Patent Application
20100081183
The invention relates to the field of industrial microbiology and expression of dihydroxy-acid dehydratase activity. More specifically, increased levels of dihydroxy-acid dehydratase activity were achieved in lactic acid bacteria, allowing increased production of compounds from pathways including dihydroxy-acid dehydratase, such as isobutanol.
Dihydroxy-acid dehydratase (DHAD), also called acetohydroxy acid dehydratase, catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate and of 2,3-dihydroxymethylvalerate to α-ketomethylvalerate. The DHAD enzyme requires binding of an iron-sulfur (Fe—S) cluster for activity, is classified as E.C. 4.2.1.9, and is part of naturally occurring biosynthetic pathways producing valine, isoleucine, leucine and pantothenic acid (vitamin B5). DHAD catalyzed conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate is also a common step in the multiple isobutanol biosynthetic pathways that are disclosed in commonly owned and co-pending US Patent Application Publication US 20070092957 A1. Disclosed therein is engineering of recombinant microorganisms for production of isobutanol. Isobutanol is useful as a fuel additive, whose availability may reduce the demand for petrochemical fuels.
High levels of DHAD activity are desired for increased production of products from biosynthetic pathways that include this enzyme activity, including for enhanced microbial production of branched chain amino acids, pantothenic acid, and isobutanol.
There is a need therefore to increase DHAD activity in lactic acid bacterial (LAB) cells to allow increased production of isobutanol and other products whose biosynthetic pathways include DHAD.
Provided herein is a recombinant lactic acid bacterial cell comprising at least one gene encoding a heterologous polypeptide having dihydroxy-acid dehydratase activity and wherein the bacterial cell is substantially free of lactate dehydrogenase activity. In some embodiments, the heterologous polypeptide having dihydroxy-acid dehydratase activity has a specific activity of at least about 0.1 μmol min−1 mg−1 total soluble protein in a crude cell extract. In other embodiments, the heterologous polypeptide having dihydroxy-acid dehydratase activity has a specific activity of at least about 0.6 μmol min−1 mg−1 total soluble protein in a crude cell extract.
In some embodiments, the dihydroxy-acid dehydratase enzyme is expressed by a nucleic acid molecule that is heterologous to the bacteria, and in some embodiments, the dihydroxy-acid dehydratase is a [2Fe-2S] dihydroxy-acid dehydratase. In some embodiments, the dihydroxy-acid dehydratase polypeptide has an amino acid sequence that matches the Profile HMM of table 7 with an E value of <10−5 wherein the polypeptide additionally comprises all three conserved cysteines, corresponding to positions 56, 129, and 201 in the amino acids sequences of the Streptococcus mutans DHAD enzyme corresponding to SEQ ID NO:168.
In some embodiments, the dihydroxyacid dehydratase polypeptide has an amino acid sequence selected from the group consisting of SEQ ID NO:310, SEQ ID NO:298, SEQ ID NO:168, SEQ ID No:164, SEQ ID NO:346, SEQ ID NO:344, SEQ ID NO:232, and SEQ ID NO:230.
Also provided herein is a recombinant lactic acid bacterial cell comprising at least one gene encoding a heterologous polypeptide having dihydroxy-acid dehydratase activity wherein the bacterial cell is substantially free of lactate dehydrogenase activity and comprising a disruption in, or some other genetic modification that reduces expression of, at least one endogenous gene encoding a polypeptide having lactate dehydrogenase activity. In some embodiments, the gene encoding lactate dehydrogenase is selected from the group consisting of IdhL, IdhD, IdhL1, and IdhL2. In some embodiments, the lactic acid bacteria is selected from the group consisting of Lactococcus, Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, and Streptococcus.
In some embodiments, the lactic acid host cell is Lactobacillus plantarum and the polypeptide having lactate dehydrogenase activity has an amino acid sequence selected from the group consisting of SEQ ID NO: 496, 498, and 500. In other embodiments, the lactic acid host cell is Lactococcus lactis and the polypeptide having lactate dehydrogenase activity has an amino acid sequence as set forth in SEQ ID NO:502. In other embodiments, the lactic acid host cell is Leuconostoc mesenteroides and the polypeptide having lactate dehydrogenase activity has an amino acid sequence as set forth in SEQ ID NO:504. In other embodiments, the lactic acid host cell is Streptococcus thermophilus and the polypeptide having lactate dehydrogenase activity has an amino acid sequence as set forth in SEQ ID NO:506. In other embodiments, the lactic acid host cell is Pediococcus pentosaceus and the polypeptide having lactate dehydrogenase activity has an amino acid sequence selected from the group consisting of SEQ ID NO:508 and 510. In other embodiments, the lactic acid host cell is Lactobacillus acidophilus and the polypeptide having lactate dehydrogenase activity has an amino acid sequence selected from the group consisting of SEQ ID NO:512, 514 and 516.
Also provided is a recombinant lactic acid bacterial cell comprising at least one gene encoding a heterologous polypeptide having dihydroxy-acid dehydratase activity wherein the bacterial cell is substantially free of lactate dehydrogenase activity and wherein the bacteria produces isobutanol. In some embodiments, the bacteria comprises an isobutanol biosynthetic pathway, and in some embodiments, the isobutanol biosynthetic pathway comprises genes encoding acetolactate synthase, acetohydroxy acid isomeroreductase, dihydroxy-acid dehydratase, branched-chain α-keto acid decarboxylase, and branched-chain alcohol dehydrogenase.
Also provided herein is a method of making isobutanol comprising providing the recombinant lactic acid bacteria described herein and growing the lactic acid bacteria under conditions wherein isobutanol is produced.
The various embodiments of the invention can be more fully understood from the following detailed description, the figures, and the accompanying sequence descriptions, which form a part of this application.
Table 7 is a table of the Profile HMM for dihydroxy-acid dehydratases based on enzymes with assayed function. Table 7 is submitted herewith electronically and is incorporated herein by reference.
The following sequences conform with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.
Mycobacterium sp. MCS
Mycobacterium gilvum PYR-GCK
Mycobacterium smegmatis str. MC2 155
Mycobacterium vanbaalenii PYR-1
Nocardia farcinica IFM 10152
Rhodococcus sp. RHA1
Mycobacterium ulcerans Agy99
Mycobacterium avium subsp.
paratuberculosis K-10
Mycobacterium tuberculosis H37Ra
Mycobacterium leprae TN *
Kineococcus radiotolerans SRS30216
Janibacter sp. HTCC2649
Nocardioides sp. JS614
Renibacterium salmoninarum ATCC
Arthrobacter aurescens TC1
Leifsonia xyli subsp. xyli str. CTCB07
marine actinobacterium PHSC20C1
Clavibacter michiganensis subsp.
michiganensis NCPPB 382
Saccharopolyspora erythraea NRRL
Acidothermus cellulolyticus 11B
Corynebacterium efficiens YS-314
Brevibacterium linens BL2
Tropheryma whipplei TW08/27
Methylobacterium extorquens PA1
Methylobacterium nodulans ORS 2060
Rhodopseudomonas palustris BisB5
Rhodopseudomonas palustris BisB18
Bradyrhizobium sp. ORS278
Bradyrhizobium japonicum USDA 110
Fulvimarina pelagi HTCC2506
Aurantimonas sp. SI85-9A1
Hoeflea phototrophica DFL-43
Mesorhizobium loti MAFF303099
Mesorhizobium sp. BNC1
Parvibaculum lavamentivorans DS-1
Loktanella vestfoldensis SKA53
Roseobacter sp. CCS2
Dinoroseobacter shibae DFL 12
Roseovarius nubinhibens ISM
Sagittula stellata E-37
Roseobacter sp. AzwK-3b
Roseovarius sp. TM1035
Oceanicola batsensis HTCC2597
Oceanicola granulosus HTCC2516
Rhodobacterales bacterium HTCC2150
Paracoccus denitrificans PD1222
Oceanibulbus indolifex HEL-45
Sulfitobacter sp. EE-36
Roseobacter denitrificans OCh 114
Jannaschia sp. CCS1
Caulobacter sp. K31
Candidatus Pelagibacter ubique
Erythrobacter litoralis HTCC2594
Erythrobacter sp. NAP1
Comamonas testosterone KF-1
Sphingomonas wittichii RW1
Burkholderia xenovorans LB400
Burkholderia phytofirmans PsJN
Bordetella petrii DSM 12804
Bordetella bronchiseptica RB50
Bradyrhizobium sp. ORS278
Bradyrhizobium sp. BTAi1
Bradhyrhizobium japonicum
Sphingomonas wittichii RW1
Rhodobacterales bacterium HTCC2654
Solibacter usitatus Ellin6076
Roseiflexus sp. RS-1
Rubrobacter xylanophilus DSM 9941
Salinispora tropica CNB-440
Acidobacteria bacterium Ellin345
Thermus thermophilus HB27
Maricaulis maris MCS10
Parvularcula bermudensis HTCC2503
Oceanicaulis alexandrii HTCC2633
Plesiocystis pacifica SIR-1
Bacillus sp. NRRL B-14911
Oceanobacillus iheyensis HTE831
Staphylococcus saprophyticus subsp.
