to generate the peptide. Examples of the amine component may include L-amino acid, C-protected L-amino acid, D-amino acid, C-protected D-amino acid and amines. As amines, not only natural amine but also non-natural amine and derivatives thereof are exemplified. As amino acids, not only natural amino acids but also non-natural amino acids and derivatives thereof are exemplified. β-, γ- and ω-Amino acids in addition to α-amino acids having different binding sites of amino groups are also exemplified.
Concentrations of the carboxy component and the amine component which are starting materials may be 1 mM to 10 M and preferably 0.05 M to 2 M. In some cases, it is preferable to add the amine component in the amount equal to or more than the amount of the carboxy component. When the reaction is inhibited by the high concentration of the substrate, the concentrations may be kept to a certain level in order to avoid inhibition of the reaction and the components may be sequentially added.
A reaction temperature may be 0 to 60° C. at which the peptide can be synthesized, and preferably 5 to 40° C. A reaction pH may be 6.5 to 10.5 at which the peptide can be synthesized, and preferably pH 7.0 to 10.0.
The method for producing the peptide of the present invention is suitable as the method for producing various peptides. Examples of the peptide may include dipeptides such as α-L-aspartyl-L-phenylalanine-β-methyl ester (i.e., α-L-(β-O-methyl aspartyl)-L-phenylalanine(abbreviation: α-AMP)), L-alanyl-L-glutamine (Ala-Gln), L-alanyl-L-phenylalanine (Ala-Phe), L-phenylalanyl-L-methionine (Phe-Met), L-leucyl-L-methionine (Leu-Met), L-isoleucyl-L-methionine (Ile-Met), L-methionyl-L-methionine (Met-Met), L-prolyl-L-methionine (Pro-Met), L-tryptophyl-L-methionine (Trp-Met), L-valyl-L-methionine (Val-Met), L-asparaginyl-L-methionine (Asn-Met), L-cysteinyl-L-methionine (Cys-Met), L-glutaminyl-L-methionine (Gln-Met), glycyl-L-methionine (Gly-Met), L-seryl-L-methionine (Ser-Met), L-threonyl-L-methionine (Thr-Met), L-tyrosyl-L-methionine (Tyr-Met), L-aspartyl-L-methionine (Asp-Met), L-arginyl-L-methionine (Arg-Met), L-histidyl-L-methionine (His-Met), L-lysyl-L-methionine (Lys-Met), L-alanyl-glycine (Ala-Gly), L-alanyl-L-threonine (Ala-Thr), L-alanyl-L-glutamic acid (Ala-Glu), L-alanyl-L-alanine (Ala-Ala), L-alanyl-L-aspartic acid (Ala-Asp), L-alanyl-L-serine (Ala-Ser), L-alanyl-L-methionine (Ala-Met), L-alanyl-L-valine (Ala-Val), L-alanyl-L-lysine (Ala-Lys), L-alanyl-L-asparagine (Ala-Asn), L-alanyl-L-cysteine (Ala-Cys), L-alanyl-L-tyrosine (Ala-Tyr), L-alanyl-L-isoleucine (Ala-Ile), L-arginyl-L-glutamine (Arg-Gln), glycyl-L-serine (Gly-Ser), glycyl-L-(t-butyl)serine (Gly-Ser(tBu)), and (2S,3R,4S)-4-hydroxylisoleucyl-phenylalanine (HIL-Phe); tripeptides such as L-alanyl-L-phenylalanyl-L-alanine (AFA), L-alanyl-glycyl-L-alanine (AGA), L-alanyl-L-histidyl-L-alanine (AHA), L-alanyl-L-leucyl-L-alanine (ALA), L-alanyl-L-alanyl-L-alanine (AAA), L-alanyl-L-alanyl-glycine (AAG), L-alanyl-L-alanyl-L-proline (AAP), L-alanyl-L-alanyl-L-glutamine (AAQ), L-alanyl-L-alanyl-L-tyrosine (AAY), glycyl-L-phenylalanyl-L-alanine (GFA), L-alanyl-glycyl-glycine (AGG), L-threonyl-glycyl-glycine (TGG), glycyl-glycyl-glycine (GGG), and L-alanyl-L-phenylalanyl-glycine (AFG); tetrapeptides such as glycyl-glycyl-L-phenylalanyl-L-methionine (GGFM); and pentapeptides such as L-tyrosyl-glycyl-glycyl-L-phenylalanyl-L-methionine (YGGFM).
The method for producing the peptide of the present invention is also suitable for the method for producing, for example, α-L-aspartyl-L-phenylalanine-β-methyl ester (i.e., α-L-(β-O-methyl aspartyl)-L-phenylalanine, abbreviated as α-AMP). α-AMP is an important intermediate for producing α-L-aspartyl-L-phenylalanine-α-methyl ester (product name: Aspartame) which has a large demand as a sweetener.
The present invention will be described in detail with reference to the following Examples, but the invention is not limited thereto.
An objective gene encoding a protein having a peptide-synthesizing activity was amplified by PCR with a chromosomal DNA from Sphingobacterium multivorum FERM BP-10163 strain as a template using oligonucleotides shown in SEQ ID NOS:5 and 6 as primers. An amplified DNA fragment was treated with NdeI/XbaI, and a resulting DNA fragment was ligated to pTrpT that had been treated with NdeI/XbaI. Escherichia coli JM109 was transformed with this solution containing the ligated product, and a strain having an objective plasmid was selected with ampicillin resistance as an indicator, and this plasmid was designated as pTrpT_Sm_Aet. Escherichia coli JM109 having pTrpT_Sm_Aet is also represented as pTrpT_Sm_Aet/JM109 strain.
One platinum loopful of pTrpT_Sm_Aet/JM109 strain was inoculated into a general test tube in which 3 mL of a medium (2 g/L of glucose, 10 g/L of yeast extract, 10 g/L of casamino acid, 5 g/L of ammonium sulfate, 3 g/L of potassium dihydrogen phosphate, 1 g/L of dipotassium hydrogen phosphate, 0.5 g/L of magnesium sulfate 7-hydrate, 100 mg/L of ampicillin) had been placed, and a main cultivation was performed at 25° C. for 20 hours. An AMP-synthesizing activity of 2.1 U per 1 mL of the cultured medium was found, thereby confirming that the cloned gene had been expressed in Escherichia coli. No activity was detected in transformants into which pTrpT alone had been introduced as a control.
(1) Construction of pKF_Sm_Aet
An objective gene was amplified by PCR with pTrpT_Sm_Aet plasmid as a template using the oligonucleotides shown in SEQ ID NOS:3 and 4 as the primers. This DNA fragment was treated with EcoRI/PstI, and the resulting DNA fragment was ligated to pKF18k2 (suppled from Takara Shuzo Co., Ltd.) that had been treated with EcoRI/PstI. Escherichia coli JM109 was transformed with this solution containing the ligated product, and a strain having an objective plasmid was selected with kanamycin resistance as the indicator, and this plasmid was designated as pKF_Sm_Aet. Escherichia coli JM109 having pKF_Sm_Aet is also represented as pKF_Sm_Aet/JM109 strain.
(2) Introduction of Rational Mutation into pKF_Sm_Aet
In order to construct mutant Aet, pKF_Sm_Aet plasmid was used as the template for site-directed mutagenesis using an ODA method. Mutations were introduced using “site-directed mutagenesis system Mutan Super Express kit” supplied from Takara Shuzo Co., Ltd. (Japan) in accordance with the protocol of the manufacturer using the primers (SEQ ID NOS:12 to 33) corresponding to each mutant enzyme. The 5′ terminus of the primers were phosphorylated before use with T4 polynucleotide kinase supplied from Takara Shuzo Co., Ltd. The primers were phosphorylated by adding 100 μmol DNA (primer) and 10 units of T4 polynucleotide kinase to 20 μL of 50 mM tris-hydrochloric acid buffer (pH 8.0) containing 0.5 mM ATP, 10 mM magnesium chloride and S mM DTT and warming at 37° C. for 30 minutes followed by heating at 70° C. for 5 minutes. Subsequently, 1 μL (5 pmol) of this reaction solution was used for PCR by which the mutation was introduced. The PCR was performed by adding 10 ng of ds DNA (pKF_Sm_Aet plasmid) as the template, S pmol each of Selection Primer and 5′-phosphorylated mutagenic oligonucleotides shown above as the primers and 40 units of LA-Taq to 50 μL of LA-Taq buffer II (Mg2+ plus) containing 250 μM each of dATP, dCTP, dGTP and dTTP, which was then subjected to 25 cycles of heating at 94° C. for one minute, 55° C. for one minute and 72° C. for 3 minutes. After the PCR for introducing the mutation was completed, a DNA fragment was collected by ethanol precipitation, and Escherichia coli MV1184 strain was transformed with the resulting DNA fragment. A strain having an objective plasmid: pKF_Sm_AetM containing a mutant Aet gene was selected with kanamycin resistance as the indicator.
In the present specification, Escherichia coli MV1184 strain having pKF_Sm_AetM is also represented as pKF_Sm_AetM/MV1184 strain. When referring to a specific mutant of pKF_Sm_AetM, the mutation thereof may be represented by replacing “AetM” with the type of mutation, e.g., pKF_Sm_F207V. When a mutant contains two or more mutations, the mutations may be stated continuously with “/” dividing each mutation. For example, pKF_Sm_F207V/Q441E represents a mutant in which the mutations F207V and Q441E have been introduced into the Aet gene which pKF_Sm_Aet plasmid carries.
(3) Construction of pHSG_Sm_Aet
An objective gene was amplified by PCR with pTrpT_Sm_Aet plasmid as a template using the oligonucleotides shown in SEQ ID NO:3 and 4 as primers. This DNA fragment was treated with EcoRI/PstI, and a resulting DNA fragment was ligated to pHSG298 (suppled from Takara Shuzo Co., Ltd.) that had been treated with EcoRI/PstI. Escherichia coli MV1184 strain was transformed with this solution containing the ligated product, and a strain having an objective plasmid was selected with kanamycin resistance as an indicator, and this plasmid was designated as pHSG_Sm_Aet. Escherichia coli MV1184 having pHSG_Sm_Aet is also represented as pHSG_Sm_Aet/MV1184 strain.
(4) Obtaining Microbial Cells: A
Each of pKF_Sm_Aet/JM109 strain, pKF_Sm_Aet/MV1184 strain and pHSG_Sm_Aet/MV1184 strain was precultured in an LB agar medium (10 g/L of yeast extract, 10 g/L of peptone, 5 g/L of sodium chloride, 20 g/L of agar, pH 7.0) at 30° C. for 24 hours. One platinum loopful of microbial cells of each strain obtained from the above cultivation was inoculated into a general test tube in which 3 mL of the LB medium (0.1 M IPTG and 20 mg/L of kanamycin were added to the above medium from which the agar had been omitted) had been placed, and a main cultivation was performed at 25° C. at 150 reciprocatings/minute for 20 hours.
