Natural promoters for gene expression in C1 metabolizing bacteria

FIELD OF THE INVENTION

[0001] This invention is in the field of bacterial gene expression and metabolic engineering. More specifically, the invention relates to the use of promoter regions isolated from a Methylomonas sp. for gene expression in C1 metabolizing bacteria.

BACKGROUND INFORMATION

[0002] Methanotrophic bacteria are defined by their ability to use methane as their sole source of carbon and energy under ambient conditions. This ability, in conjunction with the abundance of methane, makes the biotransformation of methane a potentially unique and valuable process. As such, several approaches have been used in attempts to harnesss the unique natural abilities of these organisms for commercial applications.

[0003] Historically, the commercial applications of biotransformation of methane have fallen broadly into three categories:

[0004] 1) Production of single cell protein (Sharpe D. H. BioProtein Manufacture (1989). Ellis Horwood series in applied science and industrial technology. New York: Halstead Press) (Villadsen, John, Recent Trends Chem. React. Eng., [Proc. Int. Chem. React. Eng. Conf.], 2nd (1987), Volume 2, pp 320-33. Editor(s): Kulkarni, B. D.; Mashelkar, R. A.; Sharma, M. M. Publisher: Wiley East., New Delhi, India; Naguib, M., Proc. OAPEC Symp. Petroprotein, [Pap.] (1980), Meeting Date 1979, pp 253-77 Publisher: Organ. Arab Pet. Exporting Countries, Kuwait, Kuwait);

[0005] 2) Epoxidation of alkenes for production of chemicals (U.S. Pat. No. 4,348,476); and

[0006] 3) Biodegradation of chlorinated pollutants (Tsien et al., Gas, Oil, Coal, Environ. Biotechnol. 2, [Pap. Int. IGT Symp. Gas, Oil, Coal, Environ. Biotechnol.], 2nd (1990), pp 83-104. Editor(s): Akin, Cavit; Smith, Jared. Publisher: Inst. Gas Technol., Chicago, Ill.; WO 9,633,821; Merkley et al., Biorem. Recalcitrant Org., [Pap. Int. In Situ On-Site Bioreclam. Symp.], 3rd (1995), pp. 165-74. Editor(s): Hinchee, Robert E; Anderson, Daniel B.; Hoeppel, Ronald E. Publisher: Battelle Press, Columbus, Ohio; Meyer et al., Microb. Releases 2(1): 11-22 (1993)).

[0007] Epoxidation of alkenes has experienced only slight commercial success due to low product yields, toxicity of products and the large amount of cell mass required to generate products.

[0008] Large-scale protein production from methane, termed single cell protein or SCP, has been technically feasible and commercialized at large scale (Villadsen, supra). Single cell protein is a relatively low value product. As such, the economic production cannot tolerate heavy bioprocessing costs. The yield of the methanotrophic strain used for producing SCP may be critical to the overall economic viability of the process. Microbial biomass produced by methanotrophic bacteria is typically very high in protein content (−70-80% by weight), which can restrict the direct use of this protein to certain types of animal feed.

[0009] In addition to the synthesis of SCP, methanotrophic cells can further build the oxidation products of methane (i.e. methanol and formaldehyde) into complex molecules such as carbohydrates and lipids. For example, under certain conditions methanotrophs are known to produce exopolysaccharides (WO 02/20797; WO 02/20728; Ivanova et al., Mikrobiologiya 57(4):600-5 (1988); Kilbane, John J., II Gas, Oil, Coal, Environ. Biotechnol. 3, [Pap. IGT's Int. Symp.], 3rd (1991), Meeting Date 1990, pp. 207-26. Editor(s): Akin, Cavit; Smith, Jared. Publisher: IGT, Chicago, Ill.). Similarly, methanotrophs are known to accumulate both isoprenoid compounds and carotenoid pigments of various carbon lengths (WO 02/20733; WO 02/20728; Urakami et al., J. Gen. Appl. Microbiol. 32(4):317-41 (1986)).

[0010] Most recently, the natural abilities of methanotrophic organisms have been stretched by the advances of genetic engineering. Odom et al. have investigated Methyolomonas sp. 16a as a microbial platform of choice for production of a variety of materials beyond single cell protein including carbohydrates, pigments, terpenoid compounds and aromatic compounds (WO 02/20728; WO 02/18617). This particular methanotrophic bacterial strain is capable of efficiently using either methanol or methane as a carbon substrate, is metabolically versatile in that it contains multiple pathways for the incorporation of carbon from formaldehyde into 3-carbon units, and is amenable to genetic engineering via bacterial conjugation using donor species such as Escherichia coli. Thus, Methyolomonas sp. 16a can be engineered to produce new classes of products other than those naturally produced from methane. Further advancement in the metabolic engineering of methanotrophs such as Methyolomonas sp. 16a, however, is currently limited by the lack of a detailed understanding of promoters useful to drive the expression of foreign and native genes in this host. Additionally, it would be useful to possess a suite of promoters that are individually regulatable under a variety of natural growth and induction conditions.

[0011] In general, prokaryotic promoters can play an important role in biotechnology, particularly for directing expression of chimeric genes to alter cellular metabolism to produce larger quantities of a natural productor new products. Producing high levels of a specific protein may also be desirable as a product. Promoters that are generally used for gene expression in E. coli may not be suitable for driving chimeric gene expression in Methylomonas, especially when a strong or inducible promoter is required. Promoters that are strong in E. coli, generally have much lower expression levels in Methylomonas. Induction systems used with inducible promoters in E. coli generally do not function well in Methylomonas.