saprophyticus ATCC 15305
Bacillus selenitireducens MLS10
Streptococcus pneumoniae SP6-BS73
Streptococcus sanguinis SK36
Streptococcus thermophilus LMG 18311
Streptococcus suis 89/1591
Streptococcus mutans UA159
Leptospira borgpetersenii serovar
Hardjo-bovis L550
Candidatus Vesicomyosocius okutanii
Candidatus Ruthia magnifica str. Cm
Methylococcus capsulatus str. Bath
Alcanivorax borkumensis SK2
Chromohalobacter salexigens DSM
Marinobacter algicola DG893
Marinobacter aquaeolei VT8
Marinobacter sp. ELB17
Pseudoalteromonas haloplanktis
Acinetobacter sp. ADP1
Opitutaceae bacterium TAV2
Flavobacterium sp. MED217
Cellulophaga sp. MED134
Kordia algicida OT-1
Flavobacteriales bacterium ALC-1
Psychroflexus torquis ATCC 700755
Flavobacteriales bacterium HTCC2170
unidentified eubacterium SCB49
Gramella forsetii KT0803
Robiginitalea biformata HTCC2501
Tenacibaculum sp. MED152
Polaribacter irgensii 23-P
Pedobacter sp. BAL39
Flavobacteria bacterium BAL38
Flavobacterium psychrophilum JIP02/86
Flavobacterium johnsoniae UW101
Lactococcus lactis subsp. cremoris SK11
Psychromonas ingrahamii 37
Microscilla marina ATCC 23134
Cytophaga hutchinsonii ATCC 33406
Rhodopirellula baltica SH 1
Blastopirellula marina DSM 3645
Planctomyces maris DSM 8797
Algoriphagus sp. PR1
Candidatus Sulcia muelleri str. Hc
Candidatus Carsonella ruddii PV
Synechococcus sp. RS9916
Synechococcus sp. WH 7803
Synechococcus sp. CC9311
Synechococcus sp. CC9605
Synechococcus sp. WH 8102
Synechococcus sp. BL107
Synechococcus sp. RCC307
Synechococcus sp. RS9917
Synechococcus sp. WH 5701
Prochlorococcus marinus str. MIT 9313
Prochlorococcus marinus str. NATL2A
Prochlorococcus marinus str. MIT 9215
Prochlorococcus marinus str. AS9601
Prochlorococcus marinus str. MIT 9515
Prochlorococcus marinus subsp.
pastoris str. CCMP1986
Prochlorococcus marinus str. MIT 9211
Prochlorococcus marinus subsp.
marinus str. CCMP1375
Nodularia spumigena CCY9414
Nostoc punctiforme PCC 73102
Nostoc sp. PCC 7120
Trichodesmium erythraeum IMS101
Acaryochloris marina MBIC11017
Lyngbya sp. PCC 8106
Synechocystis sp. PCC 6803
Cyanothece sp. CCY0110
Thermosynechococcus elongatus BP-1
Synechococcus sp. JA-2-3B′a(2-13)
Gloeobacter violaceus PCC 7421
Nitrosomonas eutropha C91
Nitrosomonas europaea ATCC 19718
Nitrosospira multiformis ATCC 25196
Chloroflexus aggregans DSM 9485
Leptospirillum sp. Group II UBA
Leptospirillum sp. Group II UBA
Halorhodospira halophila SL1
Nitrococcus mobilis Nb-231
Alkalilimnicola ehrlichei MLHE-1
Deinococcus geothermalis DSM 11300
Polynucleobacter sp. QLW-P1DMWA-1
Polynucleobacter necessarius STIR1
Azoarcus sp. EbN1
Burkholderia phymatum STM815
Burkholderia xenovorans LB400
Burkholderia multivorans ATCC 17616
Burkholderia cenocepacia PC184
Burkholderia mallei GB8 horse 4
Ralstonia eutropha JMP134
Ralstonia metallidurans CH34
Ralstonia solanacearum UW551
Ralstonia pickettii 12J
Limnobacter sp. MED105
Herminiimonas arsenicoxydans
Bordetella parapertussis
Bordetella petrii DSM 12804
Polaromonas sp. JS666
Polaromonas naphthalenivorans CJ2
Rhodoferax ferrireducens T118
Verminephrobacter eiseniae EF01-2
Acidovorax sp. JS42
Delftia acidovorans SPH-1
Methylibium petroleiphilum PM1
Tremblaya princeps
Blastopirellula marina DSM 3645
Planctomyces maris DSM 8797
Microcystis aeruginosa PCC 7806
Salinibacter ruber DSM 13855
Methylobacterium chloromethanicum
Schizosaccharomyces pombe ILV3
Saccharomyces cerevisiae ILV3
Kluyveromyces lactis ILV3
Candida albicans SC5314 ILV3
Pichia stipitis CBS 6054 ILV3
Yarrowia lipolytica ILV3
Candida galbrata CBS 138 ILV3
Chlamydomonas reinhardtii
Ostreococcus lucimarinus CCE9901
Vitis vinifera
Vitis vinifera
Arabidopsis thaliana
Oryza sativa (indica cultivar-group)
Physcomitrella patens subsp. Patens
Chaetomium globosum CBS 148.51
Neurospora crassa OR74A
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus niger
Neosartorya fischeri NRRL 181
Neosartorya fischeri NRRL 181
Aspergillus niger
Aspergillus niger
Aspergillus terreus NIH2624
Aspergillus clavatus NRRL 1
Aspergillus nidulans FGSC A4
Aspergillus oryzae
Ajellomyces capsulatus NAm1
Coccidioides immitis RS
Botryotinia fuckeliana B05.10
Phaeosphaeria nodorum SN15
Pichia guilliermondii ATCC 6260
Debaryomyces hansenii CBS767
Lodderomyces elongisporus NRRL
Vanderwaltozyma polyspora DSM
Ashbya gossypii ATCC 10895
Laccaria bicolor S238N-H82
Coprinopsis cinerea okayama 7#130
Cryptococcus neoformans var.
neoformans JEC21
Ustilago maydis 521
Malassezia globosa CBS 7966
Aspergillus clavatus NRRL 1
Neosartorya fischeri NRRL 181
Aspergillus oryzae
Aspergillus niger (hypothetical
Aspergillus terreus NIH2624
Coccidioides immitis RS (hypothetical
Paracoccidioides brasiliensis
Phaeosphaeria nodorum SN15
Gibberella zeae PH-1
Neurospora crassa OR74A
Coprinopsis cinerea okayama 7#130
Laccaria bicolor S238N-H82
Ustilago maydis 521
Escherichia coli str. K-12 substr.
Bacillus subtilis subsp. subtilis str.
Agrobacterium tumefaciens str. C58
Burkholderia cenocepacia MC0-3
Psychrobacter cryohalolentis K5
Psychromonas sp. CNPT3
Deinococcus radiodurans R1
Wolinella succinogenes DSM 1740
Zymomonas mobilis subsp. mobilis
Clostridium acetobutylicum ATCC
Clostridium beijerinckii NCIMB 8052
Pseudomonas fluorescens Pf-5
Methanococcus maripaludis C7
Methanococcus aeolicus Nankai-3
Vibrio fischeri ATCC 700601
Shewanella oneidensis MR-1 ATCC
Lactobacillus plantarum ldhD
Lactobacillus plantarum ldhL1
Lactobacillus plantarum ldhL2
Lactococcus lactis ldhL
Leuconostoc mesenteroides ldhD
Streptococcus thermophilus ldhL
Pediococcus pentosaceus ldhD
Pediococcus pentosaceus ldhL
Lactobacillus acidophilus ldhL1
Lactobacillus acidophilus ldhL2
Lactobacillus acidophilus ldhD
Vibrio cholerae KARI
Pseudomonas aeruginosa PAO1
Pseudomonas fluorescens PF5
Achromobacter xylosoxidans
Lactobacillus plantarum orotidine-
SEQ ID NO:564 is the nucleotide sequence of the Lactococcus lactis subsp lactis NCDO2118 ilvD coding region.
SEQ ID NO:566 is the nucleotide sequence of a ribosome binding site.
Provided herein is a recombinant lactic acid bacterial cell comprising at least one gene encoding a heterologous polypeptide having dihydroxy-acid dehydratase activity and wherein the bacterial cell is substantially free of lactate dehydrogenase activity. Further disclosed herein is the discovery that the specific activity of Fe—S requiring DHAD is increased in lactic acid bacterial hosts that are substantially free of lactate dehydrogenase activity.
The recombinant lactic acid bacterial (LAB) cells described herein have been engineered to have increased dihydroxy-acid dehydratase (DHAD) activity. In one embodiment, the engineered LAB cells have at least about 0.1 μmol min−1 mg−1 of DHAD activity as measured for specific activity. LAB cells with this level of DHAD activity are useful for production of compounds in biochemical pathways including DHAD, such as valine, isoleucine, leucine, pantothenic acid (vitamin B5), and isobutanol. In addition, the present invention relates to a method for producing isobutanol using the present engineered LAB cells with increased DHAD activity. Production of isobutanol in lactic acid bacteria will reduce the need for petrochemicals through use of isobutanol as a fuel additive.
The following abbreviations and definitions will be used for the interpretation of the specification and the claims.
As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, are intended to cover a non-exclusive inclusion. For example, a composition, a mixture, process, method, article, or apparatus that comprises a list of elements is not necessarily limited to only those elements but may include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
Also, the indefinite articles “a” and “an” preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances (i.e. occurrences) of the element or component. Therefore “a” or “an” should be read to include one or at least one, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.