(5) Production of Peptide Using Microbial Cells <Synthesis of AMP>
400 μL of each cultured medium obtained in Example 2 (4) was centrifuged to collect the microbial cells. The collected cells were then suspended in 200 μL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 100 mM phenylalanine, and reacted at 25° C. for 30 minutes. The concentration of α-AMP produced by the strain which expressed the wild type enzyme (such a strain will be referred to hereinbelow as the “wild strain”) in this reaction is shown in Table 3. For the dipeptide production by the strains which expressed various mutant enzymes (mutant strains), their ratios of production concentrations to those of the wild strain are shown in Table 3.
(6) Production of Peptide Using Microbial Cells <Synthesis of Ala-Gln>
100 μL of each cultured medium obtained in Example 2 (4) was centrifuged to collect the microbial cells. The collected cells were then suspended in 200 μL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 100 mM L-alanine methyl ester and 200 mM glutamine, and reacted at 25° C. for 30 minutes. The concentration of L-alanyl-L-glutamine (Ala-Gln) produced by the wild strain in this reaction is shown in Table 3. For the dipeptide production by the various mutant strains, the ratio of production concentration to that of the wild strain is shown in Table 3.
(7) Production of Peptide Using Microbial Cells <Synthesis of Phe-Met, Leu-Met>
800 μL of each cultured medium obtained in Example 2 (4) was centrifuged to collect the microbial cells. The collected cells were then suspended in 400 μL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 50 mM L-phenylalanine methyl ester hydrochloride or L-leucine methyl ester hydrochloride, and 100 mM L-methionine, and reacted at 25° C. for 20 minutes. The concentration of L-phenylalanyl-L-methionine (Phe-Met) or L-leucyl-L-methionine (Leu-Met) produced by the wild strain in this reaction is shown in Table 3. For the dipeptide synthesized by the various mutant strains, the ratio of production concentration with respect to that by the wild strain is shown in Table 3.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(8) Preparation of pTrpT_Sm_Aet Random Library
In order to construct mutant Aet, pTrpT_Sm_Aet plasmid was used as the template for random mutagenesis using error prone PCR. The mutation was introduced using “GeneMorph PCR Mutagenesis Kit” supplied from Stratagene (USA) in accordance with the protocol of the manufacturer.
The PCR was performed using the oligonucleotides shown in SEQ ID NOS:5 and 6 as primers. That is, 500 ng of ds DNA (pTrpT_Sm_Aet or pTrpT_Sm_F207V plasmid) as the template, 125 ng each of the primers and 2.5 units of Mutazyme DNA polymerase were added to 50 μL of Mutazyme reaction buffer containing 200 μM each of dATP, dCTP, dGTP and dTTP, which was then subjected to the PCR using 30 cycles at 95° C. for 30 seconds, 52° C. for 30 seconds and 72° C. for 2 minutes.
The PCR product was treated with NdeI/XbaI, and the resulting DNA fragment was ligated to pTrpT that had been treated with NdeI/XbaI. Escherichia coli JM109 (suppled from Takara Shuzo Co., Ltd.) was transformed with this solution containing the ligated product in accordance with standard methods. This was plated on an LB agar medium containing 100 μg/mL of ampicillin to make a library into which the random mutation had been introduced.
(9) Screening from pTrpT_Sm_Aet Random Library: A
Escherichia coli JM109 strain transformed with the plasmid (pTrpT_Sm_AetM) containing each mutant Aet gene and Escherichia coli JM109 strain transformed with the plasmid containing the wild type Aet were inoculated to 150 μL (dispensed in wells of 96-well plate) of the medium containing 100 μg/mL of ampicillin (2 g/L of glucose, 10 g/L of yeast extract, 10 g/L of casamino acid, 5 g/L of ammonium sulfate, 1 g/L of potassium dihydrogen phosphate, 3 g/L of dipotassium hydrogen phosphate, 0.5 g/L of magnesium sulfate 7-hydrate, pH 7.5, 100 μg/mL of ampicillin), and cultured at 25° C. for 16 hours with shaking. The cultivation was performed with shaking at 1000 rotations/minute using a bio-shaker (M/BR-1212FP) supplied from TITEC.
(10) Primary Screening
The primary screening was performed using the cultured medium obtained in Example 3 (9). Selection was performed as follows. 200 μL of a reaction solution (pH 8.2) containing 10 mM phenol, 6 mM AP, 5 mM Asp (OMe)2, 7.5 mM Phe, 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the cultured medium, which was then reacted at 25° C. for about 20 minutes. After the reaction, an absorbance at 500 nm was measured, and an amount of released methanol was calculated. Those showing the large amount of released methanol were selected as those having the enzyme with high AMP-synthesizing activity.
(11) Obtaining Microbial Cells
One platinum loopful of the strain selected in the primary screening was precultured in the LB agar medium at 25° C. for 16 hours. One platinum loopful of each strain expressing the enzyme was inoculated to 2 mL of terrific medium (12 g/L of tryptone, 24 g/L of yeast extract, 2.3 g/L of potassium dihydrogen phosphate, 12.5 g/L of dipotassium hydrogen phosphate, 4 g/L glycerol, 100 mg/L of ampicillin) in a general test tube, and the main cultivation was performed at 25° C. at 150 reciprocatings/minute for 18 hours.
(12) Secondary Screening
25 μL of the cultured broth was suspended in 500 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 75 mM phenylalanine, which was then reacted at 20° C. or 25° C. for 10 or 15 minutes to measure the amount of synthesized AMP. Among the secondary screened strains, the strains which exerted improved specific activity was analyzed as to their mutation points. As a result, the following mutation points were specified. The mutant strains comprising the mutants 4, 5, 6, 7, 8, 9, 10, 14, 15 and 16 were obtained from the library derived from the wild strain as a parent strain (template), and the mutant strains comprising the mutants 17, 18, 19 and 20 were obtained from the library derived from the F207V mutant strain as the parent strain.
(13) Production of Peptide Using Microbial Cells
The concentrations of AMP produced with the wild strain in the aforementioned reaction are shown in Table 4 (reaction time: 10 minutes), and the concentration of AMP produced with the mutant strain F207V is shown in Table 5 (reaction time: 15 minutes). For the dipeptide synthesized by each mutant strain, the ratio of the concentrations of the dipeptides synthesized by the mutant strain with respect to that by the parent strain are shown in Tables 4 and 5. Other conditions for the AMP synthesis reaction were the same as in the above Example 2 (5).
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE MOTHER STRAIN (MUTANT STRAIN F207V) IS “1”
(14) Construction of Strain in which Specified Mutation Point has been Introduced into pKF
The mutation point specified in Example 3 (12) was combined with already constructed pKF_Sm_F207V/Q441E to construct a triple mutant strain. The mutation was introduced in the same way as in Example 2 (2) using pKF_Sm_F207V/Q441E as the template and using the primers corresponding to various mutant enzymes (SEQ ID NOS:34 to 44 and 77). Resulting strains and the already constructed strains were cultured in the same way as in Example 2 (4).
(15) Production of Peptide Using Microbial Cells <AMP>
500 μL of the cultured medium obtained in Example 4 (14) was centrifuged to collect microbial cells. The collected cells were then suspended in 500 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 100 mM phenylalanine, and reacted at 25° C. for 30 minutes. The concentrations of AMP synthesized with the wild strain in this reaction are shown in Table 6. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 6.
(16) Production of Peptide Using Microbial Cells <Ala-Gln>
100 μL of the cultured medium obtained in Example 4 (14) was centrifuged to collect the microbial cells. The collected cells were then suspended in 1000 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 100 mM L-alanine methyl ester and 200 mM glutamine, and reacted at 25° C. for 10 minutes. The concentrations of Ala-Gln synthesized with the wild strain in this reaction are shown in Table 6. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 6.
(17) Production of Peptide Using Microbial Cells <Phe-Met, Leu-Met>
800 μL of the cultured medium obtained in Example 4 (14) was centrifuged to collect the microbial cells. The collected cells were then suspended in 400 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM L-phenylalanine methyl ester hydrochloride or L-leucine methyl ester hydrochloride, and 100 mM L-methionine, and reacted at 25° C. for 20 minutes. The concentrations of Phe-Met and Leu-Met synthesized with the wild strain in this reaction are shown in Table 6. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 6.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(18) Preparation of pSTV_Sm_Aet Random Library
In order to construct mutant Aet, pHSG_Sm_Aet plasmid was used as the template for random mutagenesis using error prone PCR. The mutation was introduced using “GeneMorph PCR Mutagenesis Kit” supplied from Stratagene (USA) in accordance with the protocol of the manufacturer.
The PCR was performed using the oligonucleotides shown in SEQ ID NOS:3 and 4. That is, 100 ng of ds DNA (pHSG_Sm_Aet plasmid) as the template, 1.25 pmol each of the primers 1 and 2 and 2.5 units of Murazyme DNA polymerase were added to 50 μL of Mutazyme reaction buffer containing 200 μM each of dATP, dCTP, dGTP and dTTP. The mixture was heated at 95° C. for 30 seconds and then subjected to the PCR using 25 cycles at 95° C. for 30 seconds, 52° C. for 30 seconds and 72° C. for 2 minutes.
The PCR product was treated with EcoRI/PstI, and the resulting DNA fragment was ligated to pSTV28 (suppled from Takara Shuzo Co., Ltd.) that had been treated with EcoRI/PstI. Escherichia coli JM109 was transformed with this solution containing the ligated product. This transformed strain was plated on M9 agar medium (200 mL/L of 5*M9, 1 mL/L of 0.1 M CaCl2, 1 mL/L of 1 M MgSO4, 10 mL/L of 50% glucose, 10 g/L of casamino acid, 15 g/L of agar) containing 50 μg/mL of chloramphenicol and 0.1 mM IPTG to make a library in which random mutation was introduced. At that time, for the sake of simplicity of the subsequent screening, the transformants were applied so that about 100 colonies per plate would be grown. The above “5*M9” is a solution containing 64 g/L of Na2HPO4.7H2O, 15 g/L of KH2PO4, 2.5 g/L of NaCl and 5 g/L of NH4Cl.
(19) Primary Screening from pSTV Based Random Library
In order to efficiently select the strain whose activity had been enhanced from the resulting transformants (library from mutant enzyme-expressing strain), Phe-pNA hydrolytic activity of each transformant was examined. A reaction solution (10 mM Phe-pNA, 10 mM OPT, 20 mM Tris-HCl (pH 8.2), 0.8% agar) (5 mL) was overlaid on the plate for transformant growth made in Example 5 (18), and color development by pNA produced by hydrolysis of Phe-pNA was examined (microbial cells are colored in yellow by liberation of pNA). The strongly colored colony was selected as the strain whose activity had been enhanced.
(20) Obtaining Microbial Cells
The selected strains were cultured on the LB agar medium at 30° C. for 24 hours. One platinum loopful of microbial cells of each strain was inoculated to 3 mL of the LB medium (agar was omitted from the above medium) containing 0.1 mM IPTG and 50 mg/L of chloramphenicol, and the main cultivation was performed at 25° C. at 150 reciprocatings/minute for 20 hours.
