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US20030148494A1 - Genes encoding exopolysaccharide production - Google Patents

Genes encoding exopolysaccharide production Download PDF

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US20030148494A1
US20030148494A1 US10/353,457 US35345703A US2003148494A1 US 20030148494 A1 US20030148494 A1 US 20030148494A1 US 35345703 A US35345703 A US 35345703A US 2003148494 A1 US2003148494 A1 US 2003148494A1
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Mattheos Koffas
James Odom
Siqun Wang
Tao Wang
Rich Ye
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8245—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving modified carbohydrate or sugar alcohol metabolism, e.g. starch biosynthesis
    • C12N15/8246—Non-starch polysaccharides, e.g. cellulose, fructans, levans
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/04—Polysaccharides, i.e. compounds containing more than five saccharide radicals attached to each other by glycosidic bonds

Definitions

  • This invention relates to the field of microbial production of polysaccharides. More specifically, the invention pertains to nucleic acid molecules encoding enzymes involved in biosynthesis of exopolysaccharides from Methylomonas sp.
  • Polysaccharides are sugar polymers that have been used widely as a thickener in food and non-food industries (Sanford et al. Pure & Appl. Chem . 56: 879-892 (1984); Sutherland, Trends Biotechnol , 16(1): 41-6 (1998)). They can be found in food products such as salad dressing, jam, frozen food, bakery products, canned food and dry food. Many other applications include suspending agents for pesticides, paints and other coating agents. They can act as flocculants, binders, film-formers, lubricants and friction reducers. Furthermore, exopolysaccharides are commonly used in oil field for oil recovery.
  • xanthan gum is a complex exopolysaccharide produced by a gram-negative bacterium Xanthomonas campestris pv. Campestris which is a pathogen of cruciferous plants.
  • Xanthan consists of a ⁇ -1,4-linked D-glucose backbone with trisaccharides side chains composed of mannose-( ⁇ -1,4)-glucuronic acid-( ⁇ -1,2)-mannose attached to alternate glucose residues in the backbone by ⁇ -1,3 linkages.
  • the polymerized pentasaccharide repeating units which are assembled by the sequential addition of glucose 1-phosphate, glucose, mannose, glucuronic acid, and mannose on polyprenol phosphate carrier (lelpi et al., J. Bacteriol . 175:2490-2500, 1993).
  • the biosynthetic pathway of xanthan in Xanthomonas campestris comprises five stages: (i) conversion of simple sugars to nucleotidyl derivative precursors, (ii) assembly of pentasaccharide subunits attached to the inner membrane polyprenol phosphate carrier, (iii) addition of acetyl and pyruvate groups, (iv) polymerization of pentasaccharide repeat units, and (v) secretion of polymer.
  • UDP-glucose pyrophosphorylase is the enzyme that catalyzes the reaction generating UDP-glucose (UTP+glucose-1-phosphate ⁇ -->UDP-glucose+Ppi) (Wei et al., Biochem Biophys Res Commun . 226:607-12 (1996)).
  • UDP-glucose is the building blocks for many exopolysaccharides containing glucose.
  • a cluster of gum genes are found to be required for xanthan gum synthesis in Xanthomonas campestris (Katzen et al. J. Bacteriol . 180:1607-1617 (1998); Chou, F. L., et al, Biochem. Biophys. Res. Commun . 233 (1), 265-269 (1997)).
  • GumD the glycosyltransferase
  • GumH is the protein involved in the transfer of the mannose to the lipid-linked intermediates in exopolysaccharide synthesis in Xanthomonas campestris.
  • the epsB gene encodes the EpsB protein that is probably involved in polymerization and/or export of EPS, has been sequenced in Ralstonia sola (Huang et al, Mol. Microbiol . 16: 977-989 (1995).
  • the espM gene encoding EspM protein has been found in the esp gene cluster from Streptococcus thermophilus (Stingele et al, J. Bacteiol . 178: 1680-1690 (1996)).
  • Another putative polysaccharide export protein, WZA is identified in E. coli .
  • the epsV gene encodes the EpsV protein, a transferase which transfers the sugar to polysaccharide intermediates, and it has also been sequence in Streptococcus thermophilus (Bourgoin et al. Plasmid 40: 44-49 (1998); Bourgoin, F., et al., Gene 233:151-161 (1999).
  • the problem to be solved therefore is to identify the genes relevant to exopolysaccharide synthesis in a C1 utilizing organism for the production of exopolysaccharides in both similar and unrelated microbes.
  • Applicants have solved the stated problem by isolating and characterizing a complete enzymatic pathway for the synthesis of exopolysaccharide from a Methylomonas sp.
  • the present invention provides an isolated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme, selected from the group consisting of: (a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18; (b) an isolated nucleic acid molecule that hybridizes with (a) under the following hybridization conditions: 0.1 ⁇ SSC, 0.1% SDS, 65° C. and washed with 2 ⁇ SSC, 0.1% SDS followed by 0.1 ⁇ SSC, 0.1% SDS; and (c) an isolated nucleic acid molecule that is complementary to (a) or (b).
  • a Methylomonas sp exopolysaccharide biosynthetic enzyme selected from the group consisting of: (a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4,
  • the invention provides: 1) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 293 amino acids that has at least 58% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 2, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 2) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 473 amino acids that has at least 36% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 4, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 3) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 366 amino acids that has at least 36% identity based on the
  • the invention also provides chimeric genes comprising the isolated nucleic acid molecule of any one of the instant sequences operably linked to suitable regulatory sequences.
  • the invention additionally provides polypeptides encoded by the instant genes.
  • the invention provides a transformed host cell comprising the instant chimeric genes.
  • the invention provides a method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising: (a) probing a genomic library with the nucleic acid molecule of the present invention; (b) identifying a DNA clone that hybridizes with the nucleic acid molecule of the present invention; and (c) sequencing the genomic fragment that comprises the clone identified in step (b), wherein the sequenced genomic fragment encodes a Methylomonas sp exopolysaccharide biosynthetic enzyme.
  • the invention provides a method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising: (a) synthesizing at least one oligonucleotide primer corresponding to a portion of the sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, and 17; and (b) amplifying an insert present in a cloning vector using the oligonucleotide primer of step (a); wherein the amplified insert encodes a portion of an amino acid sequence encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme.
  • the invention provides a method for the production of exopolysaccharide comprising: contacting a transformed host cell under suitable growth conditions with an effective amount of a carbon source whereby exopolysaccharide is produced, said transformed host cell comprising a set of nucleic acid molecules encoding SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18; under the control of suitable regulatory sequences.
  • the invention provides a mutated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme having an altered biological activity produced by a method comprising the steps of:
  • step (iii) incubating the denatured said mixture of restriction fragments of step (ii) with a polymerase;
  • FIG. 1 shows the DNA region containing gumD, wza, espB, espM, waaE, espV, gumH and glycosyltransferase genes in Methylomonas spp. strain 16a.
  • the gene encoding the gene ugp, UDP-glucose pyrophosphorylase, is located in a different region.
  • SEQ ID NO: 1 is the nucleotide sequence of the ugp gene.
  • SEQ ID NO: 2 is the deduced amino acid sequence of ugp gene encoded by SEQ ID NO: 1.
  • SEQ ID NO: 3 is the nucleotide sequence of ORF 1 comprising the gumD gene.
  • SEQ ID NO: 4 is the deduced amino acid sequence of the gumD gene product encoded by ORF 3.
  • SEQ ID NO: 5 is the nucleotide sequence of ORF 2 comprising the wza gene.
  • SEQ ID NO: 6 is the deduced amino acid sequence of wza the gene product encoded by ORF 5.
  • SEQ ID NO: 7 is the nucleotide sequence of ORF 3 comprising the epsB gene.
  • SEQ ID NO: 8 is the deduced amino acid sequence of epsB the gene product encoded by ORF 7.
  • SEQ ID NO: 9 is the nucleotide sequence of ORF 4 comprising the epsM gene.
  • SEQ ID NO: 10 is the deduced amino acid sequence of the epsM gene product encoded by ORF 9.
  • SEQ ID NO: 11 is the nucleotide sequence of ORF 5 comprising the waaE gene.
  • SEQ ID NO: 12 is the deduced amino acid sequence of the waaE gene product encoded by ORF 11.
  • SEQ ID NO: 13 is the nucleotide sequence of ORF 6 comprising the epsV gene.
  • SEQ ID NO: 14 is the deduced amino acid sequence of the epsV gene product encoded by ORF 13.
  • SEQ ID NO: 15 is the nucleotide sequence of ORF 7 comprising the gumH gene.
  • SEQ ID NO: 16 is the deduced amino acid sequence of the gumH gene product encoded by ORF 15.
  • SEQ ID NO: 17 is the nucleotide sequence of ORF 8 comprising the glycosyltransferase gene.
  • SEQ ID NO: 18 is the deduced amino acid sequence of the glycosyltransferase gene product encoded by ORF 17.
  • Nucleic acid fragments involved in encoding enzymes for exopolysaccharide production have been isolated from a strain of Methylomonas spp. strain 16a and identified by comparison to public databases containing nucleotide and protein sequences using the BLAST and FASTA algorithms well known to those skilled in the art.
  • genes described in present invention enable the overexpression of enzymes involved in the biosynthetic pathway of exopolysaccharide. Overexpression of genes in the present invention in either natural host, Methylomonas 16a, or in heterologous hosts will lead to improved exopolysaccharide yield, saving both and money.
  • the genes of the present invention can be mutagenized or recombined with genes from other pathways to produce enzymes with different substrate specificity, producing new polymers with novel functionality. Such novel functionality may include novel gelling properties, temperature resistance, and suspending ability.
  • exopolysaccharides are believed to play an important in facilitating bacterial adhesion and the formation of biofilms.
  • Bacterial biofilms are implicated in biofouling and clogging of pipelines in manufacturing processes that use bacteria as a production platform.
  • the formation of bacterial biofilms is problematic. For example, once a biofilm is formed on transplants or catheters, infection caused by bacteria is very difficult to eradicate. Therefore, inhibitors of biofilm formation will have very significant commercial value, and the genes or the gene products described here can be used as targets for screening potential inhibitors.
  • ORF Open reading frame
  • PCR Polymerase chain reaction
  • an “isolated nucleic acid fragment” and “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.
  • ugp refers to a gene encoding UDP-glucose pyrophosphorylase, UGP.
  • glycosyltransferase refers to a gene encoding glycosyltransferase, GumD.
  • wza refers to a gene encoding polysaccharide export protein Wza.
  • EpsB refers to a gene encoding polysaccharide export protein EpsB.
  • EpsM refers to a gene encoding polysaccharide biosynthesis related protein EpsM.
  • WaaE refers to a gene encoding glycosyltransferase, WaaE.
  • EpsV refers to a gene encoding sugar transferase EpsV.
  • GumH refers to a gene encoding galactosyltransferase, GumH.
  • UDP refers to uridine 5-diphosphate
  • UTP refers to uridine 5-triphosphate
  • exopolysaccharide or “polysaccharide” “biosynthetic pathway” means an enzymatic pathway comprising genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH as described above.
  • exopolysaccharide gene or “polysaccharide gene” will refer to anyone or all of the genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH.
  • exopolysaccharide biosynthetic enzyme or “polysaccharide biosynthetic enzyme” will refer to anyone or all of the gene products of the genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH.
  • the term “monosaccharide” will refer to single polyhydroxy aldehyde or ketone units of the general formula (CH 2 O)n. “Polysaccharides” are molecules containing many monosaccharide units joined in long linear or branched chains. The term “exopolysaccharide” will mean any biologically produced polysaccharide that is excreted from a cell.
  • Embden-Meyerhof pathway refers to the series of biochemical reactions for conversion of hexoses such as glucose and fructose to important cellular 3 carbon intermediates such as glyceraldehyde 3 phosphate, dihydroxyacetone phosphate, phosphoenol pyruvate and pyruvate. These reactions typically proceed with net yield of biochemically useful energy in the form of ATP.
  • the key enzymes unique to the Embden-Meyerhof pathway are the phosphofructokinase and fructose 1,6 bisphosphate aldolase.
  • Entner-Douderoff pathway refers to a series of biochemical reactions for conversion of hexoses suchas as glucose or fructose to important 3 carbon cellular intermediates pyruvate and glyceraldehyde 3 phosphate without any net production of biochemically useful energy.
  • the key enzymes unique to the Entner-Douderoff pathway are the 6 phosphogluconate dehydratase and the ketodeoxyphosphogluconate aldolase.
  • high growth methanotrophic bacterial strain refers to a bacterium capable of growth with methane or methanol as sole carbon and energy source which possess a functional Embden-Meyerhof carbon flux pathway resulting in yield of cell mass per gram of C1 substrate metabolized.
  • the specific “high growth methanotrophic bacterial strain” described herein is referred to as “Methylomonas 16a” or “16a”, which terms are used interchangeably.
  • substantially similar refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences.
  • a codon for the amino acid alanine, a hydrophobic amino acid may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine).
  • a codon encoding another less hydrophobic residue such as glycine
  • a more hydrophobic residue such as valine, leucine, or isoleucine
  • changes which result in substitution of one negatively charged residue for another such as aspartic acid for glutamic acid
  • one positively charged residue for another such as lysine for arginine
  • nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein.
  • substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1 ⁇ SSC, 0.1% SDS, 65° C. and washed with 2 ⁇ SSC, 0.1% SDS followed by 0.1 ⁇ SSC, 0.1% SDS), with the sequences exemplified herein.
  • Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are at least 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the DNA sequence of the nucleic acid fragments reported herein.
  • a nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule 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 , Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization.
  • Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms.
  • Post-hybridization washes determine stringency conditions.
  • One set of preferred conditions uses a series of washes starting with 6 ⁇ SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2 ⁇ SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2 ⁇ SSC, 0.5% SDS at 50° C. for 30 min.
  • a more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2 ⁇ SSC, 0.5% SDS was increased to 60° C.
  • Another preferred set of highly stringent conditions uses two final washes in 0.1 ⁇ SSC, 0.1% SDS at 65° C.
  • 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.
  • RNA:RNA, DNA:RNA, DNA:DNA 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).
  • the length for a hybridizable nucleic acid is at least about 10 nucleotides.
  • a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 30 nucleotides.
  • 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 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 (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol . 215:403-410; see also www.ncbi.nim.nih.gov/BLAST/).
  • BLAST Basic Local Alignment Search Tool
  • 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.
  • 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).
  • 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.
  • 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 partial or complete amino acid and nucleotide sequences encoding one or more particular microbial 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.
  • nucleotide bases that are capable to hybridizing to one another.
  • adenosine is complementary to thymine and cytosine is complementary to guanine.
  • the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences.
  • identity is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences.
  • 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: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D.
  • nucleic acid fragments encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein.
  • Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein.
  • 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.
  • 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. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the instant microbial polypeptides as set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18.
  • 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.
  • “Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. “Chemically synthesized”, as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.
  • Gene refers to a nucleic acid fragment that expresses a specific protein, 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 refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer.
  • 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.
  • Coding sequence 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.
  • Promoter refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA.
  • 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 “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression.
  • the polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor.
  • RNA transcript refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell.
  • Antisense RNA refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065; WO 9928508).
  • the complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, or the coding sequence.
  • “Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes.
  • 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.
  • a promoter is operably linked with a coding sequence when it is capable of affecting 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.
  • expression 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.
  • “Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed.
  • “Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals.
  • signal peptide refers to an amino terminal polypeptide preceding the secreted mature protein.
  • the signal peptide is cleaved from and is therefore not present in the mature protein.
  • Signal peptides have the function of directing and translocating secreted proteins across cell membranes.
  • Signal peptide is also referred to as signal protein.
  • Transformation refers to the transfer of a nucleic acid fragment into the genome of 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.
  • Plasmid refers 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.
  • Transformation cassette refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell.
  • Expression cassette refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.
  • altered biological activity will refer to an activity, associated with a protein encoded by a microbial nucleotide sequence which can be measured by an assay method, where that activity is either greater than or less than the activity associated with the native microbial sequence.
  • Enhanced biological activity refers to an altered activity that is greater than that associated with the native sequence.
  • Diminished biological activity is an altered activity that is less than that associated with the native sequence.
  • 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 the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol . 215:403-410 (1990), and DNASTAR (DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA).
  • GCG Genetics Computer Group
  • BLASTP BLASTP
  • BLASTN BLASTN
  • BLASTX Altschul et al., J. Mol. Biol . 215:403-410 (1990)
  • DNASTAR DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA.
  • the nucleic acid fragments of the instant invention may be used to isolate genes encoding homologous proteins from the same or other microbial species. 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, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202), ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci. USA 82, 1074, (1985)) or strand displacement amplification (SDA, Walker, et al., Proc. Nat. Acad. Sci. U.S.A ., 89, 392, (1992)).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • SDA strand displacement
  • genes encoding similar proteins or polypetides to those of the instant invention 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 bacteria using methodology well known to those skilled in the art.
  • Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis).
  • the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems.
  • 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 under conditions of appropriate stringency.
  • the primers typically 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 oligonucleotide 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 Press, Herndon, Va.); Rychlik, W. (1993) In White, B. A. (ed.), Methods in Molecular Biology , Vol. 15, pages 31-39, PCR Protocols: Current Methods and Applications. Humania Press, Inc., Totowa, N.J.)
  • two short segments of the instant 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 instant 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.
  • the second primer sequence may be based upon sequences derived from the cloning vector.
  • 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 (BRL), specific 3′ or 5′ cDNA fragments can be isolated (Ohara et al., PNAS USA 86:5673 (1989); Loh et al., Science 243:217 (1989)).
  • RACE protocol Frohman et al., PNAS USA 85:8998 (1988)
  • the instant 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 of the present invention are typically single stranded nucleic acid sequences which 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 which 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.
  • a chaotropic agent may be added. The chaotropic agent stabilizes nucleic acids by inhibiting nuclease activity.
  • chaotropic agent allows sensitive and stringent hybridization of short oligonucleotide probes at room temperature [Van Ness and Chen (1991) Nucl. Acids Res . 19:5143-5151].
  • Suitable chaotropic agents include guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide, and cesium trifluoroacetate, among others.