[0012] The problem to be solved therefore is to provide promoters that are useful for expression of chimeric genes under desired conditions in Methylomonas. Promoters with high expression during growth on methane and methanol are valuable when Methylomonas is used as a production host. Similarly, promoters induced by growth on nitrate and by change in temperature and pH conditions are very applicable in industrial settings, as each of these conditions can be adjusted easily. Applicants have solved the stated problem by identifying genes within the Methylomonas sp. 16a genome that are regulated by designated metabolic and growth conditions, and isolating the promoters from these genes. The nucleic acid sequences of the genes can be used for bioreactor monitoring in Methylomonas sp. and C1 metabolizing bacterial cultures. Specifically, applicants have used microarray technology to identify genes that are responsive to: 1.) growth on methane and methanol; 2.) induction in the presence of nitrate; 3.) induction by change in growth temperature; and 4.) induction by modification of media pH. Homologs of these genes should be useful for similar purposes in a variety of C1 metabolizing bacteria.

SUMMARY OF THE INVENTION

[0013] The invention relates to new promoter regions isolated from inducible genes isolated from a species of Methylomonas designated herein as Methylomonas 16a. The promoter regions are derived from; a nitrogen transporter gene (nrtA) and a nitrogen regulating protein (glnB), both inducible by nitrate; a heat shock protein encoding gene (htpB), inducible at elevated temperature; a methanol dehydrogenaase gene (moxF) and a hexulose-6-phosphate syntase (hps) both highly expressed in the presence of methanol or methane. Theses promoter regions have been found to be effective for drivign the expression of a variety of coding regions in C1 metabolizing bacteria.

[0014] Accordingly the invention provides a method for the expression of a coding region of interest in a C1 metabolizing bacteria comprising:

[0015] a) providing a transformed C1 metabolizing bacterial cell having a chimeric gene comprising;

[0016] 1) a promoter region of a gene selected from the group consisting of: a nrtA gene and a glnB gene; and

[0017] 2) a coding region of interest expressible in a C1 metabolizing bacteria;

[0018] wherein the promoter region is operably linked to a coding region of interest; and

[0019] b) growing the transformed C1 metabolizing bacteria cell of step (a) in the presence of nitrate wherein the chimeric gene is expressed.

[0020] Similarly the invention provides a method for the expression of a coding region of interest in a C1 metabolizing bacteria comprising:

[0021] a) providing a transformed C1 metabolizing bacterial cell having a chimeric gene comprising;

[0022] 1) a promoter region of a glyoxil gene; and

[0023] 2) a coding region of interest expressible in a C1 metabolizing bacteria;

[0024] wherein the promoter region is operably linked to a coding region of interest; and

[0025] b) growing the transformed C1 metabolizing bacteria cell of step (a) at a pH of about 5.5 wherein the chimeric gene is expressed.

[0026] In an alternate embodiment the invention provides a method for the expression of a coding region of interest in a C1 metabolizing bacteria comprising:

[0027] a) providing a transformed C1 metabolizing bacterial cell having a chimeric gene comprising;

[0028] 1) a promoter region of a htpG gene; and

[0029] 2) a coding region of interest expressible in a C1 metabolizing bacteria;

[0030] wherein the promoter region is operably linked to a coding region of interest; and

[0031] b) growing the transformed C1 metabolizing bacteria cell of step (a) at a temperature suitable for induction of the promoter region wherein the chimeric gene is expressed.

[0032] In another embodiment the invention provides a method for the expression of a coding region of interest in a C1 metabolizing bacteria comprising:

[0033] a) providing a transformed C1 metabolizing bacterial cell having a chimeric gene comprising;

[0034] 1) a promoter region of a gene selected from the group consisting of: a moxF gene and a hps gene; and

[0035] 2) a coding region of interest expressible in a C1 metabolizing bacteria;

[0036] wherein the promoter region is operably linked to a coding region of interest; and

[0037] b) growing the transformed C1 metabolizing bacteria cell of step (a) in the presence of a C1 carbon source selected from the group consisting of methane and methanol wherein the chimeric gene of step (a) is expressed.

[0038] Preferred hosts for expression the promoter regions of the invention are methanotrophs and methylotrophs.

[0039] Preferred coding regions for expression under the control of the promoter regions of the invention are those involved in the biosynthesis of carotenoids.

[0040] The invention additionally provides an isolated nucleic acid molecule encoding a nitrate inducible gene selected from the group consisting of:

[0041] (a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:5;

[0042] (b) an isolated nucleic acid molecule that hybridizes with (a) under stringent conditions and is washed with 0.1×SSC, 0.1% SDS, 65° C.; or

[0043] an isolated nucleic acid molecule that is complementary to (a), or (b).

[0044] Similarly the invention provides an isolated nucleic acid molecule encoding a pH inducible gene selected from the group consisting of:

[0045] a) an isolated nucleic acid molecule encoding the amino acid sequence as set forth in SEQ ID NO:8;

[0046] b) an isolated nucleic acid molecule that hybridizes with (a) under stringent conditions and is washed with 0.1×SSC, 0.1% SDS, 65° C.; or

[0047] an isolated nucleic acid molecule that is complementary to (a), or (b).

[0048] In another embodiment the invention provides an isolated nucleic acid molecule encoding a temperature inducible gene selected from the group consisting of:

[0049] a) an isolated nucleic acid molecule encoding the amino acid sequence as set forth in SEQ ID NO:11;

[0050] b) an isolated nucleic acid molecule that hybridizes with (a) under stringent conditions and is washed with 0.1×SSC, 0.1% SDS, 65° C.; or an isolated nucleic acid molecule that is complementary to (a), or (b).