(21) Secondary Screening
Microbial cells were collected from 400 μL of the cultured broth obtained in Example 5 (20). The collected cells were suspended in 400 μL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 50 mM Phe-OMe and 100 mM Met, and reacted at 25° C. for 30 minutes. The amount of synthesized Phe-Met was measured, and the strains whose initial rate of the reaction was fast were selected. For the selected strains whose activity had been enhanced, the mutation point was analyzed, and the mutation points 11 and 12 were specified.
(22) Production of Peptide Using Microbial Cells <Phe-Met, Leu-Met>
800 μL of the cultured medium obtained in Example 5 (20) was centrifuged to collect the microbial cells. The collected cells were then suspended in 400 μL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 25 mM L-phenylalanine methyl ester hydrochloride or L-leucine methyl ester hydrochloride, and 50 mM L-methionine, and reacted at 25° C. for 20 minutes. The concentrations of Phe-Met and Leu-Met synthesized with the wild strain in this reaction are shown in Table 7. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 7.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(23) Construction of Plasmid with High Expression
An expression plasmid was constructed by ligating the mature peptide-synthesizing enzyme gene derived from Sphingobacterium to downstream of a modified promoter and a signal sequence of acid phosphatase derived from Enterobacter aerogenes by PCR.
The peptide-synthesizing enzyme gene was amplified by PCR using 50 μL of a reaction solution containing 0.4 mM pTrpT_Sm_Aet (Example 1) as a template, 0.4 mM each of Esp-S1 (5′-CCG TAA GGA GGA ATG TAG ATG AAA AAT ACA ATT TCG TGC C; SEQ ID NO:121) and S-AS1 (5′-GGC TGC AGT TTG CGG GAT GGA AGG CCG GC; SEQ ID NO:122) oligonucleotides as the primers, KOD plus buffer (suppled from Toyobo Co., Ltd.), 0.2 mM each of dATP, dCTP, dGTP and dTTP, 1 mM magnesium sulfate and 1 unit of KOD plus polymerase (suppled from Toyobo Co., Ltd.), by heating at 94° C. for 30 seconds followed by 25 cycles at 94° C. for 15 seconds, 55° C. for 30 seconds and 68° C. for two minutes and 30 seconds. The promoter and signal sequences of acid phosphatase were amplified by PCR using pEAP130 plasmid (see the following Reference Example 1, related patent application: JP 2004-83481) as the template, and E-S1 (5′-CCT CTA GAA TTT TTT CAA TGT GAT TT; SEQ ID NO:123) and Esp-AS1 (5′-GCA GGA AAT TGT ATT TTT CAT CTA CAT TCC TCC TTA CGG TGT TAT; SEQ ID NO:124) oligonucleotides as the primers under the same condition as the above. The reaction solutions were subjected to agarose electrophoresis, and the amplified DNA fragments were recovered using Microspin column (supplied from Amersham Pharmacia Biotech).
Then, a chimeric enzyme gene was constructed by PCR using the amplified DNA fragment mixture as the template, E-S1 and S-AS1 oligonucleotides as the primer, and the reaction solution having the same composition as the above, for 25 cycles of 94° C. for 15 seconds, 55° C. for 30 seconds and 68° C. for two minutes and 30 seconds. The amplified DNA fragment was recovered using Microspin column (supplied from Amersham Pharmacia Biotech), and digested with XbaI and PstI. This was ligated to XbaI-PstI site of pCU18 plasmid. The nucleotide sequence was determined by a dye terminator method using a DNA sequencing kit, Dye Terminator Cycle Sequencing Ready Reaction (supplied from Perkin Elmer) and 310 Genetic Analyzer (ABI) to confirm that the objective mutations had been introduced, and then this plasmid was designated as pSF_Sm_Aet plasmid.
(24) Construction of Strain in which pSF_Sm_Aet Rational Mutation has been Introduced
To construct the mutant Aet, pSF_Sm_Aet was used as the template of site-directed mutagenesis using the PCR. The mutation was introduced using QuikChange Site-Directed Mutagenesis Kit supplied from Stratagene (USA) and the primers corresponding to each mutant enzyme (SEQ ID NOS:45 to 78) in accordance with the protocol of the manufacturer. Escherichia coli JM109 strain was transformed with PCR products, and strains having objective plasmids were selected with ampicillin resistance as the indicator. Escherichia coli JM109 strain having pSF_Sm_Aet is also represented as pSF_Sm_Aet/JM109 strain.
(25) Obtaining Microbial Cells
Each mutant strain obtained in Example 6 (24) was precultured in the LB agar medium at 25° C. for 16 hours. One platinum loopful of each strain expressing the enzyme was inoculated to 2 mL of terrific medium (12 g/L of tryptone, 24 g/L of yeast extract, 2.3 g/L of potassium dihydrogen phosphate, 12.5 g/L of dipotassium hydrogen phosphate, 4 g/L glycerol, 100 mg/L of ampicillin) in a general test tube, and the main cultivation was performed at 25° C. at 150 reciprocatings/minute for 18 hours.
(26) Production of Peptide Using Microbial Cells <Ala-Gln>
The cultured broth (5 μL) obtained in (25) was added to 500 μL of borate buffer (pH 8.5 or pH 9.0) containing 50 mM L-alanine methyl ester hydrochloride (A-OMe HCl), 100 mM L-glutamine and 10 mM EDTA, and reacted at 25° C. for 10 minutes. The concentrations of Ala-Gln synthesized with the wild strain in this reaction are shown in Table 8. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 8.
(27) Production of Peptide Using Microbial Cells <AMP>
The cultured broth (25 μL) obtained in the above was suspended in 500 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 75 mM phenylalanine, and reacted at 20° C. or 25° C. for 15 minutes. The concentrations of AMP synthesized with the wild strain in this reaction are shown in Table 8. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 8.
(28) Production of Peptide Using Microbial Cells <Phe-Met, Leu-Met>
The cultured broth (25 μL) obtained in the above was suspended in 500 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 25 mM L-phenylalanine methyl ester hydrochloride or L-leucine methyl ester hydrochloride, and 50 mM L-methionine, and reacted at 25° C. for 15 minutes. The concentrations of Phe-Met and Leu-Met synthesized with the wild strain in this reaction are shown in Table 8. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 8.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(29) Construction of Random Screening Mutation-Combining Strain
To construct strains where various mutations were combined, pSF_Sm_Aet was used as the template for site-directed mutagenesis using the PCR.
The mutation was introduced using “QuikChange Multi” supplied from Stratagene (USA) in accordance with the protocol of the manufacturer and using the primers (99 to 120) corresponding to each mutant enzyme. The 5′ terminus of the primers were phosphorylated before use with T4 polynucleotide kinase supplied from Takara Shuzo Co., Ltd. The primer was phosphorylated by adding 100 μmol DNA (primer) and 10 units of T4 polynucleotide kinase to 20 μL of 50 mM tris hydrochloric acid buffer (pH 8.0) containing 0.5 mM ATP, 10 mM magnesium chloride and 5 mM DTT and warming at 37° C. for 30 minutes followed by heating at 70° C. for 5 minutes.
The PCR was performed by adding 50 ng of ds DNA (pSF_Sm_Aet plasmid) as the template, 50 or 100 ng each of the 5′-phosphorylated mutagenic oligonucleotides (100 ng when the number of sort of primers in the combination is up to 3 types, and 50 ng when the number of sort of the primers in the combination is 4 types or more), 0.375 μL of Quik solution and 1.25 units of QuikChange Multi enzyme blend to 12.5 μL of QuikChange Multi reaction buffer containing 0.5 μL of dNTP mix, which was then subjected to the reaction of 30 cycles at 95° C. for one minute, 53.5° C. for one minute and 65° C. for 10 minutes.
Escherichia coli JM109 strain was transformed with 2 μL of the reaction solution obtained by adding 5 unites of DpnI to the PCR product (total amount: 12.5 μL) and treating at 37° C. for one hour. Transformed microbial cells were plated on the LB medium containing 100 μg/mL of ampicillin to obtain a library of randomly combined strains as ampicillin resistant strains.
(30) Screening from Library Having Combined Mutations
Escherichia coli JM109 strain transformed with the plasmid (pTrpT_Sm_AetM) containing each mutant Aet gene and Escherichia coli JM109 strain transformed with the plasmid containing the wild type Aet were inoculated to 150 μL (dispensed in wells of 96-well plate) of the medium containing 100 μg/mL of ampicillin, and cultured at 25° C. for 16 hours with shaking. The cultivation was performed with shaking at 1000 rotations/minute using a bio-shaker (M/BR-1212FP) supplied from TITEC. Using the resulting cultured medium, the selection was performed by screening.
(31) Primary Screening
A reaction solution (200 μL) (pH 8.2) containing 10 mM phenol, 6 mM AP, 5 mM Asp (OMe)2, 7.5 mM Phe, 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of resulting microbial medium, which was then reacted at 25° C. for about 20 minutes. After the reaction, the absorbance at 500 nm was measured, and the amount of released methanol was calculated. Those showing the large amount of released methanol were selected as those having the enzyme with high AMP-synthesizing activity.
(32) Secondary Screening
After the primary screening described above, the selected strains were cultured by the method described in Example 6 (25). 10 μL or 50 μL of each cultured broth was suspended in 1 mL of 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM Asp(OMe)2 and 75 mM Phe, and reacted at 20° C. or 25° C. for 10 minutes. The amount of synthesized AMP was measured and strains that exerted a large synthesis amount were selected. The combination of the mutation points was determined in the selected strains by sequencing. The obtained strains and the combinations of the primers used for obtaining the strains are shown in Table 9.
(33) Production of Peptide Using Microbial Cells
The combination strains obtained in the above were evaluated. The cultured broth (25 μL) obtained in the above was suspended in 500 μL of 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM dimethyl aspartate and 75 mM phenylalanine, and reacted at 20° C. for 15 minutes. The concentration of AMP synthesized with the wild strain in this reaction is shown in Table 10. For the dipeptide synthesized by various mutant strains, the ratio of the specific activity of the dipeptide synthesized by the mutant strain with respect to the specific activity as to the wild strain being 1 is shown in Table 10.
(34) Study of Substrate Specificity Using Mutant Enzyme
The production of peptides was examined in the cases of using various amino acid methyl ester for the carboxy component and L-methionine for the amine component. The cultured broth (25 μL) prepared by the method described in Example 6 (25) was added to 500 μL of borate buffer (pH 8.5) containing 25 mM L-amino acid methyl ester hydrochloride (X-OMe-HCl) shown in Table 11, 50 mM L-methionine and 10 mM EDTA. The mixture was then reacted at 25° C. for 15 minutes or 3 hours. The amounts of various peptides synthesized with the wild strain in this reaction are shown in Tables 11-1 and 11-2. The amount of the produced peptide with a mark “+” was shown in terms of estimated reference value of the peak, tentatively determining an area value of 8000 in HPLC being 1 mg/L. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Tables 11-1 and 11-2.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(35) Screening from pTrpT_Sm_Aet Random Library: B
The library produced in Example 3 (8) was cultured in the same way as in Example 3 (9), and two types of screenings were performed using the cultured medium.
