DIHYDROXY-ACID DEHYDRATASE ACTIVITY IN LACTIC ACID BACTERIA

CROSS-REFERENCE TO RELATED APPLICATIONS This application is related to and claims the benefit of priority of U.S. Provisional Application No. 61/100,809, filed September 29, 2008, the entirety of which is herein incorporated by reference. FIELD OF THE INVENTION

The invention relates to the field of microbiology. More specifically, lactic acid bacteria are disclosed expressing high levels of dihydroxy-acid dehydratase activity in the presence of introduced iron-sulfur cluster forming proteins. BACKGROUND OF THE INVENTION

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 Pub No. 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, however since DHAD enzymes are Fe-S cluster requiring they must be expressed in a host having the genetic machinery to produce Fe-S proteins.

[2Fe-2S] 2+ and [4Fe-4S] 2+ clusters can form spontaneously in vitro (Malkin and Rabinowitz (1966) Biochem. Biophys. Res. Comm. 23: 822-827). However, likely due to the toxic nature of both free Fe(II) and sulfide, biogenesis systems have evolved to form Fe-S clusters and insert them into their target apoproteins in vivo. The biogenesis of iron sulfur clusters is not completely understood but is known generally to include liberation of sulfur from the amino acid cysteine by a cysteine desulfurase enzyme, combination of the sulfur with Fe(II) on a scaffold protein, and transfer of the formed Fe-S clusters, frequently in a chaperone-dependent manner, to the proteins and enzymes that require them. The Isc, Suf and Nif operons have been found to encode proteins involved in Fe-S cluster formation in different bacteria (Johnson et al. Annu. Rev. Biochem. 74:247-281 (2005)).

Lactic acid bacteria are well characterized and are used commercially in a number of industrial processes. Although it is known that some lactic acid bacteria possess Fe-S cluster requiring enzymes (Liu et al., Journal of Biological Chemistry (2000), 275(17), 12367-12373) and therefore posses the genetic machinery to produce Fe-S clusters, little is known about the ability of lactic acid bacteria to insert Fe-S clusters into heterologous enzymes, and little is known about the facility with which Fe- S cluster forming proteins can be expressed in lactic acid bacteria. To obtain high levels of product in a lactic acid bacteria from a biosynthetic pathway including DHAD activity, high expression of DHAD activity is desired. The activity of the Fe-S requiring DHAD enzyme in a host cell may be limited by the availability of Fe-S cluster in the cell. There remains a need therefore to engineer a lactic acid bacteria, which is a good industrial host, to provide sufficient levels of Fe-S cluster forming proteins to accommodate the expression of Fe-S requiring proteins such as DHAD. SUMMARY OF THE INVENTION

Provided herein are lactic acid bacterial cells comprising a functional dihydroxy-acid dehydratase polypeptide and at least one recombinant genetic expression element encoding iron-sulfur cluster forming proteins. In some embodiments, the functional dihydroxy-acid dehydratase polypeptide is encoded by a nucleic acid molecule that is heterologous to the bacteria. In some embodiments, the functional dihydroxyacid dehydratase polypeptide is a [2Fe-2S] 2+ dihydroxy-acid dehydratase, while in other embodiments, the functional dihydroxyacid dehydratase polypeptide is a [4Fe-4S] 2+ dihydroxy-acid dehydratase.

In one embodiment, the dihydroxyacid 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 one embodiment, 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.

In some embodiments, the recombinant genetic expression element encoding iron-sulfur cluster forming proteins contains coding regions of an operon selected from the group consisting of Isc, Suf and Nif operons. In some embodiments, the Suf operon comprises at least one coding region selected from the group consisting of SufC, Suf D, Suf S, SufU, Suf B, SufA and yseH, and in some embodiments, the Isc operon comprises at least one coding region selected from the group consisting of IscS, IscU, IscA, IscX, HscA, HscB, and Fdx. In some embodiments the Nif operon comprises at least one coding region selected from the group consisting of NifS and NifU. In some embodiments, the Suf operon has the nucleotide sequence selected from the group consisting of SEQ ID NO:881 and SEQ ID NO:589. In some embodiments, the Suf operon is derived from Lactococcus lactis and comprises at least one coding region encoding a polypeptide having an amino acid sequenced selected from the group consisting of SEQ ID NO: 598 (SufC), SEQ ID NO: 604 (SufD), SEQ ID NO: 610 (SufB), and SEQ ID NO: 618 (YseH). In some embodiments, the Suf operon is derived from Lactoabcillus plantarum and comprises at least one coding region encoding a polypeptide having an amino acid sequenced selected from the group consisting of SEQ ID NO: 596 (SufC), SEQ ID NO: 602 (SufD), SEQ ID NO: 624 (SufS), SEQ ID NO: 620 (SufU) and SEQ ID NO: 608 (SufB). In some embodiments, the lsc operon is derived from E. CoIi and comprises at least one coding region encoding a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 528 (IscS), SEQ ID NO: 530 (IscU), SEQ ID NO: 532 s(lscA), SEQ ID NO:534 (HscB), SEQ ID NO: 536 (hscA), SEQ ID NO: 538 (Fdx), and SEQ ID NO: 540 (IscX). In some embodiments the Nif operon is derived from Wolinella succinogenes and comprises at least one coding region encoding a polypeptide having an amino acid sequence selected from the group consisting of: SEQ ID NO: 542 (NifS) and SEQ ID NO: 544 (NifU).

In some embodiments, the lactic acid bacterial cell provided herein is a member of a genus selected from the group consisting of Lactococcus, Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, and Streptococcus. In some embodiments, the bacteria produces isobutanol, and in some embodiments, the bacteria comprises an isobutanol biosynthetic pathway. 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 for increasing the activity of a heterologous dihydroxyacid dehydratase polypeptide in a lactic acid bacterial cell comprising: a) providing a lactic acid bacterial cell comprising: 1 ) a nucleic acid molecule encoding a heterologous dihydroxyacid dehydratase polypeptide; 2) a recombinant genetic expression element encoding iron-sulfur cluster forming proteins, wherein the proteins are expressed; and b) growing the lactic acid bacterial cell of (a) under conditions whereby the dihydroxy-acid dehydratase polypeptide is expressed in functional form having a specific activity greater than the same dihydroxy-acid dehydratase polypeptide expressed in the same bacterial cell lacking the recombinant genetic expression element encoding iron-sulfur cluster forming proteins. In one embodiment, the specific activity of the expressed dihydroxyacid dehydratase polypeptide is at least about two fold greater than the specific activity of the same dihydroxyacid dehydratase polypeptide expressed in the same bacteria lacking the recombinant genetic expression element encoding iron-sulfur cluster forming proteins.