  • the chaotropic agent will be present at a final concentration of about 3M. If desired, one can add formamide to the hybridization mixture, typically 30-50% (v/v).
  • 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 1M sodium chloride, about 0.05 to 0.1M buffers, such as sodium citrate, Tris-HCl, PIPES or HEPES (pH range about 6-9), about 0.05 to 0.2% detergent, such as sodium dodecylsulfate, or between 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kilodaltons), polyvinylpyrrolidone (about 250-500 kdal), and serum albumin.
  • 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 which include a variety of polar water-soluble or swellable agents, such as polyethylene glycol, anionic polymers such as polyacrylate or polymethylacrylate, and anionic saccharidic polymers, such as 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.
  • genes and gene products of the instant sequences may be produced in heterologous host cells, particularly in the cells of microbial hosts.
  • Expression in recombinant microbial hosts may be useful for the expression of various pathway intermediates; for the modulation of pathways already existing in the host for the synthesis of new products heretofore not possible using the host. Additionally the gene products may be useful for conferring higher growth yields of the host or for enabling alternative growth mode to be utilized.
  • Preferred heterologous host cells for express of the instant genes and nucleic acid molecules are microbial hosts that can be found broadly within the fungal or bacterial families and which grow over a wide range of temperature, pH values, and solvent tolerances. Because of transcription, translation and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, functional genes are expressed irrespective of carbon feedstock used to generate cellular biomass. Large scale microbial growth and functional gene expression may utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, saturated hydrocarbons such as methane or carbon dioxide in the case of photosynthetic or chemoautotrophic hosts.
  • the functional genes may be regulated, repressed or depressed by specific growth conditions, which may include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions.
  • the regulation of functional genes may be achieved by the presence or absence of specific regulatory molecules that are added to the culture and are not typically considered nutrient or energy sources. Growth rate may also be an important regulatory factor in gene expression.
  • host strains include but are not limited to fungal or yeast species such as Aspergillus, Trichoderma, Saccharomyces, Pichia, Candida, Hansenula, or bacterial species such as Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, Pseudomonas, Methylomonas, Methylobacter, Alcaligenes, Synechocystis, Anabaena, Thiobacillus, Methanobacterium and Klebsiella.
  • fungal or yeast species such as Aspergillus, Trichoderma, Saccharomyces, Pichia, Candida, Hansenula, or bacterial species such as Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, Pseudomonas, Methylomonas, Methylobacter, Alcaligenes, Synechocystis, Anaba
  • the present strain contains several anomalies in the carbon utilization pathway. For example, based on genome sequence data, the strain is shown to contain genes for two pathways of hexose metabolism.
  • the Entner-Douderoff athway which utilizes the keto-deoxy phosphogluconate aldolase enzyme is present in the strain. Is generally well accepted that this is the operative pathway in obligate methanotrophs. Also present, however, is the Embden-Meyerhof pathway which utilizes the Fructose bisphosphate aldolase enzyme. It is well known that this pathway is either not present or not operative in obligate methanotrophs.
  • the latter pathway is most favorable and allows greater yield of biologically useful energy and ultimately production of cell mass and other cell mass-dependent products in Methylomonas 16a.
  • the activity of this pathway in the present 16a strain has been confirmed through microarray data and biochemical evidence measuring the reduction of ATP.
  • the 16a strain has been shown to possess both the Embden-Meyerhof and the Entner-Douderoff pathway enzymes the data suggests that the Embden-Meyerhof pathway enzymes are more strongly expressed than the Entner-Douderoff pathway enzymes. This result is surprising and counter to existing beliefs on the glycolytic metabolism of methanotrophic bacteria.
  • methanotrophic bacteria having this characteristic, including for example, Methylomonas clara and Methylosinus sporium . It is likely that this activity has remained undiscovered in methanotrophs due to the lack of activity of the enzyme with ATP, the typical phosphoryl donor for the enzyme in most bacterial systems.
  • a particularly novel and useful feature of the Embden-Meyerhof pathway in strain 16a is that the key phosphofructokinase step is pyrophosphate dependent instead of ATP dependent. This feature adds to the energy yield of the pathway by using pyrophosphate instead of ATP. Because of it's significance in providing an energetic advantage to the strain this gene in the carbon flux pathway is considered diagnostic for the present strain.
  • methane is converted to biomolecules via a cyclic set of reaction known as the ribulose monophosphate pathway or RuMP cycle.
  • This pathway is comprised of three phases, each phases being a series of enzymatic steps.
  • the first step is “fixation” or incorporation of C-1 (formaldehyde) into a pentose to form a hexose or six carbon sugar. This occurs via a condensation reaction between a carbon sugar (pentose) and formaldehyde and is catalyzed by hexulose monophosphate synthase.
  • the second phase is termed “cleavage” and results in splitting of that hexose into two 3 carbon molecules.
  • the RuMP pathway may occur as one of three variants. However only two of these variants are commonly found.
  • the FBP/TA structurallyse bisphosphotase/Transaldolase
  • the KDPG/TA keto deoxy phosphogluconate/transaldolase
  • the present strain is unique in the way it handles the “cleavage” steps where genes were found that carry out this conversion via fructose bisphosphate as a key intermediate.
  • the genes for fructose bisphosphate aldolase and transaldolase were found clustered together on one piece of DNA.
  • the genes for the other variant involving the keto deoxy phosphogluconate intermediate were also found clustered together.
  • Available literature teaches that these organisms (obligate methylotrophs and methanotrophs) rely solely on the KDPG pathway and that the FBP-dependent fixation pathway is utilized by facultative methylotrophs (Dijkhuizen et al., supra). Therefore the latter observation is expected whereas the former is not.
  • the finding of the FBP genes in and obligate methane utilizing bacterium is both surprising and suggestive of utility.
  • the FBP pathway is energetically favorable to the host microorganism due to the fact that more energy (ATP) is utilized than is utilized in the KDPG pathway.
  • organisms that utilize the FBP pathway may have an energetic advantage and growth advantage over those that utilize the KDPG pathway. This advantage may also be useful for energy-requiring production pathways in the strain.
  • a methane-utilizing bacterium may have an advantage over other methane utilizing organisms as production platforms for either single cell protein or for any other product derived from the flow of carbon through the RuMP pathway.
  • the present invention provides a method for the production of exopolysaccharide using an energetically, favoralbe Methylomonas strain which
  • (b) comprises a functional Embden-Meyerhof carbon pathway
  • said pathway comprising a gene encoding a pyrophosphate dependent phosphofructokinase enzyme.
  • Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of the any of the gene products of the instant sequences. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the enzymes.
  • the instant genes will be effective in altering the properties of the host microbe. It is expected, for example, host cells can be transformed with chimeric genes encoding one or more of the instant sequences in order to induce the overexpression of exopolysaccharide, or to manipulate production of exopolysaccharides by changing the biosynthesis pathway of exopolysaccharide in host cell to reduce the exopolysaccharide production in host cells to reduce the biofilm formation.
  • Vectors or cassettes useful for the transformation of suitable host cells are well known in the art.
  • the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration.
  • Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
  • Initiation control regions or promoters which are useful to drive expression of the instant ORF's in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, ara, tet, trp, IP L , IP R , T7, tac, and trc (useful for expression in Escherichia coli ) as well as the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus.
  • Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included.
  • the present genes may be used in various methanotrophic strains to modulate or regulate the production of exopolysaccharides. These genes and their sequences may be used in a variety of ways to modulate existing polysaccharide pathways. Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particularly pathway may be upregulated or down regulated by variety of methods. Additionally, competing pathways organism may be eliminated or sublimated by gene disruption and similar techniques.
  • a key genetic pathway may be upregulated to increase the output of the pathway.
  • the target genes may be modified so as to be under the control of non-native promoters.
  • regulated or inducible promoters may be used to replace the native promoter of the target gene.
  • the native or endogenous promoter may be modified to increase gene expression.
  • endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868).
  • Antisense technology is another method of down regulating genes where the sequence of the target gene is known. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the protein of interest.
  • the person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan.
  • transposoable elements are genetic elements that insert randomly in DNA but can be latter retrieved on the basis of sequence to determine where the insertion has occurred.
  • Transposase enzyme enzyme that catalyzes the synthesis of a transposable element.
  • the transposable element or transposon is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the nucleic acid fragment.
  • the technique is useful for random mutageneis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element.
  • Kits for in vitro transposition are commercially available (see for example The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass.; based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element.
  • the present strain has the ability to product polysaccharides in large amounts. This process is governed by a set of genes including the ugp gene, gumD and H genes, the epsB, M, and V genes and the waaD gene. In this pathway it may be of particular importance to up-regulate the espB gene involved in polymerization and/or export of the polysaccharide, or the epsV gene which controls the transfer of sugar to polysaccharide intermediates.
  • a classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process.
  • the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system.
  • a “batch” culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration.
  • the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated.
  • cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die.
  • Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post-exponential phase production can be obtained in other systems.
  • a variation on the standard batch system is the Fed-Batch system.
  • Fed-Batch culture 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 culture 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. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO 2 .
  • Batch and Fed-Batch culturing methods are common and well known in the art and examples may be found in Thomas D.
  • Continuous cultures are an open system where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in log phase growth.
  • continuous culture may be practiced with immobilized cells where carbon and nutrients are continuously added, and valuable products, by-products or waste products are continuously removed from the cell mass. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials.
  • Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration.
  • one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate.
  • a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant.
  • Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture.
  • Methods of modulating nutrients and growth factors for continuous culture 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.
  • Fermentation media in the present invention must contain suitable carbon substrates.
  • suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, 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.
  • the carbon substrate may also be one-carbon substrates such as carbon dioxide, methane or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated.
  • methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity.
  • methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C 1 Compd ., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK).
  • various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol . 153:485-489 (1990)).
  • the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
  • Plants and algae are also known to produce polysaccharides.
  • the nucleic acid fragments of the instant invention may be used to create transgenic plants having the ability to express the microbial protein.
  • Preferred plant hosts will be any variety that will support a high production level of the instant proteins. Suitable green plants will included but are not limited to of soybean, rapeseed ( Brassica napus, B.
  • campestris sunflower ( Helianthus annus ), cotton ( Gossypium hirsutum ), corn, tobacco ( Nicotiana tabacum ), alfalfa ( Medicago sativa ), wheat (Triticum sp), barley ( Hordeum vulgare ), oats ( Avena sativa , L), sorghum ( Sorghum bicolor ), rice ( Oryza sativa ), Arabidopsis, cruciferous vegetables (broccoli, cauliflower, cabbage, parsnips, etc.), melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, grass seed crops, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses.
  • Algal species include but not limited to commercially significant hosts such as Spirulina and Dunalliela.
  • Overexpression of the proteins of the instant invention may be accomplished by first constructing chimeric genes in which the coding region are operably linked to promoters capable of directing expression of a gene in the desired tissues at the desired stage of development.
  • the chimeric genes may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals must also be provided.
  • the instant chimeric genes may also comprise one or more introns in order to facilitate gene expression.
  • any combination of any promoter and any terminator capable of inducing expression of a coding region may be used in the chimeric genetic sequence.
  • Some suitable examples of promoters and terminators include those from nopaline synthase (nos), octopine synthase (ocs) and. cauliflower mosaic virus (CaMV) genes.
  • One type of efficient plant promoter that may be used is a high level plant promoter. Such promoters, in operable linkage with the genetic sequences or the present invention should be capable of promoting expression of the present gene product.
  • High level plant promoters that may be used in this invention include the promoter of the small subunit (ss) of the ribulose-1,5-bisphosphate carboxylase from example from soybean (Berry-Lowe et al., J. Molecular and App. Gen ., 1:483-498 1982)), and the promoter of the chlorophyll a/b binding protein. These two promoters are known to be light-induced in plant cells (See, for example, Genetic Engineering of Plants, an Agricultural Perspective , A. Cashmore, Plenum, N.Y. (1983), pages 29-38; Coruzzi, G. et al., The Journal of Biological Chemistry , 258:1399 (1983), and Dunsmuir, P. et al., Journal of Molecular and Applied Genetics , 2:285 (1983)).
  • ss small subunit of the ribulose-1,5-bisphosphate carboxylase from example from soybean (Berry-Lowe et al.
  • Plasmid vectors comprising the instant chimeric genes can then constructed.
  • the choice of plasmid vector depends upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) EMBO J . 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern.
  • Such screening may be accomplished by Southern analysis of DNA blots (Southern, J. Mol. Biol . 98, 503, (1975)). Northern analysis of mRNA expression (Kroczek, J. Chromatogr. Biomed. Appl ., 618 (1-2) (1993) 133-145), Western analysis of protein expression, or phenotypic analysis.
  • the chimeric genes described above may be further supplemented by altering the coding sequences to encode enzymes with appropriate intracellular targeting sequences such as transit sequences (Keegstra, K., Cell 56:247-253 (1989)), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels, J. J., Ann. Rev. Plant Phys. Plant Mol. Biol . 42:21-53 (1991)), or nuclear localization signals (Raikhel, N. Plant Phys . 100:1627-1632 (1992)) added and/or with targeting sequences that are already present removed. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future that are useful in the invention.
  • the present nucleotide may be used to produce gene products having enhanced or altered activity.
  • Various methods are known for mutating a native gene sequence to produce a gene product with altered or enhanced activity including but not limited to error prone PCR (Melnikov et al., Nucleic Acids Research , (Feb. 15, 1999) Vol. 27, No. 4, pp. 1056-1062); site directed mutagenesis (Coombs et al., Proteins (1998), 259-311, 1 plate. Editor(s): Angeletti, Ruth Hogue. Publisher: Academic, San Diego, Calif.) and “gene shuffling” (U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; and 5,837,458, incorporated herein by reference).
  • the method of gene shuffling is particularly attractive due to its facile implementation, and high rate of mutagenesis and ease of screening.
  • the process of gene shuffling involves the restriction endonuclease cleavage of a gene of interest into fragments of specific size in the presence of additional populations of DNA regions of both similarity to or difference to the gene of interest. This pool of fragments will then be denatured and reannealed to create a mutated gene. The mutated gene is then screened for altered activity.
  • the instant microbial sequences of the present invention may be mutated and screened for altered or enhanced activity by this method.
  • the sequences should be double stranded and can be of various lengths ranging form 50 bp to 10 kb.
  • the sequences may be randomly digested into fragments ranging from about 10 bp to 1000 bp, using restriction endonucleases well known in the art (Maniatis supra).
  • populations of fragments that are hybridizable to all or portions of the microbial sequence may be added.
  • a population of fragments which are not hybridizable to the instant sequence may also be added.
  • these additional fragment populations are added in about 10 to 20 fold excess by weight as compared to the total nucleic acid. Generally if this process is followed the number of different specific nucleic acid fragments in the mixture will be about 100 to about 1000.
  • the mixed population of random nucleic acid fragments are denatured to form single-stranded nucleic acid fragments and then reannealed. Only those single-stranded nucleic acid fragments having regions of homology with other single-stranded nucleic acid fragments will reanneal.
  • the random nucleic acid fragments may be denatured by heating. One skilled in the art could determine the conditions necessary to completely denature the double stranded nucleic acid. Preferably the temperature is from 80° C. to 100° C.
  • the nucleic acid fragments may be reannealed by cooling. Preferably the temperature is from 20° C. to 75° C. Renaturation can be accelerated by the addition of polyethylene glycol (“PEG”) or salt. A suitable salt concentration may range from 0 mM to 200 mM.
  • PEG polyethylene glycol
  • a suitable salt concentration may range from 0 mM to 200 mM.
  • the annealed nucleic acid fragments are then incubated in the presence of a nucleic acid polymerase and dNTP's (i.e. dATP, dCTP, dGTP and dTTP).
  • the nucleic acid polymerase may be the Klenow fragment, the Taq polymerase or any other DNA polymerase known in the art.
  • the polymerase may be added to the random nucleic acid fragments prior to annealing, simultaneously with annealing or after annealing.
  • the cycle of denaturation, renaturation and incubation in the presence of polymerase is repeated for a desired number of times. Preferably the cycle is repeated from 2 to 50 times, more preferably the sequence is repeated from 10 to 40 times.
  • the resulting nucleic acid is a larger double-stranded polynucleotide ranging from about 50 bp to about 100 kb and may be screened for expression and altered activity by standard cloning and expression protocol. (Manatis supra).
  • a hybrid protein can be assembled by fusion of functional domains using the gene shuffling (exon shuffling) method (Nixon et al, PNAS, 94:1069-1073 (1997)).
  • the functional domain of the instant gene can be combined with the functional domain of other genes to create novel enzymes with desired catalytic function.
  • a hybrid enzyme may be constructed using PCR overlap extension method and cloned into the various expression vectors using the techniques well known to those skilled in art.
  • nucleic acid fragments of the instant invention may also be used as probes for gene expression monitoring and gene expression profiling.
  • Many external changes such as changes in growth condition, exposure to chemicals, can cause induction or repression of genes in the cell.
  • the induction or repression of gene can be used for a screening system to determine the best growth condition for production organism, drug discovery with similar mode of action compound, just to mention a few.
  • amplifying or disrupting genes one can manipulate the production of the amount of cellular products, biofilm formation as well as the timeline.
  • all or a portion of the instant nucleic acid fragments may be immobilized on a nylon membrane or a glass slide.
  • a Generation II DNA spotter (Molecular Dynamics) is one of the available technology to array the DNA samples onto the coated glass slides. Other array methods are also available and well known in the art.
  • Fluorescent or radioactive labeled target cDNA can be made by reverse transcription of mRNA.
  • the target mixture is hybridized to the probes, washed using conditions well known in the art.
  • the amount of the target gene expression is quantified by the intensity of radioactivity or fluorescence label (e.g., confocal laser microscope: Molecular Dynamics).
  • the intensities of radioactivity or fluorescent label at the immobilized probes are measured using the technology well known in the art.
  • the two color fluorescence detection scheme e.g., Cy3 and Cy5
  • the two fluorescent images obtained with the appropriate excitation and emission filters constitute the raw data from differential gene expression ratio values are calculated.
  • the intensity of images are analyzed using the available software (e.g., Array Vision 4.0: Imaging Research Inc.) well known in the art and normalized to compensate for the differential efficiencies of labeling and detection of the label.