[0051] Similarly the invention provides an isolated nucleic acid molecule encoding a methane or methanol inducible gene selected from the group consisting of:

[0052] (a) an isolated nucleic acid molecule encoding the amino acid sequence selected from the group consisting of SEQ ID NO:14, and 17;

[0053] (b) an isolated nucleic acid molecule that hybridizes with (a) under stringent conditions and is washed with 0.1×SSC, 0.1% SDS, 65° C.; or an isolated nucleic acid molecule that is complementary to (a), or (b).

[0054] In specific embodiments the invention provides promoter regions isolated from the subject genes having the nucleic acid sequences as set forth in SEQ ID NO:3 and SEQ ID NO:6, SEQ ID NO:9, SEQ ID NO:12, SEQ ID NO:15, and SEQ ID NO:18.

[0055] In addition to the nucleic acids of the invention, the invention provides polypeptides encoded thereby, chimeric genes comprising the nucleic acids of the invention, and host cells transformed therewith.

BRIEF DESCRIPTION OF THE FIGURES, SEQUENCE DESCRIPTIONS, AND BIOLOGICAL DEPOSITS

[0056]
FIG. 1 is a plasmid map of pTJS75LacZKam with insertion of the moxF promoter drawn.

[0057]
FIG. 2A schematically illustrates the plasmid map of pHPS, while FIG. 2B is a plasmid map for pCRT18. FIG. 2C shows HPLC results demonstrating the presence of zeaxanthin glucosides in Methylomonas cells transformed with pCRT18.

[0058]
FIG. 3A is a plasmid map of pCRT24. FIG. 3B shows HPLC results confirming the presence of zeaxanthin in Methylomonas cells transformed with pCRT24.

[0059] The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions, which form a part of this application.

[0060] The following sequences conform with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.

[0061] SEQ ID NOs:1-18 are full length coding regions (open reading frames, or ORFs), proteins, or promoter fragments, as identified in Table 1.

1TABLE 1Summary of DNA and Protein SEQ ID NumbersSEQ IDNucleic acidSEQ IDSEQ ID(PromoterDescriptionNucleic acidPeptideFragment)Nitrogen transporter (nrtA)123Nitrogen regulating PII-protein456(glnB)Glyoxalase ii (glyoxII)789Heat shock protein (htpG)101112Methanol dehydrogenase131415(moxF)Hexulose-6-phosphate161718syntase (hps)

[0062] SEQ ID NOs:19 and 20 are primers used for amplification of the moxF promoter.

[0063] SEQ ID NOs:21 and 22 are primers used for amplification of the hps promoter.

[0064] SEQ ID NOs:23-26 are primers used for deletion of the crtX coding region.

[0065] Applicants made the following biological deposits under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure:

2InternationalDepositor IdentificationDepositoryReferenceDesignationDate of DepositMethylomonas 16aATCC PTA 2402Aug. 22, 2000

DETAILED DESCRIPTION OF THE INVENTION

[0066] The present invention describes the isolation and characterization of inducible genes and their promoters from a high growth methanotrophic bacterial strain, Methylomonas sp. 16a. These promoters that are responsive to growth on methane and methanol and induction by the presence of nitrate, a change in growth temperature, or modification of media pH, will be useful to regulate the production of biomass including proteins, carbohydrates and pigments in Methylomonas sp. 16a and other C1 metabolizing bacteria. Thus, the present invention advances the art by providing:

[0067] (i) A method for the expression of a coding region of interest in a C1 metabolizing bacteria by nitrate induction;

[0068] (ii) A method for the expression of a coding region of interest in a C1 metabolizing bacteria by low pH (˜5.5) induction;

[0069] (iii) A method for the expression of a coding region of interest in a C1 metabolizing bacteria by elevating growth temperature as an inducing condition; and

[0070] (iv) A method for the expression of a coding region of interest in a C1 metabolizing bacteria by growth in methane or methanol.

[0071] In addition, nucleic acid sequences homologous to the present coding regions, or ORFs, and promoter fragments of the invention are expected to function in a similar manner for related applications in other C1 metabolizing bacteria.

[0072] Definitions

[0073] In this disclosure, a number of terms and abbreviations are used. The following definitions are provided.

[0074] “Open reading frame” is abbreviated ORF.

[0075] “Polymerase chain reaction” is abbreviated PCR.

[0076] The term “genomic DNA” refers to the total DNA from an organism.

[0077] The term “total RNA” refers to the non-fractionated RNA from an organism.

[0078] “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” or “mRNA” refers to 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 a RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to a 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.

[0079] The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from a coding sequence. Expression may also refer to translation of mRNA into a polypeptide.

[0080] The term “up-regulated” as applied to gene expression means the mRNA transcriptional level of a particular gene or region in the test condition is increased relative to the control condition. In contrast, the term “down-regulated” as applied to gene expression means the mRNA transcriptional level of a particular gene or region in the test condition is decreased relative to the control condition.

[0081] The term “growth cycle” as applied to a cell refers to the metabolic cycle through which a cell moves in culture conditions. The cycle may be divided into various stages known as the exponential phase, the end of exponential phase, and the stationary phase.

[0082] The term “exponential growth”, “exponential phase growth”, “log phase” or “log phase growth” refer to the rate at which microorganisms are growing and dividing. When growing in log phase microorganisms are growing at the maximal rate possible given their genetic potential, the nature of the medium, and the conditions under which they are grown. Microorganism rate of growth is constant during exponential phase and the microorganism divides and doubles in number at regular intervals. Cells that are “actively growing” are those that are growing in log phase. In contrast to the definition of “exponential growth”, the term “stationary phase” refers to the growth cycle phase where cell growth in a culture slows or even ceases. The term “growth-altering environment” refers to energy, chemicals, or living things that have the capacity to either inhibit cell growth or kill cells. Inhibitory agents may include, but are not limited to: mutagens, antibiotics, UV light, gamma-rays, x-rays, extreme temperature, phage, macrophages, organic chemicals and inorganic chemicals.