Also provided herein is a method of making isobutanol comprising providing a lactic acid bacterial cell disclosed herein and growing said cell under conditions wherein isobutanol is produced.

BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE DESCRIPTIONS

The invention can be more fully understood from the following detailed description, figure, and the accompanying sequence descriptions, which form a part of this application.

Figure 1 shows a schematic drawing of the coding regions in the Suf operon from Lactobacillus plantarum as well as the adjacent coding regions feoA and ORF (A), and the portion of the Suf operon that was deleted in Example 1 (B).

Figure 2 shows a schematic drawing of the coding regions in the Suf operon from Lactococcus lactis, with each coding region named by the designation from the publicly available genomic sequence and the corresponding coding region identified by sequence homology. No homologous protein is identified for the hypothetical protiein.

Figure 3 shows a schematic drawing of the coding regions in the Suf operon from E. coli. Figure 4 shows a schematic drawing of the coding regions of the lsc operon from E. coli, and the adjacent iscR gene. Figure 5 shows a schematic drawing of the coding regions of the Nif operon from Wolinella succinogenes, with the bounding ORF1 and ORF2.

Figure 6 shows biosynthetic pathways for biosynthesis of isobutanol.

Table 7 is a table of the Profile HMM for dihydroxy-acid dehydratases based on enzymes with assayed function prepared as described in Example 1. Table 8 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.

Table 1. SEQ ID NOs of representative bacterial [2Fe-2S] 2+ DHAD proteins and encoding sequences

Table 2. SEQ ID NOs of representative fungal and plant [2Fe-2S] 2+ DHAD proteins and encoding sequences

Table 3. SEQ ID NOs of representative [4Fe-4S] 2+ DHAD proteins and encoding sequences

Table 4. SEQ ID NOs of representative Suf operon Fe-S cluster forming proteins and encoding sequences.

Annotations in μuoiic αaiaoases may nave a αiπereπi protein iπαicaieα τor some of the SufS proteins above. Annotation as Class V aminotransferase refers to the same protein as cysteine desulfurase.

Table 5. SEQ ID NOs of representative lsc and Nif operon Fe-S cluster forming proteins and encoding sequences

Table 6. SEQ ID NOs of additional proteins and encoding sequences

SEQ ID NOs:554 - 570, 572, 573, 575, 576, 578 - 588, 592 and 593 are nucleotide sequences of primers used in the Examples.

SEQ ID NOs:553, 571 , 574, 577 and 594 are nucleotide sequences of vectors used in the Examples.

SEQ ID NO:589 is the nucleotide sequence of the Suf operon from Lactobacillus plantarum PN0512.

SEQ ID NO:590 is the nucleotide sequence of a ribosome binding sequence used in the Examples.

SEQ ID NO:591 is the nucleotide sequence of the promoter region of the IdhU gene from Lactobacillus plantarum PN0512.

SEQ ID NO:881 is the nucleotide sequence of the Suf operon from Lactococcus lactis subsp lactis NCDO2118.

DETAILED DESCRIPTION OF THE INVENTION

The present invention solves the stated problem by providing recombinant lactic acid bacterial cells that express DHAD and that express at least one recombinant genetic element encoding Fe-S cluster forming proteins. These cells have increased DHAD activity as compared to DHAD activity in cells without the recombinant genetic element. In these cells, products synthesized by a pathway that includes DHAD activity may be increased, including amino acids valine, leucine and isoleucine, vitamin B5, and isobutanol. The amino acids and vitamin B5 may be used as nutritional supplements, and isobutanol may be used as a fuel additive to reduce demand for petrochemicals.

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 "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. Foreign genes 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. The term "recombinant genetic expression element" refers to a nucleic acid fragment that expresses one or more specific proteins, including regulatory sequences preceding (5' non-coding sequences) and following (3' termination sequences) coding sequences for the proteins. A chimeric gene is a recombinant genetic expression element. The coding regions of an operon may form a recombinant genetic expression element, along with an operably linked promoter and termination region.

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.

The term "overexpression" ", as used herein, refers to expression that is higher than endogenous expression of the same or related gene. A heterologous gene is overexpressed if its expression is higher than that of a comparable endogenous gene.

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, 2" ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, NY (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 6X SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2X SSC, 0.5% SDS at 45 ⁰ C for 30 min, and then repeated twice with 0.2X SSC, 0.5% SDS at 50 ⁰ 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 0.2X SSC, 0.5% SDS was increased to 60 ⁰ C. Another preferred set of highly stringent conditions uses two final washes in 0.1 X SSC, 0.1 % SDS at 65 ⁰ C. An additional set of stringent conditions include hybridization at 0.1 X SSC, 0.1 % SDS, 65 ⁰ C and washes with 2X SSC, 0.1 % SDS followed by 0.1X 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 hybhdizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybhdizable 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. MoI. 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.) Biocomputinq: 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: NJ (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, Wl). 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=I O and GAP LENGTH PENALTY=IO. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method are KTUPLE=I , 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)) and found in the MegAlign™ v6.1 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). Default parameters for multiple alignment (GAP PENALTY=IO, GAP LENGTH PENALTY=0.2, Delay Divergen Seqs(%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Mathx=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: 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 55% to 100% may be useful in describing the present invention, such as 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, Wl); 2.) BLASTP, BLASTN, BLASTX (Altschul et al., J. MoI. Biol., 215:403-410 (1990)); 3.) DNASTAR (DNASTAR, Inc. Madison, Wl); 4.) Sequencher (Gene Codes Corporation, Ann Arbor, Ml); 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, NY). 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, NY (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, NY (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc, and Wiley-lnterscience (1987).

The invention provides recombinant lactic acid bacterial cells expressing a functional dihydroxy-acid dehydratase polypeptide where the lactic acid bacterial cell is also expressing at least one recombinant genetic element encoding iron-sulfur cluster forming proteins. It has been discovered that the co-expression of a dihydroxy-acid dehydratase polypeptide with a recombinant genetic expression element encoding iron- sulfur cluster forming proteins results in increased specific activity of dihydroxy-acid dehydratase. Specific activity is based on concentration of total soluble protein in a crude cell extract. Lactic Acid Bacterial cells Lactic acid bacteria (LAB) which may be used as hosts in the present disclosure include, but are not limited to, Lactococcus, Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, and Strept ococcus. These and any LAB cells that are amenable to genetic manipulation may be modified as disclosed herein for increased DHAD activity. Expression of DHAD activity

In the disclosed LAB cells, DHAD activity may be provided by natural expression of an endogenous DHAD protein, by expression of an introduced heterologous DHAD gene, or both. For example, cells of

Lactococcus, Streptococcus, and Leuconostoc. have endogenous genes encoding DHAD, and may have this endogenous activity enhanced by introduction of a heterologous DHAD encoding gene. DHAD genes are not known in cells of Lactobacillus, Pediococcus, and Oenococcus, which then are engineered for DHAD expression through introduction of a heterologous DHAD encoding gene.