(36) Primary Screening: A
A reaction solution (200 μL) (pH 8.2) containing 10 mM phenol, 6 mM AP, S mM Asp(OMe)2, 5 mM Ala-OEt, 7.5 mM Phe, 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial medium, which was then reacted at 25° C. for about 20 minutes. After the reaction, the absorbance at 500 nm was measured, and an amount of released methanol was calculated. Herein, those showing the large amount of released methanol were selected as those having the enzyme which tends to synthesize AMP more abundantly than Ala-Phe.
(37) Primary Screening: B
A reaction solution (200 μL) (pH 8.2) containing 10 mM phenol, 6 mM AP, 5 mM Asp(OMe)2, 5 mM A(M), 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial medium, which was then reacted at 25° C. for about 20 minutes. After the reaction, the absorbance at 500 nm was measured, and an amount of released methanol was calculated. Herein, those showing the small amount of released methanol were selected as enzymes which has less tendency to produce AM (AM).
(38) Secondary Screening
The strains selected in Example 9 (36) and (37) were cultured in the same way as in Example 6 (25), and 50 μL of each cultured broth was suspended in 1 mL of 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM Asp(OMe)2, 50 mM Ala-OMe and 75 mM Phe, and reacted 20° C. for 10 minutes. The amounts of synthesized AMP and Ala-Phe were measured, and the strains whose initial rate of the reaction was fast were selected. Likewise, 50 μL of each cultured broth was suspended in 1 mL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 50 mM Asp(OMe)2, and 75 mM Phe, and reacted at 20° C. for 10 minutes. The yields of synthesized AMP were measured, and the strains exerting the high yield were selected. The mutation 21 was selected as the valid mutation point.
(39) Introduction of Mutation into V184
The mutation point, V184A obtained in Example 9 was introduced into pSF_Sm_Aet, and also introduced into an existing construct, pSF_Sm_M35-4. V184X strains were also constructed by substituting V184 with other amino acids. The mutation was introduced in the same way as in (2) using pSF_Sm_Aet or pSF_Sm_M35-4 as the template and using the primers (SEQ ID NO:79 to 98) corresponding to each mutant enzyme. The resulting strains were cultured by the method described in Example 6 (25).
(40) Production of Peptide Using Microbial Cells <AMP>
The cultured broth (25 μL) prepared by the method described in Example 6 (24) was suspended in 500 μL of 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 75 mM phenylalanine, and reacted at 20° C. for 10 minutes. The concentrations of AMP synthesized with the wild strain in this reaction are shown in Table 12. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized by the mutant strain with respect to that by the wild strain is shown in Table 12.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THAT SYNTHESIZED DIPEPTIDE CONCENTRATION IN THE WILD STRAIN IS “1”
(41) Production of Peptide Using Microbial Cells <AMP>
The cultured broth obtained by the method described in Example 6 (25) was suspended in 100 mM borate buffer (pH 8.5 or pH 9.0) containing 10 mM EDTA, 50 mM dimethyl aspartate and 75 mM phenylalanine, and reacted at 20° C. The yields of AMP synthesized with the wild strain and various mutant strains in this reaction are shown in Table 13.
(42) pH Stability of Enzymes
pH Stability was examined by incubating the enzyme at a certain pH for a certain period of time and subsequently synthesizing AMP from dimethyl L-aspartate hydrochloride and L-phenylalanine. The cultured broth (10 μL) prepared by the method described in Example 6 (25) was mixed with 190 μL of each of buffers at a variety of pH's (8.5, 9.0, 9.5) (as to M9-9 and M12-1, pH 8.0 was also tested), incubated for 30 minutes, and subsequently added to 400 μL of 450 mM borate buffer containing 75 mM dimethyl L-aspartate, 112.5 mM L-phenylalanine and 15 mM EDTA, which was then reacted at 20° C. for 20 minutes. The concentrations of synthesized AMP are shown in
(43) Optimal Reaction Temperature of Enzymes
Effects of the reaction temperature on the reaction to synthesize AMP from dimethyl L-aspartate hydrochloride and L-phenylalanine were examined. The cultured broth (20 μL) prepared by the method described in Example 6 (25) was added to 980 μL of 100 mM borate buffer (pH 8.5) containing 50 mM dimethyl L-aspartate, 75 mM L-phenylalanine and 10 mM EDTA, and reacted at each temperature (20, 25, 30, 35, 40, 45, 50, 55, 60° C.) for 5 minutes. The concentrations of synthesized AMP are shown in
(44) Temperature Stability of Enzymes
Temperature stability was examined by incubating the enzymes at a certain temperature for a certain period of time and subsequently synthesizing AMP from dimethyl L-aspartate hydrochloride and L-phenylalanine. The cultured broth (20 μL) that had been prepared by the method described in Example 6 (25) was incubated at each temperature (35, 40, 45, 50, 55, 60° C.) for 30 minutes, and was subsequently added to 980 μL of 100 mM borate buffer (pH 8.5) containing 50 mM dimethyl L-aspartate, 100 mM L-phenylalanine and 10 mM EDTA, which was then reacted at 20° C. for 5 minutes. The concentrations of AMP synthesized thereby are shown in
<Analysis of Products>
In the aforementioned Examples, the products were quantified by the high performance liquid chromatography, details of which are as follows. Column: Inertsil ODS-3 (supplied from GL Sciences), eluants: i) aqueous solution of phosphoric acid containing 5.0 mM sodium 1-octanesulfonate (pH 2.1): methanol=100:15 to 50, ii) aqueous solution of phosphoric acid containing 5.0 mM sodium 1-octanesulfonate (pH 2.1): acetonitrile=100:15 to 30, flow rate: 1.0 mL/minute, and detection: 210 nm.
In accordance with the description of Journal of Bioscience and Bioengineering, 92(1):50-54, 2001 (or JP H10-201481 A publication), a DNA fragment of 1.6 kbp which contains an acid phosphatase gene region was cleaved out and isolated with restriction enzymes SalI and KpnI from a chromosomal DNA derived from Enterobacter aerogenes IFO 12010 strain. The fragment was ligated to pUC118 to construct a plasmid DNA which was designated as pEAP120. The nucleotide sequences encoding the promoter and the signal peptide of acid phosphatase were incorporated into the plasmid pEAP120. The strain to which IFO number was given has been deposited to Institute for Fermentation (17-85 Joso-honnmachi, Yodogawa-ku, Osaka, Japan), but, its operation has been transferred to NITE Biological Resource Center (NBRC), Department of Biotechnology (DOB), National Institute of Technology and Evaluation since Jun. 30, 2002, and the strain can be furnished from NBRC with reference to the above IFO number.
Subsequently, it was attempted to enhance the activity by partially modifying the promoter sequence present upstream of this gene. The site-directed mutation was introduced using QuikChange Site-Directed Mutagenesis Kit (supplied from Stratagene) to replace −10 region of the putative promoter sequence of the acid phosphatase gene from AAAAAT to TATAAT. Oligonucleotide primers for PCR, EM1 (5′-CTT ACA GAT GAC TAT AAT GTG ACT AAA AAC: SEQ ID NO:125) and EMR1 (5′-GTT TTT AGT CAC ATT ATA GTC ATC TGT AAG: SEQ ID NO:126) designed for introducing the mutation were synthesized. In accordance with the method of the instructions, the mutation was introduced using pEAP120 as the template. The nucleotide sequence was determined by the dye termination method using DNA Sequencing Kit Dye Terminator Cycle Sequencing Ready Reaction (supplied from Perkin Elmer) and using 310 Genetic analyzer (ABI) to confirm that the objective mutation had been introduced, and this plasmid was designated as pEAP130. The plasmid pEAP130 has the nucleotide sequences encoding the signal peptide and the modified promoter derived from the N terminal region of acid phosphatase.
(45) Construction of pSFN_Sm_Aet Strain
In order to construct a plasmid pSFN_Sm_Aet from which a fragment of an Aet enzyme gene can be cut out by the treatment with restriction enzymes, pSF_Sm_Aet (Example 6) was used as a template of the site-directed mutagenesis using PCR. The mutation was introduced using “QuikChange Site-Directed Mutagenesis Kit” supplied from Stratagene (USA) in accordance with the manufacturer's protocol and using various primers. First, the base at position 4587 on pSF_Sm_Aet plasmid was substituted (from “a” to “g”) by introducing the mutation using the oligonucleotides shown in SEQ ID NOS:127 and 128 as the primers, to delete NdeI site. Subsequently, the base at position 2363 on pSF_Sm_Aet plasmid was substituted (from “tag” to “atg”) by introducing the mutation using the oligonucleotides shown in SEQ ID NOS:129 and 130, to introduce NdeI site. Escherichia coli JM109 was transformed with the PCR product, and a strain having the objective plasmid pSFN_Sm_Aet was selected using ampicillin resistance as an indicator.
(46) Introduction of pKF_Sm_Aet Rational Mutation
In order to construct a mutant Aet, pKF_Sm_Aet plasmid (Example 2 (1)) was used as the template of the site-directed mutagenesis using the ODA method. The mutation was introduced by the same method as in Example 2 (2) using the primers (SEQ ID NOS:131 to 137) corresponding to various mutant enzymes, and the strains having the objective plasmid pKF_Sm_Aet containing the mutant Aet gene was selected.
(47) Introduction into pSFN_Sm_Aet
The objective gene was amplified by PCR with the plasmid pKF_Sm_AetM containing the mutant Aet gene as the template using the oligonucleotides shown in SEQ ID NOS:129 and 122 as the primers. This DNA fragment was treated with NdeI/PstI, and the resulting DNA fragment was ligated to pSFN_Sm_Aet which had been treated with NdeI/PstI. Escherichia coli JM109 was transformed with this solution containing the ligated product, and a strain having the objective plasmid was selected using ampicillin resistance as the indicator. The resulting strain and the already constructed strains were cultured by the same method as in Example 6 (25).