[0083] “State of the cell” refers to metabolic state of the organism when grown under different conditions.

[0084] The term “expression profile” refers to the expression of groups of genes under a given set of conditions.

[0085] The term “gene expression profile” refers to the expression of an individual gene and of suites of individual genes.

[0086] The term “DNA microarray” or “DNA chip” means the assembling of PCR products of a group of genes or all genes within a genome on a solid surface in a high density format or array. General methods for array construction and use are available (for example, see Schena M., et al. Science. 270(5235): 467-70 (1995). A DNA microarray allows for analysis of gene expression patterns or profiles of many genes to be performed simultaneously by hybridizing the DNA microarray comprising these genes or PCR products of these genes with cDNA probes prepared from the sample to be analyzed. DNA microarray or “chip” technology permits examination of gene expression on a genomic scale, allowing transcription levels of many genes to be measured simultaneously. Briefly, the technology comprises arraying microscopic amounts of DNA complementary to genes of interest or open reading frames on a solid surface at defined positions. This solid surface is generally a glass slide or a membrane (e.g., nylon). The DNA sequences may be arrayed by spotting or by photolithography. Two separate fluorescently-labeled probe mixes prepared from the two sample(s) to be compared are hybridized to the microarray. The presence and amount of the bound probes are detected by fluorescence, following laser excitation using a scanning confocal microscope, and quantitated using a laser scanner and appropriate array analysis software packages. Cy3 (green) and Cy5 (red) fluorescent labels are routinely used in the art; however, other similar fluorescent labels may also be employed. To obtain and quantitate a gene expression profile or pattern between the two compared samples, the ratio between the signals in the two channels (red:green) is calculated with the relative intensity of Cy5/Cy3 probes taken as a reliable measure of the relative abundance of specific mRNAs in each sample. Materials for the construction of DNA microarrays are commercially available: Affymetrix (Santa Clara, Calif.); Sigma Chemical Company (St. Louis, Mo.); Genosys (The Woodlands, Tex.); Clontech (Palo Alto, Calif.); and Corning (Corning, N.Y.). In addition, custom-made DNA microarrays can be prepared by commercial vendors such as Affymetrix, Clontech, and Corning.

[0087] The term “C1 carbon substrate” refers to any carbon-containing molecule that lacks a carbon-carbon bond. Examples are methane, methanol, formaldehyde, formic acid, formate, methylated amines (e.g., mono-, di-, and tri-methyl amine), methylated thiols, and carbon dioxide.

[0088] The term “C1 metabolizer” refers to a microorganism that has the ability to use a single carbon substrate as its sole source of energy and biomass. C1 metabolizers will typically be methylotrophs and/or methanotrophs.

[0089] The term “C1 metabolizing bacteria” refers to bacteria that have the ability to use a single carbon substrate as their sole source of energy and biomass. C1 metabolizing bacteria, a subset of C1 metabolizers, will typically be methylotrophs and/or methanotrophs.

[0090] The term “methylotroph” means an organism capable of oxidizing organic compounds that do not contain carbon-carbon bonds. Where the methylotroph is able to oxidize CH4, the methylotroph is also a methanotroph.

[0091] The term “methanotroph” or “methanotrophic bacteria” means a prokaryote capable of utilizing methane as its primary source of carbon and energy. Complete oxidation of methane to carbon dioxide occurs by aerobic degradation pathways. Typical examples of methanotrophs useful in the present invention include but are not limited to the genera Methylomonas, Methylobacter, Methylococcus, and Methylosinus.

[0092] The term “high growth methanotrophic bacterial strain” refers to a bacterium capable of growth with methane or methanol as the sole carbon and energy source and which possesses a functional Embden-Meyerof carbon flux pathway, resulting in a high rate of growth and yield of cell mass per gram of C1 substrate metabolized (see WO 02/20728). The specific “high growth methanotrophic bacterial strain” described herein is referred to as “Methylomonas 16a”, “16a” or “Methylomonas sp. 16a”, which terms are used interchangeably and which refer to the Methylomonas strain used in the present invention.

[0093] A “nucleic acid” is a polymeric compound comprised of covalently linked subunits called nucleotides. Nucleic acids include polyribonucleic acid (RNA) and polydeoxyribonucleic acid (DNA), both of which may be single-stranded or double-stranded. DNA includes cDNA, genomic DNA, synthetic DNA, and semi-synthetic DNA.

[0094] As used herein, an “isolated nucleic acid fragment” is 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.

[0095] A nucleic acid fragment is “hybridizable” to another nucleic acid fragment, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid fragment can anneal to the other nucleic acid fragment under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Ed., 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. An additional set of stringent conditions include hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS, for example.

[0096] 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 complementarity, 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 the length of the probe.

[0097] The term “oligonucleotide” refers to a nucleic acid, generally of at least 18 nucleotides, that is hybridizable to a genomic DNA molecule, a cDNA molecule, or an mRNA molecule. Oligonucleotides can be labeled, e.g., with 32P-nucleotides or nucleotides to which a label, such as biotin, has been covalently conjugated. In one embodiment, a labeled oligonucleotide can be used as a “probe” to detect the presence of a nucleic acid according to the invention. Thus, the term “probe” refers to a single-stranded nucleic acid molecule that can base pair with a complementary single stranded target nucleic acid to form a double-stranded molecule. The term “label” will refer to any conventional molecule which can be readily attached to mRNA or DNA and which can produce a detectable signal, the intensity of which indicates the relative amount of hybridization of the labeled probe to the DNA fragment. Preferred labels are fluorescent molecules or radioactive molecules. A variety of well-known labels can be used.