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] 2+ cluster or a [2Fe-2S] 2+ 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=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix. Additional [2Fe-2S] 2+ DHADs may be identified using the analysis described in commonly owned and co-pending US Patent Application 61/100792, 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 DHA Ds 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. MoI. 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] 2+ DHADs, [2Fe-2S] 2+ DHADs, arabonate 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] ²⁺ cluster. Proteins having the three conserved cysteines include arabonate dehydratases and [2Fe-2S] 2+ DHADs. The [2Fe-2S] 2+ DHADs may be distinguished from the arabonate dehydratases by analyzing for signature conserved amino acids found to be present in the [2Fe-2S] 2+ DHADs or in the arabonate dehydratases at positions corresponding to the following positions in the Streptococcus mutans DHAD amino acid sequence. These signature amino acids are in [2Fe-2S] 2+ DHADs or in arabonate 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), MuIMs et al., U.S. Patent 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, NJ). 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-HCI, 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 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 ldhL1and 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)-hydroxymyhstoyl-[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.anύ 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 pAMβi 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 et al. Appl. Environ. Microbiol. 2005 Mar; 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)).

Fe-S cluster forming proteins

Disclosed herein are recombinant LAB cells that express DHAD and are engineered for expression of proteins involved in formation of Fe- S clusters. Two or more proteins are involved in several systems that are known to form Fe-S clusters, which may include proteins that acquire iron and sulfur, assemble Fe-S clusters, and transfer Fe-S clusters to apoproteins. The DHAD protein requires either a [2Fe-2S] 2+ cluster or a [4Fe-4S] 2+ cluster to be active, depending on the specific DHAD. Applicants have found that increasing the expression of Fe-S cluster forming proteins effectively increased the activity of DHAD in LAB cells.

Expression of any set of proteins for Fe-S cluster formation may be used to increase DHAD activity in LAB cells. There are three known groups of Fe-S cluster forming proteins. These proteins are encoded by three types of operons: the Suf operon, the lsc operon, and the Nif operon.

The putative Suf operons of Lactococcus lactis and of Lactobacillus plantarum were identified by applicants by the presence of coding regions with sequence homologies to suf coding regions from other organisms. Disclosed herein is the first demonstration that expression of the set of genes including putative sufC, putative sufD, putative sufS, putative sufU, and putative suf B of L. plantarum affect function of an Fe-S protein. Similarly, disclosed herein is the first demonstration that expression of the set of genes including putative sufC, putative sufD, putative sufS, yseH (encoding hypothetical protein), putative nifU, and putative sufB of L. lactis affect function of an Fe-S protein. Applicants have shown in Example 3 herein, that expression of the identified Lactococcus lactis suf operon in a Lactobacillus plantarum strain with the endogenous suf operon deleted allowed expression of activity of an introduced DHAD while there as no DHAD acitvity in the Lactobacillus plantarum deletion strain with no Lactococcus lactis suf operon. Applicants have shown in Example 5 herein, that increased expression of the identified endogenous Lactobacillus plantarum suf operon provided increased activity of an expressed DHAD.

The Suf operons of L. plantarum and L. lactis are shown in Figures 1 and 2, respectively. SufS is a cysteine desulfurase which provides the sulfur for the cluster, and SufU is a scaffold protein that acts as a sulfur and iron acceptor. Functions of SufC and SufD are not established, though SufC has ATPase activity, Suf B has cysteine desulfurase activator activity and a SufBCD complex has similarity to components of ATP- binding cassette transporter proteins. The E. co// Suf operon, shown in Figure 3, includes SufE, another cysteine desulfurase activator. In addition, SufU is not present and is replaced by a different scaffold protein, SufA. Thus there is some variation in the set of Fe-S cluster forming proteins that is included in a Suf operon depending on the source organism. Any set of Fe-S cluster forming Suf operon proteins may be expressed in the LAB cells disclosed herein. Representative examples of these proteins and their coding regions, with SEQ ID NOs, are given in Table 4. Typically a set of coding regions that is used in preparing the LAB cells disclosed herein is derived from a single operon. However, coding regions for proteins that have high sequence identities may be interchanged for one another in a set of Fe-S cluster forming proteins. For example, the SufS protein from L. lactis may be used together with the SufC, SufD, SufU, and Suf B proteins of Lactobacillus reuteri whose SufS has 74% identity, or of Lactobacillus fermentum whose SufS has 72% identity, each to the SufS of L lactis. Also the SufS of L. plantarum may be interchanged. Though it has 62% identity with SufS of L. lactis, considering conservative amino acid changes the similarity is 80%. One skilled in the art will recognize that generally proteins with sequence identities of at least about 70%, 75%, 80%, 85%, 90%, 95% or greater may be substituted for each other in a set of Fe-S cluster forming proteins. With similarities of about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or greater, Suf proteins may be interchangeable if the amino acid changes are conservative for a final similarity of 70%, 75%, 80%, 85%, 90%, 95% or greater based on the Clustal W method of alignment using the default parameters of GAP PENALTY=I O, GAP LENGTH PENALTY=O.1 , and Gonnet 250 series of protein weight matrix over the full length of the protein sequence.

Proteins of a Suf operon derived from a wide variety of LAB and other related bacteria may be used in the LAB cells disclosed herein. The SufS proteins and coding regions representing the Fe-S cluster forming protein operons of a variety of organisms that may be used herein are given in Table 4. Each of the sufS coding regions given in Table 4 is a part of a Suf operon. One skilled in the art can readily use the sufS coding region or protein sequence of an organism that is given in Table 4 as a sequence probe to identify the entire Suf operon from that organism in publicly available sequence databases. Each individual suf gene coding region may be identified using BLAST sequence analysis of individual coding or protein sequences, as described above, to identify the corresponding coding sequence from a desired organism. The suf gene sequences given in Table 4, for example, may be used as the gene probe sequences. Alternatively, annotations present in publicly available databases may be used to identify suf genes.

Fe-S cluster forming proteins may also be found in an lsc operon. The lsc operon of E. coli, for example, includes coding regions for the proteins IscS, IscU, IscA, HscB, HscA, Fdx and IscX, whose sequences are listed in Table 5, with SEQ ID NOs, and operon diagram is shown in Figure 4. Expression of the operon is negatively regulated by IscR, encoded by an adjacent sequence (Figure 4) but that is not part of the Fe- S cluster forming set of proteins in the lsc operon. IscS is a cysteine desulfurase that transfers sulfur to the scaffold protein IscU. IscA binds iron and provides iron to IscU. HscA, also called Hsc66, is a chaperone (member of the Hsp70 protein family) whose ATPase activity is stimulated by IscU in the presence of the co-chaperone HscB, also called Hsc20. FdX is a ferredoxin which may function as an intermediate site for Fe-S cluster assembly. IscX interacts with IscS, but may not be necessary for Fe-S cluster formation. Any lsc operon Fe-S cluster forming proteins may be used in the LAB cells disclosed herein.