  • the original environmental sample containing the isolate was obtained from pond sediment from the nature preserve in Pennsylvania.
  • the pond sediment was inoculated directly into a defined mineral medium under 25% methane in air.
  • Methane was the sole source of carbon and energy. Growth was followed until the optical density at 660 nm was stable whereupon the culture was transferred to fresh medium such that a 1:100 dilution was achieved.
  • methane was the sole source of carbon and energy source
  • the culture was plated onto defined minimal medium agar and incubated under 25% methane in air.
  • Methylomonas 16a was selected as the organism to study due to the rapid growth of colonies and large colony size. The genus of the selected organism was confirmed by 16SrRNA analysis.
  • 16SrRNA extracted from the strain was sequenced and compared to known 16SrRNAs from other microorganisms.
  • the data shows 96% similarity to sequences from Methylomonas sp. KSP III and Methylomonas sp. Strain LW13
  • Genomic DNA was isolated from Methylomonas 16a according to standard protocols.
  • Genomic DNA and library construction were prepared according to published protocols (Friseur et al., The Minimal Gene Complement of Mycoplasma genitalium ; Science 270, 1995). A cell pellet was resuspended in a solution containing 100 mM Na-EDTA pH 8.0, 10 mM tris-HCl pH 8.0, 400 mM NaCl, and 50 mM MgCl 2 .
  • Genomic DNA preparation After resuspension, the cells were gently lysed in 10% SDS, and incubated for 30 min at 55° C. After incubation at room temperature, proteinase K was added to 100 ⁇ g/mL and incubated at 37° C. until the suspension was clear. DNA was extracted twice with tris-equilibrated phenol and twice with chloroform. DNA was precipitated in 70% ethanol and resuspended in a solution containing 10 mM tris-HCl and 1 mM Na-EDTA (TE) pH 7.5. The DNA solution was treated with a mix of RNAases, then extracted twice with tris-equilibrated phenol and twice with chloroform. This was followed by precipitation in ethanol and resuspension in TE.
  • Sequence was generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP 272007) using a combination of vector and insert-specific primers. Sequence editing was performed in either DNAStar (DNA Star Inc.) or the Wisconsin GCG program (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.) and the CONSED package (version 7.0). All sequences represent coverage at least two times in both directions.
  • ORFs encoding ugp, gumD, wza, epsB, epsM, waaE, epsV, gumH, and glycosyltransferase of Methylomonas 16a were initially identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol .
  • the DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTP algorithm (Altschul, S. F., et al., Nucleic Acid Res . 25:3389-3402) (1997) provided by the NCBI.

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Abstract

Genes have been isolated from a Methylomonas sp encoding elements of the exopolysaccharide biosynthetic pathway. The genes and gene products are the first isolated from an organisms capable of utilizing single carbon (C1) substrates as energy sources. The genes are useful for engineering other C1 utilizing microorganisms to make altered levels of exopolysaccharide which is used in a variety of commercial applications.

Description

  • This application claims the benefit of U.S. Provisional Application No. 60/229,944, filed Sep. 1, 2000.[0001]
    • FIELD OF THE INVENTION
  • This invention relates to the field of microbial production of polysaccharides. More specifically, the invention pertains to nucleic acid molecules encoding enzymes involved in biosynthesis of exopolysaccharides from Methylomonas sp. [0002]
    • BACKGROUND OF THE INVENTION
  • Polysaccharides are sugar polymers that have been used widely as a thickener in food and non-food industries (Sanford et al. [0003] Pure & Appl. Chem. 56: 879-892 (1984); Sutherland, Trends Biotechnol, 16(1): 41-6 (1998)). They can be found in food products such as salad dressing, jam, frozen food, bakery products, canned food and dry food. Many other applications include suspending agents for pesticides, paints and other coating agents. They can act as flocculants, binders, film-formers, lubricants and friction reducers. Furthermore, exopolysaccharides are commonly used in oil field for oil recovery.
  • Traditionally, industrially useful polysaccharides have been derived from algal and plant sources. Over the past decade polysaccharides derived from microbes have been found increased usage (Sanford et al. [0004] Pure & Appl. Chem. 56: 879-892 (1984)); Sutherland, Trends Biotechnol, 16(1): 41-6 (1998)). One of the commercially well-known microbial exopolysaccharide is xanthan gum. Xanthan gum is a complex exopolysaccharide produced by a gram-negative bacterium Xanthomonas campestris pv. Campestris which is a pathogen of cruciferous plants. Xanthan consists of a β-1,4-linked D-glucose backbone with trisaccharides side chains composed of mannose-(β-1,4)-glucuronic acid-(β-1,2)-mannose attached to alternate glucose residues in the backbone by α-1,3 linkages. The polymerized pentasaccharide repeating units which are assembled by the sequential addition of glucose 1-phosphate, glucose, mannose, glucuronic acid, and mannose on polyprenol phosphate carrier (lelpi et al., J. Bacteriol. 175:2490-2500, 1993).
  • One of the most characterized pathways for the production of microbial exopolysaccharides is found in Xanthomonas. For example, the biosynthetic pathway of xanthan in [0005] Xanthomonas campestris comprises five stages: (i) conversion of simple sugars to nucleotidyl derivative precursors, (ii) assembly of pentasaccharide subunits attached to the inner membrane polyprenol phosphate carrier, (iii) addition of acetyl and pyruvate groups, (iv) polymerization of pentasaccharide repeat units, and (v) secretion of polymer.
  • Several enzymes or proteins involved in biosynthesis of xanthan and other exopolysaccharides are well known in the art. UDP-glucose pyrophosphorylase is the enzyme that catalyzes the reaction generating UDP-glucose (UTP+glucose-1-phosphate<-->UDP-glucose+Ppi) (Wei et al., [0006] Biochem Biophys Res Commun. 226:607-12 (1996)). UDP-glucose is the building blocks for many exopolysaccharides containing glucose.
  • A cluster of gum genes are found to be required for xanthan gum synthesis in [0007] Xanthomonas campestris (Katzen et al. J. Bacteriol. 180:1607-1617 (1998); Chou, F. L., et al, Biochem. Biophys. Res. Commun. 233 (1), 265-269 (1997)). For example, GumD, the glycosyltransferase, is responsible for the transfer of the first glucose to the lipid-linked intermediates in exopolysaccharide biosynthesis in Xanthomonas campestris. GumH is the protein involved in the transfer of the mannose to the lipid-linked intermediates in exopolysaccharide synthesis in Xanthomonas campestris.
  • Many other genes involved in exopolysaccharide biosynthesis have been characterized or sequenced from other organisms. The epsB gene encodes the EpsB protein that is probably involved in polymerization and/or export of EPS, has been sequenced in [0008] Ralstonia sola (Huang et al, Mol. Microbiol. 16: 977-989 (1995). The espM gene encoding EspM protein has been found in the esp gene cluster from Streptococcus thermophilus (Stingele et al, J. Bacteiol. 178: 1680-1690 (1996)). Another putative polysaccharide export protein, WZA, is identified in E. coli. (Blattner et al., Science 277: 1453-1474 (1997)). Finally, the epsV gene encodes the EpsV protein, a transferase which transfers the sugar to polysaccharide intermediates, and it has also been sequence in Streptococcus thermophilus (Bourgoin et al. Plasmid 40: 44-49 (1998); Bourgoin, F., et al., Gene 233:151-161 (1999).
  • In spite of the abundance of information regarding gene encoding microbial exopolysaccharides, no genes involved in this pathway have been isolated or characterized from C1 utilizing organisms, such as Methylomonas. As noted above, microbial exopolysaccharides have a variety of uses and it would be an advantage to synthesize this material from an abundance and inexpensive carbon source such as methane. [0009]
  • The problem to be solved therefore is to identify the genes relevant to exopolysaccharide synthesis in a C1 utilizing organism for the production of exopolysaccharides in both similar and unrelated microbes. Applicants have solved the stated problem by isolating and characterizing a complete enzymatic pathway for the synthesis of exopolysaccharide from a Methylomonas sp. [0010]
    • SUMMARY OF THE INVENTION
  • The present invention provides an isolated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme, selected from the group consisting of: (a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18; (b) an isolated nucleic acid molecule that hybridizes with (a) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS; and (c) an isolated nucleic acid molecule that is complementary to (a) or (b). [0011]
  • Specifically the invention provides: 1) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 293 amino acids that has at least 58% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 2, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 2) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 473 amino acids that has at least 36% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 4, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 3) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 366 amino acids that has at least 36% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 6, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 4) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 779 amino acids that has at least 35% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 8, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 5) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 472 amino acids that has at least 23% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 10, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 6) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 272 amino acids that has at least 28% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 12, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 7) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 284 amino acids that has at least 21% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 14, or a second nucleotide sequence comprising the complement of the first nucleotide sequence; 8) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 398 amino acids that has at least 26% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 16, or a second nucleotide sequence comprising the complement of the first nucleotide sequence, and 9) an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 317 amino acids that has at least 51% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 18, or a second nucleotide sequence comprising the complement of the first nucleotide sequence. [0012]
  • The invention also provides chimeric genes comprising the isolated nucleic acid molecule of any one of the instant sequences operably linked to suitable regulatory sequences. The invention additionally provides polypeptides encoded by the instant genes. [0013]
  • Similarly the invention provides a transformed host cell comprising the instant chimeric genes. [0014]
  • Additionally the invention provides a method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising: (a) probing a genomic library with the nucleic acid molecule of the present invention; (b) identifying a DNA clone that hybridizes with the nucleic acid molecule of the present invention; and (c) sequencing the genomic fragment that comprises the clone identified in step (b), wherein the sequenced genomic fragment encodes a Methylomonas sp exopolysaccharide biosynthetic enzyme. [0015]
  • Alternatively the invention provides a method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising: (a) synthesizing at least one oligonucleotide primer corresponding to a portion of the sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, and 17; and (b) amplifying an insert present in a cloning vector using the oligonucleotide primer of step (a); wherein the amplified insert encodes a portion of an amino acid sequence encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme. [0016]
  • In one embodiment the invention provides a method for the production of exopolysaccharide comprising: contacting a transformed host cell under suitable growth conditions with an effective amount of a carbon source whereby exopolysaccharide is produced, said transformed host cell comprising a set of nucleic acid molecules encoding SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18; under the control of suitable regulatory sequences. [0017]
  • In an alternate embodiement the invention provides a mutated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme having an altered biological activity produced by a method comprising the steps of: [0018]
  • (i) digesting a mixture of nucleotide sequences of the present invention or 5-13 with restriction endonucleases wherein said mixture comprises: [0019]
  • a) a native microbial gene; [0020]
  • b) a first population of nucleotide fragments which will hybridize to said native microbial sequence; [0021]
  • c) a second population of nucleotide fragments which will not hybridize to said native microbial sequence; [0022]
  • wherein a mixture of restriction fragments are produced; [0023]
  • (ii) denaturing said mixture of restriction fragments; [0024]
  • (iii) incubating the denatured said mixture of restriction fragments of step (ii) with a polymerase; [0025]
  • (iv) repeating steps (ii) and (iii) wherein a mutated microbial gene is produced encoding a protein having an altered biological activity. [0026]
    • BRIEF DESCRIPTION OF THE DRAWINGS, SEQUENCE DESCRIPTIONS AND BIOLOGICAL DEPOSITS
  • FIG. 1 shows the DNA region containing gumD, wza, espB, espM, waaE, espV, gumH and glycosyltransferase genes in Methylomonas spp. strain 16a. The gene encoding the gene ugp, UDP-glucose pyrophosphorylase, is located in a different region.[0027]
  • The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions which form a part of this application. [0028]
  • The following sequence descriptions and sequences listings attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. §1.821-1.825. The Sequence Descriptions contain the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IYUB standards described in [0029] Nucleic Acids Research 13:3021-3030 (1985) and in the Biochemical Journal 219 (No. 2):345-373 (1984) which are herein incorporated by reference. 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.
  • SEQ ID NO: 1 is the nucleotide sequence of the ugp gene. [0030]
  • SEQ ID NO: 2 is the deduced amino acid sequence of ugp gene encoded by SEQ ID NO: 1. [0031]
  • SEQ ID NO: 3 is the nucleotide sequence of [0032] ORF 1 comprising the gumD gene.
  • SEQ ID NO: 4 is the deduced amino acid sequence of the gumD gene product encoded by [0033] ORF 3.
  • SEQ ID NO: 5 is the nucleotide sequence of [0034] ORF 2 comprising the wza gene.
  • SEQ ID NO: 6 is the deduced amino acid sequence of wza the gene product encoded by [0035] ORF 5.
  • SEQ ID NO: 7 is the nucleotide sequence of [0036] ORF 3 comprising the epsB gene.
  • SEQ ID NO: 8 is the deduced amino acid sequence of epsB the gene product encoded by [0037] ORF 7.
  • SEQ ID NO: 9 is the nucleotide sequence of [0038] ORF 4 comprising the epsM gene.
  • SEQ ID NO: 10 is the deduced amino acid sequence of the epsM gene product encoded by ORF 9. [0039]
  • SEQ ID NO: 11 is the nucleotide sequence of [0040] ORF 5 comprising the waaE gene.
  • SEQ ID NO: 12 is the deduced amino acid sequence of the waaE gene product encoded by ORF 11. [0041]
  • SEQ ID NO: 13 is the nucleotide sequence of [0042] ORF 6 comprising the epsV gene.
  • SEQ ID NO: 14 is the deduced amino acid sequence of the epsV gene product encoded by ORF 13. [0043]
  • SEQ ID NO: 15 is the nucleotide sequence of [0044] ORF 7 comprising the gumH gene.
  • SEQ ID NO: 16 is the deduced amino acid sequence of the gumH gene product encoded by ORF 15. [0045]
  • SEQ ID NO: 17 is the nucleotide sequence of [0046] ORF 8 comprising the glycosyltransferase gene.
  • SEQ ID NO: 18 is the deduced amino acid sequence of the glycosyltransferase gene product encoded by ORF 17. [0047]
  • Applicants made the following biological deposits under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for the Purposes of Patent Procedure: [0048]
    International
    Depositor Identification Depository
    Reference Designation Date of Deposit
    Methylomonas 16a ATCC PTA 2402 Aug. 21, 2000
    • DETAILED DESCRIPTION OF THE INVENTION
  • Nucleic acid fragments involved in encoding enzymes for exopolysaccharide production have been isolated from a strain of Methylomonas spp. strain 16a and identified by comparison to public databases containing nucleotide and protein sequences using the BLAST and FASTA algorithms well known to those skilled in the art. [0049]
  • The genes described in present invention enable the overexpression of enzymes involved in the biosynthetic pathway of exopolysaccharide. Overexpression of genes in the present invention in either natural host, Methylomonas 16a, or in heterologous hosts will lead to improved exopolysaccharide yield, saving both and money. In addition, the genes of the present invention can be mutagenized or recombined with genes from other pathways to produce enzymes with different substrate specificity, producing new polymers with novel functionality. Such novel functionality may include novel gelling properties, temperature resistance, and suspending ability. [0050]
  • In some circumstances the production of exopolysaccharides is detrimental and a system of screening for inhibitors of exopolysaccharides synthesis will be useful. For example, in nature, exopolysaccharides are believed to play an important in facilitating bacterial adhesion and the formation of biofilms. Bacterial biofilms are implicated in biofouling and clogging of pipelines in manufacturing processes that use bacteria as a production platform. Similarly in medical environments the formation of bacterial biofilms is problematic. For example, once a biofilm is formed on transplants or catheters, infection caused by bacteria is very difficult to eradicate. Therefore, inhibitors of biofilm formation will have very significant commercial value, and the genes or the gene products described here can be used as targets for screening potential inhibitors. [0051]
  • In this disclosure, a number of terms and abbreviations are used. The following definitions are provided. [0052]
  • “Open reading frame” is abbreviated ORF. [0053]
  • “Polymerase chain reaction” is abbreviated PCR. [0054]
  • As used herein, the terms an “isolated nucleic acid fragment” and “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. [0055]
  • The term “ugp” refers to a gene encoding UDP-glucose pyrophosphorylase, UGP. [0056]
  • The term “gumD” refers to a gene encoding glycosyltransferase, GumD. [0057]
  • The term “wza” refers to a gene encoding polysaccharide export protein Wza. [0058]
  • The term “epsB” refers to a gene encoding polysaccharide export protein EpsB. [0059]
  • The term “epsM” refers to a gene encoding polysaccharide biosynthesis related protein EpsM. [0060]
  • The term “waaE” refers to a gene encoding glycosyltransferase, WaaE. [0061]
  • The term “epsV” refers to a gene encoding sugar transferase EpsV. [0062]
  • The term “gumH” refers to a gene encoding galactosyltransferase, GumH. [0063]
  • The term “UDP” refers to uridine 5-diphosphate. [0064]
  • The term “UTP” refers to uridine 5-triphosphate. [0065]
  • As used herein the term “exopolysaccharide” or “polysaccharide” “biosynthetic pathway” means an enzymatic pathway comprising genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH as described above. The term “exopolysaccharide gene” or “polysaccharide gene” will refer to anyone or all of the genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH. The term “exopolysaccharide biosynthetic enzyme” or “polysaccharide biosynthetic enzyme” will refer to anyone or all of the gene products of the genes ugp, gumD, wza, epsB, epsM, waaE, epsV, and gumH. [0066]
  • The term “monosaccharide” will refer to single polyhydroxy aldehyde or ketone units of the general formula (CH[0067] 2O)n. “Polysaccharides” are molecules containing many monosaccharide units joined in long linear or branched chains. The term “exopolysaccharide” will mean any biologically produced polysaccharide that is excreted from a cell.
  • The term “Embden-Meyerhof pathway” refers to the series of biochemical reactions for conversion of hexoses such as glucose and fructose to important cellular 3 carbon intermediates such as [0068] glyceraldehyde 3 phosphate, dihydroxyacetone phosphate, phosphoenol pyruvate and pyruvate. These reactions typically proceed with net yield of biochemically useful energy in the form of ATP. The key enzymes unique to the Embden-Meyerhof pathway are the phosphofructokinase and fructose 1,6 bisphosphate aldolase.