[0098] A “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol. 215:403-410 (1993). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches 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.

[0099] The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. 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.

[0100] 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: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, NY (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, NY (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 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.

[0101] 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.

[0102] “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, 5, 8, 11, 14, 17, and 20. 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.

[0103] “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. Chimeric genes of the present invention will typically comprise an inducible promoter operably linked to a coding region of interest. “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.

[0104] The term “inducible gene” means any gene with high expression in response to a specific stress, stimulus, or growth condition. Inducible genes of the present invention include the genes identified as nrtA, glnB, glyoxil, htpg, moxF, and hps of Methlomonas sp. 16a.

[0105] “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.

[0106] The term “homolog”, as applied to a gene, means any gene derived from the same or a different microbe having the same function. A homologous gene may have significant sequence similarity.

[0107] “Coding sequence” or “coding region of interest” refers to a DNA sequence that codes for a specific amino acid sequence.

[0108] “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 sites, effector binding sites and stem-loop structures.

[0109] “Transcriptional and translational control sequences” are DNA regulatory sequences, such as promoters, enhancers, terminators, and the like, that provide for the expression of a coding sequence in a host cell. In eukaryotic cells, polyadenylation signals are control sequences.

[0110] “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. “Inducible promoter” means any promoter that is responsive to a particular stimulus. Inducible promoters of the present invention will typically be derived from the “inducible genes” and will be responsive to various metabolic conditions (growth substrate, nutrient composition, or environmental stress such as pH and temperature changes).

[0111] The terms “subfragment that is functionally equivalent” and “functionally equivalent subfragment” are used interchangeably herein. These terms refer to a portion or subsequence of an isolated nucleic acid fragment that retains the ability to confer gene expression or produce a certain phenotype. For example, the fragment or subfragment can be used for the expression of chimeric genes to produce the desired phenotype in a transformed host. The subfragment retains the promoter activity of the original full nucleic acid promoter fragment.

[0112] 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.

[0113] 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., 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.

[0114] “Mature” protein refers to a post-translationally processed polypeptide (i.e., 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.

[0115] The term “signal peptide” refers to an amino terminal polypeptide preceding a 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. A signal peptide is also referred to as a signal protein.

[0116] “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.

[0117] The terms “plasmid” and “vector” 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 fragments. 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 vector” refers to a specific plasmid containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. “Expression cassette” refers to a DNA fragment containing a coding region and having elements in addition to the coding region that allow for expression of that coding region in a specific host.

[0118] 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.

[0119] 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., J. Mol. Biol. 215:403410 (1990); DNASTAR (DNASTAR, Inc., Madison, Wis.); and the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, the results of the analysis are 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.

[0120] Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).

[0121] Identification of Natural Methylomonas sp. 16a Promoters

[0122] The present invention identifies a number of inducible genes contained within the Methylomonas genome that are responsive to various metabolic conditions. These genes are regulated in response to nitrate, pH, temperature, or growth in methane or methanol. More specifically, promoter regions that regulate nrtA, glnB, glyoxil, htpg, moxF and hps have been identified as useful for driving expression of any suitable coding region of interest in C1 metabolizing bacteria.

[0123] Application of Microarrays

[0124] Investigation of promoter activity in Methylomonas or any other bacterium often employs Northern blots, enzymatic assays, and reporter genes. These methods permit monitoring of the effect of environmental changes on gene expression by comparing expression levels of a limited number of genes. Although they often enable investigation of one or a subset of the physiological conditions, these methods typically fail to monitor the comprehensive responses of a preponderance of individual genes in the genome of an organism in a reliable and useful manner.

[0125] With the advances in genomic research, a powerful new way to identify promoters is the use of DNA microarrays. DNA microarray technology is used to explore gene expression profiles on a genome-wide scale (DeRisi, J. L., et al., Science 278: 680-686 (1997)). It allows for the identification of genes that are expressed in different growth stages or environmental conditions. Promoters isolated from the identified genes can then be used to express other coding regions in the growth stage or under the environmental conditions characteristic of the promoter. The gene sequences themselves may be used as probes to follow gene expression activity, which is valuable for industrial environments where the conditions for promoter induction must be convenient, cost effective and compatible with a specific bio-manufacturing process. Thus the identified gene sequences may be used to analyze the state of the biomass and cell response to growth conditions in a bioreactor.

[0126] Generation of Microarrays

[0127] The invention identifies a number of Methylomonas sp. 16a genes as being responsive to various conditions not heretofore appreciated. The identification of these genes as being regulated by the new inducing conditions was made by means of the application of DNA microarray technology to the Methylomonas sp. 16a genome. Any C1 metabolizing bacterial species may be used, however Methylomonas sp. strain 16a is preferred.

[0128] The generation of DNA microarrays is common and well known in the art (e.g., Brown et al., U.S. Pat. No. 6,110,426). Typically, the generation of a microarray begins by providing a nucleic acid sample representing the genome of the organism of interest. Typically, the ORFs of this nucleic acid sample are amplified to produce DNA fragments of the same sequence by methods of primer directed amplification such as, for example: polymerase chain reaction (PCR) (U.S. Pat. No. 4,683,202 (1987, Mullis, et al.) and U.S. Pat. No. 4,683,195 (1986, Mullis, et al.); ligase chain reaction (LCR) (Tabor et al., Proc. Acad. Sci. U.S.A., 82:1074-1078 (1985)); and/or, strand displacement amplification (Walker et al., Proc. Natl. Acad. Sci. U.S.A., 89: 392 (1992)). The denatured, amplified ORF DNA fragments are then spotted on slides comprised of glass or some other solid substrate by methods well known in the art to form a micro-array. Methods of forming high-density arrays of oligonucleotides, with a minimal number of synthetic steps are known (see for example Brown et al., U.S. Pat. No. 6,110,426). The oligonucleotide analogue array can be synthesized on a solid substrate by a variety of methods, including, but not limited to: light-directed chemical coupling and mechanically directed coupling. See Pirrung et al., U.S. Pat. No. 5,143,854 (also PCT Application No. WO 90/15070) and Fodor et al., PCT Publication NOs. WO 92/10092 and WO 93/09668, which disclose methods of forming vast arrays of peptides, oligonucleotides and other molecules using, for example, light-directed synthesis techniques. See also, Fodor et al., Science, 251:767-77 (1991).