Fe-S cluster forming proteins may also be found in a Nif operon. The Nif operon of Wolinella succinogenes, for example, includes coding regions for the proteins NifS and NifU, whose sequences are listed in Table 5 and operon diagram is shown in Figure 5. NifS is a cysteine desulfurase and NifU is a scaffold protein. Any Nif operon Fe-S cluster forming proteins may be used in the LAB cells disclosed herein. A set of Fe-S cluster forming proteins, as described above, may be expressed in LAB cells as one recombinant genetic expression element that includes the coding regions as they are present in their natural operon, operably linked to a promoter and 3' termination sequence. Alternatively, a set of Fe-S cluster forming proteins may be expressed in more than one operon or each as an individual chimeric gene, all of which are called recombinant genetic expression elements. One skilled in the art can readily choose and implement any of these methods of expressing two or more proteins that are a set of Fe-S cluster forming proteins.

An additional approach to increase the expression of Fe-S cluster forming proteins comprises replacing or augmenting the promoter of an endogenous gene whose product is known or predicted to be involved in Fe-S cluster assembly or the promoter for an operon containing genes whose products are known or predicted to be involved in Fe-S cluster assembly. The endogenous promoter may be replaced by a high expression promoter or augmented by additional copies of the native promoter or a non-native promoter. Suitable promoters and methods are well known in the art.

Promoters, termination control regions, and vectors used for expressing Fe-S cluster forming proteins as recombinant genetic expression elements that are individual chimeric genes or one or multiple operons in LAB cells are the same as described above for expression of DHAD coding regions. lsobutanol and other products lsobutanol 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 a functional dihydroxy- acid dehydratase polypeptide and at least one recombinant genetic expression element encoding iron-sulfur cluster forming proteins. 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 α-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 US 6177264. 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 Publication 20070092957 A1 , which is herein incorporated by reference. A diagram of the disclosed isobutanol biosynthetic pathways is provided in Figure 6. Production of isobutanol in a strain disclosed herein benefits from increased DHAD activity. As described in US 20070092957 A1 , steps in an example isobutanol biosynthetic pathway include conversion of: - pyruvate to acetolactate (Fig. 6 pathway step a), as catalyzed for example by acetolactate synthase,

- acetolactate to 2,3-dihydroxyisovalerate (Fig. 6 pathway step b) as catalyzed for example by acetohydroxy acid isomeroreductase;

- 2,3-dihydroxyisovalerate to α-ketoisovalerate (Fig. 6 pathway step c) as catalyzed for example by acetohydroxy acid dehydratase, also called dihydroxy-acid dehydratase (DHAD);

- α-ketoisovalerate to isobutyraldehyde (Fig. 6 pathway step d) as catalyzed for example by branched-chain α-keto acid decarboxylase ;and

- isobutyraldehyde to isobutanol (Fig. 6 pathway step e) as catalyzed for example by branched-chain alcohol dehydrogenase.

The substrate to product conversions and enzymes involved in these reactions, and for steps f, g, h, I, j, and k of alternative pathways shown in Figure 6, are described in US 20070092957 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 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 commonly owned and co-pending US Patent Pub No. 20080261230. Examples of high activity KARIs disclosed therein are those from Vibrio cholerae (TJNA: SEQ ID NO:545; protein SEQ ID NO:546), Pseudomonas aeruginosa PAO1, (TJNA: SEQ ID NO:551 ; protein SEQ ID NO:552), and Pseudomonas fluorescens PF5 (DNA: SEQ ID NO:547; protein SEQ ID NO:548).

Additionally described in US 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. Growth for production

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, including 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 U.S. Patent Application Publication No. 2007/0031918A1 , 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

⁰ C to about 40 ⁰ 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, MA., 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.

EXAMPLES 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), "μg" 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. GENERAL METHODS:

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-lnterscience, N. Y., 1987. Materials and methods suitable for the maintenance and growth of bacterial cultures are also well known in the art. Techniques suitable for use in the following Examples may be found in Manual of Methods for General Bacteriology, Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds., American Society for Microbiology, Washington, DC, 1994, or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, MA, 1989. All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wl), BD Diagnostic Systems (Sparks, MD), Life Technologies (Rockville, MD), or Sigma Chemical Company (St. Louis, MO), unless otherwise specified.

Example 1

Lactobacillus plantarum PN0512 suf operon deletion The purpose of this example is to describe the deletion of the suf operon in Lactobacillus plantarum PN0512 (ATCC strain # PTA-7727) to create the Lactobacillus plantarum strain PN0512Δsuf. This operon contains genes whose products are predicted to be involved in Fe-S cluster assembly. The coding regions of the operon were identified by sequence homology to suf gene coding regions that are present in publicly available sequence databases. The deletion was constructed by a two-step homologous recombination procedure to yield an unmarked deletion using methods previously described (Ferain et al., 1994, J. Bad 176:596). The procedure utilized a shuttle vector, pFP996 (SEQ ID NO:553). 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 (Hohnouchi and Weisblum J. Bacterid. (1982) 150(2):804-814). In pFP996, the multiple cloning sites (nucleotides #1 to 50) contain restriction sites for EcoRI, BgIII, Xhol, Smal, CIaI, Kpnl, and Hindlll. 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 containing sequences upstream and downstream of the intended deletion were cloned into the plasmid to provide the regions of homology for two genetic crossovers. The initial single crossover integrated the plasmid into the chromosome. The second crossover event yielded either the wild type sequence or the intended gene deletion.

The recombination 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, MA). DNA fragments were purified with Qiaquick PCR Purification Kit (Qiagen Inc., Valencia, CA). Plasmid DNA was prepared with QIAprep Spin Miniprep Kit (Qiagen Inc., Valencia, CA). L. plantarum PN0512 genomic DNA was prepared with MasterPure DNA Purification Kit (Epicentre, Madison, Wl). Oligoucleotides were synthesized by Sigma-Genosys (Woodlands, TX). The vector construct was confirmed by DNA sequencing.