  • The term “Entner-Douderoff pathway” refers to a series of biochemical reactions for conversion of hexoses suchas as glucose or fructose to important 3 carbon cellular intermediates pyruvate and [0069] glyceraldehyde 3 phosphate without any net production of biochemically useful energy. The key enzymes unique to the Entner-Douderoff pathway are the 6 phosphogluconate dehydratase and the ketodeoxyphosphogluconate aldolase.
  • The term “high growth methanotrophic bacterial strain” refers to a bacterium capable of growth with methane or methanol as sole carbon and energy source which possess a functional Embden-Meyerhof carbon flux pathway resulting in yield of cell mass per gram of C1 substrate metabolized. The specific “high growth methanotrophic bacterial strain” described herein is referred to as “Methylomonas 16a” or “16a”, which terms are used interchangeably. [0070]
  • As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. “Substantially similar” also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences. [0071]
  • For example, it is well known in the art that alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein are common. For the purposes of the present invention substitutions are defined as exchanges within one of the following five groups: [0072]
  • 1. Small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr (Pro, Gly); [0073]
  • 2. Polar, negatively charged residues and their amides: Asp, Asn, Glu, Gln; [0074]
  • 3. Polar, positively charged residues: His, Arg, Lys; [0075]
  • 4. Large aliphatic, nonpolar residues: Met, Leu, Ile, Val (Cys); and [0076]
  • 5. Large aromatic residues: Phe, Tyr, Trp. [0077]
  • Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product. [0078]
  • In many cases, nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein. [0079]
  • Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS), with the sequences exemplified herein. Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are at least 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the DNA sequence of the nucleic acid fragments reported herein. [0080]
  • A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule 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. [0081] Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferable a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 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 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 (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) [0082] J. Mol. Biol. 215:403-410; see also www.ncbi.nim.nih.gov/BLAST/). 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 partial or complete amino acid and nucleotide sequences encoding one or more particular microbial 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 to hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences. [0083]
  • 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: [0084] Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, NJ (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, NY (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments using the Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
  • Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. 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. [0085]
  • “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. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the instant microbial polypeptides as set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18. 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. [0086]
  • “Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. “Chemically synthesized”, as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available. [0087]
  • “Gene” refers to a nucleic acid fragment that expresses a specific protein, 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 refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. 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. [0088]
  • “Coding sequence” 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. [0089]
  • “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. [0090]
  • The “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. [0091]
  • “RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065; WO 9928508). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, or the coding sequence. “Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes. [0092]
  • 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 affecting 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. [0093]
  • 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. [0094]
  • “Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. “Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals. [0095]
  • The term “signal peptide” refers to an amino terminal polypeptide preceding the secreted mature protein. The signal peptide is cleaved from and is therefore not present in the mature protein. Signal peptides have the function of directing and translocating secreted proteins across cell membranes. Signal peptide is also referred to as signal protein. [0096]
  • “Transformation” refers to the transfer of a nucleic acid fragment into the genome of 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. [0097]
  • The terms “plasmid”, “vector” and “cassette” 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. “Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitates transformation of a particular host cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host. [0098]
  • The term “altered biological activity” will refer to an activity, associated with a protein encoded by a microbial nucleotide sequence which can be measured by an assay method, where that activity is either greater than or less than the activity associated with the native microbial sequence. “Enhanced biological activity” refers to an altered activity that is greater than that associated with the native sequence. “Diminished biological activity” is an altered activity that is less than that associated with the native sequence. [0099]
  • 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 the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX (Altschul et al., [0100] J. Mol. Biol. 215:403-410 (1990), and DNASTAR (DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA). 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 which 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., [0101] Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Cold Press Spring Harbor, NY (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987). Isolation of Homologs
  • The nucleic acid fragments of the instant invention may be used to isolate genes encoding homologous proteins from the same or other microbial species. 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, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202), ligase chain reaction (LCR), Tabor, S. et al., [0102] Proc. Acad. Sci. USA 82, 1074, (1985)) or strand displacement amplification (SDA, Walker, et al., Proc. Nat. Acad. Sci. U.S.A., 89, 392, (1992)).
  • For example, genes encoding similar proteins or polypetides to those of the instant invention 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 bacteria using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as 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 under conditions of appropriate stringency. [0103]
  • 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 oligonucleotide as specific hybridization probes in the Diagnosis of Genetic Disorders”, in [0104] Human Genetic Diseases: A Practical Approach, K. E. Davis Ed., (1986) pp. 33-50 IRL Press, Herndon, Va.); Rychlik, W. (1993) In White, B. A. (ed.), Methods in Molecular Biology, Vol. 15, pages 31-39, PCR Protocols: Current Methods and Applications. Humania Press, Inc., Totowa, N.J.)
  • Generally two short segments of the instant 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 instant 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., [0105] 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 (BRL), 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 instant 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 of the present invention are typically single stranded nucleic acid sequences which 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. [0106]
  • Hybridization methods are well defined. Typically the probe and sample must be mixed under conditions which 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 (1991) [0107] Nucl. Acids Res. 19:5143-5151]. 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 3M. 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 1M sodium chloride, about 0.05 to 0.1M buffers, such as sodium citrate, Tris-HCl, PIPES or HEPES (pH range about 6-9), about 0.05 to 0.2% detergent, such as sodium dodecylsulfate, or between 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kilodaltons), 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 which include a variety of polar water-soluble or swellable agents, such as polyethylene glycol, anionic polymers such as polyacrylate or polymethylacrylate, and anionic saccharidic polymers, such as dextran sulfate. [0108]
  • 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. [0109]
  • Recombinant Expression—Microbial [0110]
  • The genes and gene products of the instant sequences may be produced in heterologous host cells, particularly in the cells of microbial hosts. Expression in recombinant microbial hosts may be useful for the expression of various pathway intermediates; for the modulation of pathways already existing in the host for the synthesis of new products heretofore not possible using the host. Additionally the gene products may be useful for conferring higher growth yields of the host or for enabling alternative growth mode to be utilized. [0111]
  • Preferred heterologous host cells for express of the instant genes and nucleic acid molecules are microbial hosts that can be found broadly within the fungal or bacterial families and which grow over a wide range of temperature, pH values, and solvent tolerances. Because of transcription, translation and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, functional genes are expressed irrespective of carbon feedstock used to generate cellular biomass. Large scale microbial growth and functional gene expression may utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, saturated hydrocarbons such as methane or carbon dioxide in the case of photosynthetic or chemoautotrophic hosts. However, the functional genes may be regulated, repressed or depressed by specific growth conditions, which may include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions. In addition, the regulation of functional genes may be achieved by the presence or absence of specific regulatory molecules that are added to the culture and are not typically considered nutrient or energy sources. Growth rate may also be an important regulatory factor in gene expression. Examples of host strain s include but are not limited to fungal or yeast species such as Aspergillus, Trichoderma, Saccharomyces, Pichia, Candida, Hansenula, or bacterial species such as Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, Pseudomonas, Methylomonas, Methylobacter, Alcaligenes, Synechocystis, Anabaena, Thiobacillus, Methanobacterium and Klebsiella. [0112]
  • Of particular interest in the present invention are high growth obligate methanotrophs having an energetically favorable carbon flux pathway. For example Applicants have discovered a specific strain of methanotroph having several pathway features which make it particularly useful for carbon flux manipulation. This type of strain has served as the host in present application and is known as Methylomonas 16a (A TCC PTA 2402). [0113]
  • The present strain contains several anomalies in the carbon utilization pathway. For example, based on genome sequence data, the strain is shown to contain genes for two pathways of hexose metabolism. The Entner-Douderoff athway which utilizes the keto-deoxy phosphogluconate aldolase enzyme is present in the strain. Is generally well accepted that this is the operative pathway in obligate methanotrophs. Also present, however, is the Embden-Meyerhof pathway which utilizes the Fructose bisphosphate aldolase enzyme. It is well known that this pathway is either not present or not operative in obligate methanotrophs. Energetically, the latter pathway is most favorable and allows greater yield of biologically useful energy and ultimately production of cell mass and other cell mass-dependent products in Methylomonas 16a. The activity of this pathway in the present 16a strain has been confirmed through microarray data and biochemical evidence measuring the reduction of ATP. Although the 16a strain has been shown to possess both the Embden-Meyerhof and the Entner-Douderoff pathway enzymes the data suggests that the Embden-Meyerhof pathway enzymes are more strongly expressed than the Entner-Douderoff pathway enzymes. This result is surprising and counter to existing beliefs on the glycolytic metabolism of methanotrophic bacteria. Applicants have discovered other methanotrophic bacteria having this characteristic, including for example, [0114] Methylomonas clara and Methylosinus sporium. It is likely that this activity has remained undiscovered in methanotrophs due to the lack of activity of the enzyme with ATP, the typical phosphoryl donor for the enzyme in most bacterial systems.
  • A particularly novel and useful feature of the Embden-Meyerhof pathway in strain 16a is that the key phosphofructokinase step is pyrophosphate dependent instead of ATP dependent. This feature adds to the energy yield of the pathway by using pyrophosphate instead of ATP. Because of it's significance in providing an energetic advantage to the strain this gene in the carbon flux pathway is considered diagnostic for the present strain. [0115]
  • In methanotrophic bacteria methane is converted to biomolecules via a cyclic set of reaction known as the ribulose monophosphate pathway or RuMP cycle. This pathway is comprised of three phases, each phases being a series of enzymatic steps. The first step is “fixation” or incorporation of C-1 (formaldehyde) into a pentose to form a hexose or six carbon sugar. This occurs via a condensation reaction between a carbon sugar (pentose) and formaldehyde and is catalyzed by hexulose monophosphate synthase. The second phase is termed “cleavage” and results in splitting of that hexose into two 3 carbon molecules. One of those three carbon molecules is recycled back through the RuMP pathway and the other 3 carbon fragment is utilized for cell growth. In methanotrophs and methylotrophs the RuMP pathway may occur as one of three variants. However only two of these variants are commonly found. The FBP/TA (fructose bisphosphotase/Transaldolase) or the KDPG/TA (keto deoxy phosphogluconate/transaldolase) pathway. (Dijkhuizen L., G. E. Devries. The Physiology and biochemistry of aerobic methanol-utilizing gram negative and gram positive bacteria. In: Methane and Methanol Utilizers 1992, ed Colin Murrell and Howard Dalton Plenum Press NY). [0116]
  • The present strain is unique in the way it handles the “cleavage” steps where genes were found that carry out this conversion via fructose bisphosphate as a key intermediate. The genes for fructose bisphosphate aldolase and transaldolase were found clustered together on one piece of DNA. Secondly the genes for the other variant involving the keto deoxy phosphogluconate intermediate were also found clustered together. Available literature teaches that these organisms (obligate methylotrophs and methanotrophs) rely solely on the KDPG pathway and that the FBP-dependent fixation pathway is utilized by facultative methylotrophs (Dijkhuizen et al., supra). Therefore the latter observation is expected whereas the former is not. The finding of the FBP genes in and obligate methane utilizing bacterium is both surprising and suggestive of utility. The FBP pathway is energetically favorable to the host microorganism due to the fact that more energy (ATP) is utilized than is utilized in the KDPG pathway. Thus organisms that utilize the FBP pathway may have an energetic advantage and growth advantage over those that utilize the KDPG pathway. This advantage may also be useful for energy-requiring production pathways in the strain. By using this pathway a methane-utilizing bacterium may have an advantage over other methane utilizing organisms as production platforms for either single cell protein or for any other product derived from the flow of carbon through the RuMP pathway. [0117]
  • Accordingly the present invention provides a method for the production of exopolysaccharide using an energetically, favoralbe Methylomonas strain which [0118]
  • (a) grows on a C1 carbon substrate selected from the group consisting of methane and methanol; and [0119]
  • (b) comprises a functional Embden-Meyerhof carbon pathway, [0120]
  • said pathway comprising a gene encoding a pyrophosphate dependent phosphofructokinase enzyme. [0121]
  • Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of the any of the gene products of the instant sequences. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the enzymes. [0122]
  • Additionally, the instant genes will be effective in altering the properties of the host microbe. It is expected, for example, host cells can be transformed with chimeric genes encoding one or more of the instant sequences in order to induce the overexpression of exopolysaccharide, or to manipulate production of exopolysaccharides by changing the biosynthesis pathway of exopolysaccharide in host cell to reduce the exopolysaccharide production in host cells to reduce the biofilm formation. [0123]
  • Vectors or cassettes useful for the transformation of suitable host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a [0124] region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
  • Initiation control regions or promoters, which are useful to drive expression of the instant ORF's in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, ara, tet, trp, IP[0125] L, IPR, T7, tac, and trc (useful for expression in Escherichia coli) as well as the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus.
  • Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included. [0126]
  • Pathway Engineering [0127]
  • In a preferred embodiment the present genes may be used in various methanotrophic strains to modulate or regulate the production of exopolysaccharides. These genes and their sequences may be used in a variety of ways to modulate existing polysaccharide pathways. Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particularly pathway may be upregulated or down regulated by variety of methods. Additionally, competing pathways organism may be eliminated or sublimated by gene disruption and similar techniques. [0128]
  • Once a key genetic pathway has been identified and sequenced specific genes may be upregulated to increase the output of the pathway. For example, additionally copies of the targeted genes may be introduced into the host cell on multicopy plasmids such as pBR322. Alternatively the target genes may be modified so as to be under the control of non-native promoters. Where it is desired that a pathway operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters may used to replace the native promoter of the target gene. Similarly, in some case the native or endogenous promoter may be modified to increase gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868). [0129]
  • Alternatively it may be necessary to reduce or eliminate the expression of certain genes in the target pathway or in competing pathways that may serve as competing sinks for energy or carbon. Methods of down-regulating genes for this purpose have been explored. Where sequence of the gene to be disrupted is known, one of the most effective methods gene down regulation is targeted gene disruption where foreign DNA is inserted into a structural gene so as to disrupt transcription. This can be effected by the creation of genetic cassettes comprising the DNA to be inserted (often a genetic marker) flanked by sequence having a high degree of homology to a portion of the gene to be disrupted. Introduction of the cassette into the host cell results in insertion of the foreign DNA into the structural gene via the native DNA replication mechanisms of the cell. (See for example Hamilton et al. (1989) [0130] J. Bacteriol. 171:4617-4622, Balbas et al. (1993) Gene 136:211-213, Gueldener et al. (1996) Nucleic Acids Res. 24:2519-2524, and Smith et al. (1996) Methods Mol. Cell. Biol. 5:270-277.)
  • Antisense technology is another method of down regulating genes where the sequence of the target gene is known. To accomplish this, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the protein of interest. The person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. [0131]
  • Although targeted gene disruption and antisense technology offer effective means of down regulating genes where the sequence is known, other less specific methodologies have been developed that are not sequence based. For example, cells may be exposed to a UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect nonreplicating DNA such as HNO[0132] 2 and NH2OH, as well as agents that affect replicating DNA such as acridine dyes, notable for causing frameshift mutations. Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See for example Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36, 227, (1992).
  • Another non-specific method of gene disruption is the use of transposoable elements or transposons. Transposons are genetic elements that insert randomly in DNA but can be latter retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vitro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme. When the transposable element or transposon, is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the nucleic acid fragment. The technique is useful for random mutageneis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see for example The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass.; based upon the bacterial transposon Tn7; and the EZ::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element. [0133]
  • Within the context of the present invention it may be useful to modulate the expression of the exopolysaccharaide pathway. As has been noted the present strain has the ability to product polysaccharides in large amounts. This process is governed by a set of genes including the ugp gene, gumD and H genes, the epsB, M, and V genes and the waaD gene. In this pathway it may be of particular importance to up-regulate the espB gene involved in polymerization and/or export of the polysaccharide, or the epsV gene which controls the transfer of sugar to polysaccharide intermediates. [0134]
  • Industrial Scale Production [0135]
  • Where commercial production of exopolysaccharides are desired a variety of culture methodologies may be applied. For example, large scale production may be produced by both batch or continuous culture methodologies. [0136]
  • A classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system. Typically, however, a “batch” culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post-exponential phase production can be obtained in other systems. [0137]
  • A variation on the standard batch system is the Fed-Batch system. Fed-Batch culture 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 culture 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. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO[0138] 2. Batch and Fed-Batch culturing methods are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36, 227, (1992), herein incorporated by reference.
  • Commercial production of exopolysaccharides may also be accomplished with a continuous culture. Continuous cultures are an open system where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in log phase growth. Alternatively continuous culture may be practiced with immobilized cells where carbon and nutrients are continuously added, and valuable products, by-products or waste products are continuously removed from the cell mass. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials. [0139]
  • Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture. Methods of modulating nutrients and growth factors for continuous culture 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. [0140]
  • Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, 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. Additionally the carbon substrate may also be one-carbon substrates such as carbon dioxide, methane or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., [0141] Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol. 153:485-489 (1990)). Hence it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
  • Recombinant Production—Plants [0142]
  • Plants and algae are also known to produce polysaccharides. The nucleic acid fragments of the instant invention may be used to create transgenic plants having the ability to express the microbial protein. Preferred plant hosts will be any variety that will support a high production level of the instant proteins. Suitable green plants will included but are not limited to of soybean, rapeseed ([0143] Brassica napus, B. campestris), sunflower (Helianthus annus), cotton (Gossypium hirsutum), corn, tobacco (Nicotiana tabacum), alfalfa (Medicago sativa), wheat (Triticum sp), barley (Hordeum vulgare), oats (Avena sativa, L), sorghum (Sorghum bicolor), rice (Oryza sativa), Arabidopsis, cruciferous vegetables (broccoli, cauliflower, cabbage, parsnips, etc.), melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, grass seed crops, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses. Algal species include but not limited to commercially significant hosts such as Spirulina and Dunalliela. Overexpression of the proteins of the instant invention may be accomplished by first constructing chimeric genes in which the coding region are operably linked to promoters capable of directing expression of a gene in the desired tissues at the desired stage of development. For reasons of convenience, the chimeric genes may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals must also be provided. The instant chimeric genes may also comprise one or more introns in order to facilitate gene expression.