[0129] The ORF DNA fragments are arrayed in high density on at least one glass microscope slide. Once all the ORFs from the genome are amplified, and the amplified DNA fragments are isolated and arrayed, a set of probes, bearing a signal generating label are synthesized. Typically probes are generated from mRNA transcript(s) of the gene(s), or nucleic acids derived from the mRNA transcript(s), of the organism of interest. As used herein, a nucleic acid derived from an mRNA transcript refers to the nucleic acid produced from a particular mRNA transcript or a sub-sequence thereof (i.e., the mRNA transcript serves as a template for the nucleic acid so derived). Thus, a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from the cDNA, an RNA transcribed from the amplified DNA, etc., are all derived from the mRNA transcript and detection using such derived products is indicative of the presence and/or abundance of the original transcript in a sample. Thus, suitable samples include, but are not limited to: mRNA transcripts of the gene(s), cDNA reverse transcribed from the mRNA, cRNA transcribed from the cDNA, DNA amplified from the gene(s), RNA transcribed from amplified DNA, and the like. Probes may be randomly generated or may be synthesized based on the sequence of specific open reading frames. Probes are typically single stranded nucleic acid sequences that are complementary to the nucleic acid sequences to be detected. Probes are “hybridizable” to the ORF DNA fragments of the array. 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.

[0130] Signal-generating labels that may be incorporated into the probes are well known in the art. For example, labels may include (but are not limited to): fluorescent moieties, chemiluminescent moieties, particles, enzymes, radioactive tags, or light emitting moieties or molecules. Fluorescent moieties are preferred. Most preferred are fluorescent dyes capable of attaching to nucleic acids and emitting a fluorescent signal. A variety of dyes are known in the art such as fluorescein, Texas Red, and rhodamine. Preferred are the mono reactive dyes Cy3 and Cy5, both available commercially (i.e. Amersham Pharmacia Biotech, Arlington Heights, Ill.). Suitable dyes are discussed in U.S. Pat. No. 5,814,454, hereby incorporated by reference.

[0131] Labels may be incorporated by any of a number of means well known to those of skill in the art. However, in a preferred embodiment, the label is simultaneously incorporated during the amplification step in the preparation of the probe nucleic acids. Thus, for example, polymerase chain reaction (PCR) with labeled primers or labeled nucleotides will provide a labeled amplification product. In a preferred embodiment, reverse transcription or replication using a labeled nucleotide (e.g. dye-labeled UTP and/or CTP) incorporates a label into the transcribed nucleic acids.

[0132] Alternatively, a label may be added directly to the original nucleic acid sample (e.g., mRNA, polyA mRNA, cDNA, etc.) or to the amplification product after the synthesis is completed. Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example, nick translation or end-labeling (e.g. with a labeled RNA) by treatment of the nucleic acid with kinase and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to the label (e.g., a fluorophore).

[0133] Following incorporation of the label into the probe the probes are then hybridized to the micro-array using standard conditions where hybridization results in a double stranded nucleic acid, one strand being a nucleic acid spotted on the array and one strand being a probe, generating a detectable signal from the label at the site of hybridization of the probe on the array. Typically, the probe and array must be mixed with each other under conditions that permit nucleic acid hybridization. This involves contacting the probe and array in the presence of an inorganic or organic salt under the proper concentration and temperature conditions. The probe and array 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 array in the mixture will determine the time necessary for hybridization to occur. The higher the probe or array concentration the shorter the hybridization incubation time needed. Optionally a chaotropic agent may be added. The chaotropic agent stabilizes nucleic acids by inhibiting nuclease activity. Furthermore, the chaotropic agent allows sensitive and stringent hybridization of short oligonucleotide probes at room temperature (Van Ness and Chen. Nucl. Acids Res. 19:5143-5151(1991)). Suitable chaotropic agents include: guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide, and cesium trifluoroacetate, among others. Typically, the chaotropic agent will be present at a final concentration of about 3 M. If desired, one can add formamide to the hybridization mixture, typically 30-50% (v/v).

[0134] Various hybridization solutions can be employed. Typically, these comprise from about 20 to 60% volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30-50% v/v formamide, about 0.15 to 1 M sodium chloride, about 0.05 to 0.1 M buffers, 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 that include a variety of polar water-soluble or swellable agents (e.g., polyethylene glycol), anionic polymers (e.g., polyacrylate or polymethylacrylate), and anionic saccharidic polymers (e.g., dextran sulfate). Methods of optimizing hybridization conditions are well known to those of skill in the art (see, for example, Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y., (1993); and Maniatis, supra).

[0135] Identification of Inducible Genes

[0136] The basis of gene expression profiling via microarray technology relies on comparing mRNAs present in an organism under a variety of conditions that result in alterations of the gene expression patterns. Within the context of the present invention separate populations of cells were exposed to different stresses that resulted in the alteration of gene expression patterns. The stresses or inducing conditions analyzed included: 1) nitrate; 2) low pH (˜5.5); 3) elevated temperature (about 41-42° C.) - -); and 4) growth in methane or methanol. Non-stressed cells were used for generation of “control” array data and stressed cells were used to generate “experimental”, “stressed” or “induced” array data.