The homologous DNA arms were designed such that the deletion would encompass the majority of the first gene through the 5' end of the last gene in the operon, which is shown in Figure 1 A. The deleted sequence, as shown in Figure 1 B, started at 94 base pairs into the sufC coding sequence through 215 base pairs of the sufB coding sequence. The homologous arms cloned into the plasmid were approximately 1100 (left arm) and 1200 (right arm) base pairs long separated by 12 base pairs (Xhol and Xmal restriction sites). The suf operon left homologous arm was amplified from L. plantarum PN0512 genomic DNA with primers oBP97 (SEQ ID NO:554), containing an EcoRI site, and oBP98 (SEQ ID NO:555), containing an Xhol site using Phusion High-Fidelity PCR Master Mix. The suf operon right homologous arm was amplified from L. plantarum PN0512 genomic DNA with primers oBP101 (SEQ ID NO:556), containing an Xmal site and oBP102 (SEQ ID NO:557), containing a Kpnl site using Phusion High-Fidelity PCR Master Mix. The suf operon left homologous arm was digested with EcoRI and Xhol and the suf operon right homologous arm was digested with Xmal and Kpnl. The two homologous arms were ligated with T4 DNA Ligase into the corresponding restriction sites of pFP996, after digestion with the appropriate restriction enzymes, to generate the vector pFP996-suf-arms.

Deletion of the suf operon was obtained by transforming Lactobacillus plantarum PN0512 with pFP996-suf-arms. 5 ml of Lactobacilli MRS medium (7406, Accumedia, Neogen Corporation,

Lansing, Ml) containing 1 % glycine (G8898, Sigma-AIdrich, St. Louis, MO) was inoculated with PN0512 and grown overnight at 3O ⁰ 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 3O ⁰ C. Cells were harvested at 3700xg for 8 min at 4 ⁰ C, washed with 100 ml cold 1 mM

MgCI ₂ (M8266, Sigma-AIdrich, St. Louis, MO), centrifuged at 3700xg for 8 min at 4 ⁰ C, washed with 100 ml cold 30% PEG-1000 (81188, Sigma- AIdrich, St. Louis, MO), recentrifuged at 3700xg for 20 min at 4 ⁰ C, then resuspended in 1 ml cold 30% PEG-1000. 60 μl of cells were mixed with -100 ng of plasmid DNA in a cold 1 mm gap electroporation cuvette and electroporated in a BioRad Gene Pulser (Hercules, CA) at 1.7 kV, 25 μF, and 400 Ω. Cells were resuspended in 1 ml MRS medium containing 500 mM sucrose (S9378, Sigma-AIdrich, St. Louis, MO) and 100 mM MgCI ₂ , incubated at 3O ⁰ C for 2 hrs, and then plated on MRS medium plates containing 2 μg/ml of erythromycin (E5389, Sigma-AIdrich, St. Louis, MO).

Transformants were screened by PCR using plasmid specific primers oBP42 (SEQ ID ON:558) and oBP57 (SEQ ID NO:559). Transformants were grown at 3O ⁰ C in Lactobacilli MRS medium with erythromycin (3 μg/ml) for approximately 10 generations and then at 37 ⁰ C for approximately 45 generations by serial inoculations in Lactobacilli MRS medium. The cultures were plated on Lactobacilli MRS medium with erythromycin (1 μg/ml).The isolates were screened by colony PCR for a single crossover with chromosomal specific primer oBP125 [SEQ ID No. 560] and plasmid specific primer oBP42 (SEQ ID NO:558), and chromosomal specific primer oBP127 9SEQ ID NO:561 ) and plasmid specific primer oBP57 (SEQ ID NO:559).

Subsequently, single crossover integrants were grown at 37 ⁰ C for approximately 44 generations by serial inoculations in Lactobacilli MRS medium. The cultures were plated on MRS medium. Colonies were patched to MRS plates and grown at 37 ⁰ C. The isolates were then patched onto MRS medium with erythromycin (1 μg/ml). Erythromycin sensitive isolates were screened by (colony) PCR for the presence of a wild-type or deletion second crossover using chromosomal specific primers oBP125 (SEQ ID NO:560) and oBP127 (SEQ ID NO:561 ). A wild- type sequence yielded a 6400 bp product and a deletion sequence yielded a 2500 bp product. The deletion was confirmed by sequencing the PCR product while the absence of plasmid was tested by colony PCR using plasmid specific primers oBP42 (SEQ ID NO:558) and oBP57 (SEQ ID NO:559).

Example 2 Construction of plasmid pDM1 -HvD(L. lactis)-suf(L lactis) The purpose of this example is to describe cloning of the HvD coding region (SEQ ID NO:231 ) and suf operon (SEQ ID NO:881 ) from Lactococcus lactis subsp lactis NCDO2118 (NCIMB 702118) [Godon et al., J. Bacterid. (1992) 174:6580-6589]. The Lactococcus lactis suf operon comprises ysfB (sufC), ysfB (sufC), ysfA (sufD), ysel (sufS), yseH (hypothetical protein), nifU, and yseF (sufB) genes as diagrammed in Figure 2)

A shuttle vector pDM1 (SEQ ID NO:571 ) was used for cloning and expression of the HvD coding region and suf operon from Lactococcus lactis subsp lactis NCDO2118 (NCIMB 702118) in Lactobacillus plantarum PN0512 (ATCC PTA-7727). Plasmid pDM1 contains a minimal pLF1 replicon (-0.7 Kbp) and pemK-peml toxin-antitoxin(TA) from Lactobacillus plantarum ATCC14917 plasmid pLF1 , a P15A replicon from pACYC184, chloramphenicol resistance 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 L. lactis suf operon (6,108 bp) was PCR-amplified from genomic DNA of L. lactis subsp lactis NCDO2118 (NCIMB 702118) with T- sufLI(Notl) (SEQ ID NO:572) and B-sufLI(Spel) (SEQ ID NO:573) primers. L. lactis subsp lactis NCDO2118 genomic DNA was prepared with a Puregene Gentra Kit (QIAGEN, CA). The resulting suf PCR fragment containing ysfB (sufC), ysfB (sufC), ysfA (sufD), ysel (sufS), yseH, nifU, and yseF (sufB) coding regions was digested with Notl and Spel, and the 6.1 Kbp suf operon fragment was gel-purified. A cloning plasmid pTnCm (SEQ ID NO:574) was digested with Notl and Spel, and ligated with 6.1 Kbp suf operon fragment. pTnCm contains a pE194 replicon, pBR322 replicon, ampicillin resistance marker for selection in E. coli, and chloramphenicol resistance marker for selection in L. plantarum. The ligation mixture was transformed into the E. coli Top10 strain (Invitrogen, CA), and spread on LB plates containing 100 μg/ml ampicillin for selection. Positive clones were screened by Xhol digestion, giving two fragments with an expected size of 5,136bp and 8,413bp. The correct plasmid was named pTnCm-suf(L. lactis).