(48) Production of Peptide Using Microbial Cells <X-Met>
A cultured broth (40 μL) obtained in (47) was suspended in 400 μL of 100 mM borate buffer (pH 8.5 or 9.0) containing 10 mM EDTA, 50 mM amino acid methylester and 100 mM Met, and reacted at 20° C. for one hour. Concentrations of various dipeptides synthesized in this reaction with the wild strain are shown in Table 14. For the dipeptide synthesized by various mutant enzyme-expressing strains (referred to as mutant strains), the ratio of the concentration of the dipeptides synthesized thereby with respect to that by the wild strain is shown in Table 14.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM] IN THE WILD STRAIN IS “1”
(49) Production of Dipeptide Using Microbial Cells <Ala-X>
The production of the peptide when alanine methyl ester was used as the carboxy component and various L-amino acids were used as the amine component was examined. As the mutant enzymes, the mutant strains made in Examples 7 (32), 10 (39) and 12 (47) were used. The cultured broth (20 μL) obtained by the cultivation method described in Example 6 (25) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM alanine methyl ester hydrochloride (Ala-OMe HCl), 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. The concentrations (mM) of various dipeptides synthesized in this reaction with the wild strain are shown in Table 15. For the dipeptide synthesized by various mutant strains, the ratio of the concentration of the dipeptides synthesized thereby with respect to that by the wild strain is shown in Table 15. In Table 15, the synthesis of Ala-Gly and Ala-Thr was measured by the reaction for 10 minutes, and the synthesis of the other dipeptides was measured by the reaction for 15 minutes.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM] IN THE WILD STRAIN IS “1”
(50) Production of Dipeptide Using Microbial Cells <Ala-X>
The cultured broth (20 μL) obtained in Example 12 (47) was added to 400 μL of 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM alanine methyl ester, and 100 mM L-amino acid, and reacted at 20° C. for 15 minutes. The concentrations (mM/O.D.) of various dipeptides synthesized in this reaction with the wild strain are shown in Table 16. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptides synthesized thereby to that by the wild strain is shown in Table 16.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM/O.D.] IN THE WILD STRAIN IS “1”
(51) Construction of pSF_Sm_Aet Rational Mutant Strain
In order to construct mutant Aet, pSF_Sm_Aet was used as the template of the site-directed mutagenesis using PCR. The mutation was introduced by the same method as in Example 12 (45) using the primers (SEQ ID NOS:138 to 157, 160 to 167) corresponding to various mutant enzymes. Escherichia coli JM109 was transformed with the PCR product, and strains having the objective plasmid were selected using ampicillin resistance as the indicator. The resulting strain and the already constructed strains (Example 10 (39)) were cultured by the same method as in Example 6(25).
(52) Production of Peptide Using Microbial Cells <Ala-X>
The cultured broth (20 μL) obtained in (51) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM alanine methyl ester hydrochloride (Ala-OMe HCl), 100 mm 1-amino acid and 10 mM EDTA, and reacted at 20° C. for 15 minutes. The concentrations (mM/O.D.) of various dipeptides (Ala-X) synthesized in this reaction with the wild strain are shown in Table 17. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptides synthesized thereby with respect to that by the wild strain is shown in Table 17.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM/O.D.] IN THE WILD STRAIN IS “1”
(53) Production of Peptide Using Microbial Cells <Ala-X>
Mutation points V184A and V184P whose effects had been observed in (52) were introduced into pSF_Sm_M7-35. V257Y was introduced into pSF_Sm_M7-35 and pSF_Sm_V184A. The mutation was introduced by the same method as in (45) using pSF_Sm_M7-35 or pSF_Sm_V184A as the template and using the primers corresponding to various mutant enzymes (SEQ ID NOS:79, 80, 93, 94, 156, 157). The resulting strains were cultured by the method described in Example 6 (25).
(54) Production of Peptide Using Microbial Cells <Ala-X>
The mutation points W187A, F211A, Q441E, Q441K and N442D whose effects had been observed in Table 11 in Example 8 (34) and Table 16 in Example 13 (50) were introduced into the already-constructed pSF_Sm_M7-35. Double substitution and a triple substitution such as pSF_Sm_V184A/W187A, V184A/N442D and V184A/N442D/L439V were also constructed. In addition, the mutant strain obtained by introducing F207V into pSF_Sm_M7-35/V184A was also constructed. The mutation was introduced by the same method as in Example 12 (45) using pSF_Sm_M7-35, pSF_Sm_V184A or pSF_Sm_M7-35/V184A as the template and using the primers (SEQ ID NOS:131, 158, 134, 159, 14, 170, 168, 169) corresponding to various mutant enzymes. The resulting strains and already-constructed strains were cultured by the method described in Example 6 (25).
(55) Production of Peptide Using Microbial Cells <Ala-X>
The cultured broth (20 μL) obtained in (53) or (54) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM alanine methyl ester hydrochloride (Ala-OMe HCl), 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for 15 minutes. The concentrations (mM/O.D.) of various dipeptides (Ala-X) synthesized in this reaction with the wild strain are shown in Table 18. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized thereby with respect to that by the wild strain is shown in Table 18.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM/O.D.] IN THE WILD STRAIN IS “1”
(56) Production of Peptide Using Microbial Cells <Ala-X>
The mutation points K83A, W187A, F211A, and N442D whose effects had been observed in Example 14 (49) were introduced into pSF_Sm_M7-35/V184A. Double substitution obtained by introducing N442D into pSF_Sm_V184P was also constructed. The mutation was introduced by the same method as in (45) using pSF_Sm_M35-4/V184A or pSF_Sm_V184P as the template and using the primers corresponding to various mutant enzymes. The resulting strains were cultured by the method described in Example 6 (25).
(57) Production of Peptide Using Microbial Cells <Ala-X>
The cultured broth (20 μL) obtained in (56) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM alanine methyl ester hydrochloride (Ala-OMe HCl), 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for 15 minutes. The concentrations (mM) of various dipeptides (Ala-X) synthesized in this reaction with the wild strain are shown in Table 19. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized thereby with respect to that by the wild strain is shown in Table 19.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM] IN THE WILD STRAIN IS “1”
※MUTATION Q441E OF M35-4/V184A IS A STRAIN WHICH RETURNS FROM “E” TO “Q”
(58) Preparation of pTrpT_Sm_Aet Random Library
In order to construct mutant Aet, pTrpT_Sm_Aet or pSF_Sm_M35-4/V184A plasmid was used as the template for random mutagenesis using error prone PCR. The library in which the mutation had been introduced was made by the same method as in Example 3 (8).
(59) Screening of pSFN_Sm_Aet Random Library
Selection was performed by performing two screenings (A/B or A/C) selected from the primary screenings (A) to (C) shown below using the cultured solution obtained by culturing the library made in (58) by the same method as in Example 3 (9).
(60) Primary Screening (A)
A reaction solution (pH 8.2) (200 μL) containing 10 mM phenol, 6 mM AP, S mM Asp(OMe)2, 5 mM Ala-OEt, 7.5 mM Phe, 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial solution, and reacted at 25° C. for about 20 minutes. Subsequently, absorbance at 500 nm was measured to calculate the released amount of methanol. Those in which methanol had been abundantly released were selected as the enzyme which tend to produce AMP rather than Ala-Phe.
(61) Primary Screening (B)
In the same manner as in (60), the reaction solution (pH 8.2) (200 μL) containing 10 mM phenol, 6 mM AP, 5 mM Asp(OMe)2, 5 mM A(M), 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial solution, and reacted at 25° C. for about 20 minutes. Subsequently, absorbance at 500 nm was measured to calculate the released amount of methanol. Those in which the amount of released methanol had been low were selected as the enzyme which has less tendency to produce AM(AM).
(62) Primary Screening (C)
In the same manner as in (60), the reaction solution (pH 8.2) (200 μL) containing 10 mM phenol, 6 mM AP, 5 mM Asp(OMe)2, 3.6 U/mL of peroxidase, 0.16 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial solution, and reacted at 25° C. for about 20 minutes. Subsequently, absorbance at 500 nm was measured to calculate a released amount of methanol. Those in which the amount of released methanol had been low were selected as the enzyme which has less tendency to decompose Asp(OMe)2.
(63) Secondary Screening
The strains selected in (60), (61) and (62) were cultured by the same method as in Example 6 (25). 50 μL of each cultured broth was suspended in 1 mL of 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM Asp(OMe)2, 50 mM Ala-OMe and 75 mM Phe. The mixture was reacted at 20° C. for 10 minutes, and the amounts of produced AMP and Ala-Phe were measured. The strain which had exhibited a fast initial reaction rate was selected.
The cultured broth obtained in the same way as the above was also suspended (2.2 U/mL reaction solution) in 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 50 mM Asp(OMe)2 and 75 mM Phe. The mixture was reacted at 20° C., and the yield of produced AMP was measured. The mutation point was analyzed in the strains which exhibited the high yield, and the following mutation points were specified. The mutant strains having the mutations 21, 22 and 23 (P214T, Q202E and Y494F) were obtained from the library using pTrpT_Sm_Aet as the template. The mutant strains having the mutations 354, 346, 347, 350, 351, 352, 343, 354, 348, 349 and 353 (combining each mutation of A182G, K314R, A515V, K484I, V213A, A245S, V178G, L263M, L66F, S315R and P214H with M35-4/V184A) were obtained from the library using pSF_Sm_M35-4/V184A as the template. The yields of AMP in this reaction 20, 40 and 70 minutes after the onset of the reaction in each mutant strain are shown in Tables 20-1 and 20-2. M35-4/V184A may be referred to hereinbelow as “A1”.
(64) Introduction of Mutation into A182, P183 and T185
Since the yield was enhanced in the strain carrying the V184A mutation, the strains carrying the mutation at around position 184 were constructed. The mutation was introduced by the same method as in (45) using pSF_Sm_M35-4/V184A as the template and using the primers (SEQ ID NOS:171 to 192) corresponding to various mutant enzymes.
(65) Production of Peptides Using Microbial Cells <AMP>
The strains obtained in Example 15 (63) and the aforementioned (64) were cultured by the method described in Example 6 (25). The cultured broth was suspended (10 U/mL reaction solution) in 100 mM borate buffer (pH 8.5) containing 400 mM Asp(OMe)2 hydrochloride and 600 mM Phe, and reacted at 25° C. with keeping pH 8.5 using NaOH. The yields of produced AMP was measured 20, 40 and 80 minutes after the onset of the reaction. The AMP yields in this reaction are shown in Table 21.
(66) Production of Peptides Using Microbial Cells <Ala-X>
The strains obtained in Example 15 (63) and the aforementioned (64) were cultured by the method described in Example 6 (25). The cultured broth (20 μL) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM Ala-OMe.HCl, 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for 15 minutes. The concentrations (mM) of various dipeptides (Ala-X) synthesized in this reaction with pSF_Sm_M35-4/V184A are shown in Table 22. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized thereby with respect to that by pSF_Sm_M35-4/V184A is shown in Table 22.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM] IN M35-4/V184A IS “1”
(67) Construction of Combined Mutant Strain
The mutation points T185F and A182G which had exhibited the effect when combined with M35-4/V184A (A1) were introduced into pSF_Sm_M35-4/V184A, pSF_Sm_M7-35/V184A and pSF_Sm_M3S-4/V184A/N442D. The mutation was introduced by the same method as in (45) using the primers (SEQ ID NOS:185, 186, 193, 194, 199, 200) corresponding to various mutant enzymes. The resulting strains were cultured by the method described in Example 6 (25).