The term “invention” or “present invention” as used herein is a non-limiting term and is not intended to refer to any single embodiment of the particular invention but encompasses all possible embodiments as described in the specification and the claims.
As used herein, the term “about” modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like. The term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about”, the claims include equivalents to the quantities. In one embodiment, the term “about” means within 10% of the reported numerical value, preferably within 5% of the reported numerical value.
The term “isobutanol biosynthetic pathway” refers to an enzyme pathway to produce isobutanol from pyruvate.
The term “lactate dehydrogenase” refers to a polypeptide (or polypeptides) having an enzyme activity that catalyzes the conversion of pyruvate to lactate. Lactate dehydrogenases are known as EC 1.1.1.27 (L-lactate dehydrogenase) or EC 1.1.1.28 (D-lactate dehydrogenase), and are further characterized herein.
The term “substantially free” when used in reference to the presence or absence of lactate dehydrogenase enzyme activity means that the level of the enzyme activity is substantially less than that of the same enzyme in the wild-type host, where less than 50% of the wild-type level is preferred and less than about 90% of the wild-type level is most preferred. The reduced level of enzyme activity may be attributable to genetic modification genes encoding this enzyme such that expression levels of the enzyme are reduced.
The term “a facultative anaerobe” refers to a microorganism that can grow in both aerobic and anaerobic environments.
The term “carbon substrate” or “fermentable carbon substrate” refers to a carbon source capable of being metabolized by host organisms of the present invention and particularly carbon sources selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, and one-carbon substrates or mixtures thereof.
The term “gene” refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign gene” or “heterologous gene” refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. “Heterologous gene” includes a native coding region, or portion thereof, that is reintroduced into the source organism in a form that is different from the corresponding native gene. For example, a heterologous gene may include a native coding region that is a portion of a chimeric gene including non-native regulatory regions that is reintroduced into the native host. Also a foreign gene can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.
As used herein the term “coding region” refers to a DNA sequence that codes for a specific amino acid sequence. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.
The term “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.
The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of effecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.
The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide.
As used herein the term “transformation” refers to the transfer of a nucleic acid fragment into a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.
The terms “plasmid” and “vector” as used herein, refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell.
As used herein the term “codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The term “codon-optimized” as it refers to genes or coding regions of nucleic acid molecules for transformation of various hosts, refers to the alteration of codons in the gene or coding regions of the nucleic acid molecules to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the DNA.
As used herein, an “isolated nucleic acid fragment” or “isolated nucleic acid molecule” will be used interchangeably and will mean a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
A nucleic acid fragment is “hybridizable” to another nucleic acid fragment, such as a cDNA, genomic DNA, or RNA molecule, when a single-stranded form of the nucleic acid fragment can anneal to the other nucleic acid fragment under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms). Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. An additional set of stringent conditions include hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washes with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS, for example.
Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.
A “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Altschul, S. F., et al., J. Mol. Biol., 215:403-410 (1993)). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches the complete amino acid and nucleotide sequence encoding particular proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.
The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine.
The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including but not limited to those described in: 1.) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2.) Biocomputing: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3.) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humania: N.J. (1994); 4.) Sequence Analysis in . Molecular Biology (von Heinje, G., Ed.) Academic (1987); and 5.) Sequence Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY (1991).
Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the MegAlign™program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences is performed using the “Clustal method of alignment” which encompasses several varieties of the algorithm including the “Clustal V method of alignment” corresponding to the alignment method labeled Clustal V (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). For multiple alignments, the default values correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. After alignment of the sequences using the Clustal V program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program. Additionally the “Clustal W method of alignment” is available and corresponds to the alignment method labeled Clustal W (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci. 8:189-191(1992), Thompson, J. D., Higgins, D. G., and Gibson T. J. (1994) Nuc. Acid Res. 22: 4673 4680) and found in the MegAlign™ v 6.1 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). Default parameters for multiple alignment (GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergen Seqs (%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB). After alignment of the sequences using the Clustal W program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the same program.
It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides, from other species, wherein such polypeptides have the same or similar function or activity. Useful examples of percent identities include, but are not limited to: 24%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 24% to 100% may be useful in describing the present invention, such as 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.
The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1.) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol., 215:403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc. Madison, Wis.); 4.) Sequencher (Gene Codes Corporation, Ann Arbor, Mich.); and 5.) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.](1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters that originally load with the software when first initialized.
Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).
The invention relates to the engineering of a lactic acid bacterial cell such that the cell is substantially free of lactic acid dehydrogenase (LDH) activity and has DHAD activity. Surprisingly, it was found that expression of the Fe—S cluster requiring DHAD enzyme in a host cell substantially lacking LDH activity resulted in increased specific activity as compared to the activity of the same DHAD enzyme when expressed in a host containing LDH activity.
Lactic acid bacteria cells substantially free of lactic acid dehydrogenase and expressing DHAD enzymes having a specific activity level of at least about 0.1 μmol min−1 mg−1 where mg is the amount of total soluble protein in a crude cell extract. In addition, DHAD specific activities of at least about 0.2 μmol min−1 mg−1, and of at least about 0.4 μmol min−1 mg−1 may be achieved in LAB cells, where specific activities of at least about 0.6 μmol min−1 mg−1 are reasonably expected. Disclosed herein are LAB cells having these levels of DHAD activity.
In the disclosed LAB cells, any gene encoding a DHAD enzyme may be used to provide expression of DHAD activity in a LAB cell. DHAD, also called acetohydroxy acid dehydratase, catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate and of 2,3-dihydroxymethylvalerate to α-ketomethylvalerate and is classified as E.C. 4.2.1.9. Coding sequences for DHADs that may be used herein may be derived from bacterial, fungal, or plant sources. DHADs that may be used may have a [4Fe-4S] cluster or a [2Fe-2S] cluster bound by the apoprotein. Tables 1, 2, and 3 list SEQ ID NOs for coding regions and proteins of representative DHADs that may be used in the present invention. Proteins with at least about 95% identity to those listed sequences have been omitted for simplification, but it is understood that the omitted proteins with at least about 95% sequence identity to any of the proteins listed in Tables 1, 2, and 3 and having DHAD activity may be used as disclosed herein. Additional DHAD proteins and their encoding sequences may be identified by BLAST searching of public databases, as well known to one skilled in the art. Typically BLAST (described above) searching of publicly available databases with known DHAD sequences, such as those provided herein, is used to identify DHADs and their encoding sequences that may be expressed in the present cells. For example, DHAD proteins having amino acid sequence identities of at least about 80-85%, 85%-90%, 90%-95% or 98% sequence identity to any of the DHAD proteins of Table 1 may be expressed in the present cells.
Identities are based on the Clustal W method of alignment using the default parameters of GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight matrix over the full length of the protein sequence.
Additional [2Fe-2S] DHADs may be identified using the analysis described in co-pending U.S. Patent Application 61/100,792, which is herein incorporated by reference. The analysis is as follows: A Profile Hidden Markov Model (HMM) was prepared based on amino acid sequences of eight functionally verified DHADs. These DHADs are from Nitrosomonas europaea (DNA SEQ ID NO:309; protein SEQ ID NO:310), Synechocystis sp. PCC6803 (DNA SEQ ID:297; protein SEQ ID NO:298), Streptococcus mutans (DNA SEQ ID NO:167; protein SEQ ID NO:168), Streptococcus thermophilus (DNA SEQ ID NO:163; SEQ ID No:164), Ralstonia metallidurans (DNA SEQ ID NO:345; protein SEQ ID NO:346), Ralstonia eutropha (DNA SEQ ID NO:343; protein SEQ ID NO:344), and Lactococcus lactis (DNA SEQ ID NO:231; protein SEQ ID NO:232). In addition the DHAD from Flavobacterium johnsoniae (DNA SEQ ID NO:229; protein SEQ ID NO:230) was found to have dihydroxy-acid dehydratase activity when expressed in E. coli and was used in making the Profile. The Profile HMM is prepared using the HMMER software package (The theory behind profile HMMs is described in R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998; Krogh et al., 1994; J. Mol. Biol. 235:1501-1531), following the user guide which is available from HMMER (Janelia Farm Research Campus, Ashburn, Va.). The output of the HMMER software program is a Profile Hidden Markov Model (HMM) that characterizes the input sequences. The Profile HMM prepared for the eight DHAD proteins is given in Table 7. Any protein that matches the Profile HMM with an E value of <10−5 is a DHAD related protein, which includes [4Fe-4S] DHADs, [2Fe-2S] DHADs, aldonic acid dehydratases, and phosphogluconate dehydratases. Sequences matching the Profile HMM are then analyzed for the presence of the three conserved cysteines, corresponding to positions 56, 129, and 201 in the Streptococcus mutans DHAD. The presence of all three conserved cysteines is characteristic of proteins having a [2Fe-2S] cluster. Proteins having the three conserved cysteines include arabonate dehydratases and [2Fe-2S] DHADs and are members of a [2Fe-2S] DHAD/aldonic acid dehydratase group. The [2Fe-2S] DHADs may be distinguished from the aldonic acid dehydratases by analyzing for signature conserved amino acids found to be present in the [2Fe-2S] DHADs or in the aldonic acid dehydratases at positions corresponding to the following positions in the Streptococcus mutans DHAD amino acid sequence. These signature amino acids are in [2Fe-2S] DHADs or in aldonic acid dehydratases, respectively, at the following positions (with greater than 90% occurance): 88 asparagine vs glutamic acid; 113 not conserved vs glutamic acid; 142 arginine or asparagine vs not conserved; 165: not conserved vs glycine; 208 asparagine vs not conserved; 454 leucine vs not conserved; 477 phenylalanine or tyrosine vs not conserved; and 487 glycine vs not conserved.