The L. lactis HvD coding region was PCR-amplified from genomic DNA of L lactis subsp lactis NCDO2118 (NCIMB 702118) with T- NvDLI(BamHI) (SEQ ID NO:575) and B-ilvDLI(NotlBamHI) (SEQ ID NO:576) primers. The resulting HvD PCR fragment was digested with BamHI and Notl, This 1.7Kbp HvD coding region fragment was gel- purified, and ligated into BamHI and Notl sites of plasmid pAMAC8-Papha (SEQ ID NO:577), which contained the Papha promoter from the pJH1 plasmid of Enterococcus faecalis (Trieu-Cuot, P. & Courvalin, P. Gene (1983) 23:331 -341 ). pAMACδ carries a pAMβi replication origin (Renault et al., Gene 183:175-182 (1996); and O'Sullivan et al., Gene 137:227-231 (1993)), P15A replicon from pACYC184, chloramphenicol resistance gene from Staphylococcus aureusplasmid pC194 for selection in L. plantarum, and ampicillin gene for selection in E. coli. As a result of the ligation, pAMAC8-Papha-ilvD (L.lactis) was generated. Plasmid pAMAC8-Papha- NvD(L lactis) was then digested with Xhol and Notl, and the 2,147 bp Papha-ilvDLI fragment was gel-purified. The 2,147 bp Papha-ilvDLI fragment was ligated into Sail and Notl sites of pTnCm-suf(L. lactis). The ligation mixture was transformed into E. coli Top10 cells (Invitrogen, CA), which were spread on LB plates containing 100 μg/ml ampicillin for selection. Positive clones were screened by BamHI and Notl digestion, giving two fragments with an expected size of 13,934 bp and 1 ,742 bp. The correct plasmid was named pTnCm-Papha-ilvD(L. lactis)-suf(L. lactis).

The NvD(L lactis)-suf(L lactis) cassette (SEQ ID NO:594) was isolated from pTnCm-Papha-ilvD(L lactis)-suf(L actis). Plasmid pTnCm- Papha-ilvD(L lactis)-suf(L lactis) was digested with Spel, treated with Klenow fragment of DNA polymerase to make blunt ends, and then digested with BamHI. The 7.9 Kbp NvD(L lactis)-suf(L lactis) cassette

(SEQ ID NO: 594) was gel-purified, and ligated into BamHI and Smal sites of pDM1 to clone the NvD(L lactis)-suf(L lactis) cassette under the control of the P30 promoter in pDM1. The ligation mixture was transformed into E. coli Top10 cells (Invitrogen, CA), and spread on LB plates containing 25 μg/ml chloramphenicol for selection. Positive clones were screened by ApaLI digestion, giving two fragments with an expected size of 8,040bp and 3,562bp. The correct plasmid was named pDM1 - NvD(L. lactis)-suf(L. lactis). The sequence of the NvD(L. lactis)-suf(L. lactis) cassette in pDM1 -NvD(L. lactis)-suf(L. lactis) was confirmed with sequence primers, DLM (R) (SEQ ID NO:578), DLI2 (SEQ ID NO:579), DLI3 (SEQ ID NO:580), Sufi (SEQ ID NO:581 ), Suf2 (SEQ ID NO:582), Suf3 (SEQ ID NO:583), Suf4 (SEQ ID NO:584), Suf5 (SEQ ID NO:585), Suf6 (SEQ ID NO:586), Suf7 (SEQ ID NO:587), and Suf8 (SEQ ID NO:588). Plasmid pDM1 -HvD(L. lactis)-suf(L.lactis) was digested with ApaLI and Notl, treated with Klenow fragment of DNA polymerase to make blunt ends, and the 5.3 Kbp fragment containing pDM1 -HvD(L. lactis) was gel- purified. The gel-purified pDM1 -ilvDLI fragment was self-ligated to create pDM1 -HvD(L. lactis). Positive clones were screened by Sail digestion, giving one fragment with an expected size of 5,262 bp.

Example 3 Recombinant co-expression of Lactococcus lactis sufoperon with Lactococcus lactis HvD restores DHAD activity in Lactobacillus plantarum

PN0512Δsαf strain

The purpose of this example is to describe co-expression of the Lactococcus lactis HvD coding region and Lactococcus lactis sufoperon in the Lactobacillus plantarum PN0512 Asuf strain. Construction of Lactobacillus plantarum PN0512 Asuf operon deletion mutant and that of plasmids pDM1 -HvD(L. lactis)-suf(L. lactis) and pDM1 -HvD(L. lactis) are described in examples 1 and 2, respectively.

L. plantarum PN0512 was transformed with plasmid pDM1 -HvD(L. lactis)-suf(L. lactis) or pDM1 -HvD(L. lactis) by electroporation. Electro- competent cells were prepared by the following procedure. 5 ml of Lactobacilli MRS medium containing 1 % glycine was inoculated with PN0512 cells and grown overnight at 3O ⁰ C. 100 ml MRS medium with 1 % glycine was inoculated with the overnight culture to an OD600 = 0.1 and grown to an OD600 = 0.7 at 3O ⁰ C. Cells were harvested at 3700xg for 8 min at 4 ⁰ C, washed with 100 ml cold 1 mM MgCI ₂ , centrifuged at 3700xg for 8 min at 4 ⁰ C, washed with 100 ml cold 30% PEG-1000 (81188, Sigma- Aldrich, St. Louis, MO), recentrifuged at 3700xg for 20 min at 4 ⁰ C, and 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, CA) at 1.7 kV, 25 μF, and 400 Ω. Cells were resuspended in 1 ml MRS medium containing 500 mM sucrose and 100 mM MgCI ₂ , incubated at 3O ⁰ C for 2 hrs, and then plated on MRS medium plates containing 10 μg/ml of chloramphenicol for selection.