(68) Production of Peptides Using Microbial Cells <Ala-X>
The cultured broth (20 μL) obtained in (67) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM Ala-OMe HCl, 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for 15 minutes. The concentrations (mM) of the dipeptides (Ala-X) synthesized in this reaction with the wild strain are shown in Table 23. For the dipeptides synthesized by various mutant strains, the ratio of the concentration of the dipeptide synthesized thereby with respect to that by the wild strain is shown in Table 23.
*THIS SHOWS RATIO OF THE SYNTHESIZED DIPEPTIDE CONCENTRATION IN VARIOUS MUTANT STRAINS WHEN THE SYNTHESIZED DIPEPTIDE CONCENTRATION [mM] IN THE WILD STRAIN IS “1”
※MUTATION Q441E OF M35-4 + V184A IS A STRAIN WHICH RETURNS FROM “E” TO “Q”
(69) Production of Peptides with Increased Amount of Substrate <Ala-X>
pSF_Sm_Aet, pSF_Sm_M35-4/V184A and pSF_Sm_M7-35/V184A/A182G were cultured by the method shown in Example 6 (25). The cultured broth (5 μL or 20 μL) was added to 400 μL of borate buffer (pH 8.5) containing 50 mM Ala-OMe HCl, 100 mM to 400 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for one hour. The concentrations (mM) of the dipeptides (Ala-X) synthesized in this reaction are shown in Table 24.
(70) Production of Various Dipeptides Using Mutant Enzymes
The production of the peptide with various L-amino acid methyl esters as the carboxy component and L-amino acid as the amine component was examined. The cultured broth (20 μL or 40 μL) cultured by the method described in Example 6 (25) was added to 400 μL of borate buffer (pH 8.5 or 9.0) containing 50 mM L-amino acid methyl ester hydrochloride (X-OMe HCl), 100 mM L-amino acid shown in Table 25 and 10 mM EDTA, and reacted at 20° C. The amounts of various dipeptides produced in this reaction are shown in Table 25. As the enzymes, those derived from pSF_Sm_Aet, pSF_Sm_M12-1 (Example 7 (32)) and pSF_Sm_M35-4/V184A (Example 10 (39)) were used. In the synthesis reaction of Val-Met and Met-Met, enzymes derived from pSF_Sm_F207V (Example 6 (24)) and pSF_Sm_M35-4/V184A/F207V were also used.
*1F207V
*2M35-4/V184A/F207V
*3Asp(OMe)2
(71) Production of Peptides Using Microbial Cells <Arg-Gln>
pSF_Sm_Aet and pSF_Sm_M35-4/V184A were cultured in the method described in Example 6 (25). The cultured broth (1 mL) was suspended in 9 mL of 100 mM borate buffer (pH 9.0) containing 10 mM EDTA, 100 or 200 mM arginine methyl ester and 150 to 300 mL Gln, and reacted at 20° C. for 3 hours. As the reaction proceeds, a pH value was lowered. Thus, the reaction was performed with keeping pH to 9.0 using a 25% NaOH solution. The concentrations and the yields of Arg-Gln produced in this reaction are shown in Table 26.
Reaction time; 180 min
(72) Purification of Enzymes
The wild strain, the pSF_Sm_M35-4/V184A strain and the pSF_Sm_M7-35/V184A/A182G strain were refreshed on LB plates. One platinum loopful thereof was inoculated to 50 mL of terrific broth, and cultured at 25° C. for 18 hours. Microbial cells were collected from the cultured solution, suspended in 100 mM KPB (pH 6.5) and disrupted by a sonicator (180 W/30 minutes). The solution was collected and the supernatant was collected as a soluble fraction by ultracentrifugation at 200,000 g at 4° C. for 20 minutes.
The following manipulations were performed at 4° C. or on ice unless otherwise particularly specified. AKTA explorer 100 was used for the following column fractionation.
The resulting soluble fraction was subjected to CHT5-1 (5 mL, 10×64 mm) which had previously been equilibrated with 100 mM KPB (pH 6.5). Unabsorbed proteins were eluted with 100 mM KPB buffer at a flow rate of 1 mL/minute, and subsequently the absorbed protein was eluted with 25 times volume of the column volume of 100 to 500 mM KPB buffer having a linear gradient.
The active fraction separated by hydroxyapatite chromatography was subjected to preparation so that the final ammonium sulfate concentration became 2 M, and then subjected to Hic-resource-Phe (1 mL) which had previously been equilibrated with 100 mM KPB (pH 6.5) and 2 M ammonium sulfate. The unabsorbed proteins were eluted at a flow rate of 1 mL/minute, and subsequently the absorbed protein was eluted with KPB buffer (60 times volume of the column volume) containing 2M to 0M ammonium sulfate in a linear gradient.
The fraction separated by hydrophobic chromatography was subjected to HiLoad 16/60 Superdex-200 pg (column volume: 120 mL, 16 mm×600 mm) which had previously been equilibrated with 20 mM Hepes (pH 6.5) and 500 mM NaCl. The protein was eluted at a flow rate of 0.75 mL/minute to collect the active fraction. The active fraction was concentrated, and then dialyzed against 20 mM Hepes (pH 6.5). The “unit” shown below indicates the unit in Ala-Gln synthesis reaction.
(73) Production of Peptides Using Purified Enzyme <HIL-Phe>
The purified enzyme (0.84 or 4.2 U, 1 or 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 9.0) containing 50 mM lactonized HIL [{2S,3R,4S)-hydroxyisoleucine], 100 mM Phe and 10 mM EDTA, and reacted at 20° C. for one hour. The concentrations of HIL-Phe synthesized in this reaction are shown in Table 27.
(74) Production of Peptides Using Purified Enzyme <Gly-Ser(tBu)>
The purified enzyme (0.84 or 4.2 U, 1 or 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 8.5) containing 50 mM Gly-OMe, 100 mM Ser(tBu) and 10 mM EDTA, and reacted at 20° C. The concentrations of Gly-Ser(tBu) synthesized in this reaction calculated in terms of Gly-Ser are shown in Table 28.
*Gly-Ser conversion
(75) Production of Tripeptides Using Purified Enzymes <Ala-X-X>
The purified enzyme (0.84 or 4.2 U, 1 or 5 μL) obtained from pSF_Sm_M35-4/V184A or pSF_Sm_M7-35/V184A/A182G was added to 150 μL of borate buffer (pH 9.0) containing 50 mM Ala-OMe, 100 X-X and 10 mM EDTA, and reacted at 20° C. The concentrations of tripeptides (Ala-X-X) synthesized in this reaction are shown in Table 29.
(76) Production of Tripeptides Using Purified Enzyme
The purified enzyme (0.84 or 4.2 U, 1 or 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 9.0) containing 50 mM Ala-OMe, 50 mM X-X and 10 mM EDTA, and reacted at 20° C. The concentrations of the tripeptides synthesized in this reaction are shown in Table 30.
Substrate 50 mM XOMe+50 mM XX
(77) Production of Peptides Using Purified Enzyme <Ala-X-X>
The purified enzyme (0.84 or 4.2 U, 1 or 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 9.0) containing 100 mM Ala-OMe, 100 mM X-X and 10 mM EDTA, and reacted at 20° C. The concentrations of the tripeptides (Ala-X-X) synthesized in this reaction are shown in Table 31.
Substrate 100 mM AlaOMe+100 mM XX
(78) Production of Tetrapeptide Using Purified Enzyme <GGFM>
The purified enzyme (4.2 U, 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 9.0) containing 100 mM Gly-OMe, 40 mM GFM and 10 mM EDTA, and reacted at 20° C. The concentrations of the tetrapeptide (GGFM) synthesized in this reaction are shown in Table 32.
(79) Production of Pentapeptide Using Purified Enzyme <Met-Enkephalin>
The purified enzyme (4.2 U, 5 μL) obtained from pSF_Sm_M35-4/V184A was added to 150 μL of borate buffer (pH 8.5) containing 50 mM Tyr-OMe, 5 mM GGFM and 10 mM EDTA, and reacted at 20° C. The concentrations of the pentapeptide (YGGFM) synthesized in this reaction are shown in Table 33.
(1) 1 L of Escherichia coli (E. coli) JM109 Strain in which the Protein Having the Amino Acid Sequence of SEQ ID NO:209 was Expressed at High Level was Cultured, and the Protein was Purified from Microbial Cells by the Following Procedure.
(1-1) Hydroxyapatite Chromatography
The microbial cells obtained in the above were disrupted in “100 mM potassium phosphate buffer (pH 6.5)” (buffer A), and 100 mL of the soluble fraction was subjected to a hydroxyapatite column Bio-Scale CHT-I (supplied from Bio-Rad, CV=5 mL) which had been equilibrated with the buffer A, to absorb to the carrier.
The absorbed protein was eluted by linearly changing the concentration of potassium phosphate buffer from 100 mM to 500 mM (25CV). A peak of the protein was detected by absorbance at 280 nm, and the fraction was collected.
(1-2) Hydrophobic Chromatography
The fraction fractionated in (1-1) was mixed with the 5 time volume of “100 mM potassium phosphate buffer (pH 6.5) containing 2M ammonium sulfate” (buffer B). This solution was subjected to a hydrophobic chromatographic column RESOURCE PHE (supplied from Amersham, CV=1 mL) which had been equilibrated with the buffer B. The objective protein was absorbed to the carrier by this manipulation. Subsequently, the protein was eluted by a linear gradient from 2M to 0 M of ammonium sulfate (60CV), and the fraction was fractionated.
(1-3) Cation Exchange Chromatography: Resource S
The fraction fractionated in (1-2) was dialyzed against “20 mM sodium acetate buffer (pH 5.0)” (buffer C) overnight. This solution was subjected to a cation exchange column RESOURCE S (supplied from Amersham, CV=1 mL) which had been equilibrated with the buffer C. The absorbed protein was eluted by linearly changing the concentration of sodium chloride from 0 mM to 500 mM (50CV). The peak of the protein was detected by absorbance at 280 nm, and the fraction was fractionated.
The fractions in respective purification stages were confirmed by SDS-PAGE. As a result, the purified protein obtained after (1-3) was detected as an almost single band at a position of about 70 kDa by CBBR staining. The solution the protein thus obtained was dialyzed against 20 mM HEPES buffer (pH 7.0) at 4° C. overnight. About 30 mg of the purified protein was obtained by the aforementioned manipulations.
(2) Crystallization of Protein Having Amino Acid Sequence of SEQ ID NO:209
The purified protein solution obtained in (1) was concentrated to about 40 mg/mL at 4° C. using an ultrafiltrator AmiconUltra (supplied from Millipore, fractioning molecular weight: 10 kDa). Using the obtained concentrated protein solution, crystallization conditions were searched by changing various parameters such as a protein concentration, a precipitating agent, pH, temperature and additives. As a result, hexagonal-cylindrical crystals were obtained which had grown to the 0.2 mm×0.2 mm×0.2 mm crystal in about one week by the hanging drop vapor diffusion method in which a droplet which is a mixture of 1 μL of the protein solution and 1 μL of the precipitating agent containing 0.2% octyl β D-glucopyranoside is equilibrated at 20° C. in the precipitating agent having the composition of 12 to 18% PEG 6000 and 0.1 M Tris-HCl (pH 8.0).