Additionally, the sequences of DHAD coding regions provided herein may be used to identify other homologs in nature. For example each of the DHAD encoding nucleic acid fragments described herein may be used to isolate genes encoding homologous proteins. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to: 1.) methods of nucleic acid hybridization; 2.) methods of DNA and RNA amplification, as exemplified by various uses of nucleic acid amplification technologies [e.g., polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202; ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci. USA 82:1074 (1985); or strand displacement amplification (SDA), Walker, et al., Proc. Natl. Acad. Sci. U.S.A., 89:392 (1992)]; and 3.) methods of library construction and screening by complementation.
For example, genes encoding similar proteins or polypeptides to the DHAD encoding genes provided herein could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired organism using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the disclosed nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis, supra). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan (e.g., random primers DNA labeling, nick translation or end-labeling techniques), or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of (or full-length of) the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full-length DNA fragments by hybridization under conditions of appropriate stringency.
Typically, in PCR-type amplification techniques, the primers have different sequences and are not complementary to each other. Depending on the desired test conditions, the sequences of the primers should be designed to provide for both efficient and faithful replication of the target nucleic acid. Methods of PCR primer design are common and well known in the art (Thein and Wallace, “The use of oligonucleotides as specific hybridization probes in the Diagnosis of Genetic Disorders”, in Human Genetic Diseases: A Practical Approach, K. E. Davis Ed., (1986) pp 33-50, IRL: Herndon, Va.; and Rychlik, W., In Methods in Molecular Biology, White, B. A. Ed., (1993) Vol. 15, pp 31-39, PCR Protocols: Current Methods and Applications. Humania: Totowa, N.J.).
Generally two short segments of the described sequences may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the described nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding microbial genes.
Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., PNAS USA 85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the instant sequences. Using commercially available 3′ RACE or 5′ RACE systems (e.g., BRL, Gaithersburg, Md.), specific 3′ or 5′ cDNA fragments can be isolated (Ohara et al., PNAS USA 86:5673 (1989); Loh et al., Science 243:217 (1989)).
Alternatively, the provided DHAD encoding sequences may be employed as hybridization reagents for the identification of homologs. The basic components of a nucleic acid hybridization test include a probe, a sample suspected of containing the gene or gene fragment of interest, and a specific hybridization method. Probes are typically single-stranded nucleic acid sequences that are complementary to the nucleic acid sequences to be detected. Probes are “hybridizable” to the nucleic acid sequence to be detected. The probe length can vary from 5 bases to tens of thousands of bases, and will depend upon the specific test to be done. Typically a probe length of about 15 bases to about 30 bases is suitable. Only part of the probe molecule need be complementary to the nucleic acid sequence to be detected. In addition, the complementarity between the probe and the target sequence need not be perfect. Hybridization does occur between imperfectly complementary molecules with the result that a certain fraction of the bases in the hybridized region are not paired with the proper complementary base.
Hybridization methods are well defined. Typically the probe and sample must be mixed under conditions that will permit nucleic acid hybridization. This involves contacting the probe and sample in the presence of an inorganic or organic salt under the proper concentration and temperature conditions. The probe and sample nucleic acids must be in contact for a long enough time that any possible hybridization between the probe and sample nucleic acid may occur. The concentration of probe or target in the mixture will determine the time necessary for hybridization to occur. The higher the probe or target concentration, the shorter the hybridization incubation time needed. Optionally, a chaotropic agent may be added. The chaotropic agent stabilizes nucleic acids by inhibiting nuclease activity. Furthermore, the chaotropic agent allows sensitive and stringent hybridization of short oligonucleotide probes at room temperature (Van Ness and Chen, Nucl. Acids Res. 19:5143-5151 (1991)). Suitable chaotropic agents include guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide and cesium trifluoroacetate, among others. Typically, the chaotropic agent will be present at a final concentration of about 3 M. If desired, one can add formamide to the hybridization mixture, typically 30-50% (v/v).
Various hybridization solutions can be employed. Typically, these comprise from about 20 to 60% volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30-50% v/v formamide, about 0.15 to 1 M sodium chloride, about 0.05 to 0.1 M buffers (e.g., sodium citrate, Tris-HCl, PIPES or HEPES (pH range about 6-9)), about 0.05 to 0.2% detergent (e.g., sodium dodecylsulfate), or between 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kdal), polyvinylpyrrolidone (about 250-500 kdal) and serum albumin. Also included in the typical hybridization solution will be unlabeled carrier nucleic acids from about 0.1 to 5 mg/mL, fragmented nucleic DNA (e.g., calf thymus or salmon sperm DNA, or yeast RNA), and optionally from about 0.5 to 2% wt/vol glycine. Other additives may also be included, such as volume exclusion agents that include a variety of polar water-soluble or swellable agents (e.g., polyethylene glycol), anionic polymers (e.g., polyacrylate or polymethylacrylate) and anionic saccharidic polymers (e.g., dextran sulfate).
Nucleic acid hybridization is adaptable to a variety of assay formats. One of the most suitable is the sandwich assay format. The sandwich assay is particularly adaptable to hybridization under non-denaturing conditions. A primary component of a sandwich-type assay is a solid support. The solid support has adsorbed to it or covalently coupled to it immobilized nucleic acid probe that is unlabeled and complementary to one portion of the sequence.
LAB cells that may be engineered to create cells of the present invention include, but are not limited to, Lactococcus, Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, and Streptococcus.
LAB cells are genetically modified for expression of DHAD activity using methods well known to one skilled in the art. Expression of DHAD is generally achieved by transforming suitable LAB host cells with a sequence encoding a DHAD protein. Typically the coding sequence is part of a chimeric gene used for transformation, which includes a promoter operably linked to the coding sequence as well as a ribosome binding site and a termination control region. The coding region may be from the host cell for transformation and combined with regulatory sequences that are not native to the natural gene encoding DHAD. Alternatively, the coding region may be from another host cell.
Codons may be optimized for expression based on codon usage in the selected host, as is known to one skilled in the art. Vectors useful for the transformation of a variety of host cells are common and described in the literature. Typically the vector contains a selectable marker and sequences allowing autonomous replication or chromosomal integration in the desired host. In addition, suitable vectors may comprise a promoter region which harbors transcriptional initiation controls and a transcriptional termination control region, between which a coding region DNA fragment may be inserted, to provide expression of the inserted coding region. Both control regions may be derived from genes homologous to the transformed host cell, although it is to be understood that such control regions may also be derived from genes that are not native to the specific species chosen as a production host.
Initiation control regions or promoters, which are useful to drive expression of a DHAD coding region in LAB are familiar to those skilled in the art. Some examples include the amy, apr, and npr promoters; nisA promoter (useful for expression Gram-positive bacteria (Eichenbaum et al. Appl. Environ. Microbiol. 64(8):2763-2769 (1998)); and the synthetic P11 promoter (useful for expression in Lactobacillus plantarum, Rud et al., Microbiology 152:1011-1019 (2006)). In addition, the IdhL1and fabZ1 promoters of L plantarum are useful for expression of chimeric genes in LAB. The fabZ1 promoter directs transcription of an operon with the first gene, fabZ1, encoding (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase.
Termination control regions may also be derived from various genes, typically from genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included.
Vectors useful in LAB include vectors having two origins of replication and one or two selectable markers which allow for replication and selection in both Escherichia coli and LAB. Examples are pFP996(SEQ ID NO:565) and pDM1 (SEQ ID NO:563), which are useful in L. plantarum and other LAB. Many plasmids and vectors used in the transformation of Bacillus subtilis and Streptococcus may be used generally for LAB. Non-limiting examples of suitable vectors include pAMβ1 and derivatives thereof (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)); pMBB1 and pHW800, a derivative of pMBB1 (Wyckoff et al. Appl. Environ. Microbiol. 62:1481-1486 (1996)); pMG1, a conjugative plasmid (Tanimoto et al., J. Bacteriol. 184:5800-5804 (2002)); pNZ9520 (Kleerebezem et al., Appl. Environ. Microbiol. 63:4581-4584 (1997)); pAM401 (Fujimoto et al., Appl. Environ. Microbiol. 67:1262-1267 (2001)); and pAT392 (Arthur et al., Antimicrob. Agents Chemother. 38:1899-1903 (1994)). Several plasmids from Lactobacillus plantarum have also been reported (e.g., van Kranenburg R, Golic N, Bongers R, Leer R J, de Vos W M, Siezen R J, Kleerebezem M. Appl. Environ. Microbiol. March 2005; 71(3): 1223-1230).