Lactobacilli MRS medium (7406, Accumedia, Neogen Corporation, Lansing, Ml)) was inoculated with L. plantarum PN0512 Asuf transformants carrying pDM1 -NvD(L. lactis)-suf(L.lactis) or pDM1 - ilvD(L.lactis) and grown overnight at 3O ⁰ C. 120 ml MRS medium with 40 μM ferric citrate (F3388, Sigma-Aldrich, St. Louis, MO) , 0.5 mM L- cysteine (30089, Sigma-Aldrich, St. Louis, MO), and 10 μg/ml chloramphenicol was inoculated with overnight culture to an OD600 of 0.1 and grown to an OD600 of 2-3 anaerobically at 30 ⁰ C in a 50 ml conical tube. Cultures were centrifuged at 3700xg for 10 min at 4 ⁰ C, the pellets washed with 50 mM potassium phosphate buffer pH 6.2 (6.2 g/L KH ₂ PO ₄ and 1.2 g/L K ₂ HPO ₄ ) and re-centrifuged. Pellets were frozen and stored at -8O ⁰ C until assayed for DHAD activity. Cell extract samples were assayed for DHAD activity using a dinitrophenylhydrazine based method as follows. Enzymatic activity of the crude extract was assayed at 37 ⁰ C as follows. Cells to be assayed for DHAD were suspended in 2-5 volumes of 50 mM Tris, 10 mM MgSO ₄ , pH 8.0 (TM8) buffer, then broken by sonication at 0 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 N ₂ and stored at -80 ⁰ 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 Piece 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. Plasmid expression of the L. lactis HvD coding region showed 0.004 μmol min ^"1 mg ^"1 DHAD activity in L. plantarum PN0512. Plasmid expression of the L. lactis HvD coding region, however, showed no DHAD activity in L. plantarum PN0512 Asuf. Co-expression in L.plantarum PN0512 Asuf of L. lactis sufoperon with L. lactis /VvD from pDM1-ilvD(L.lactis)-suf(L. lactis) restored the DHAD activity to 0.004 μmol min ^"1 mg ^"1 . The data indicate that either L. plantarum native sufoperon or L. lactis sufoperon is involved in Fe-S cluster biogenesis for DHAD activity in L. plantarum PN0512. Table 8. DHAD activity in L. plantarum PN0512 Asuf.

Strain/Plasmid Specific Activity

(μmol min ^"1 mg ^"1 ) L. plantarum PN0512 / pDM1 -NvD(L lactis) 0.004

L. plantarum PN0512 Asuf I pDM1 -NvD(L lactis) 0.000

L. plantarum PN0512 Asuf I pDM1 -ilvD(L.lactis)-suf(Llactis) 0.004

Example 4

Construction of plasmids for co-expression of Lactococcus lactis HvD and the Lactobacillus plantarum PN0512 suf operon.

The purpose of this example is to describe the construction of plasmids used for the co-expression of Lactococcus lactis HvD(SEQ ID NO:231 ) and the Lactobacillus plantarum PN0512 sufoperon (SEQ ID NO:589). A shuttle vector pDM1 (SEQ ID NO:571 ), described in Example 2, was used for cloning and expression of the HvD coding region from Lactococcus lactis subsp lactis NCDO2118 (NCIMB 702118) [Godon et al., J. Bacteriol. (1992) 174:6580-6589] and the sufoperon from Lactobacillus plantarum PN0512.

Plasmids were 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, MA). DNA fragments were purified with Qiaquick PCR Purification Kit (Qiagen Inc., Valencia, CA). Plasmid DNA was prepared with QIAprep Spin Miniprep Kit (Qiagen Inc., Valencia, CA). L. plantarum PN0512 genomic DNA was prepared with MasterPure DNA Purification Kit (Epicentre, Madison, Wl). Oligoucleotides were synthesized by Sigma- Genosys (Woodlands, TX). All vector constructs were confirmed by DNA sequencing.

Vector pDM1 was modified by deleting nucleotides 3281 -3646 spanning the lacZ region which were replaced with a multi cloning site. Primers oBP120 [SEQ ID NO:562], containing an Xhol site, and oBP182 [SEQ ID NO:563], containing Drdl, Pstl, Hindlll, and BamHI sites, were used to amplify the P30 promoter from pDM1 with Phusion High-Fidelity PCR Master Mix. The resulting PCR product and pDM1 vector were digested with Xhol and Drdl, which drops out lacZ and P30. The PCR product and the large fragment of the pDM1 digestion were ligated to yield vector pDM20 in which the P30 promoter was reinserted, bounded by Xhol and Drdl restriction sites.

The HvD coding region (SEQ ID NO:231 ) from Lactococcus lactis and a ribosome binding sequence (SEQ ID NO:590) were cloned into pDM20 to create vector pDM20-ilvD(L. lactis). Primers oBP190 (SEQ ID NO:564), containing a BamHI site and ribosome binding sequence, and oBP192 (SEQ ID NO:565), containing a Pstl site, were used to amplify the HvD coding region from pDM1 -ilvD(L. lactis) with Phusion High-Fidelity PCR Master Mix. Construction of pDM1 -ilvD (L. lactis) is described in Example 2. The resulting PCR product and pDM20 were ligated after digestion with BamHI and Pstl to yield vector pDM20-ilvD(L. lactis) in which the ilvD coding region is expressed from the P30 promoter.

The promoter region of the IdhU gene (SEQ ID NO:591 ) from Lactobacillus plantarum PN0512 with a multi cloning site and the suf operon containing sufC, sufD, sufS, sufU, and sufB (SEQ ID NO:589) from Lactobacillus plantarum PN0512 were cloned into pDM20-ilvD(LI) by two consecutive steps to create vector pDM20-ilvD(LI)-Pldhl_1-suf(Lp)]. sufC was preceded by a ribosome binding sequence (SEQ ID NO:590). Primers AA178 (SEQ ID NO567), containing Drdl, Sail and AfIII sites, and AA179 (SEQ ID NO:568), containing Drdl, Pmel, Sad, Avrll, Pad, Kasl, and Not I sites, were used to amplify the IdhLI promoter from L. plantarum PN0512 genomic DNA using Phusion High-Fidelity PCR Master Mix. The resulting PCR product and pDM20-ilvD(LI) were ligated after digestion with Drdl. Clones were screened by PCR for inserts that were in the same orientation as the HvD coding region using primers AA178 (SEQ ID NO:567) and AA177 (SEQ ID NO:566). A clone that had the correctly oriented insert was named pDM20-ilvD(LI)-Pldhl_1. Primers oBP211 (SEQ ID NO:569), containing a Notl site and hbosome binding sequence, and OBP195 (SEQ ID NO:570), containing a Pad site, were used to amplify the suf operon from L. plantarum PN0512 genomic DNA using Phusion High-Fidelity PCR Master Mix. The resulting PCR product and pDM20- ilvD(LI)-Pldhl_1 were ligated after digestion with Notl and Pad to yield vector pDM20-ilvD(LI)-Pldhl_1 -suf(Lp), where the suf operon is expressed from the IdhLI promoter.

Example 5

Increased DHAD activity with co-expression of Lactococcus lactis HvD and the Lactobacillus plantarum PN0512 suf operon in a wild-type PN0512 strain background The purpose of this example is to demonstrate the effect of co- expression of the Lactobacillus plantarum PN0512 suf operon, containing the Fe-S cluster assembly genes, with Lactococcus lactis HvD on DHAD activity in wild-type Lactobacillus plantarum PN0512.