  • Any combination of any promoter and any terminator capable of inducing expression of a coding region may be used in the chimeric genetic sequence. Some suitable examples of promoters and terminators include those from nopaline synthase (nos), octopine synthase (ocs) and. cauliflower mosaic virus (CaMV) genes. One type of efficient plant promoter that may be used is a high level plant promoter. Such promoters, in operable linkage with the genetic sequences or the present invention should be capable of promoting expression of the present gene product. High level plant promoters that may be used in this invention include the promoter of the small subunit (ss) of the ribulose-1,5-bisphosphate carboxylase from example from soybean (Berry-Lowe et al., [0144] J. Molecular and App. Gen., 1:483-498 1982)), and the promoter of the chlorophyll a/b binding protein. These two promoters are known to be light-induced in plant cells (See, for example, Genetic Engineering of Plants, an Agricultural Perspective, A. Cashmore, Plenum, N.Y. (1983), pages 29-38; Coruzzi, G. et al., The Journal of Biological Chemistry, 258:1399 (1983), and Dunsmuir, P. et al., Journal of Molecular and Applied Genetics, 2:285 (1983)).
  • Plasmid vectors comprising the instant chimeric genes can then constructed. The choice of plasmid vector depends upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) [0145] EMBO J. 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA blots (Southern, J. Mol. Biol. 98, 503, (1975)). Northern analysis of mRNA expression (Kroczek, J. Chromatogr. Biomed. Appl., 618 (1-2) (1993) 133-145), Western analysis of protein expression, or phenotypic analysis.
  • For some applications it will be useful to direct the instant proteins to different cellular compartments. It is thus envisioned that the chimeric genes described above may be further supplemented by altering the coding sequences to encode enzymes with appropriate intracellular targeting sequences such as transit sequences (Keegstra, K., [0146] Cell 56:247-253 (1989)), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels, J. J., Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53 (1991)), or nuclear localization signals (Raikhel, N. Plant Phys. 100:1627-1632 (1992)) added and/or with targeting sequences that are already present removed. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future that are useful in the invention.
  • Protein Engineering [0147]
  • It is contemplated that the present nucleotide may be used to produce gene products having enhanced or altered activity. Various methods are known for mutating a native gene sequence to produce a gene product with altered or enhanced activity including but not limited to error prone PCR (Melnikov et al., [0148] Nucleic Acids Research, (Feb. 15, 1999) Vol. 27, No. 4, pp. 1056-1062); site directed mutagenesis (Coombs et al., Proteins (1998), 259-311, 1 plate. Editor(s): Angeletti, Ruth Hogue. Publisher: Academic, San Diego, Calif.) and “gene shuffling” (U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; and 5,837,458, incorporated herein by reference).
  • The method of gene shuffling is particularly attractive due to its facile implementation, and high rate of mutagenesis and ease of screening. The process of gene shuffling involves the restriction endonuclease cleavage of a gene of interest into fragments of specific size in the presence of additional populations of DNA regions of both similarity to or difference to the gene of interest. This pool of fragments will then be denatured and reannealed to create a mutated gene. The mutated gene is then screened for altered activity. [0149]
  • The instant microbial sequences of the present invention may be mutated and screened for altered or enhanced activity by this method. The sequences should be double stranded and can be of various lengths ranging form 50 bp to 10 kb. The sequences may be randomly digested into fragments ranging from about 10 bp to 1000 bp, using restriction endonucleases well known in the art (Maniatis supra). In addition to the instant microbial sequences, populations of fragments that are hybridizable to all or portions of the microbial sequence may be added. Similarly, a population of fragments which are not hybridizable to the instant sequence may also be added. Typically these additional fragment populations are added in about 10 to 20 fold excess by weight as compared to the total nucleic acid. Generally if this process is followed the number of different specific nucleic acid fragments in the mixture will be about 100 to about 1000. The mixed population of random nucleic acid fragments are denatured to form single-stranded nucleic acid fragments and then reannealed. Only those single-stranded nucleic acid fragments having regions of homology with other single-stranded nucleic acid fragments will reanneal. The random nucleic acid fragments may be denatured by heating. One skilled in the art could determine the conditions necessary to completely denature the double stranded nucleic acid. Preferably the temperature is from 80° C. to 100° C. The nucleic acid fragments may be reannealed by cooling. Preferably the temperature is from 20° C. to 75° C. Renaturation can be accelerated by the addition of polyethylene glycol (“PEG”) or salt. A suitable salt concentration may range from 0 mM to 200 mM. The annealed nucleic acid fragments are then incubated in the presence of a nucleic acid polymerase and dNTP's (i.e. dATP, dCTP, dGTP and dTTP). The nucleic acid polymerase may be the Klenow fragment, the Taq polymerase or any other DNA polymerase known in the art. The polymerase may be added to the random nucleic acid fragments prior to annealing, simultaneously with annealing or after annealing. The cycle of denaturation, renaturation and incubation in the presence of polymerase is repeated for a desired number of times. Preferably the cycle is repeated from 2 to 50 times, more preferably the sequence is repeated from 10 to 40 times. The resulting nucleic acid is a larger double-stranded polynucleotide ranging from about 50 bp to about 100 kb and may be screened for expression and altered activity by standard cloning and expression protocol. (Manatis supra). [0150]
  • Furthermore, a hybrid protein can be assembled by fusion of functional domains using the gene shuffling (exon shuffling) method (Nixon et al, PNAS, 94:1069-1073 (1997)). The functional domain of the instant gene can be combined with the functional domain of other genes to create novel enzymes with desired catalytic function. A hybrid enzyme may be constructed using PCR overlap extension method and cloned into the various expression vectors using the techniques well known to those skilled in art. [0151]
  • Gene Expression Profiling [0152]
  • All or portion of the nucleic acid fragments of the instant invention may also be used as probes for gene expression monitoring and gene expression profiling. Many external changes such as changes in growth condition, exposure to chemicals, can cause induction or repression of genes in the cell. The induction or repression of gene can be used for a screening system to determine the best growth condition for production organism, drug discovery with similar mode of action compound, just to mention a few. On the other hand, by amplifying or disrupting genes, one can manipulate the production of the amount of cellular products, biofilm formation as well as the timeline. [0153]
  • For example, all or a portion of the instant nucleic acid fragments may be immobilized on a nylon membrane or a glass slide. A Generation II DNA spotter (Molecular Dynamics) is one of the available technology to array the DNA samples onto the coated glass slides. Other array methods are also available and well known in the art. After the cells were grown in various growth conditions or treated with potential candidates, cellular RNA is purified. Fluorescent or radioactive labeled target cDNA can be made by reverse transcription of mRNA. The target mixture is hybridized to the probes, washed using conditions well known in the art. The amount of the target gene expression is quantified by the intensity of radioactivity or fluorescence label (e.g., confocal laser microscope: Molecular Dynamics). The intensities of radioactivity or fluorescent label at the immobilized probes are measured using the technology well known in the art. The two color fluorescence detection scheme (e.g., Cy3 and Cy5) has the advantage over radioactively labeled targets of allowing rapid and simultaneous differential expression analysis of independent samples. In addition, the use of ratio measurements compensates for probe to probe variation of intensity due to DNA concentration and hybridization efficiency. In the case of fluorescence labeling, the two fluorescent images obtained with the appropriate excitation and emission filters constitute the raw data from differential gene expression ratio values are calculated. The intensity of images are analyzed using the available software (e.g., Array Vision 4.0: Imaging Research Inc.) well known in the art and normalized to compensate for the differential efficiencies of labeling and detection of the label. There are many different ways known in the art to normalize the signals. One of the ways to normalize the signal is by correcting the signal against internal controls. Another way is to run a separate array with labeled genomic driven DNA and compare the signal with mRNA driven signals. This method also allows to measure the transcript abundance. The array data of individual gene is examined and evaluated to determine the induction or repression of the gene under the test condition. [0154]
    • 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 usages and conditions. [0155]
  • General Methods [0156]
  • 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. [0157] Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, (1989) (Maniatis) and 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, pub. by Greene Publishing Assoc. and Wiley-Interscience (1987).
  • Materials and methods suitable for the maintenance and growth of bacterial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in [0158] 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, D.C. (1994)) or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition, Sinauer Associates, Inc., Sunderland, Mass. (1989). All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), or Sigma Chemical Company (St. Louis, Mo.) unless otherwise specified.
  • Manipulations of genetic sequences were accomplished using the suite of programs available from the Genetics Computer Group Inc. (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.). Where the GCG program “Pileup” was used the gap creation default value of 12, and the gap extension default value of 4 were used. Where the CGC “Gap” or “Bestfit” programs were used the default gap creation penalty of 50 and the default gap extension penalty of 3 were used. In any case where GCG program parameters were not prompted for, in these or any other GCG program, default values were used. [0159]
  • Multiple alignment of the sequences was performed using the the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, [0160] Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y.).
  • The meaning of abbreviations is as follows: “h” means hour(s), “min” means minute(s), “sec” means second(s), “d” means day(s), “mL” means milliliters, “L” means liters. [0161]
  • Isolation of Strain Methylomonas 16a [0162]
  • The original environmental sample containing the isolate was obtained from pond sediment from the nature preserve in Pennsylvania. The pond sediment was inoculated directly into a defined mineral medium under 25% methane in air. Methane was the sole source of carbon and energy. Growth was followed until the optical density at 660 nm was stable whereupon the culture was transferred to fresh medium such that a 1:100 dilution was achieved. After 3 successive transfers with methane as sole carbon and energy source the culture was plated onto defined minimal medium agar and incubated under 25% methane in air. Methylomonas 16a was selected as the organism to study due to the rapid growth of colonies and large colony size. The genus of the selected organism was confirmed by 16SrRNA analysis. 16SrRNA extracted from the strain was sequenced and compared to known 16SrRNAs from other microorganisms. The data shows 96% similarity to sequences from Methylomonas sp. KSP III and Methylomonas sp. Strain LW13 [0163]
    • Example 1
  • Preparation of Genomic DNA for Sequencing and Sequence Generation [0164]
  • Genomic DNA was isolated from Methylomonas 16a according to standard protocols. [0165]
  • Genomic DNA and library construction were prepared according to published protocols (Friseur et al., The Minimal Gene Complement of [0166] Mycoplasma genitalium; Science 270, 1995). A cell pellet was resuspended in a solution containing 100 mM Na-EDTA pH 8.0, 10 mM tris-HCl pH 8.0, 400 mM NaCl, and 50 mM MgCl2.
  • Genomic DNA preparation. After resuspension, the cells were gently lysed in 10% SDS, and incubated for 30 min at 55° C. After incubation at room temperature, proteinase K was added to 100 μg/mL and incubated at 37° C. until the suspension was clear. DNA was extracted twice with tris-equilibrated phenol and twice with chloroform. DNA was precipitated in 70% ethanol and resuspended in a solution containing 10 mM tris-HCl and 1 mM Na-EDTA (TE) pH 7.5. The DNA solution was treated with a mix of RNAases, then extracted twice with tris-equilibrated phenol and twice with chloroform. This was followed by precipitation in ethanol and resuspension in TE. [0167]
  • Library construction. 200 to 500 μg of chromosomal DNA was resuspended in a solution of 300 mM sodium acetate, 10 mM tris-HCl, 1 mM Na-EDTA, and 30% glycerol, and sheared at 12 psi for 60 sec in an Aeromist Downdraft Nebulizer chamber (IBI Medical products, Chicago, Ill.). The DNA was precipitated, resuspended and treated with Bal31 nuclease. After size fractionation, a fraction (2.0 kb, or 5.0 kb) was excised, cleaned and a two-step ligation procedure was used to produce a high titer library with greater than 99% single inserts. [0168]
  • Sequencing. A shotgun sequencing strategy approach was adopted for the sequencing of the whole microbial genome (Fleischmann, Robert et al., Whole-Genome Random sequencing and assembly of [0169] Haemophilus influenzae Rd Science, 269:1995).
  • Sequence was generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP 272007) using a combination of vector and insert-specific primers. Sequence editing was performed in either DNAStar (DNA Star Inc.) or the Wisconsin GCG program (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.) and the CONSED package (version 7.0). All sequences represent coverage at least two times in both directions. [0170]
    • Example 2
  • Identification and Characterization of Bacterial ORF's [0171]
  • ORFs encoding ugp, gumD, wza, epsB, epsM, waaE, epsV, gumH, and glycosyltransferase of Methylomonas 16a were initially identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) [0172] J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant (nr) GenBank CDS translations, sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank, the SWISS-PROT protein sequence database, EMBL, and DDBJ databases). The sequences obtained in Example 1 were analyzed for similarity to all publicly available DNA sequences contained in the “nr” database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTP algorithm (Altschul, S. F., et al., Nucleic Acid Res. 25:3389-3402) (1997) provided by the NCBI.
  • All initial comparisons were done using either the BLASTNnr or BLASTPnr algorithm. A refined similarity search was performed using FASTA (version 3.2) with the default parameters settings (BLOSUM 50 scoring matrix, word size ktup=2, gap penalty=−12 for the first residue and −2 for every additional residue in the gap). The results of the FASTA comparison is given in Table 1 which summarize the sequences to which they have the most similarity. Table 1 displays data based on the FASTA algorithm with values reported in expect values. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected in a search of a database of this size absolutely by chance. [0173]
  • Gene clusters of genes, gumD, wza, epsB, epsM, waaE, epsV, gumH, and glycosyltransferase, are shown in FIG. 1. [0174]
    TABLE 1
    Gene SEQ ID SEQ ID % %
    ORF Name Name Similarity Identified base Peptide Identitya Similarityb E-valuec Citation
    ugp ugp ( Xanthomonas  1  2 58% 82% 3.2 e-60 Wei et al., Biochem. Biophys.
    campestris) Res. Commun. 226 (3), 607-
    612 (1996)
    ORF 1 gumD gumD ( Xanthomonas  3  4 36% 69% 2.5 e-52 Chou, F.L., et el, Biochem.
    campestris) Biophys. Res. Commun. 233
    (1), 265-269 (1997)
    ORF 2 wza wza (Escherichia coli)  5  6 36% 69% 5.8 e-39 Blattner, F.R. et al., Science
    277 (5331), 1453-1474 (1997)
    ORF 3 epsB epsB ( Pseudomonas  7  8 35% 67%   2 e-74 Huang, J. and Schell, M., Mol.
    solanacearum) Microbiol. 16 (5), 977-989
    (1995)
    ORF 4 epsM epsM (Streptococcus  9 10 23% 55% 1.3 e-05 Stingele, F. et al.,
    thermophilus) J. Bacteriol. 178 (6), 1680-
    1690 (1996)
    ORF 5 waaE waaE (Serratia 11 12 28% 55% 8.6 e-09 Pique, N et al., Unpublished
    marcescens) Genbank number: AAC44433
    ORF
    6 epsV epsV (Streptococcus 13 14 21% 56% 2.3 e-05 Bourgoin, F. et al., Plasmid 40
    thermophilus) (1), 44-49 (1998)
    ORF 7 gumH gumH (Rhizobium 15 16 26% 55% 0.00088 Becker, A. et al., Mol.
    meliloti) Microbiol. 16 (2), 191-203
    (1995)
    ORF 8 glycosyl Glycosyltransferase 17 18 51% 80% 1.7 e-62 Nakano, Y, Biochem. Biophys.