Vectors may be introduced into a host cell using methods known in the art, such as electroporation (Cruz-Rodz et al. Molecular Genetics and Genomics 224:1252-154 (1990), Bringel, et al. Appl. Microbiol. Biotechnol. 33: 664-670 (1990), Alegre et al., FEMS Microbiology letters 241:73-77 (2004)), and conjugation (Shrago et al., Appl. Environ. Microbiol. 52:574-576 (1986)). A chimeric DHAD gene can also be integrated into the chromosome of LAB using integration vectors (Hols et al., Appl. Environ. Microbiol. 60:1401-1403 (1990), Jang et al., Micro. Lett. 24:191-195 (2003)).
DHAD activity of at least about 0.1, 0.2, 0.4 or 0.6 μmol min−1 mg−1 may be achieved in a LAB cell by modifying the cell such that it is substantially free of lactate dehydrogenase enzyme activity. Lactate dehydrogenases are known as EC 1.1.1.27 (L-lactate dehydrogenase) or EC 1.1.1.28 (D-lactate dehydrogenase). At least one genetic modification is made in a LAB cell to render it substantially free of lactate dehydrogenase activity. DHAD is expressed as described above in the so modified LAB cell.
Endogenous lactate dehydrogenase activity in lactic acid bacteria (LAB) converts pyruvate to lactate. LAB may have one or more genes, typically one, two or three genes, encoding lactate dehydrogenase. For example, Lactobacillus plantarum has three genes encoding lactate dehydrogenase which are named IdhL2 (protein SEQ ID NO: 500, coding region SEQ ID NO: 499), IdhD (protein SEQ ID NO: 496, coding region SEQ ID NO: 495), and IdhL1 (protein SEQ ID NO: 498, coding region SEQ ID NO: 497). Lactococcus lactis has one gene encoding lactate dehydrogenase which is named IdhL (protein SEQ ID NO: 502, coding region SEQ ID NO: 501), and Pediococcus pentosaceus has two genes named IdhD (protein SEQ ID NO: 508, coding region SEQ ID NO: 507) and IdhL (protein SEQ ID NO: 510, coding region SEQ ID NO: 509).
In the present LAB strains, lactate dehydrogenase activity is reduced so that the cells are substantially free of lactate dehydrogenase activity. Genetic modification is made in at least one gene encoding lactate dehydrogenase to reduce activity. When more than one lactate dehydrogenase gene is active under the growth conditions to be used, each of these active genes may be modified to reduce expression. For example, in L. plantarum IdhL1 and IdhD genes are modified. It is not necessary to modify the third gene, IdhL2, for growth in typical conditions as this gene appears to be inactive in these conditions. Typically, expression of one or more genes encoding lactate dehydrogenase is disrupted to reduce expressed enzyme activity. Examples of LAB lactate dehydrogenase genes that may be targeted for disruption are represented by the coding regions of SEQ ID NOs: 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, and 515 listed in Table 4. Other target genes, such as those encoding lactate dehydrogenase proteins having at least about 80-85%, 85%-90%, 90%-95%, or 98% sequence identity to the lactate dehydrogenases of SEQ ID NOs:496, 498, 500, 502, 504, 506, 508, 510, 512, 514, and 516 listed in Table 4 may be identified in the literature and using bioinformatics approaches, as is well known to the skilled person, since lactate dehydrogenases are well known. Typically BLAST (described above) searching of publicly available databases with known lactate dehydrogenase amino acid sequences, such as those provided herein, is used to identify lactate dehydrogenases, and their encoding sequences, that may be targets for disruption to reduce lactate dehydrogenase activity. Identities are based on the Clustal W method of alignment using the default parameters of GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight matrix.
Additionally, the sequences described herein or those recited in the art may be used to identify other homologs in nature in other LAB strains as described above for DHAD homolog analysis.
In the present LAB strains, at least one modification is engineered that results in cells substantially free of lactate dehydrogenase activity. This may be accomplished by eliminating expression of at least one endogenous gene encoding lactate dehydrogenase. Any genetic modification method known by one skilled in the art for reducing the expression of a protein may be used to alter lactate dehydrogenase expression. Methods include, but are not limited to, deletion of the entire or a portion of the lactate dehydrogenase encoding gene, inserting a DNA fragment into the lactate dehydrogenase encoding gene (in either the promoter or coding region) so that the encoded protein cannot be expressed, introducing a mutation into the lactate dehydrogenase coding region which adds a stop codon or frame shift such that a functional protein is not expressed, and introducing one or more mutations into the lactate dehydrogenase coding region to alter amino acids so that a non-functional protein is expressed. In addition lactate dehydrogenase expression may be blocked by expression of an antisense RNA or an interfering RNA, and constructs may be introduced that result in cosuppression. All of these methods may be readily practiced by one skilled in the art making use of the known lactate dehydrogenase encoding sequences such as those of SEQ ID NOs: 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, and 515.
For some methods genomic DNA sequences that surround a lactate dehydrogenase encoding sequence are useful, such as for homologous recombination-based methods. These sequences may be available from genome sequencing projects such as for Lactobacillus plantarum, which is available through the National Center for Biotechnology Information (NCBI) database, with Genbank™ identification gi|28376974|ref|NC—004567.1|[28376974]. Adjacent genomic DNA sequences may also be obtained by sequencing outward from a lactate dehydrogenase coding sequence using primers within the coding sequence, as well known to one skilled in the art.
A particularly suitable method for creating a genetically modified LAB strain with substantially no lactate dehydrogenase activity, as exemplified herein in Example 1, is using homologous recombination mediated by lactate dehydrogenase coding region flanking DNA sequences to delete the entire gene. The flanking sequences are cloned adjacent to each other so that a double crossover event using these flanking sequences deletes the lactate dehydrogenase coding region.
Isobutanol and any other product made from a biosynthetic pathway including DHAD activity may be produced with greater effectiveness in a LAB cell disclosed herein having at least about 0.1, 0.2, or 0.4 μmol min−1 mg−1 DHAD activity. Such products include, but are not limited to valine, isoleucine, leucine, pantothenic acid (vitamin B5), 2-methyl-1-butanol, 3-methyl-1-butanol, and isobutanol.
For example, biosynthesis of valine includes steps of acetolactate conversion to 2,3-dihydroxy-isovalerate by acetohydroxyacid reductoisomerase (ilvC), conversion of 2,3-dihydroxy-isovalerate to α-ketoisovalerate (also called 2-keto-isovalerate) by dihydroxy-acid dehydratase (ilvD), and conversion of a-ketoisovalerate to valine by branched-chain amino acid aminotransferase (ilvE). Biosynthesis of leucine includes the same steps to α-ketoisovalerate, followed by conversion of α-ketoisovalerate to leucine by enzymes encoded by leuA (2-isopropylmalaate synthase), leuCD (isopropylmalate isomerase), leuB (3-isopropylmalate dehydrogenase), and tyrB/ilvE (aromatic amino acid transaminase). Biosynthesis of pantothenate includes the same steps to α-ketoisovalerate, followed by conversion of α-ketoisovalerate to pantothenate by enzymes encoded by panB (3-methyl-2-oxobutanoate hydroxymethyltransferase), panE (2-dehydropantoate reductae), and panC (pantoate-beta-alanine ligase). Engineering expression of enzymes for enhanced production of pantothenic acid in microorganisms is described in U.S. Pat. No. 6,177,264.
Increased conversion of 2,3-dihydroxy-isovalerate to α-ketoisovalerate will increase flow in these pathways, particularly if one or more additional enzymes of a pathway is overexpressed. Thus it is desired for production of, for example, valine, leucine, or pantothenate to use an engineered LAB cell disclosed herein.
The α-ketoisovalerate product of DHAD is an intermediate in isobutanol biosynthetic pathways disclosed in commonly owned and co-pending US Patent Pub No. 20070092957 A1, which is herein incorporated by reference. A diagram of the disclosed isobutanol biosynthetic pathways is provided in
The substrate to product conversions, and enzymes involved in these reactions, for steps f, g, h, I, j, and k of alternative pathways are described in US Patent Pub No. US20070092957 A1.
Genes that may be used for expression of the pathway step enzymes named above other than the DHADs disclosed herein, as well as those for two additional isobutanol pathways, are described in US Patent Pub No. 20070092957 A1, and additional genes that may be used can be identified by one skilled in the art through bioinformatics or experimentally as described above. The preferred use in all three pathways of ketol-acid reductoisomerase (KARI) enzymes with particularly high activities is disclosed in co-pending US Patent Pub No. US20080261230 A1. Examples of high activity KARIs disclosed therein are those from Vibrio cholerae (DNA: SEQ ID NO:517; protein SEQ ID NO:518), Pseudomonas aeruginosa PAO1, (DNA: SEQ ID NO:523; protein SEQ ID NO:524), and Pseudomonas fluorescens PF5 (DNA: SEQ ID NO:519; protein SEQ ID NO:520).
Additionally described in US Patent Pub No. 20070092957 A1 are construction of chimeric genes and genetic engineering of bacteria for isobutanol production using the disclosed biosynthetic pathways. Expression of these enzymes in LAB is as described above for expression of DHADs.
Recombinant LAB cells disclosed herein may be used for fermentation production of isobutanol and other products as follows. The recombinant cells are grown in fermentation media which contains suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, or mixtures of monosaccharides that include C5 sugars such as xylose and arabinose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt.