Lactobacillus plantarum PN0512 was transformed separately with vectors pDM20-ilvD(LI) and pDM20-ilvD(LI)-Pldhl_1-suf(l_p). Lactobacillus plantarum PN0512 was transformed as in Example 1 , except transformants were selected for on MRS medium plates containing 10 μg/ml of chloramphenicol (C0378, Sigma-Aldrich, St. Louis, MO). Strains PN0512/pDM20-ilvD(LI) and PN0512/pDM20-ilvD(LI)-PldhL1 -suf(Lp) were grown overnight in Lactobacilli MRS medium (7406, Accumedia, Neogen Corporation, Lansing, Ml) with 10 μg/ml chloramphenicol (C0378, Sigma- Aldrich, St. Louis, MO) at 3O ⁰ C. 120 ml of MRS medium supplemented with 100 mM MOPS (M1254, Sigma-Aldrich, St. Louis, MO), 40 μM ferric citrate (F3388, Sigma-Aldrich, St. Louis, MO), 0.5 mM L-cysteine (30089, Sigma-Aldrich, St. Louis, MO), and 10 μg/ml chloramphenicol adjusted to pH 7.5 with KOH was inoculated with overnight culture to an OD600 -0.05-0.1 in a 125 ml screw cap flask. The cultures were placed in an anaerobic chamber (Coy Laboratories Inc., Grass Lake, Ml) for 1 hour with the caps loose or the cultures were inoculated in the anaerobic chamber using medium which had been stored in the anaerobic chamber. The caps on the flask were sealed tight and the cultures were incubated at 37 ⁰ C until reaching an OD600 ~ 1.0-2.0. Cultures were centrifuged at 3700xg for 10 min at 4 ⁰ C. Pellets were washed with 50 mM potassium phosphate buffer pH 6.2 (6.2 g/L KH ₂ PO ₄ (P5379, Sigma-Aldrich, St. Louis, MO) and 1.2 g/L K ₂ HPO ₄ (P8281 , Sigma-Aldrich, St. Louis, MO)) and re- centhfuged. Pellets were frozen and stored at -8O ⁰ C until assayed for DHAD activity. Samples were assayed for DHAD activity using a dinitrophenylhydrazine based method as described in Example 3. The DHAD activity results are given in Table 9. The presence of the overexpressed suf operon led to a two-fold increase in DHAD activity in the PN0512 strain background .

Table 9. Co-expression of HvD and the suf operon in wild-type Lactobacillus plantarum PN0512. DHAD activity in μmoles KIVA/min/mg total protein. Data represent the average of two independent experiments.

Example 6 (Prophetic)

Construction of plasmid for co-expression of Bacillus subtilis ilvD and the

Lactococcus lactis suf operon

The purpose of this example is to describe how to clone the HvD coding region (SEQ ID NO:497) from Bacillus subtilis 168 (ATCC 23857) and suf operon (SEQ ID NO:881 ) from Lactococcus lactis subsp lactis NCDO2118 (NCIMB 702118) [Godon et al., J. Bacterid. (1992) 174:6580- 6589] into pDML

Plasmid pDM1 -HvD(B. subtilis)-suf(L.lactis) is constructed by swapping the NvD(L lactis) coding region of pDM1 -NvD(B. subtilis)- suf(L. lactis) with a B. subtilis HvD coding region. The B. subtilis HvD coding region including a ribosomal binding site (RBS) is PCR-amplified from genomic DNA of Bacillus subtilis 168 with primers T-ilvDBs(BamHI) (SEQ ID NO:592) and B-ilvDBs(Notl) (SEQ ID NO:593). Bacillus subtilis 168 genomic DNA is prepared with a Puregene Gentra Kit (QIAGEN, CA). The B. subtilis HvD PCR product is digested with BamHI and Notl, and the 1.7kbp B. subtilis HvD fragment is gel-purified. Plasmid pDM1- NvD(L. lactis)-suf(L. lactis) is digested with BamHI and Notl, and 9.8 kbp fragment containing pDM1 -suf(L. lactis) is gel-purified. The construction of pDM1 -NvD(L. lactis)-suf(L. lactis) is described in Example 2. The resulting 9.8 kbp pDM1 -suf(L. lactis) fragment is ligated with the 1.7 kbp B. subtilis HvD fragment. The ligation mixture is transformed into E. coli Top10 strain (Invitrogen, CA), and spread on LB plates containing 25 μg/ml chloramphenicol for selection. Positive clones are screened by colony PCR with primers T-ilvDBs(BamHI) and B-ilvDBs(Notl), giving a PCR product with an expected size of 1.7kbp. The positive plasmid is named as pDM1 -NvD(B. subtilis)-suf(L.lactis). Plasmid pDM1 -NvD(B. subtilis)- suf(L. lactis) is digested with ApaLI and Notl, treated with Klenow fragment of DNA polymerase to make blunt ends, and then the 5.3 Kbp fragment containing pDM1 -NvD(B. subtilis) is gel-purified. The gel-purified fragment is self-ligated to create pDM1 -NvD(B. subtilis). Positive clones are screened by Sail digestion, giving one fragment with an expected size of 5.3 kbp.

Example 7 (Prophetic) Co-expression of Bacillus subtilis HvD with Lactococcus lactis suf operon in Lactobacillus plantarum PN0512 The purpose of this example is to describe how to express Bacillus subtilis HvD with Lactococcus lactis suf operon in Lactobacillus plantarum PN0512.

L. plantarum PN0512 is transformed with plasmid pDM1 -NvD(B. subtilis)-suf(L. lactis) or pDM1 -NvD(B. subtilis) by electrophoration. Preparation of electro-competent cells and electro-transformation are performed as described in Example 1.

L. plantarum PN0512 transformants carrying pDM1 -NvD(B. subtilis)- suf(L. lactis) or pDM1 -NvD(B. subtilis) are grown overnight in Lactobacilli MRS medium at 3O ⁰ C. 120 ml of MRS medium supplemented with 40 μM ferric citrate, 0.5 mM L-cysteine, and 10 μg/ml chloramphenicol is inoculated with overnight culture to an OD600 = 0.1 in a 50 ml conical tube for each overnight sample. Cultures are anaerobically incubated at 3O ⁰ C until reaching an OD600 of 2-3. Cultures are centrifuged at 3700xg for 10 min at 4 ⁰ C. Pellets are washed with 50 mM potassium phosphate buffer pH 6.2 (6.2 g/L KH ₂ PO ₄ and 1.2 g/L K ₂ HPO ₄ ) and re-centhfuged. Pellets are frozen and stored at -8O ⁰ C until assayed for DHAD activity. Cell extract samples are assayed for DHAD activity using a dinitrophenylhydrazine based method as in Example 3. In preferred embodiments, DHAD activity is higher in the cells transformed with pDM1 - NvD(B. subtilis)-suf(L. lactis) than in those transformed with pDM1 -NvD(B. subtilis).

Table 7