    transferase (Actinobacillus Acta 1442:409-414 (1998)
    actinimycetemcomitans)
  • [0175]
  • 1 18 1 873 DNA Methylomonas 16a 1 atgaaagtta ccaaagccgt ttttcccgtt gccggactgg gcacccggtc attgcccgca 60 accaaggccg ttgccaagga aatgttgccg gtggtggaca agccgctgat tcagtatgcg 120 gtggaagagg ccgtggccgc cggcatcgac acgatgattt tcgtgatcgg tagaaacaag 180 gaatccattg ccaaccattt cgataaatcc tacgaactgg aaaaggaact ggaaaaaagc 240 ggcaagaccg atttgctgaa aatgctgcgg gagattttgc ccgcgcatgt gtcctgcgta 300 ttcgtgcgtc aagcggaggc tctgggtttg gggcatgcgg tgcattgcgc caagccggtg 360 gtcggcaacg agccgtttgc ggtgatcttg ccggatgact tgatcgagga cggcgagcgc 420 ggttgcatga agcagatggt ggatttgttc gacaaagagc aaagcagcgt attgggggta 480 gagcgggtcg atcccaagga aacccataag tacggcatcg tcgaacatgc cgaaacctcg 540 cccagagtcg gttggttgag ttccatcgtc gagaaaccca aacccgaagt ggcgccctcc 600 aatatcgcgg tggtcgggcg ctacatcttg acgccggcca tttttcaaaa aatcgagaac 660 acggggcgcg gcgccggcgg cgaaattcaa ttgaccgatg cgattgccgc gttgatgaaa 720 gacgaacgcg ttttgtccta tgaattcgaa ggcaatcgct acgactgcgg ttccaagttt 780 ggttttttgt tggccaatgt cgaatatggc ttgctgcaca aggaaatcaa agccgaattc 840 gccaactatc tgaaacaacg cgtcagcaaa atc 873 2 293 PRT Methylomonas 16a 2 Met Thr Met Lys Val Thr Lys Ala Val Phe Pro Val Ala Gly Leu Gly 1 5 10 15 Thr Arg Ser Leu Pro Ala Thr Lys Ala Val Ala Lys Glu Met Leu Pro 20 25 30 Val Val Asp Lys Pro Leu Ile Gln Tyr Ala Val Glu Glu Ala Val Ala 35 40 45 Ala Gly Ile Asp Thr Met Ile Phe Val Ile Gly Arg Asn Lys Glu Ser 50 55 60 Ile Ala Asn His Phe Asp Lys Ser Tyr Glu Leu Glu Lys Glu Leu Glu 65 70 75 80 Lys Ser Gly Lys Thr Asp Leu Leu Lys Met Leu Arg Glu Ile Leu Pro 85 90 95 Ala His Val Ser Cys Val Phe Val Arg Gln Ala Glu Ala Leu Gly Leu 100 105 110 Gly His Ala Val His Cys Ala Lys Pro Val Val Gly Asn Glu Pro Phe 115 120 125 Ala Val Ile Leu Pro Asp Asp Leu Ile Glu Asp Gly Glu Arg Gly Cys 130 135 140 Met Lys Gln Met Val Asp Leu Phe Asp Lys Glu Gln Ser Ser Val Leu 145 150 155 160 Gly Val Glu Arg Val Asp Pro Lys Glu Thr His Lys Tyr Gly Ile Val 165 170 175 Glu His Ala Glu Thr Ser Pro Arg Val Gly Trp Leu Ser Ser Ile Val 180 185 190 Glu Lys Pro Lys Pro Glu Val Ala Pro Ser Asn Ile Ala Val Val Gly 195 200 205 Arg Tyr Ile Leu Thr Pro Ala Ile Phe Gln Lys Ile Glu Asn Thr Gly 210 215 220 Arg Gly Ala Gly Gly Glu Ile Gln Leu Thr Asp Ala Ile Ala Ala Leu 225 230 235 240 Met Lys Asp Glu Arg Val Leu Ser Tyr Glu Phe Glu Gly Asn Arg Tyr 245 250 255 Asp Cys Gly Ser Lys Phe Gly Phe Leu Leu Ala Asn Val Glu Tyr Gly 260 265 270 Leu Leu His Lys Glu Ile Lys Ala Glu Phe Ala Asn Tyr Leu Lys Gln 275 280 285 Arg Val Ser Lys Ile 290 3 1419 DNA Methylomonas 16a 3 atgccactcg gtttgggaaa tatcttcaac gggctgttca agcaatacgg gcacacggtg 60 atcctgttgt tgagggttat cgacgtggtc atgttattgg gcgcggcctg gctggcgcat 120 tatttttggt tgcatgacag cgtcatcgat cagcattacc gtttcgtgat tgccctgggt 180 atcttgggtg cgatcatatt tttcgagatc ggccaggtgt atcggccgtg gcgcaatgac 240 gcgatgcgcg gcgaaattcc ccgcatcatc agagcctggt tgctggcctt gctgacggtg 300 gtgtccatcg tggccctggt cagattgcat ttttggtttg gttccagtta tcgctggatc 360 gcctcctggg gcggtttggg gctgttcttc gtactggcgg cccgcggtgt gctggcacag 420 gtgttgaagt ggttgcgtgc acggggctgg agccaggggc gcatcattct ggtgggtttg 480 aatcagatgg ccgtcgccgt cagtcggcaa ttgaatcact cttcctgggc cggtttgcag 540 gtgattggtt atgtcgatga ccgggccgaa gaccggctgg cggtggcgga ttattcgctg 600 ccacgcctgg gcaagttgag cgatctgcct cgtctggttt ccagacaagc cgtggatgaa 660 gtctgggtgg cgtttcctgg cgcttcgctg gccgagcggg tacagcacga attgcgccat 720 ttgccggtca gcattcgcct ggtgatcgat tgctttgcct ttaaacaaag caaattcctc 780 agtctgaaca cggtggccgg tatcccgacg ctggacgtct cggtgtcgcc gctgcatggc 840 gtcaatcgct atatcaagga aatcgaggac cgcttgctgg ccttgctgtt gttgttgctg 900 atcagcccgt tgatgctggt cattgcgctt ggcgtgaaac tgagttctcc gggcccggtg 960 ttttacaagc aggtcagagt gggctggaac aatcgcaaat tcacgatgct gaagtttcgt 1020 tcgatgccgg tcgatgccga ggccaaaacc ggcgcggtct gggccaggcc cggcgaaaac 1080 cgtgcaaccc ggtttggggc cttcctgcgc aaaaccagtc tggacgagtt gccgcagttg 1140 atcaatgtgc tcaagggcga catgtcgctg gtcggcccgc gccctgaacg gcccgatttc 1200 gtcgaggtgt tcaaggatca agtacccaat tacatgaaaa aacacatggt caaggcgggc 1260 attaccggtt gggcacaagt caacggctgg cgcggtgata ccgacctgaa tcgccgcatc 1320 gaacacgatc tgtattacat ccagcattgg tcggtctggt tcgatctgga gattgccttt 1380 cgcaccgtgt tgaccggctt tatcaacaaa aatgcctat 1419 4 473 PRT Methylomonas 16a 4 Met Pro Leu Gly Leu Gly Asn Ile Phe Asn Gly Leu Phe Lys Gln Tyr 1 5 10 15 Gly His Thr Val Ile Leu Leu Leu Arg Val Ile Asp Val Val Met Leu 20 25 30 Leu Gly Ala Ala Trp Leu Ala His Tyr Phe Trp Leu His Asp Ser Val 35 40 45 Ile Asp Gln His Tyr Arg Phe Val Ile Ala Leu Gly Ile Leu Gly Ala 50 55 60 Ile Ile Phe Phe Glu Ile Gly Gln Val Tyr Arg Pro Trp Arg Asn Asp 65 70 75 80 Ala Met Arg Gly Glu Ile Pro Arg Ile Ile Arg Ala Trp Leu Leu Ala 85 90 95 Leu Leu Thr Val Val Ser Ile Val Ala Leu Val Arg Leu His Phe Trp 100 105 110 Phe Gly Ser Ser Tyr Arg Trp Ile Ala Ser Trp Gly Gly Leu Gly Leu 115 120 125 Phe Phe Val Leu Ala Ala Arg Gly Val Leu Ala Gln Val Leu Lys Trp 130 135 140 Leu Arg Ala Arg Gly Trp Ser Gln Gly Arg Ile Ile Leu Val Gly Leu 145 150 155 160 Asn Gln Met ala Val Ala Val Ser Arg Gln Leu Asn His Ser Ser Trp 165 170 175 Ala Gly Leu Gln Val Ile Gly Tyr Val Asp Asp Arg Ala Glu Asp Arg 180 185 190 Leu Ala Val Ala Asp Tyr Ser Leu Pro Arg Leu Gly Lys Leu Ser Asp 195 200 205 Leu Pro Arg Leu Val Ser Arg Gln Ala Val Asp Glu Val Trp Val Ala 210 215 220 Phe Pro Gly Ala Ser Leu Ala Glu Arg Val Gln His Glu Leu Arg His 225 230 235 240 Leu Pro Val Ser Ile Arg Leu Val Ile Asp Cys Phe Ala Phe Lys Gln 245 250 255 Ser Lys Phe Leu Ser Leu Asn Thr Val Ala Gly Ile Pro Thr Leu Asp 260 265 270 Val Ser Val Ser Pro Leu His Gly Val Asn Arg Tyr Ile Lys Glu Ile 275 280 285 Glu Asp Arg Leu Leu Ala Leu Leu Leu Leu Leu Leu Ile Ser Pro Leu 290 295 300 Met Leu Val Ile Ala Leu Gly Val Lys Leu Ser Ser Pro Gly Pro Val 305 310 315 320 Phe Tyr Lys Gln Val Arg Val Gly Trp Asn Asn Arg Lys Phe Thr Met 325 330 335 Leu Lys Phe Arg Ser Met Pro Val Asp Ala Glu Ala Lys Thr Gly Ala 340 345 350 Val Trp Ala Arg Pro Gly Glu Asn Arg Ala Thr Arg Phe Gly Ala Phe 355 360 365 Leu Arg Lys Thr Ser Leu Asp Glu Leu Pro Gln Leu Ile Asn Val Leu 370 375 380 Lys Gly Asp Met Ser Leu Val Gly Pro Arg Pro Glu Arg Pro Asp Phe 385 390 395 400 Val Glu Val Phe Lys Asp Gln Val Pro Asn Tyr Met Lys Lys His Met 405 410 415 Val Lys Ala Gly Ile Thr Gly Trp Ala Gln Val Asn Gly Trp Arg Gly 420 425 430 Asp Thr Asp Leu Asn Arg Arg Ile Glu His Asp Leu Tyr Tyr Ile Gln 435 440 445 His Trp Ser Val Trp Phe Asp Leu Glu Ile Ala Phe Arg Thr Val Leu 450 455 460 Thr Gly Phe Ile Asn Lys Asn Ala Tyr 465 470 5 1098 DNA Methylomonas 16a 5 atgtttagac taattcccat catgctggtt ttactgttgc caggctgttt cctggcaccg 60 ggtatggata tgcagaccga tggcgacttg acagaaatcg agctgccaac catgaagggc 120 gggcagttgg tcaaggagaa aacccgcatt cagccgatca ccgccgattt gatcatcgag 180 cgtgaagtcg cacggcggca agccgtcaac aatctaccgc cgatggacga aacccggacc 240 agttatcgca tcggtccgca ggacaggttg caaatcacgg tatgggagca tcccgaactg 300 aacgatcccg gcggcgagaa aatcctgccg gaactggccg gcaaggtcgt ggacgataac 360 ggcgatttgt attaccccta tgtcggtacc cttcatgtcg gcggcaagac cgtcaccgaa 420 gtgcgcgagg aattgacccg cgaactgtcc aaatacttca aaaaggtcaa actcgacatt 480 cgtgtgctgt cgttccaggc tcaccgcgtc gcggtggtcg gtgaagtcag aaatcccggc 540 atcgtcgcga tgaccgaaac gccgttgacg gtggcagaag ccatcagcag ggccggcggc 600 gccacgcaag attccgattt gaacaacgtc gcgctggccc gcggcggccg gttgtacaaa 660 ctggatgtgc aagccttgta tgaaaaaggc ctgaccacgc aaaacctgct gttgcgggat 720 ggcgatgtgc tgaacgtcgg cgatcagaaa gacagcaagg tttatgtgat gggcgaggtc 780 ggccggcagc aggccatcca gatcaacaag ggccggatga gtctggctca ggcgctggcc 840 gaagcctatg gcgtcgattt caacacctcg cgtcccggcg atatttacgt gctgcgcgcc 900 ggcgacatgc agccggagat tttccagctg gacgccgaat cgcccgacgc gatgatcctg 960 gccgagcaat tcccgttgca gccgcacgac acgctattcg tcggtacggc cggggtcacg 1020 caatggtcca gggtgctgaa tcagattctg ccgggttcgt ttaccgccat catgtcgcaa 1080 gccgcgatga tggggatg 1098 6 366 PRT Methylomonas 16a 6 Met Phe Arg Leu Ile Pro Ile Met Leu Val Leu Leu Leu Pro Gly Cys 1 5 10 15 Phe Leu Ala Pro Gly Met Asp Met Gln Thr Asp Gly Asp Leu Thr Glu 20 25 30 Ile Glu Leu Pro Thr Met Lys Gly Gly Gln Leu Val Lys Glu Lys Thr 35 40 45 Arg Ile Gln Pro Ile Thr Ala Asp Leu Ile Ile Glu Arg Glu Val Ala 50 55 60 Arg Arg Gln Ala Val Asn Asn Leu Pro Pro Met Asp Glu Thr Arg Thr 65 70 75 80 Ser Tyr Arg Ile Gly Pro Gln Asp Arg Leu Gln Ile Thr Val Trp Glu 85 90 95 His Pro Glu Leu Asn Asp Pro Gly Gly Glu Lys Ile Leu Pro Glu Leu 100 105 110 Ala Gly Lys Val Val Asp Asp Asn Gly Asp Leu Tyr Tyr Pro Tyr Val 115 120 125 Gly Thr Leu His Val Gly Gly Lys Thr Val Thr Glu Val Arg Glu Glu 130 135 140 Leu Thr Arg Glu Leu Ser Lys Tyr Phe Lys Lys Val Lys Leu Asp Ile 145 150 155 160 Arg Val Leu Ser Phe Gln Ala His Arg Val Ala Val Val Gly Glu Val 165 170 175 Arg Asn Pro Gly Ile Val Ala Met Thr Glu Thr Pro Leu Thr Val Ala 180 185 190 Glu Ala Ile Ser Arg Ala Gly Gly Ala Thr Gln Asp Ser Asp Leu Asn 195 200 205 Asn Val Ala Leu Ala Arg Gly Gly Arg Leu Tyr Lys Leu Asp Val Gln 210 215 220 Ala Leu Tyr Glu Lys Gly Leu Thr Thr Gln Asn Leu Leu Leu Arg Asp 225 230 235 240 Gly Asp Val Leu Asn Val Gly Asp Gln Lys Asp Ser Lys Val Tyr Val 245 250 255 Met Gly Glu Val Gly Arg Gln Gln Ala Ile Gln Ile Asn Lys Gly Arg 260 265 270 Met Ser Leu Ala Gln Ala Leu Ala Glu Ala Tyr Gly Val Asp Phe Asn 275 280 285 Thr Ser Arg Pro Gly Asp Ile Tyr Val Leu Arg Ala Gly Asp Met Gln 290 295 300 Pro Glu Ile Phe Gln Leu Asp Ala Glu Ser Pro Asp Ala Met Ile Leu 305 310 315 320 Ala Glu Gln Phe Pro Leu Gln Pro His Asp Thr Leu Phe Val Gly Thr 325 330 335 Ala Gly Val Thr Gln Trp Ser Arg Val Leu Asn Gln Ile Leu Pro Gly 340 345 350 Ser Phe Thr Ala Ile Met Ser Gln Ala Ala Met Met Gly Met 355 360 365 7 2337 DNA Methylomonas 16a 7 atgccgccct tgaatcccgt gatgatgcag gagcctggcg tcagcatccg cgattatgtc 60 gatctgttga tcgagggcaa gaagacaata ctgttgacgt tggccatcgt gctgagcgtg 120 acgatgattt atttggtttt ggccccgcgc acttacaagg ccgatgcctt gctgcgtatc 180 gacaaaaata aagccttgtt ggcggccaat ttgcgtagcg agggcaatgg tacgccaacg 240 gaggcggaaa accccagggc gcaacgggaa gtggaaattt tgcgctcgcg ttcggtgctg 300 ggcaaggtgg tggaggattt gaatctagtc gtggaggcgt cgccacgata ctttcccatc 360 atcggcgaaa ccctggcccg caagcacgac aaacatgagg gcgtagccgg cgcctggtgg 420 ggattcagcc gttgggcctg gggcggggaa aaactgaaaa tcgagcgttt cgaggtgccc 480 gatcgttacc tggacaaggc ttttactttg gtggcgctgg aagcagggcg ttttcaatta 540 ttgagcccta agggcgaggt gctggccgaa ggtttgctcg gtgaaacgct gaccgccgac 600 atcggcgaag ccagtcccgt cgtcgtcaac gtcgctgatt tgcaggcgca ttacggcacc 660 gagttcgagt tgcggcgcaa aacctcgctg gcggccatag aaaccctgca aaaagccttt 720 tcggtcaagg aagtgtccaa ggataccaat attctgagtg tcgaactcaa ggggcgcgat 780 cccgagcaat tggccaaatc ggtcaacgac atcgccagta tttacgtcaa cgccacggtg 840 aattgggaat cggcggaagc ctcgcaaaag ctgaatttcc tggagagcca gttgccgctg 900 gtgaaggaga atctggaaaa ggctgagcaa gccttgagcg cttaccggca gcaacatggc 960 gcggtggata tttccgccga agccgaaatc ctgctgaaac aggcctcgga aatggaaacc 1020 ttgagcatac aactcaagca aaagtacgac gagcaaagcc agcgtctgga atcggagcat 1080 ccggacatga tcgccaccaa tgcgcaaatc cgccgggtga gcaataaatt ggcggccttg 1140 gaaaagcgca tcaaggactt gccgaagacg cagcaaaaca tggtcagcct gtcgcgcgat 1200 gtgcaggtca ataccgagct ttacacctcg ttgctgaaca gcgcgcagga gcaacgcatc 1260 gccgcggccg gttccctggg taattcgcgc atcgtcgatt tcgcggtggt tccggaaaaa 1320 ccttattggc ccaagcccgg tttgctgttg gcgattgccg gtttgctggg catcagtctg 1380 ggttcggcgc tgatattcct gagacattcg ttgcagcgcc atgacaatta tccggccttg 1440 ctggaatacc aggtcggctt gccgctgttc gccgccattc cgcacagcaa gaaacaaaga 1500 cgcttggcac gcctgctgga tcagggcaag gagcgggata ccgcgattct ggtcagccac 1560 gatccgctgg atatttcggt cgaatccttg cgcggcttgc gcactacgct ggaagcgacg 1620 ctggccagcg atgaaagcaa ggtcatcatg gtcagcagtc cggcgccggg catgggtaaa 1680 tccttcatca gcaccaattt ggcggctctg ttggccagca tacgcaagcg ggtgctgatc 1740 atcgacgccg acatgcgcaa cggccgcctg catgaaacct ttgccattgc caagcaaccg 1800 ggcttgtccg atctgctgtc cggcaaggtc agcctgggcg acgtgatcgt cagtttgccg 1860 gagataggcg tggatttgat tcccaggggc gagatggtgc tgaatccggc cgaattgttg 1920 gtgctgggcg atctggccga taccttggag caactgaaga gcttttacaa ccatatcgtc 1980 atcgattcgc cgccgatctt gggcgccacc gacgcggcga tcatgggcaa gcattgcgat 2040 gctaccttcc tggtggtcaa ggagggccgt tataccgcgc aagagctgga ggtcagtttc 2100 aggcgcttgc agcaagtcgg cgtgaaaccc aacggtttca tcatcaacga catgaaggaa 2160 ggttcgtcct attacccgta ctacggctat gcctatcagc gggatgacat gcgacaaaaa 2220 caaaccacgg cttggcaggc gcgctttcaa aacctgaatg actggatggg gcggcaggac 2280 gccgagtatt tacccgtcgc cgacgacgcg gaagaacttc acgacagcat cagggcc 2337 8 779 PRT Methylomonas 16a 8 Met Pro Pro Leu Asn Pro Val Met Met Gln Glu Pro Gly Val Ser Ile 1 5 10 15 Arg Asp Tyr Val Asp Leu Leu Ile Glu Gly Lys Lys Thr Ile Leu Leu 20 25 30 Thr Leu Ala Ile Val Leu Ser Val Thr Met Ile Tyr Leu Val Leu Ala 35 40 45 Pro Arg Thr Tyr Lys Ala Asp Ala Leu Leu Arg Ile Asp Lys Asn Lys 50 55 60 Ala Leu Leu Ala Ala Asn Leu Arg Ser Glu Gly Asn Gly Thr Pro Thr 65 70 75 80 Glu Ala Glu Asn Pro Arg Ala Gln Arg Glu Val Glu Ile Leu Arg Ser 85 90 95 Arg Ser Val Leu Gly Lys Val Val Glu Asp Leu Asn Leu Val Val Glu 100 105 110 Ala Ser Pro Arg Tyr Phe Pro Ile Ile Gly Glu Thr Leu Ala Arg Lys 115 120 125 His Asp Lys His Glu Gly Val Ala Gly Ala Trp Trp Gly Phe Ser Arg 130 135 140 Trp Ala Trp Gly Gly Glu Lys Leu Lys Ile Glu Arg Phe Glu Val Pro 145 150 155 160 Asp Arg Tyr Leu Asp