Although it is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention, preferred carbon substrates are glucose, fructose, and sucrose. Sucrose may be derived from renewable sugar sources such as sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof. Glucose and dextrose may be derived from renewable grain sources through saccharification of starch based feedstocks including grains such as corn, wheat, rye, barley, oats, and mixtures thereof. In addition, fermentable sugars may be derived from renewable cellulosic or lignocellulosic biomass through processes of pretreatment and saccharification, as described, for example, in co-owned and co-pending US Patent Pub No. US20070031918A1, which is herein incorporated by reference. Biomass refers to any cellulosic or lignocellulosic material and includes materials comprising cellulose, and optionally further comprising hemicellulose, lignin, starch, oligosaccharides and/or monosaccharides. Biomass may also comprise additional components, such as protein and/or lipid. Biomass may be derived from a single source, or biomass can comprise a mixture derived from more than one source; for example, biomass may comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves. Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof.
In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the enzymatic pathway necessary for isobutanol production.
Typically cells are grown at a temperature in the range of about 25° C. to about 40° C. in an appropriate medium. Suitable growth media are common commercially prepared media such as Bacto Lactobacilli MRS broth or Agar (Difco), Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast Medium (YM) broth. Other defined or synthetic growth media may also be used, and the appropriate medium for growth of the particular bacterial strain will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2′:3′-monophosphate, may also be incorporated into the fermentation medium.
Suitable pH ranges for the fermentation are between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is preferred as the initial condition.
Fermentations may be performed under aerobic or anaerobic conditions, where anaerobic or microaerobic conditions are preferred.
Isobutanol, or other product, may be produced using a batch method of fermentation. A classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. A variation on the standard batch system is the fed-batch system. Fed-batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Batch and fed-batch fermentations are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36:227, (1992), herein incorporated by reference.
Isobutanol, or other product, may also be produced using continuous fermentation methods. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
It is contemplated that the production of isobutanol, or other product, may be practiced using batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable. Additionally, it is contemplated that cells may be immobilized on a substrate as whole cell catalysts and subjected to fermentation conditions for isobutanol production.
Methods for Isobutanol Isolation from the Fermentation Medium
Bioproduced isobutanol may be isolated from the fermentation medium using methods known in the art for ABE fermentations (see for example, Durre, Appl. Microbiol. Biotechnol. 49:639-648 (1998), Groot et al., Process. Biochem. 27:61-75 (1992), and references therein). For example, solids may be removed from the fermentation medium by centrifugation, filtration, decantation, or the like. Then, the isobutanol may be isolated from the fermentation medium using methods such as distillation, azeotropic distillation, liquid-liquid extraction, adsorption, gas stripping, membrane evaporation, or pervaporation.
The present invention is further defined in the following Examples.
It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions.
The meaning of abbreviations used is as follows: “min” means minute(s), “h” means hour(s), “sec' means second(s), “μl” means microliter(s), “ml” means milliliter(s), “L” means liter(s), “nm” means nanometer(s), “mm” means millimeter(s), “cm” means centimeter(s), “μm” means micrometer(s), “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “μmole” means micromole(s), “g” means gram(s), “pg” means microgram(s), “mg” means milligram(s), “rpm” means revolutions per minute, “w/v” means weight/volume, “OD” means optical density, and “OD600” means optical density measured at a wavelength of 600 nm.
Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1984, and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, Greene Publishing Assoc. and Wiley-Interscience, N.Y., 1987. Additional methods used in the Examples are described in manuals including Advanced Bacterial Genetics (Davis, Roth and Botstein, Cold Spring Harbor Laboratory, 1980), Experiments with Gene Fusions (Silhavy, Berman and Enquist, Cold Spring Harbor Laboratory, 1984), Experiments in Molecular Genetics (Miller, Cold Spring Harbor Laboratory, 1972) Experimental Techniques in Bacterial Genetics (Maloy, in Jones and Bartlett, 1990), and A Short Course in Bacterial Genetics (Miller, Cold Spring Harbor Laboratory 1992).
The purpose of this example is to describe how to clone and express a gene encoding dihydroxy-acid dehydratase (ilvD) from different bacterial sources in Lactobacillus plantarum PN0512 (ATCC PTA-7727) and Lactobacillus plantarum PN0512 carrying a double lactate dehydrogenase deletion, ΔIdhDΔIdhL1.
A Lactobacillus plantarum PN0512 strain that is deleted for the two genes that encode the major lactate dehydrogenases was prepared as follows. The major end product of fermentation in Lactobacillus plantarum is lactic acid. Pyruvate is converted to lactate by the action of two lactate dehydrogenases encoded by the IdhD and IdhL1 genes. A double deletion of IdhD and IdhL1 was made in Lactobacillus plantarum PN0512 (ATCC strain #PTA-7727).
Gene knockouts were constructed using a process based on a two-step homologous recombination procedure to yield unmarked gene deletions (Ferain et al., 1994, J. Bact. 176:596). The procedure utilized a shuttle vector, pFP996 (SEQ ID NO:565). pFP996 is a shuttle vector for gram-positive bacteria. It can replicate in both E. coli and gram-postive bacteria. It contains the origins of replication from pBR322 (nucleotides #2628 to 5323) and pE194 (nucleotides #43 to 2627). pE194 is a small plasmid isolated originally from a gram positive bacterium, Staphylococcus aureus (Horinouchi and Weisblum J. Bacteriol. (1982) 150(2):804-814). In pFP996, the multiple cloning sites (nucleotides #1 to 50) contain restriction sites for EcoRI, BglII, XhoI, SmaI, ClaI, KpnI, and HindIII. There are two antibiotic resistance markers; one is for resistance to ampicillin and the other for resistance to erythromycin. For selection purposes, ampicillin was used for transformation in E. coli and erythromycin was used for selection in L. plantarum.
Two segments of DNA, each containing 900 to 1200 bp of sequence either upstream or downstream of the intended deletion, were cloned into the plasmid to provide the regions of homology for the two genetic cross-overs. Cells were grown for an extended number of generations (30-50) to allow for the cross-over events to occur. The initial cross-over (single cross-over) integrated the plasmid into the chromosome by homologous recombination through one of the two homology regions on the plasmid. The second cross-over (double cross-over) event yielded either the wild-type sequence or the intended gene deletion. A cross-over between the sequences that led to the initial integration event would yield the wild-type sequence, while a cross-over between the other regions of homology would yield the desired deletion. The second cross-over event was screened for by antibiotic sensitivity. Single and double cross-over events were analyzed by PCR and DNA sequencing.
All restriction enzymes, DNA modifying enzymes and Phusion High-Fidelity PCR Master Mix were purchased from NEB Inc. (Ipswich, Mass.). PCR SuperMix and Platinum PCR SuperMix High Fidelity were purchased from Invitrogen Corp (Carlsbad, Calif.). DNA fragments were gel purified using Zymoclean™ Gel DNA Recovery Kit (Zymo Research Corp, Orange, Calif.) or Qiaquick PCR Purification Kit (Qiagen Inc., Valencia, Calif.). Plasmid DNA was prepared with QIAprep Spin Miniprep Kit (Qiagen Inc., Valencia, Calif.). Oligoucleotides were synthesized by Sigma-Genosys (Woodlands, Tex.) or Invitrogen Corp (Carlsbad, Calif.). L. plantarum PN0512 genomic DNA was prepared with MasterPure DNA Purification Kit (Epicentre, Madison, Wis.).
Lactobacillus plantarum PN0512 was transformed by the following procedure: 5 ml of Lactobacilli MRS medium (Accumedia, Neogen Corporation, Lansing, Mich.) containing 1% glycine (Sigma-Aldrich, St. Louis, Mo.) was inoculated with PN0512 cells and grown overnight at 30° C. 100 ml MRS medium with 1% glycine was inoculated with overnight culture to an OD600 of 0.1 and grown to an OD600 of 0.7 at 30° C. Cells were harvested at 3700×g for 8 min at 4° C., washed with 100 ml cold 1 mM MgCl2 (Sigma-Aldrich, St. Louis, Mo.), centrifuged at 3700×g for 8 min at 4° C., washed with 100 ml cold 30% PEG-1000 (Sigma-Aldrich, St. Louis, Mo.), recentrifuged at 3700×g for 20 min at 4° C., then resuspended in 1 ml cold 30% PEG-1000. 60 μl cells were mixed with ˜100 ng plasmid DNA in a cold 1 mm gap electroporation cuvette and electroporated in a BioRad Gene Pulser (Hercules, Calif.) at 1.7 kV, 25 μF, and 400Ω. Cells were resuspended in 1 ml MRS medium containing 500 mM sucrose (Sigma-Aldrich, St. Louis, Mo.) and 100 mM MgCl2, incubated at 30° C. for 2 hrs, plated on MRS medium plates containing 1 or 2 μg/ml of erythromycin (Sigma-Aldrich, St. Louis, Mo.), then placed in an anaerobic box containing a Pack-Anaero sachet (Mitsubishi Gas Chemical Co., Tokyo, Japan) and incubated at 30° C.