(3) X-Ray Crystal Structure Analysis of Protein Having Amino Acid Sequence of SEQ ID NO:209
X-ray diffraction intensity was measured at low temperature because the protein crystal is deteriorated in the measurement by X-ray damage at ambient temperature and the resolution thereby gradually decreases. The crystal was transferred into the solution containing 20% glycerol, 20% PEG 6000, 0.1 M Tris-HCl (pH 8.0) and 0.4% octyl 0 D-glucopyranoside. Then nitrogen gas at −173° C. was sprayed thereto for rapid cooling. X-ray diffraction data of the crystal were obtained using a CCD detector of 315 type supplied from ADSC, placed in the beam line 5 in Photon Factory in Inter-University Research Institute Corporation, High Energy Accelerator Research Organization (Tsukuba-shi). The wavelength of the X-ray was set up to 1.0 angstrom, and a distance from the crystal to the CCD detector was 450 mm. Image data per one frame was taken with exposure for 20 seconds and an oscillation angle of 1.0°. The data for 150 frames were collected. Crystallographic parameters were as follows: a space group was P6522, and lattice constants were a=104.324 angstroms and c=615.931 angstroms. Given that two protein molecules are contained in an asymmetric unit, a water content rate of the crystal is 65%. The crystal was diffracted to about 3.0 angstroms. The data were processed using the program HKL 2000 (Methods Enzymol., 276:307-326, 1997). The values of Rmerge which is the indicator of data quality were 0.106 at the resolution of 50.0 to 3.0 angstroms and 0.450 at the outmost shell at the resolution of 3.11 to 3.00 angstroms. Completeness of the data were 97.2% at the resolution of 50.0 to 3.0 angstroms and 81.1% at the outmost shell at the resolution of 3.11 to 3.00 angstroms.
The structure was analyzed by a molecular replacement method. The program for the molecular replacement AMORE (Acta Crystallogr., Sect. A, 50:157-163, 1994) included in program package CCP4 for protein structure analysis (Acta Crystallogr., Sect. D, 50:760-763, 1994) was used. As a reference structure, the S205A mutant of α-amino acid ester hydrolase (entry number of Protein Data Bank: 1NX9) was utilized. The α-amino acid ester hydrolase has a tetramer structure whereas the protein having the amino acid sequence of SEQ ID NO:209 has a dimer structure. When a monomer structure of the α-amino acid ester hydrolase was used as a model, no promising solution was obtained. It is possible to cut out 3 types of the dimer structures from the α-amino acid ester hydrolase tetramer. Thus, the molecular replacement was attempted using these three types of dimers. As a result, when the dimer composed of A molecule and D molecule in 1NX9 coordinate data was used as the model, the promising solution was found from several standpoints (good contrast in the first solution, clear difference in space groups, no bad contact between the molecules). The electron density map at the resolution of 3.0 angstroms was calculated based on the resulting initial phase, and the electron density map was depicted on a computer graphic program QUANTA supplied from Accelrys. The structural analysis was carried forward by repeating modification of the molecular model on the graphics and by refinement using the program CNX supplied from Accelrys.
(4) Crystallization of Protein Having the Amino Acid Sequence of SEQ ID NO:209 in which Lys Residues were Reductively Dimethylated
It has been reported that the crystal quality is sometimes improved when the Lys residue of the protein is reductively dimethylated (Biochemistry 32:9851-9858, 1993). In accordance with this method, the Lys residues of the purified protein solution obtained in the above were reductively dimethylated using hydrogenated sodium boron and formaldehyde, and subsequently this protein was subjected to the crystallization experiment. As a result, platy crystals were obtained which had grown to the 0.4 mm×0.2 mm×0.1 mm crystal in about one week by the hanging drop vapor diffusion method in which a droplet which is a mixture of 1 μL of the protein solution and 1 μL of the precipitating agent containing 0.2% octyl β D-glucopyranoside is equilibrated in the precipitating agent having the composition of 15% PEG 6000 and 0.1 M Tris-HCl (pH 8.0).
(5) X-Ray Crystal Structure Analysis of Protein Having the Amino Acid Sequence of SEQ ID NO:209 in which Lys Residues were Reductively Dimethylated
The crystal was transferred into the solution containing 20% glycerol, 20% PEG 6000, 0.1 M Tris-HCl (pH 8.0) and 0.4% octyl β D-glucopyranoside. Then nitrogen gas at −173° C. was sprayed thereto for rapid cooling. X-ray diffraction data of the crystal were obtained using R-AXIS V type imaging plate detector supplied from Rigaku and placed in beam line 24XU in Synchrotron Orbit Radiation Facility, SPring 8 in Japan Synchrotron Radiation Research Institute (Hyogo Prefecture, Sayo-gun). The wavelength of the X-ray was set up to 0.827 angstrom, and the distance from the crystal to the imaging plate detector was 500 mm. Image data per one frame was taken with exposure for 90 seconds and an oscillation angle of 1.0°. The data for 180 frames were collected. Crystallographic parameters were as follows: the space group was P21, and lattice constants were a=74.476 angstroms, b=213.892 angstroms and c=90.427 angstroms. Given that four protein molecules are contained in the asymmetric unit, the water content rate of the crystal is 53%. The crystal was diffracted to about 3.0 angstroms. The data were processed using the program CrystalClear supplied from Rigaku. The values of Rmerge which is the indicator of data quality were 0.097 at a resolution of 40.0 to 3.0 angstroms and 0.309 at the outermost shell at a resolution of 3.11 to 3.00 angstroms. Completeness of the data were 96.8% at a resolution of 40.0 to 3.0 angstroms and 95.8% at the outmost shell at a resolution of 3.11 to 3.00 angstroms.
The structure was analyzed by the molecular replacement method. The program for the molecular replacement AMORE (Acta Crystallogr., Sect. A, 50:157-163, 1994) included in program package CCP4 for protein structure analysis (Acta Crystallogr., Sect. D, 50:760-763, 1994) was used. As a reference structure, the S205A mutant of α-amino acid ester hydrolase (entry number of Protein Data Bank: 1NX9) was utilized. When the monomer structure of the α-amino acid ester hydrolase was used as the model, no promising solution was obtained. Thus, the molecular replacement was attempted using three types of dimers cut out from the α-amino acid ester hydrolase tetramer. As a result, when the dimer composed of A molecule and D molecule in 1NX9 coordinate data was used as the model as with the above, the solution was found. This result indicates success of the molecular replacement method as well as the dimer structure of the protein having the amino acid sequence of SEQ ID NO:209. The electron density map at the resolution of 3.0 angstroms was calculated based on the resulting initial phase, and the electron density map was depicted on the computer graphic program QUANTA supplied from Accelrys. The structural analysis was carried forward by repeating modification of the molecular model on the graphics and by refinement using the program CNX supplied from Accelrys. Atomic coordinates of the present crystal structure were are in
Modified proteins were made by introducing rational mutation concerning 134 residues which are close to the active site (colored in black) in the amino acid sequence of SEQ ID NO:208, in accordance with the following Example 22.
(1) Rational Mutation Method Based on Tertiary Structure Information
In order to increase the production amount of AMP, the site-directed mutation was introduced into the amino acid sequence of SEQ ID NO:208 (referred to hereinbelow as pA1) based on the tertiary structure information. The protein having the amino acid sequence of SEQ ID NO:209 has high homology with the protein having the amino acid sequence of SEQ ID NO:208, i.e., only four substitutions are given. Thus, the tertiary structure information of mutant peptide-synthesizing enzymes expressed by pA1 (represented as A1) was predicted from the protein having the amino acid sequence of SEQ ID NO:209, and 134 amino acid residues (colored in black in
(2) Preparation of Single Mutation Strains
In order to obtain the mutant A1, pA1 was used as the template of the site-directed mutagenesis using PCR. The mutation was introduced using “QuikChange Site-Directed Mutagenesis Kit” supplied from Stratagene (USA) in accordance with the manufacturer's protocol. The primer of 33mer comprising a mutation codon at a center and 15mers sandwiching the mutation codon was used for the introduction of the site-directed mutagenesis in each residue. The primers used for each mutation point are shown in Table 46. The nucleotide sequences which configure the primers in Table 46 are also shown in Sequence Listing. SEQ ID NOS:210 to 483 correspond to primers in Table 46 in the order of the forward primer and the reverse primer in the direction from upper to lower rows in the table. The codon corresponding to each amino acid to be substituted is placed as the mutation codon “xxx” in the center of each primer sequence (“nnn” part in nucleotide sequences of SEQ ID NOS:210 to 483). That is, depending on the type of amino acid residue to be introduced, each primer includes the corresponding codon sequence introduced into “xxx” part. Each codon corresponding to the amino acid residue is as shown in Table 44. Escherichia coli JM109 was transformed with the PCR product, and the strain having the objective plasmid was selected using ampicillin resistance as the indicator.
(3) Obtaining Microbial Cells
One platinum loopful of each mutant strain was inoculated into a usual test tube in which 2 mL of terrific medium (12 g/L of tryptone, 24 g/L of yeast extract, 2.3 g/L of potassium dihydrogen phosphate, 12.5 g/L of dipotassium hydrogen phosphate, 4 g/L of glycerol and 100 mg/L of ampicillin) had been placed, and main cultivation was performed at 25° C. at 150 reciprocations/minute for 18 hours.
(4) Measurement of Specific Activity in Each Mutant Strain
The broth (50 μL) of each mutant strain was added to 1 mL of a low concentration reaction solution (50 mM dimethyl aspartate, 75 mM phenylalanine), and reacted at 20° C. at initial pH of 8.5. The amount of produced AMP 15 minutes after the start of the reaction was quantified by HPLC, and the specific activity (U/mL) in each single mutation strain was calculated. For the unit (U) of the enzyme, the amount of the enzyme which can produce 1 μmol of the product AMP in one minute was defined as 1 U.
(5) Measurement of AMP Yield in Each Single Mutation Strain in Low Concentration Reaction Solution
Based on the resulting specific activity data, the amount of the broth necessary for obtaining 2 U was calculated as to each mutant strain. Subsequently, the calculated amount of the broth was added to 1 mL of the low concentration reaction solution, and reacted at a temperature of 20° C. at initial pH of 8.5. The amounts of produced AMP 25 and 45 minutes after the start of the reaction were quantified by HPLC, and the mutant strains listed on Tables 32-1 to 35-7 exhibited higher yield than A1. These were found out to be the important mutant strains which contribute to the reaction of AMP synthesis.