[0137] Using the above described method of DNA microarray technology and comparing gene expression patterns in induced versus non-induced cultures of Methylomonas sp. 16a, using a variety of different inducing conditions, it was determined that:

[0138] (a) the genes nrtA and glnB are induced by growth in the presence of nitrate;

[0139] (b) the glyoxil gene is induced by growth in the presence of low pH (˜5.5);

[0140] (c) the htpG gene is induced by growth at elevated temperatures (e.g., 42° C. in the mesophilic Methylomonas sp. 16a); and

[0141] (d) the genes hps and moxF are constitutively expressed when grown in the presence of methanol and/or methane.

[0142] Comparison of the amino acid sequence encoded by the Methylomonas sp. 16a nitrogen transporter nrtA coding region sequence to public databases reveals that the most similar known sequence is 34% identical to the amino acid sequence of nrtA reported herein over the length of 464 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, N.Y.). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 60%-70% identity to the amino acid sequence herein, where about 70%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred nrtA encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of nrtA reported herein. More preferred nrtA nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are nrtA nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0143] Comparison of the amino acid sequence encoded by the Methylomonas sp. 16a nitrogen regulator protein glnB coding region sequence to public databases reveals that the most similar known sequence is 76% identical to the amino acid sequence of glnB reported herein over the length of 112 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson supra). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 78%-90% identity to the sequence herein, where about 80%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred glnB encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of glnB reported herein. More preferred glnB nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are glnB nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0144] Comparison of the amino acid sequence encoded by the Methylomonas sp. 16a putative glyoxalase II glyoxII coding region sequence to public databases reveals that the most similar known sequence is 51% identical to the amino acid sequence of glyoxil reported herein over the length of 231 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 70%-80% identity to the sequence herein, where about 80%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred glyoxil encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of glyoxil reported herein. More preferred glyoxil nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are glyoxil nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0145] Comparison of the amino acid sequence encoded by the Methylomonas sp. 16a heat shock protein htpG coding region sequence to public databases reveals that the most similar known sequence is 57% identical to the amino acid sequence of htpG reported herein over the length of 644 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 70%-80% identity to the sequence herein, where about 80%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred htpG encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of htpG reported herein. More preferred htpG nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are htpG nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0146] Comparison of amino acid sequence encoded by the Methylomonas sp. 16a methanol dehydrogenase subunit moxF coding region sequence to public databases reveals that the most similar known sequence is 60% identical to the amino acid sequence of moxF reported herein over the length of 89 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 70%-80% identity to the sequence herein, where about 80%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred moxF encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of moxF reported herein. More preferred moxF nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are moxF nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0147] Comparison of the amino acid sequence encoded by the Methylomonas sp. 16a hexulose-6-phosphate synthase (hps) coding region sequence to public databases reveals that the most similar known sequence is 55% identical to the amino acid sequence of hps reported herein over the length of 215 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, supra). Preferred nucleic acid fragments of the invention encode a polypeptide of at least about 70%-80% identity to the sequence herein, where about 80%-90% is more preferred. Most preferred are nucleic acid fragments that encode a polypeptide of at least 95% identity to the amino acid sequence reported herein. Similarly, preferred hps encoding nucleic acid sequences corresponding to the instant ORF are those encoding functional proteins, and which are at least 80% identical to the nucleic acid sequence of hps reported herein. More preferred hps nucleic acid fragments are at least 90% identical to the sequence herein. Most preferred are hps nucleic acid fragments that are at least 95% identical to the nucleic acid sequence reported herein.

[0148] Isolation of Homologs to the Inducible Genes

[0149] It will be appreciated by a person of skill in the art that the genes of the present invention have homologs in a variety of C1 metabolizing bacterial species; and, the use of the gene promoters for heterologous gene expression and the gene or ORF nucleic acid sequences for monitoring of bioreactor health and production are not limited to those genes derived from Methylomonas sp. 16a, but extend to homologs in any C1 metabolizing bacterial species. For example, the invention encompasses homologs derived from species including, but not limited to: Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylocyctis, Methylomicrobium, Methanomonas, Methylophilus, Methylobacillus, Methylobacterium, Hyphomicrobium, Xanthobacter, Bacillus, Paracoccus, Nocardia, Arthrobacter, Rhodopseudomonas, and Pseudomonas.

[0150] As is well known in the art, isolation of homologous genes using sequence-dependent protocols is readily possible using various techniques. Examples of sequence-dependent protocols include, but are not limited to: 1.) methods of nucleic acid hybridization; and 2.) methods of DNA and RNA amplification (described previously). 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, supra). Moreover, nucleic acvid sequences of the invention 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.

[0151] 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 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, pp 31-39, PCR Protocols: Current Methods and Applications; Humania Press, Inc., Totowa, N.J.).

[0152] 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.

[0153] Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., PNAS USA 85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the instant sequences. Using commercially available 3′ RACE or 5′ RACE systems (Gibco/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)).

[0154] Optionally, 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. Techniques are similar to those employed for microarray hybridization.