Lys Ala Phe Thr Leu Val Ala Leu Glu Ala Gly 165 170 175 Arg Phe Gln Leu Leu Ser Pro Lys Gly Glu Val Leu Ala Glu Gly Leu 180 185 190 Leu Gly Glu Thr Leu Thr Ala Asp Ile Gly Glu Ala Ser Pro Val Val 195 200 205 Val Asn Val Ala Asp Leu Gln Ala His Tyr Gly Thr Glu Phe Glu Leu 210 215 220 Arg Arg Lys Thr Ser Leu Ala Ala Ile Glu Thr Leu Gln Lys Ala Phe 225 230 235 240 Ser Val Lys Glu Val Ser Lys Asp Thr Asn Ile Leu Ser Val Glu Leu 245 250 255 Lys Gly Arg Asp Pro Glu Gln Leu Ala Lys Ser Val Asn Asp Ile Ala 260 265 270 Ser Ile Tyr Val Asn Ala Thr Val Asn Trp Glu Ser Ala Glu Ala Ser 275 280 285 Gln Lys Leu Asn Phe Leu Glu Ser Gln Leu Pro Leu Val Lys Glu Asn 290 295 300 Leu Glu Lys Ala Glu Gln Ala Leu Ser Ala Tyr Arg Gln Gln His Gly 305 310 315 320 Ala Val Asp Ile Ser Ala Glu Ala Glu Ile Leu Leu Lys Gln Ala Ser 325 330 335 Glu Met Glu Thr Leu Ser Ile Gln Leu Lys Gln Lys Tyr Asp Glu Gln 340 345 350 Ser Gln Arg Leu Glu Ser Glu His Pro Asp Met Ile Ala Thr Asn Ala 355 360 365 Gln Ile Arg Arg Val Ser Asn Lys Leu Ala Ala Leu Glu Lys Arg Ile 370 375 380 Lys Asp Leu Pro Lys Thr Gln Gln Asn Met Val Ser Leu Ser Arg Asp 385 390 395 400 Val Gln Val Asn Thr Glu Leu Tyr Thr Ser Leu Leu Asn Ser Ala Gln 405 410 415 Glu Gln Arg Ile Ala Ala Ala Gly Ser Leu Gly Asn Ser Arg Ile Val 420 425 430 Asp Phe Ala Val Val Pro Glu Lys Pro Tyr Trp Pro Lys Pro Gly Leu 435 440 445 Leu Leu Ala Ile Ala Gly Leu Leu Gly Ile Ser Leu Gly Ser Ala Leu 450 455 460 Ile Phe Leu Arg His Ser Leu Gln Arg His Asp Asn Tyr Pro Ala Leu 465 470 475 480 Leu Glu Tyr Gln Val Gly Leu Pro Leu Phe Ala Ala Ile Pro His Ser 485 490 495 Lys Lys Gln Arg Arg Leu Ala Arg Leu Leu Asp Gln Gly Lys Glu Arg 500 505 510 Asp Thr Ala Ile Leu Val Ser His Asp Pro Leu Asp Ile Ser Val Glu 515 520 525 Ser Leu Arg Gly Leu Arg Thr Thr Leu Glu Ala Thr Leu Ala Ser Asp 530 535 540 Glu Ser Lys Val Ile Met Val Ser Ser Pro Ala Pro Gly Met Gly Lys 545 550 555 560 Ser Phe Ile Ser Thr Asn Leu Ala Ala Leu Leu Ala Ser Ile Arg Lys 565 570 575 Arg Val Leu Ile Ile Asp Ala Asp Met Arg Asn Gly Arg Leu His Glu 580 585 590 Thr Phe Ala Ile Ala Lys Gln Pro Gly Leu Ser Asp Leu Leu Ser Gly 595 600 605 Lys Val Ser Leu Gly Asp Val Ile Val Ser Leu Pro Glu Ile Gly Val 610 615 620 Asp Leu Ile Pro Arg Gly Glu Met Val Leu Asn Pro Ala Glu Leu Leu 625 630 635 640 Val Leu Gly Asp Leu Ala Asp Thr Leu Glu Gln Leu Lys Ser Phe Tyr 645 650 655 Asn His Ile Val Ile Asp Ser Pro Pro Ile Leu Gly Ala Thr Asp Ala 660 665 670 Ala Ile Met Gly Lys His Cys Asp Ala Thr Phe Leu Val Val Lys Glu 675 680 685 Gly Arg Tyr Thr Ala Gln Glu Leu Glu Val Ser Phe Arg Arg Leu Gln 690 695 700 Gln Val Gly Val Lys Pro Asn Gly Phe Ile Ile Asn Asp Met Lys Glu 705 710 715 720 Gly Ser Ser Tyr Tyr Pro Tyr Tyr Gly Tyr Ala Tyr Gln Arg Asp Asp 725 730 735 Met Arg Gln Lys Gln Thr Thr Ala Trp Gln Ala Arg Phe Gln Asn Leu 740 745 750 Asn Asp Trp Met Gly Arg Gln Asp Ala Glu Tyr Leu Pro Val Ala Asp 755 760 765 Asp Ala Glu Glu Leu His Asp Ser Ile Arg Ala 770 775 9 1416 DNA Methylomonas 16a 9 atgttgggca aagggcattc ggacaaggct aatttaaagg aaggtttcat gctggattgg 60 ttgaggcaaa agaacttgtt gggtgacgcc tgttgggcgc tggcgggaca gttattgtcg 120 gcactggctt tgcttgcggg cacgcgcatc ctgaccgaat tggtgacgcc ggcggttttc 180 gggcacgtgg cgttgctgaa tggcttcgtc gcgctggggg tggcggtgtt tgcctatccc 240 ttcatctgcg ccgggatgcg tttcaccaat gaatgccgaa atttccgcga gcgggcggca 300 ttgcatggat tggtgtttgc gctgacgacg cgatcgacgg cattggccat taccttgctg 360 ctgctgggcg gcgcgctgta ttgctatttt gtcggtagtg aaatcggctt gttcgtgttg 420 accggattgc tgttagccgt caccgttcgc cgcgagttgg gcattcagct gatgataggc 480 gaacgcaagc aacgcggcgc cgcgctttgg caaaccagcg acagcatcct gcggccggtg 540 atggcgattt ggctggtatg gggtttgggg caaagtccgg aagcggtgtt gttgggctat 600 gtctgtgcca gcgtgctggc caatacgctg tggacgatcg taagcgatgc atggcaaaaa 660 aagcctaccg gcgatcgcgg cttcctgggg cggcaattcg agcgcggcct ttgggcttat 720 gccttgccgt tgatcccgat ggaattgatg ttctggctca acggcctggg cgaccgttac 780 gtgatcggtt atttcctaac ggcggctgaa gtgggggtgt acgcggccgc ttatacgctg 840 gtcaacgaag ccttcaatcg tagcgcgatg gtgttgttgc gcacgtttca gccggcctat 900 tttcaagcgg tttcccaagg caaaagcaaa gatgcatgtt cgctgctatg gctgtggata 960 ggggcggtcg tcgtgatgag tgttctgggc gtgacgctgg tctggttgtg caaggactgg 1020 ctggtcgcag gcttgttggc agaaccctat catgcggccg gcgcgctgat gccggttatc 1080 gccgcgggca cggccttgca tgccctgggc accgtgatgt cccagccgct gctggcgaga 1140 aaacgcacgc cgatcttgct gcgcgggcgt atctgtgggg cgttggcggc gctcatcacg 1200 ctgcctttgc tggtggcgca ttttggcctg ttcggggcgg ccttggccaa tcccgtatat 1260 ttcggcatcg aagcgctggt gttggccttg ctggccaagc cctggcgcaa gctccgcacg 1320 ggacggcagg cgcggatcgt tcaatccgaa gcggcgatgc ccgaacccga ctttgacgcc 1380 atcggagtga gagcggcggc gttctccaac gaatcc 1416 10 472 PRT Methylomonas 16a 10 Met Leu Gly Lys Gly His Ser Asp Lys Ala Asn Leu Lys Glu Gly Phe 1 5 10 15 Met Leu Asp Trp Leu Arg Gln Lys Asn Leu Leu Gly Asp Ala Cys Trp 20 25 30 Ala Leu Ala Gly Gln Leu Leu Ser Ala Leu Ala Leu Leu Ala Gly Thr 35 40 45 Arg Ile Leu Thr Glu Leu Val Thr Pro Ala Val Phe Gly His Val Ala 50 55 60 Leu Leu Asn Gly Phe Val Ala Leu Gly Val Ala Val Phe Ala Tyr Pro 65 70 75 80 Phe Ile Cys Ala Gly Met Arg Phe Thr Asn Glu Cys Arg Asn Phe Arg 85 90 95 Glu Arg Ala Ala Leu His Gly Leu Val Phe Ala Leu Thr Thr Arg Ser 100 105 110 Thr Ala Leu Ala Ile Thr Leu Leu Leu Leu Gly Gly Ala Leu Tyr Cys 115 120 125 Tyr Phe Val Gly Ser Glu Ile Gly Leu Phe Val Leu Thr Gly Leu Leu 130 135 140 Leu Ala Val Thr Val Arg Arg Glu Leu Gly Ile Gln Leu Met Ile Gly 145 150 155 160 Glu Arg Lys Gln Arg Gly Ala Ala Leu Trp Gln Thr Ser Asp Ser Ile 165 170 175 Leu Arg Pro Val Met ala Ile Trp Leu Val Trp Gly Leu Gly Gln Ser 180 185 190 Pro Glu Ala Val Leu Leu Gly Tyr Val Cys Ala Ser Val Leu Ala Asn 195 200 205 Thr Leu Trp Thr Ile Val Ser Asp Ala Trp Gln Lys Lys Pro Thr Gly 210 215 220 Asp Arg Gly Phe Leu Gly Arg Gln Phe Glu Arg Gly Leu Trp Ala Tyr 225 230 235 240 Ala Leu Pro Leu Ile Pro Met Glu Leu Met Phe Trp Leu Asn Gly Leu 245 250 255 Gly Asp Arg Tyr Val Ile Gly Tyr Phe Leu Thr Ala Ala Glu Val Gly 260 265 270 Val Tyr Ala Ala Ala Tyr Thr Leu Val Asn Glu Ala Phe Asn Arg Ser 275 280 285 Ala Met Val Leu Leu Arg Thr Phe Gln Pro Ala Tyr Phe Gln Ala Val 290 295 300 Ser Gln Gly Lys Ser Lys Asp Ala Cys Ser Leu Leu Trp Leu Trp Ile 305 310 315 320 Gly Ala Val Val Val Met Ser Val Leu Gly Val Thr Leu Val Trp Leu 325 330 335 Cys Lys Asp Trp Leu Val Ala Gly Leu Leu Ala Glu Pro Tyr His Ala 340 345 350 Ala Gly Ala Leu Met Pro Val Ile Ala Ala Gly Thr Ala Leu His Ala 355 360 365 Leu Gly Thr Val Met Ser Gln Pro Leu Leu Ala Arg Lys Arg Thr Pro 370 375 380 Ile Leu Leu Arg Gly Arg Ile Cys Gly Ala Leu Ala Ala Leu Ile Thr 385 390 395 400 Leu Pro Leu Leu Val Ala His Phe Gly Leu Phe Gly Ala Ala Leu Ala 405 410 415 Asn Pro Val Tyr Phe Gly Ile Glu Ala Leu Val Leu Ala Leu Leu Ala 420 425 430 Lys Pro Trp Arg Lys Leu Arg Thr Gly Arg Gln Ala Arg Ile Val Gln 435 440 445 Ser Glu Ala Ala Met Pro Glu Pro Asp Phe Asp Ala Ile Gly Val Arg 450 455 460 Ala Ala Ala Phe Ser Asn Glu Ser 465 470 11 816 DNA Methylomonas 16a 11 ccgataaaca ggtgtgaacc attgaacagc ttgaccatag tcattttgac gctgaacgag 60 gccgccaatc tgccccggtg cctggcggcg attccgcaac gttaccctgt cgtgatcttg 120 gattccggga gcagcgatga cacgctgtcg atcgcggaag gccacggctg caagatttat 180 caaaatcctt ggcccggctt tgccgagcag cgcaattttg cgttgaatca atgcgatatc 240 gagacgccgt gggtgttgtt cgtcgatgcc gacgaaatct acccgcaagt cttttatcag 300 catttcgaca gtggaatgct gcaaaccgga gagatcgatg tgctgatggt gccgtccatt 360 ttgtttttgc gcggcaaacg cctgcatcat gcgccgggtt atccgatcta tcacccgcgc 420 ctggttcggc gggaaacgac ccgcttcgtg cgtaatcata ccggtcacgg cgaggccgtc 480 atggatagtt gccgcatcgg ctacaccgat attccctatg atcattactt ttacgacggc 540 gagatcatcc agtggatgca taagcatgtc gacaaagccg ctcaggaagt tcggctcaaa 600 ccgacccagg gcgcgttgat gacgacccgc gggcgcttga gcgtaatgct ggggcgttca 660 tggagccgaa tcctggccag gtttgtttac cactatctgc tgcgcggcgg ctttttggac 720 ggcgcggcgg gattggaatt tacgctgatg tttacctggt atgaagccag catctatctg 780 caagccaaag ccgctgcaca agcaagggga acagca 816 12 272 PRT Methylomonas 16a 12 Pro Ile Asn Arg Cys Glu Pro Leu Asn Ser Leu Thr Ile Val Ile Leu 1 5 10 15 Thr Leu Asn Glu Ala Ala Asn Leu Pro Arg Cys Leu Ala Ala Ile Pro 20 25 30 Gln Arg Tyr Pro Val Val Ile Leu Asp Ser Gly Ser Ser Asp Asp Thr 35 40 45 Leu Ser Ile Ala Glu Gly His Gly Cys Lys Ile Tyr Gln Asn Pro Trp 50 55 60 Pro Gly Phe Ala Glu Gln Arg Asn Phe Ala Leu Asn Gln Cys Asp Ile 65 70 75 80 Glu Thr Pro Trp Val Leu Phe Val Asp Ala Asp Glu Ile Tyr Pro Gln 85 90 95 Val Phe Tyr Gln His Phe Asp Ser Gly Met Leu Gln Thr Gly Glu Ile 100 105 110 Asp Val Leu Met Val Pro Ser Ile Leu Phe Leu Arg Gly Lys Arg Leu 115 120 125 His His Ala Pro Gly Tyr Pro Ile Tyr His Pro Arg Leu Val Arg Arg 130 135 140 Glu Thr Thr Arg Phe Val Arg Asn His Thr Gly His Gly Glu Ala Val 145 150 155 160 Met Asp Ser Cys Arg Ile Gly Tyr Thr Asp Ile Pro Tyr Asp His Tyr 165 170 175 Phe Tyr Asp Gly Glu Ile Ile Gln Trp Met His Lys His Val Asp Lys 180 185 190 Ala Ala Gln Glu Val Arg Leu Lys Pro Thr Gln Gly Ala Leu Met Thr 195 200 205 Thr Arg Gly Arg Leu Ser Val Met Leu Gly Arg Ser Trp Ser Arg Ile 210 215 220 Leu Ala Arg Phe Val Tyr His Tyr Leu Leu Arg Gly Gly Phe Leu Asp 225 230 235 240 Gly Ala Ala Gly Leu Glu Phe Thr Leu Met Phe Thr Trp Tyr Glu Ala 245 250 255 Ser Ile Tyr Leu Gln Ala Lys Ala Ala Ala Gln Ala Arg Gly Thr Ala 260 265 270 13 852 DNA Methylomonas 16a 13 atgaaagtgt cattgatatt ggctacgctc ggcagggacc tggaactgct ggattttttg 60 aaatccttgc tgtttcagac ctacaagaac ttcgagttga tcgtcatcga ccagaatcaa 120 gacggcaaaa tcgatcggat tgccgagcaa tatagccaat gcctcgatct gaaacacgtc 180 aaggtgaatt tcaccggtaa tgcccgagcc agggatcatg gcatcgcctt ggcccagggc 240 gacatcatcg cctttccgga cgatgattgc gtgtatgaaa aggatgtgct ggaaaaagtg 300 gtaggcgaat ttgcatgcca gccaacgttg tcgattctgg tagccgggtc ctacgatttt 360 tccgcgaaac acttcagcat aggcgtcaac agccgtaaag cgcgttattt ttcccggttg 420 aacatgatgg gggtggagtt cacgcagttt tttgcgctgg cgcgtatcga caggcggcag 480 ttttatttgg accacgattt cggcatcggc tccaaatatg ccggggcgga aggcttcgag 540 ttgctgtatc gcctgctgcg cgcgggcggg cgggcgttct acaagccgga tatcaaaatc 600 tatcacgcca acaaggacca ttacacgctg ggtaccgcgc gcatgctgaa atattccacc 660 ggtattggcg cctatatccg caaattcgcc aatcagcatg atccctatat cggctattac 720 atcctgcgca agatgctgat agccccgact ctgaaaatgc tgctggcctt gttgacgttc 780 aacccgggaa aactcgccta ttcgttttat aacctggtgg gcatatggcg cggatttttt 840 gcctatgggc gc 852 14 284 PRT Methylomonas 16a 14 Met Lys Val Ser Leu Ile Leu Ala Thr Leu Gly Arg Asp Leu Glu Leu 1 5 10 15 Leu Asp Phe Leu Lys Ser Leu Leu Phe Gln Thr Tyr Lys Asn Phe Glu 20 25 30 Leu Ile Val Ile Asp Gln Asn Gln Asp Gly Lys Ile Asp Arg Ile Ala 35 40 45 Glu Gln Tyr Ser Gln Cys Leu Asp Leu Lys His Val Lys Val Asn Phe 50 55 60 Thr Gly Asn Ala Arg Ala Arg Asp His Gly Ile Ala Leu Ala Gln Gly 65 70 75 80 Asp Ile Ile Ala Phe Pro Asp Asp Asp Cys Val Tyr Glu Lys Asp Val 85 90 95 Leu Glu Lys Val Val Gly Glu Phe Ala Cys Gln Pro Thr Leu Ser Ile 100 105 110 Leu Val Ala Gly Ser Tyr Asp Phe Ser Ala Lys His Phe Ser Ile Gly 115 120 125 Val Asn Ser Arg Lys Ala Arg Tyr Phe Ser Arg Leu Asn Met Met Gly 130 135 140 Val Glu Phe Thr Gln Phe Phe Ala Leu Ala Arg Ile Asp Arg Arg Gln 145 150 155 160 Phe Tyr Leu Asp His Asp Phe Gly Ile Gly Ser Lys Tyr Ala Gly Ala 165 170 175 Glu Gly Phe Glu Leu Leu Tyr Arg Leu Leu Arg Ala Gly Gly Arg Ala 180 185 190 Phe Tyr Lys Pro Asp Ile Lys Ile Tyr His Ala Asn Lys Asp His Tyr 195 200 205 Thr Leu Gly Thr Ala Arg Met Leu Lys Tyr Ser Thr Gly Ile Gly Ala 210 215 220 Tyr Ile Arg Lys Phe Ala Asn Gln His Asp Pro Tyr Ile Gly Tyr Tyr 225 230 235 240 Ile Leu Arg Lys Met Leu Ile Ala Pro Thr Leu Lys Met Leu Leu Ala 245 250 255 Leu Leu Thr Phe Asn Pro Gly Lys Leu Ala Tyr Ser Phe Tyr Asn Leu 260 265 270 Val Gly Ile Trp Arg Gly Phe Phe Ala Tyr Gly Arg 275 280 15 1194 DNA Methylomonas 16a 15 atggaactgg gtattgtgac gacacatgta ccgccggcca agggctacgg tggcgtctcg 60 gtgacttgcg gcgtcttgac cagggcgtgg gcggaaatgg ggctagagat ggcgctggtt 120 tcgtcggatg aatccatcga tgggtgcttg aaaccggcgg acgtcaagct gggcgcaagc 180 gtggatgtcg atttgtaccg ctgttatggc ttcaggcgct gggggttcgg cttgggagcg 240 atacccagcc tgctgcgcct gtgctggcaa gccccgctcg tgtatatcca tggcgtcgcc 300 acctggccgt cgaccttggc ggcgcttttt tgctgcctgc tgcgcaagcc gttcatggtg 360 gcggtgcatg gcggcctgat gcctgagcat gtggcactga tcaagcggaa aaaacggcat 420 aaatggtggt attacaaact gctgactttt ccgaccttgc gccgcgcgat tgccgtgcat 480 tgcaccagtg ataccgaggt tgagggcgtg cgtgacgtac tgggcgaaaa cgcgcgggtg 540 ttgctggtgc ccaacggcat cgacagccgg ggtgtcgagg aggcccctta tccggcaggc 600 gaaggcatgc aactgtgttt tttgggtcac gtgcagcagg aaaagggcat caacgctttc 660 atccgggcct ggctcgaggt ccggcggccg ggcgatcgtc tggtcgtcgc cggccgtagc 720 gtggacgggg attattttgc cgagttttgt tccctggtcg aacgggcaaa cggcgcgatc 780 cgctattgcg gctatctgca gcgtgacgac gtgatggcct tgctggcgca aagtcatttt 840 ctggtattgc cgtccggttt ggagcaggtc ggcggcatgc gggagaattt cggtaacgtg 900 gtggcggaag ccctggcggc gggacggccg gtgctggttg tcaggggctt ggcctgggat 960 catttgccgg cattgaatgc gggcttggtt tttgacaggg acgaggccgc cgtccaagcc 1020 gtgctacgcc gggctcaggc gctcgatcaa gccgactggc tgcgcatgtc gcaagcgggc 1080 cggcgccatg ttcaacagca gctcgatccg gtcaaactgg cggagcgcgt ctggcaagca 1140 atgacggcgg cggtaccggt tgacgaggcc aaggtgttgg ccgaggagcc gaaa 1194 16 398 PRT Methylomonas 16a 16 Met Glu Leu Gly Ile Val Thr Thr His Val Pro Pro Ala Lys Gly Tyr 1 5 10 15 Gly Gly Val Ser Val Thr Cys Gly Val Leu Thr Arg