The knockout cassette to delete the IdhD gene was created by amplifying from PN0512 genomic DNA an upstream flanking region with primers Top D F1 (SEQ ID NO:572) containing an EcoRI site and Top D R1 (SEQ ID NO:573). The downstream homology region including part of the coding sequence of IdhD was amplified with primers Bot D F2 (SEQ ID NO:574) and Bot D R2 (SEQ ID NO:575) containing an XhoI site. The two homology regions were joined by PCR SOE as follows. The 0.9 kbp upstream and downstream PCR products were gel-purifed. The PCR products were mixed in equal amounts in a PCR reaction and re-amplifed with primers Top D F1 and Bot D R2. The final 1.8 kbp PCR product was gel-purifed and TOPO cloned into pCR4BluntII-TOPO (Invitrogen) to create vector pCRBluntII::IdhD. To create the integration vector carrying the internal deletion of the IdhD gene, pFP996 was digested with EcoRI and XhoI and the 5311-bp fragment gel-purified. Vector pCRBluntII::IdhD was digested with EcoRI and XhoI and the 1.8 kbp fragment gel-purified. The IdhD knockout cassette and vector were ligated using T4 DNA ligase, resulting in vector pFP996::IdhD ko.
Electrocompetent Lactobacillus plantarum PN0512 cells were prepared, transformed with pFP996::IdhD ko, and plated on MRS containing 1 μg/ml of erythromycin. To obtain the single-crossover event (sco), transformants were passaged for approximately 50 generations in MRS medium at 37° C. After growth, aliquots were plated for single colonies on MRS containing 1 μg/ml of erythromycin. The erythromycin-resistant colonies were screened by PCR amplification with primers IdhD Seq F1 (SEQ ID NO:576) and D check R (SEQ ID NO:577) to distinguish between wild-type and clones carrying the sco event. To obtain clones with a double crossover, the sco strains were passaged for approximately 30 generations in MRS medium with 20 mM D, L-lactate (Sigma, St. Louis, Mo.) at 37° C. and then plated for single colonies on MRS with lactate. Colonies were picked and patched onto MRS with lactate and MRS with lactate containing 1 μg/ml of erythromycin to find colonies sensitive to erythromycin. Sensitive colonies were screened by PCR amplification using primer D check R (SEQ ID NO:577) and D check F3 (SEQ ID NO:578). Wild-type colonies gave a 3.2 kbp product and deletion clones, called PN0512ΔIdhD, gave a 2.3 kbp PCR product.
A deletion of the IdhL1 gene was made in the PN0512ΔIdhD strain background in order to make a double ΔIdhL1ΔIdhD deletion strain. The knockout cassette to delete the IdhL1 gene was amplified from PN0512 genomic DNA. The IdhL1 left homologous arm was amplified using primers oBP31 (SEQ ID NO:579) containing a BglII restriction site and oBP32 (SEQ ID NO:580) containing an XhoI restriction site. The IdhL1 right homologous arm was amplified using primers oBP33 (SEQ ID NO:581) containing an XhoI restriction site and oBP34 (SEQ ID NO:582) containing an XmaI restriction site. The IdhL1 left homologous arm was cloned into the BglII/XhoI sites and the IdhL1 right homologous arm was cloned into the XhoI/XmaI sites of pFP996pyrFΔerm, a derivative of pFP996. pFP996pyrFΔerm contains the pyrF sequence (SEQ ID NO:571) encoding orotidine-5′-phosphate decarboxylase from Lactobacillus plantarum PN0512 in place of the erythromycin coding region in pFP996. The plasmid-borne pyrF gene, in conjunction with the chemical 5-fluoroorotic acid in a ΔpyrF strain, can be used as an effective counter-selection method in order to isolate the second homologous crossover. The XmaI fragment containing the IdhL1 homologous arms was isolated following XmaI digestion and cloned into the XmaI restriction site of pFP996, yielding a 900 by left homologous region and a 1200 by right homologous region resulting in vector pFP996-IdhL1-arms.
PN0512ΔIdhD was transformed with pFP996-IdhL1-arms and grown at 30° C. in Lactobacilli MRS medium with lactate (20 mM) and erythromycin (1 μg/ml) for approximately 10 generations. Transformants were then grown under non-selective conditions at 37° C. for about 50 generations by serial inoculations in MRS+lactate before cultures were plated on MRS containing lactate and erythromycin (1 μg/ml). Isolates were screened by colony PCR for a single crossover using chromosomal specific primer oBP49 (SEQ ID NO:583) and plasmid specific primer oBP42 (SEQ ID NO:584). Single crossover integrants were grown at 37° C. for approximately 40 generations by serial inoculations under non-selective conditions in MRS with lactate before cultures were plated on MRS medium with lactate. Isolates were patched to MRS with lactate plates, grown at 37° C., and then patched onto MRS plates with lactate and erythromycin (1μg/ml). Erythromycin sensitive isolates were screened by colony PCR for the presence of a wild-type or deletion second crossover using chromosomal specific primers oBP49 (SEQ ID NO:583) and oBP56 (SEQ ID NO:585). A wild-type sequence yielded a 3505 by product and a deletion sequence yielded a 2545 by product. The deletions were confirmed by sequencing the PCR product and absence of plasmid was tested by colony PCR with primers oBP42 (SEQ ID NO:584) and oBP57 (SEQ ID NO:586).
The Lactobacillus plantarum PN0512 double IdhDIdhL1 deletion strain was designated PNP0001. The ΔIdhD deletion included 83 by upstream of where the IdhD start codon was through amino acid 279 of 332. The ΔIdhL1 deletion included the fMet through the final amino acid.
ilvD Expression
The E. coli-L. plantarum shuttle vector pDM1 (SEQ ID NO:563) was used for cloning and expression of ilvD coding regions from Lactococcus lactis subsp lactis NCDO2118 (NCIMB #702118) [Godon et al., J. Bacteriol. (1992) 174:6580-6589] and Streptococcus mutans ATCC #700610 in L. plantarum PN0512. Plasmid pDM1 contains a minimal pLF1 replicon (˜0.7 Kbp) and pemK-pemI toxin-antitoxin(TA) from Lactobacillus plantarum ATCC14917 plasmid pLF1, a P15A replicon from pACYC184, chloramphenicol marker for selection in both E. coli and L. plantarum, and P30 synthetic promoter [Rud et al, Microbiology (2006) 152:1011-1019]. Plasmid pLF1 (C.-F. Lin et al., GenBank accession no. AF508808) is closely related to plasmid p256 [Sørvig et al., Microbiology (2005) 151:421-431], whose copy number was estimated to be ˜5-10 copies per chromosome for L. plantarum NC7. A P30 synthetic promoter was derived from L. plantarum rRNA promoters that are known to be among the strongest promoters in lactic acid bacteria (LAB) [Rud et al. Microbiology (2005) 152:1011-1019].
The Lactococcus lactis ilvD coding region (SEQ ID NO:564) was PCR-amplified from Lactococcus lactis subsp lactis NCDO2118 genomic DNA with primers 3T-ilvDLI(BamHI) (SEQ ID NO:557) and 5B-ilvDLI(NotI) (SEQ ID NO:558). L. lactis subsp lactis NCDO2118 genomic DNA was prepared with a Puregene Gentra Kit (QIAGEN; Valencia,Calif.). The 1.7 Kbp L. lactis ilvD PCR product (ilvDLI) was digested with NotI and treated with the Klenow fragment of DNA polymerase to make blunt ends. The resulting L. lactis ilvD coding region fragment was digested with BamHI and gel-purified using a QIAGEN gel extraction kit (QIAGEN). Plasmid pDM1 was digested with ApaLI, treated with the Klenow fragment of DNA polymerase to make blunt ends, and then digested with BamHI. The gel purified L. lactis ilvD coding region fragment was ligated into the BamHI and ApaLI(blunt) sites of the plasmid pDM1.The ligation mixture was transformed into E. coli Top10 cells (Invitrogen; Carlsbad, Calif.). Transformants were plated for selection on LB chloramphenicol plates. Positive clones were screened by SalI digestion, giving one fragment with an expected size of 5.3 Kbp. The positive clones were further confirmed by DNA sequencing. The correct clone was named pDM1-ilvD(L. lactis), which has the L. lactis ilvD coding region expressed from P30.
The S. mutans ATCC 700610 ilvD coding region was PCR-amplified with a specific forward primer with an NheI restriction site (SEQ ID NO:559) and a specific reverse primer with a NotI restriction site (SEQ ID NO:560). The genomic DNA of Streptococcus mutans ATCC 700610 was used as a template. Genomic DNA was prepared using a MasterPure DNA Purification Kit (Epicentre, Madison, Wis.). The plasmid vector pET28a (Novagen, Germany) was amplified with primers pET28a-F(NotI) (SEQ ID NO:561) and pET28a-R(NheI) (SEQ ID NO:562). Both coding region and plasmid fragments were digested with NheI and NotI, and ligated. The ligation mixture was transformed into E. coli (Top 10) competent cells (Invitrogen). Transformants were grown on LB agar plates supplemented with 50 μg/ml of kanamycin. Positive clones were confirmed by DNA sequencing. The S. mutans ilvD coding region from the plasmid pET28a was then sub-cloned into the E. coli-L. plantarum shuttle vector pDM1. The plasmid pET28a containing the S. mutans ilvD was digested with XbaI and NotI, treated with the Klenow fragment of DNA polymerase to make blunt ends, and a 1,759 by fragment containing the S. mutans ilvD coding region was gel-purified. Plasmid pDM1 was digested with BamHI, treated with the Klenow fragment of DNA polymerase to make blunt ends, and then digested with PvuII. The gel purified fragment containing S. mutans ilvD coding region was ligated into the BamHI(blunt) and PvuII sites of the plasmid pDM1. The ligation mixture was transformed into E. coli Top10 cells (Invitrogen, Carlsbad, Calif.). Transformants were plated for selection on LB chloramphenicol plates. Positive clones were screened by ClaI digestion, giving one fragment with an expected size of 5.5 Kbp. The correct clone was named pDM1-ilvD(S. mutans), which has the S. mutans ilvD coding region expressed from P30.