(6) Calculation of Yield Enhancement Probability
Among 1137 single mutation mutants, 335 mutants were found to be the mutants exhibiting improved yield when compared with A1. The yield enhancement probability was 335×1137=0.29. Meanwhile, the results of calculating the yield enhancement probability for each residue are summarized in Tables 36 and 37. The values of yield enhancement probability were largely different depending on the residues. For example, probability of yield increase by mutation at each of 47 positions was 40% or more, at each of 59 positions was 30% or more, and at each of 71 positions was 20% or more. The position which brings about the yield enhancement probability of 20% or more can enhance the yield with very high probability and may be determined to be an industrially very important mutation point.
(7) Preparation of Double Mutation Strains
For the purpose of obtaining the strains capable of giving further enhanced yield, double mutation strains were made by mutually combining the mutation points by which the enhanced yield had been obtained (Table 37). For example, in the case of combining I157L and Y328F which were the mutation points which had contributed to enhanced yield of AMP, PCR and the transformation were performed by the methods described in Example 22 (2) using the primers used for introducing Y328F into A1/I157L, and the strains having the objective plasmid were selected using the ampicillin resistance as the indicator.
(8) Measurement of Specific Activity in Double Mutation Strain
The specific activity (U/mL) in the double mutation strains was calculated by the methods described in Example 22 (4), and is shown in Table 38.
(9) Measurement of AMP Yield in Each Double Mutation Strain in Low Concentration Reaction Solution
Based on the resulting specific activity data, the amount of the broth necessary for obtaining 2 U was calculated as to each mutant strain. Subsequently, the calculated amount of the broth was added to 1 mL of the low concentration reaction solution, and reacted at a temperature of 20° C. at initial pH of 8.5. The amounts of produced AMP 25 and 45 minutes after the start of the reaction were quantified by HPLC, and the mutant strains listed on Table 38 exhibited higher yield than A1. It has been found out that these mutations contribute to the enhancement of yield when two of these mutations are combined.
(10) Preparation of Multiple Mutation Strains
For the purpose of obtaining the strains capable of exhibiting still more enhanced yield, the combinable mutation points each of which had contributed to AMP yield enhancement were mutually combined, to produce the multiple mutation strains (Table 38). For example, mutation points I157L with Y81A/Y328F, each of which had contributed to high AMP yield enhancement, were combined by PCR and transformation in accordance with the methods described in Example 22 (2) using the primers for introducing I157L into pA1/Y81A/Y328F, and the strains having the objective plasmid were selected using the ampicillin resistance as the indicator. The amounts of produced AMP 25 and 45 minutes after the start of the reaction were quantified by HPLC, and the mutants listed on Table 38 exhibited higher yield than A1. It has been found out that these mutations contribute to the enhancement of yield when three or more of these mutations are combined.
(11) Measurement of AMP Yield in each Mutant Strain in High Concentration Reaction Solution
Based on the resulting specific activity data, the amount of the broth necessary for obtaining 200 U was calculated as to each mutant strain. Subsequently, the calculated amount of the broth was concentrated to 5 mL. The concentrated broth of each mutant strain was added to 15 mL of the high concentration reaction solution (400 mM dimethyl aspartate, 600 mM phenylalanine), and reacted at a temperature of 22° C. at initial pH of 8.5. As the reaction proceeds, the pH value was lowered, but pH was kept to 8.5 throughout the reaction by adding 6 M NaOH. The amounts of produced AMP 40, 60 and 80 minutes after the start of the reaction were quantified by HPLC. The mutants listed on Tables 39 and 40 exhibited higher yield than A1.
The strains obtained in Example 22 (A1, A1/I157L, A1/G161A, A1/Y328F) were cultured by the method described in Example 6 (25). The cultured broth (5 μL or 10 μL) was added to 200 μL of borate buffer (pH 9.0) containing 50 mM Ala-OMe HCl, 100 mM L-amino acid and 10 mM EDTA, and reacted at 20° C. for 30 minutes. The concentrations of dipeptides (Ala-X) synthesized 5, 10 and 30 minutes after the start of the reaction are shown in Table 41
substrate 50 mM AlaOMe + 100 mM X
In order to construct strains having various combinations of mutation points, pSF_Sm_M35-4/V184A/I157L (A1/I157L) was used as the template of the site-directed mutagenesis using PCR.
The mutations were introduced by the same method as in Example 7 (29) using the primers (SEQ ID NOS:193, 195 to 198) corresponding to various enzymes to yield the library of the strains having the random combination.
The library made in (F2) was cultured by the same method as in Example 3 (9). Using the cultured solution, two screenings for selection were performed (see the following (F4) and (F5)).
The reaction solution (200 μL) (pH 8.2) containing 10 mM phenol, 6 mM AP, 5 mM Asp(OMe)2, 30 mM Phe, 6.12 U/mL of peroxidase, 0.21 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of a resulting microbial solution, reacted at 25° C. for about 20 minutes, and subsequently absorbance at 500 nm was measured to calculate the released amount of methanol.
The reaction solution (200 μL) (pH 8.2) containing 10 mM phenol, 6 mM AP, S mM Asp(OMe)2, S mM Ala-OEt, 30 mM Phe, 6.12 U/mL of peroxidase, 0.21 U/mL of alcohol oxidase, 10 mM EDTA and 100 mM borate was added to 5 μL of the resulting microbial solution, reacted at 25° C. for about 20 minutes, and subsequently the absorbance at 500 nm was measured to calculate the released amount of methanol.
Both (F4) and (F5) were performed. Those having a larger value of (F4)/(F5) than that of the mother strain (A1+I157L) were selected as the enzymes which tend to produce AMP rather than Ala-Phe.
The strains screened and selected by the aforementioned primary screenings were cultured by the method described in Example 6 (25). The cultured broth (2 U) was suspended in 100 mM borate buffer (pH 8.5) containing 10 mM EDTA, 50 mM Asp(OMe)2, and 75 mM Phe such that the final volume was 1 mL, and the amount of produced AMP was measured at 20° C. The strains which produced AMP abundantly were selected. The combination of the mutation points was specified by sequencing in the selected strains, and their mutation points are described in Table 34. The selected strain was described as F22, and the amounts of produced AMP in F22 are shown in Table 42.
The mutation points Y328F, Y81A, and T210L which exhibited effect in Example 22 were introduced into F22 strain. The mutation was introduced by the same method as in (45) using the primers (SEQ ID NOS:201 to 206) corresponding to various mutant enzymes. The resulting strains were cultured by the method described in Example 6 (25). The cultured broth was suspended in the solution (18 U/mL reaction solution) containing 400 mM Asp(OMe)2 monomethyl sulfate and 400 mM Phe, and reacted at 22° C. with keeping pH 8.5 using NH4OH. The yield of produced AMP was measured. The AMP yield in this reaction is shown in Table 43.
<List of Abbreviations>
Asp(OMe)2.HCl: L-aspartic acid-α,β-dimethyl ester hydrochloric acid
Ala-OEt: L-alanine ethyl ester
Ala-OMe: L-alanine methyl ester
Tyr-OMe: L-tyrosine methyl ester
Gly-OMe: glycine methyl ester
Phe-OMe: L-phenylalanine methyl ester
AMP: α-L-aspartyl-L-phenylalanine-β-ester
Ala-Gln: L-alanyl-L-glutamine
Ala-Phe: L-alanyl-L-phenylalanine
Phe-Met: L-phenylalanyl-L-methionine
Leu-Met: L-leucyl-L-methionine
Ile-Met: L-isoleucyl-L-methionine
Met-Met: L-methionyl-L-methionine
Pro-Met: L-prolyl-L-methionine
Trp-Met: L-tryptophyl-L-methionine
Val-Met: L-valyl-L-methionine
Asn-Met: L-asparaginyl-L-methionine
Cys-Met: L-cysteinyl-L-methionine
Gln-Met: L-glutaminyl-L-methionine
Gly-Met: glycyl-L-methionine
Ser-Met: L-seryl-L-methionine
Thr-Met: L-threonyl-L-methionine
Tyr-Met: L-tyrosyl-L-methionine
Asp-Met: L-aspartyl-L-methionine
Arg-Met: L-arginyl-L-methionine
His-Met: L-histidyl-L-methionine
Lys-Met: L-lysyl-L-methionine
Ala-Gly: L-alanyl-glycine
Ala-Thr: L-alanyl-L-threonine
Ala-Glu: L-alanyl-L-glutamic acid
Ala-Ala: L-alanyl-L-alanine
Ala-Asp: L-alanyl-L-aspartic acid
Ala-Ser: L-alanyl-L-serine
Ala-Met: L-alanyl-L-methionine
Ala-Val: L-alanyl-L-valine
Ala-Lys: L-alanyl-L-lysine
Ala-Asn: L-alanyl-L-asparagine
Ala-Cys: L-alanyl-L-cysteine
Ala-Tyr: L-alanyl-L-tyrosine
Ala-Ile: L-alanyl-L-isoleucine
Arg-Gln: L-arginyl-L-glutamine
Gly-Ser: glycyl-L-serine
Gly-Ser(tBu): glycyl-L-(t-butyl)serine
HIL-Phe: (2S,3R,4S)-4-hydroxylisoleucyl-phenylalanine
AFA: L-alanyl-L-phenylalanyl-L-alanine
AGA: L-alanyl-glycyl-L-alanine
AHA: L-alanyl-L-histidyl-L-alanine
ALA: L-alanyl-L-leucyl-L-alanine
AAA: L-alanyl-L-alanyl-L-alanine
AAG: L-alanyl-L-alanyl-glycine
AAP: L-alanyl-L-alanyl-L-proline
AAQ: L-alanyl-L-alanyl-L-glutamine
AAY: L-alanyl-L-alanyl-L-tyrosine
GFA: glycyl-L-phenylalanyl-L-alanine
AGG: L-alanyl-glycyl-glycine
TGG: L-threonyl-glycyl-glycine
GGG: glycyl-glycyl-glycine
AFG: L-alanyl-L-phenylalanyl-glycine
GGFM: glycyl-glycyl-L-phenylalanyl-L-methionine
YGGFM: L-tyrosyl-glycyl-glycyl-L-phenylalanyl-L-methionine
AM: L-aspartic acid-β-methyl ester hydrochloric acid
AM(AM): L-aspartyl-L-aspartic acid-β,β-dimethyl ester
AP: 4-aminoantipyrine
OPT: 1,10-Phenanthoroline monohydrate
Single character codes of the amino acids at mutated positions and the codons used which correspond to the mutation introduction into the amino acid residues in the present specification are as shown in Table 44.
[Sequence List Free Text]
List of Primer Sequences
The present invention is useful in a variety of fields concerning, e.g., a method for producing peptides.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2004-368503 | Dec 2004 | JP | national |
This application is based upon and claims the benefit of priority from Japanese Patent Application No. 2004-368503, filed Dec. 20, 2004 and U.S. Provisional Application No. 60/638,370, filed Dec. 27, 2004, the entire contents of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60638370 | Dec 2004 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/JP05/23400 | Dec 2005 | US |
| Child | 11765926 | Jun 2007 | US |