Ala Trp Ala Glu 20 25 30 Met Gly Leu Glu Met ala Leu Val Ser Ser Asp Glu Ser Ile Asp Gly 35 40 45 Cys Leu Lys Pro Ala Asp Val Lys Leu Gly Ala Ser Val Asp Val Asp 50 55 60 Leu Tyr Arg Cys Tyr Gly Phe Arg Arg Trp Gly Phe Gly Leu Gly Ala 65 70 75 80 Ile Pro Ser Leu Leu Arg Leu Cys Trp Gln Ala Pro Leu Val Tyr Ile 85 90 95 His Gly Val Ala Thr Trp Pro Ser Thr Leu Ala Ala Leu Phe Cys Cys 100 105 110 Leu Leu Arg Lys Pro Phe Met Val Ala Val His Gly Gly Leu Met Pro 115 120 125 Glu His Val Ala Leu Ile Lys Arg Lys Lys Arg His Lys Trp Trp Tyr 130 135 140 Tyr Lys Leu Leu Thr Phe Pro Thr Leu Arg Arg Ala Ile Ala Val His 145 150 155 160 Cys Thr Ser Asp Thr Glu Val Glu Gly Val Arg Asp Val Leu Gly Glu 165 170 175 Asn Ala Arg Val Leu Leu Val Pro Asn Gly Ile Asp Ser Arg Gly Val 180 185 190 Glu Glu Ala Pro Tyr Pro Ala Gly Glu Gly Met Gln Leu Cys Phe Leu 195 200 205 Gly His Val Gln Gln Glu Lys Gly Ile Asn Ala Phe Ile Arg Ala Trp 210 215 220 Leu Glu Val Arg Arg Pro Gly Asp Arg Leu Val Val Ala Gly Arg Ser 225 230 235 240 Val Asp Gly Asp Tyr Phe Ala Glu Phe Cys Ser Leu Val Glu Arg Ala 245 250 255 Asn Gly Ala Ile Arg Tyr Cys Gly Tyr Leu Gln Arg Asp Asp Val Met 260 265 270 Ala Leu Leu Ala Gln Ser His Phe Leu Val Leu Pro Ser Gly Leu Glu 275 280 285 Gln Val Gly Gly Met Arg Glu Asn Phe Gly Asn Val Val Ala Glu Ala 290 295 300 Leu Ala Ala Gly Arg Pro Val Leu Val Val Arg Gly Leu Ala Trp Asp 305 310 315 320 His Leu Pro Ala Leu Asn Ala Gly Leu Val Phe Asp Arg Asp Glu Ala 325 330 335 Ala Val Gln Ala Val Leu Arg Arg Ala Gln Ala Leu Asp Gln Ala Asp 340 345 350 Trp Leu Arg Met Ser Gln Ala Gly Arg Arg His Val Gln Gln Gln Leu 355 360 365 Asp Pro Val Lys Leu Ala Glu Arg Val Trp Gln Ala Met Thr Ala Ala 370 375 380 Val Pro Val Asp Glu Ala Lys Val Leu Ala Glu Glu Pro Lys 385 390 395 17 951 DNA Methylomonas 16a 17 atgacgcata aggttggact cgtcgtaccc accttgaatg cgggcgcatc ctggcagggc 60 tggctggagg ccctggcggc gcaaagtcga aggccggatc gtttgttgct gatcgattcc 120 tcgtccagcg acgacacggt ggcgctggcc cgtgcgagag gatttgacgc gcatgtgatt 180 gccaaggcct cgttcaacca cggcggcact cgtcaatcgg gcgtcgatat gttggtcgac 240 atggatctga tcgtatttct gacccaggat gccttgttgg ccgaccccag cgcgatcgaa 300 aatctgttgc aggtatttgt caatccgcaa gtggccgcgg cctatggccg gcaattgccg 360 catcggaacg ctggccccat cggcgcgcat gcccggatat tcaattaccc ggcgcaaagc 420 cagttgcgca ccttgcagga ccgcgaccgc ttcggcatca agaccgtgtt catttccaat 480 tcgttcgccg cctacagacg ttgcgccctg atgcaaatcg gcggattccc ggctcacacc 540 attatgaacg aagatactta cgttgccggc aagatgctgt tgtccggctg gagcctcgcc 600 tattgcgccg acgcgcgggt gtttcattcc cacgattaca gcctgctgga agaattcagg 660 cgctatttcg atatcggggt tttccacgcg caaaacccct ggctgcaaca gacctttggc 720 ggcgcctcgg gcgaaggcgc gcgttttgtg ctctccgaaa tgcgttactt gtcgaacacg 780 gcgccctggc tgatgttttc cgcgttcctg agaacgggat tgaaatgggc ggggtataag 840 ctgggcggcc tgcatcgcgg ctggccatta gccctgagca ggcgcctcag cctgcataag 900 ggatattggg tggcaactga acgggaatac cctaatatgc ctggatgccg t 951 18 317 PRT Methylomonas 16a 18 Met Thr His Lys Val Gly Leu Val Val Pro Thr Leu Asn Ala Gly Ala 1 5 10 15 Ser Trp Gln Gly Trp Leu Glu Ala Leu Ala Ala Gln Ser Arg Arg Pro 20 25 30 Asp Arg Leu Leu Leu Ile Asp Ser Ser Ser Ser Asp Asp Thr Val Ala 35 40 45 Leu Ala Arg Ala Arg Gly Phe Asp Ala His Val Ile Ala Lys Ala Ser 50 55 60 Phe Asn His Gly Gly Thr Arg Gln Ser Gly Val Asp Met Leu Val Asp 65 70 75 80 Met Asp Leu Ile Val Phe Leu Thr Gln Asp Ala Leu Leu Ala Asp Pro 85 90 95 Ser Ala Ile Glu Asn Leu Leu Gln Val Phe Val Asn Pro Gln Val Ala 100 105 110 Ala Ala Tyr Gly Arg Gln Leu Pro His Arg Asn Ala Gly Pro Ile Gly 115 120 125 Ala His Ala Arg Ile Phe Asn Tyr Pro Ala Gln Ser Gln Leu Arg Thr 130 135 140 Leu Gln Asp Arg Asp Arg Phe Gly Ile Lys Thr Val Phe Ile Ser Asn 145 150 155 160 Ser Phe Ala Ala Tyr Arg Arg Cys Ala Leu Met Gln Ile Gly Gly Phe 165 170 175 Pro Ala His Thr Ile Met Asn Glu Asp Thr Tyr Val Ala Gly Lys Met 180 185 190 Leu Leu Ser Gly Trp Ser Leu Ala Tyr Cys Ala Asp Ala Arg Val Phe 195 200 205 His Ser His Asp Tyr Ser Leu Leu Glu Glu Phe Arg Arg Tyr Phe Asp 210 215 220 Ile Gly Val Phe His Ala Gln Asn Pro Trp Leu Gln Gln Thr Phe Gly 225 230 235 240 Gly Ala Ser Gly Glu Gly Ala Arg Phe Val Leu Ser Glu Met Arg Tyr 245 250 255 Leu Ser Asn Thr Ala Pro Trp Leu Met Phe Ser Ala Phe Leu Arg Thr 260 265 270 Gly Leu Lys Trp Ala Gly Tyr Lys Leu Gly Gly Leu His Arg Gly Trp 275 280 285 Pro Leu Ala Leu Ser Arg Arg Leu Ser Leu His Lys Gly Tyr Trp Val 290 295 300 Ala Thr Glu Arg Glu Tyr Pro Asn Met Pro Gly Cys Arg 305 310 315

Claims (34)

What is claimed is:
1. An isolated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme, selected from the group consisting of:
(a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18;
(b) an isolated nucleic acid molecule that hybridizes with (a) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS; and
(c) an isolated nucleic acid molecule that is complementary to (a) or (b).
2. The isolated nucleic acid molecule of claim 1 selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, and 17.
3. A polypeptide encoded by the isolated nucleic acid molecule of claim 1.
4. The polypeptide of claim 3 selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18.
5. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 293 amino acids that has at least 58% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 2, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
6. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 473 amino acids that has at least 36% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 4, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
7. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 366 amino acids that has at least 36% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 6, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
8. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 779 amino acids that has at least 35% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 8, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
9. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 472 amino acids that has at least 23% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 10, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
10. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 272 amino acids that has at least 28% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 12, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
11. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 284 amino acids that has at least 21% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 14, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
12. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 398 amino acids that has at least 26% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 16, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
13. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 317 amino acids that has at least 51% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO: 18, or a second nucleotide sequence comprising the complement of the first nucleotide sequence.
14. A chimeric gene comprising the isolated nucleic acid molecule of any one of claims 1 or 5-13 operably linked to suitable regulatory sequences.
15. A transformed host cell comprising the chimeric gene of claim 14.
16. The transformed host cell of claim 15 wherein the host cell is selected from the group consisting of bacteria, yeast, filamentous fungi, and green plants.
17. The transformed host cell of claim 16 wherein the host cell is selected from the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Candida, Hansenula, Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, Pseudomonas, Methylomonas, Methylobacter, Alcaligenes, Synechocystis, Anabaena, Thiobacillus, Methanobacterium and Klebsiella.
18. The transformed host cell of claim 16 wherein the host cell is selected from the group consisting of soybean, rapeseed, sunflower, cotton, corn, tobacco, alfalfa, wheat, barley, oats, sorghum, rice, Arabidopsis, cruciferous vegetables, melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, grass seed crops, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses.
19. A method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising:
(a) probing a genomic library with the nucleic acid molecule of any one of claims 1 or 5-13;
(b) identifying a DNA clone that hybridizes with the nucleic acid molecule of any one of claims 1 or 5-13; and
(c) sequencing the genomic fragment that comprises the clone identified in step (b),
wherein the sequenced genomic fragment encodes a Methylomonas sp exopolysaccharide biosynthetic enzyme.
20. A method of obtaining a nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme comprising:
(a) synthesizing an at least one oligonucleotide primer corresponding to a portion of the sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, and 17; and
(b) amplifying an insert present in a cloning vector using the oligonucleotide primer of step (a);
wherein the amplified insert encodes a portion of an amino acid sequence encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme.
21. The product of the method of claims 19 or 20.
22. A method for the production of exopolysaccharide comprising: contacting a transformed host cell under suitable growth conditions with an effective amount of a carbon source whereby exopolysaccharide is produced, said transformed host cell comprising a set of nucleic acid molecules encoding SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, and 18; under the control of suitable regulatory sequences.
23. A method according to claim 22 wherein the transformed host cell is selected form the group consisting of Aspergillus, Trichoderma, Saccharomyces, Pichia, Candida, Hansenula, Salmonella, Bacillus, Acinetobacter, Rhodococcus, Streptomyces, Escherichia, Pseudomonas, Methylomonas, Methylobacter, Alcaligenes, Synechocystis, Anabaena, Thiobacillus, Methanobacterium and Klebsiella.
24. A method according to claim 22 wherein said methanotrophic bacteria:
(a) grows on a C1 carbon substrate selected from the group consisting of methane and methanol; and
(b) comprises a functional Embden-Meyerhof carbon pathway, said pathway comprising a gene encoding a pyrophosphate dependent phosphofructokinase enzyme.
25. A method according to claim 24 wherein said methanotrophic bacteria is methylomonas 16a ATCC PTA 2402.
26. A method according to claim 22 wherein the transformed host cell is selected form the group consisting of: soybean, rapeseed, sunflower, cotton, corn, tobacco, alfalfa, wheat, barley, oats, sorghum, rice, Arabidopsis, cruciferous vegetables, melons, carrots, celery, parsley, tomatoes, potatoes, strawberries, peanuts, grapes, grass seed crops, sugar beets, sugar cane, beans, peas, rye, flax, hardwood trees, softwood trees, and forage grasses.
27. A method according to claim 22 wherein the carbon source is selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, carbon dioxide, methanol, methane, formaldehyde, formate, and carbon-containing amines.
28. A method according to claim 22 wherein the transformed host is selected from the group consisting of Methylomonas, Methylobacter and Methanobacterium and the carbon source is selected from the group consisting of methane and methanol.
29. A method of regulating exopolysaccharide biosynthesis in an organism comprising, over-expressing at least one isoprenoid gene selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, and 17 in an organism such that the exopolysaccharide biosynthesis is altered in the organism.
30. A method according to claim 29 wherein said exopolysaccharide gene is over-expressed on a multicopy plasmid.
31. A method according to claim 29 wherein said exopolysaccharide gene is operably linked to an inducible or regulated promoter.
32. A method according to claim 29 wherein said exopolysaccharide gene is expressed in antisense orientation.
33. A method according to claim 29 wherein said exopolysaccharide gene is disrupted by insertion of foreign DNA into the coding region.
34. A mutated nucleic acid molecule encoding a Methylomonas sp exopolysaccharide biosynthetic enzyme having an altered biological activity produced by a method comprising the steps of:
(i) digesting a mixture of nucleotide sequences of any one of claims 1 or 5-13 with restriction endonucleases wherein said mixture comprises:
a) a native microbial gene;
b) a first population of nucleotide fragments which will hybridize to said native microbial sequence;
c) a second population of nucleotide fragments which will not hybridize to said native microbial sequence;
 wherein a mixture of restriction fragments are produced;
(ii) denaturing said mixture of restriction fragments;
(iii) incubating the denatured said mixture of restriction fragments of step (ii) with a polymerase;
(iv) repeating steps (ii) and (iii) wherein a mutated microbial gene is produced encoding a protein having an altered biological activity.
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EP1358333A2 (en) 2003-11-05
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US20030166171A1 (en) 2003-09-04
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US6537786B2 (en) 2003-03-25

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