L. plantarum PN0512 and L. plantarum PN0512 ΔIdhDΔIdhL1 were transformed with plasmid pDM1-ilvD(L. lactis) or pDM1-ilvD(S. mutans) by electroporation. Electro-competent cells were prepared by the following procedure. 5 ml of Lactobacilli MRS medium was inoculated with PN0512 colonies from a freshly grown MRS plate and grown overnight at 30° C. 100 ml MRS medium was inoculated with the overnight culture to an OD600=0.1 and grown to an OD600=0.7 at 30° C. Cells were harvested at 3700×g for 8 min at 4° C., washed with 100 ml cold 1 mM MgCl2, centrifuged at 3700×g for 8 min at 4° C., washed with 100 ml cold 30% PEG-1000 (81188, Sigma-Aldrich, St. Louis, Mo.), recentrifuged at 3700×g for 20 min at 4° C., then resuspended in 1 ml cold 30% PEG-1000. 60 μl of electro-competent cells were mixed with ˜100 ng plasmid DNA in a cold 1 mm gap electroporation cuvette and electroporated in a BioRad Gene Pulser (Hercules, Calif.) at 1.7 kV, 25 μF, and 400Ω. Cells were resuspended in 1 ml MRS medium containing 500 mM sucrose and 100 mM MgCl2, incubated at 30° C. for 2 hrs, and then plated on MRS medium plates containing 10 μg/ml of chloramphenicol.
L. plantarum PN0512 and L. plantarum PN0512 ΔIdhDΔIdhL1, which carried pDM1-ilvD(L. lactis) or pDM1-ilvD(S. mutans), as well as control transformants with the pDM1 vector alone, were grown overnight in Lactobacilli MRS medium at 30° C. 120 ml of MRS medium supplemented with 100 mM MOPS (pH7.5), 40 μM ferric citrate, 0.5 mM L-cysteine, and 10 μg/ml chloramphenicol was inoculated with overnight culture to an OD600=0.1 in a 125 ml screw cap flask, for each overnight sample. The cultures were anaerobically incubated at 37° C. until reaching an OD600 of 1-2. Cultures were centrifuged at 3700×g for 10 min at 4° C. Pellets were washed with 50 mM potassium phosphate buffer pH 6.2 (6.2 g/L KH2PO4 and 1.2 g/L K2HPO4) and re-centrifuged. Pellets were frozen and stored at −80° C. until assayed for DHAD activity.
Enzymatic activity of the crude extract was assayed at 37° C. as follows. Cells to be assayed for DHAD were suspended in 2-5 volumes of 50 mM Tris, 10 mM MgSO4, pH 8.0 (TM8) buffer, then broken by sonication at 0° C. The crude extract from the broken cells was centrifuged to pellet the cell debris. The supernatants were removed and stored on ice until assayed (initial assay was within 2 hrs of breaking the cells). It was found that the DHADs assayed herein were stable in crude extracts kept on ice for a few hours. The activity was also preserved when small samples were frozen in liquid N2 and stored at −80° C.
The supernatants were assayed using the reagent 2,4-dinitrophenyl hydrazine as described in Flint and Emptage (J. Biol. Chem. (1988) 263: 3558-64). When the activity was so high that it became necessary to dilute the crude extract to obtain an accurate assay, the dilution was done in 5 mg/ml BSA in TM8. Protein assays were performed using the Pierce Better Bradford reagent (cat #23238) using BSA as a standard. Dilutions for protein assays were made in TM8 buffer when necessary.
The DHAD activity results are given in Table 8. Specific activity of L. lactis DHAD and S. mutans DHAD in L. plantarum PN0512 showed 0.014 and 0.067 μmol min−1 mg−1, respectively, while the vector control sample exhibited no detectable activity. Specific activity of L. lactis DHAD and S. mutans DHAD in L. plantarum PN0512 ΔIdhDΔIdhL1 showed 0.052 and 0.106 μmol min−1 mg−1, respectively, which increased 3.7 fold and 1.6 fold in the specific activity as compared to the activity in PN0512.
Lactococcus lactis subsp
lactis NCDO2118
Streptococcus mutans
The purpose of this example is to describe the construction of another plasmid used for the expression of Lactococcus lactis ilvD (SEQ ID NO:564). The shuttle vector pDM1 (SEQ ID NO:563), described in Example 1, was used for construction of the plasmid for expression of the ilvD gene from Lactococcus lactis subsp lactis NCDO2118 (NCIMB 702118) [Godon et al., J. Bacteriol. (1992) 174:6580-6589]. The plasmid was constructed using standard molecular biology methods known in the art. All restriction and modifying enzymes and Phusion High-Fidelity PCR Master Mix were purchased from New England Biolabs (Ipswich, Mass.). DNA fragments were purified with Qiaquick PCR Purification Kit (Qiagen Inc., Valencia, Calif.). Plasmid DNA was prepared with QIAprep Spin Miniprep Kit (Qiagen Inc., Valencia, Calif.). Oligoucleotides were synthesized by Sigma-Genosys (Woodlands, Tex.). All vector constructs were confirmed by DNA sequencing.
Vector pDM1 was modified by deleting nucleotides 3281-3646 spanning the lacZ region and replacing with a multi cloning site. Primers oBP120 (SEQ ID NO:567), containing an XhoI site, and oBP182 (SEQ ID NO:568), containing DrdI, PstI, HindIII, and BamHI sites, were used to amplify the P30 promoter from pDM1 with Phusion High-Fidelity PCR Master Mix. The resulting PCR product and vector pDM1 were digested with XhoI and DrdI. This digestion cuts out the lacZ region and P30. The PCR product and the large fragment of the pDM1 digestion were ligated to yield vector pDM20, which has P30 restored along with addition of the multi cloning site.
The ilvD coding region (SEQ ID NO:564) from Lactococcus lactis subsp lactis and a ribosome binding sequence (SEQ ID NO:566) were cloned into pDM20 to create vector pDM20-ilvD(LI). Primers oBP190 (SEQ ID NO:569), containing a BamHI site and ribosome binding sequence, and oBP192 (SEQ ID NO:570), containing a PstI site, were used to amplify the ilvD coding region from vector pDM1-ilvD(L. lactis), which was described in Example 1, with Phusion High-Fidelity PCR Master Mix. The resulting PCR product and pDM20 were ligated after digestion with BamHI and PstI to yield vector pDM20-ilvD(LI), with the ilvD coding region downstream of the P30 promoter.
The purpose of this example is to demonstrate the effect on DHAD activity, from expression of L. lactis ilvD, of the L. plantarum ΔIdhDΔIdhL1 background as compared to the wild-type background.
Lactobacillus plantarum PN0512 and Lactobacillus plantarum PN0512ΔIdhDΔIdhL1 were transformed with vector pDM20-ilvD(LI). Cells were transformed as in Example 1, except transformants were selected for on MRS medium plates containing 10 μg/ml of chloramphenicol and strain PN0512ΔIdhDΔIdhL1 was grown in the absence of glycine. The transformed strains were called PN0512/pDM20-ilvD(LI) and PN0512ΔIdhDΔIdhL1/pDM20-ilvD(LI). These two strains were grown in 50 ml of Lactobacilli MRS medium supplemented with 100 mM MOPS (Sigma-Aldrich, St. Louis, Mo.), 40 μM ferric citrate (Sigma-Aldrich, St. Louis, Mo.), 0.5 mM L-cysteine (Sigma-Aldrich, St. Louis, Mo.), and 10 μg/ml chloramphenicol adjusted to pH 7 with KOH, which had been deoxygenated in an anaerobic chamber (Coy Laboratories Inc., Grass Lake, Mich.), in 50 ml conical tubes at 37° C. in the anaerobic chamber until reaching an OD600 of approximately 1.5-2.8. Cultures were centrifuged at 3700×g for 10 min at 4° C. Pellets were washed with 50 mM potassium phosphate buffer pH 6.2 (6.2 g/L KH2PO4 (Sigma-Aldrich, St. Louis, Mo.) and 1.2 g/L K2HPO4 (Sigma-Aldrich, St. Louis, Mo.)) and re-centrifuged. Pellets were frozen and stored at −80° C. until assayed for DHAD activity. Samples were assayed for DHAD activity using a dinitrophenylhydrazine based method as described in Example 2, except cells were broken using a bead beater with Lysing Matrix B (MP Biomedicals, Solon, Ohio).
The two strains were grown and assayed using the same conditions three separate times. The DHAD activity results for each experiment, as well as the average, are given in Table 9. Expression of the L. lactis DHAD in the L. plantarum ΔIdhDΔIdhL1 background led on average to approximately a 10-fold increase in DHAD activity compared to expression in the wild-type background.
plantarum PN0512 and Lactobacillus plantarum
This application is related to and claims the benefit of priority of U.S. Provisional Application No. 61/100,810, filed Sep. 29, 2008, the entire contents of which is herein incorporated by reference.
| Number | Date | Country | |
|---|---|---|---|
| 61100810 | Sep 2008 | US |