[0155] Identification of Promoter Regions Based on Microarray Data

[0156] Promoter regions are generally located 5′ to the coding region in a gene. Promoter regions in bacterial genomes exist for coding regions that are the 5′ most ORF in an operon composed of multiple ORFs. Thus the location in the genome of a coding region is analyzed to determine whether a promoter region lies 5′ to that specific coding region. Specifically, the DNA sequence surrounding the coding region (both 5′ and 3′) is examined for the presence of additional ORFs. In general, when there is no ORF found 5′ and adjacent to an ORF of interest, or the next 5′ ORF is in the opposite orientation, then the ORF of interest has a promoter 5′ and adjacent to it. If there are additional ORFs in the same orientation and 3′ adjacent to the ORF of interest, then the ORF of interest is the 5′ most ORF of an operon. The upstream region to such an ORF of interest can be used as a promoter region. Typically, DNA regions containing about 100 bp downstream and 400 to 500 bp upstream from the ATG translational start site for the 5′-most coding region in an operon are used to ensure full promoter activity. Smaller fragments that do not extend as far to either 5′ or 3′ of the ATG translational start site may have full functional promoter activity. Thus subfragments of the promoter sequences of the invention, which are functionally equivalent subfragments that retain promoter activity, are also useful for expressing chimeric genes in Methylomonas and are one aspect of the invention herein.

[0157] Chimeric Gene Expression in C1 Metabolizing Bacteria

[0158] The promoter regions derived from the inducible genes identified herein (SEQ ID NOs:3, 6, 9, 12, 15, and 18) may be utilized in the construction of chimeric genes to be expressed in native host cells and heterologous host cells, particularly in the cells of C1 metabolizing bacterial hosts. The chimeric genes described herein comprise a promoter selected from one of the promoters of the invention, and a coding region of choice. Expression of chimeric genes in recombinant C1 metabolizing bacterial hosts may be useful for altering the composition of the bacterial cells. The chimeric genes are used in creating recombinant bacterial hosts using microbial transformation systems and vectors that are well known to those skilled in the art. Plasmids that can replicate in E. coli but not in Methylomonas, and can be transferred into Methylomonas can be used as vectors for integration. Using an integration vector, expression of the chimeric gene follows its integration into the bacterial genome. Alternatively, a promoter of the invention may be operably linked to a coding region of choice and cloned into a plasmid that is capable of replicating itself in a C1 metabolizing bacterium. Broad host range plasmids that are able to replicate in a variety of bacteria can be used in Methylomonas as well. The plasmid is transferred into a C1 metabolizing bacterium by conjugation using a helper bacterial strain.

[0159] Once the recombinant C1 metabolizing bacteria is established, expression of the chimeric gene can be accomplished by applying inducing conditions appropriate to the promoter used (e.g., growth on methane or methanol, nitrate addition, and/or modification of temperature or pH). One skilled in the art will readily be able to determine appropriate conditions of induction. For example, the htpG promoter (SEQ ID NO:12 for example) will likely be induced in mesophilic C1 metabolizing bacteria (those bacteria whose optimum growth temperature lies within a range generally accepted as about 20-45° C.) between the temperature range of about 41-42° C. In contrast, thermophilic bacteria (having an optimum growth temperature greater than about 45° C.) would likely require an inducing temperature of about 47-50° C. Similarly a C1 metabolizer transformed with a chimeric gene comprising a promoter region derived from the nrtA and glnB genes (SEQ ID NO:3 or SEQ ID NO:6 for example) would be expected to express this gene in the presence of nitrate. Typically levels of about 5 mM to about 15 mM will be suitable where levels of about 10 mM are preferred. In another aspect of the invention a C1 metabolizer having a chimeric gene comprising a promoter region derived from the glyoxil gene (SEQ ID NO:9 for example) will be expected to express the this gene at acidic pH's, for example at levels of about 5.5. Alternatively C1 metabolizer host cells having chimeric genes comprising promoter regions derived from the hps and moxF genes will be expected to express these genes when the cells are grown on or exposed to suitable levels of methanol and/or methane.

[0160] Vectors useful for the transformation of suitable C1 metabolizing bacterial host cells are well known in the art. Typically the vector contains a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Chimeric genes to be introduced into a host cell may be cloned into the transformation vector. Chimeric genes comprise a region 5′ of the coding region that harbors transcriptional initiation controls and a region 3′ of the coding region that 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.

[0161] Promoters which are useful to drive expression of the coding region of interest in the desired host cell are selected from those derived from the upstream portion of the nrtA, glnB, glyoxil, htpg, moxF and hps genes (SEQ ID NOs:1, 4, 7, 10, 13, and 16), as described in the instant invention as SEQ ID NOs:3, 6, 9, 12, 15, and 18. Choice of a particular promoter will depend on the method of regulation desired (induction in the presence of nitrate, temperature, or pH conditions; or by growth on methane or methanol). The promoter regions may be identified from the sequences of the inducible genes and their homologs (see Tables 5, 7, 9, and 11) and isolated according to common methods (Maniatis, supra). Once the promoter regions are identified and isolated, each may be operably linked to a coding region of interest in suitable transformation vectors.

[0162] Termination control regions may be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.

[0163] Preferred C1 Metabolizing Bacterial Hosts

[0164] Preferred heterologous host cells for expression of the instant genes and promoter fragments are C1 metabolizing bacteria that are able to use single carbon substrates as a sole energy source. Many C1 metabolizing microorganisms that are able to use a variety of single carbon substrates are known in the art. Single carbon substrates useful in the present invention include, but are not limited to: methane, methanol, formaldehyde, formic acid, methylated amines (e.g. mono-, di- and tri-methyl amine), methylated thiols, and carbon dioxide.

[0165] All C1 metabolizing microorganisms are generally classified as methylotrophs. Methylotrophs may be defined as any organisms capable of oxidizing organic compounds that do not contain carbon-carbon bonds. Facultative methylotrophs have the ability to oxidize organic compounds which do not contain carbon-carbon bonds, but may also use other carbon substrates such as sugars and complex carbohydrates for energy and biomass. Obligate methylotrophs are those organisms which are limited to the use of organic compounds that do not contain carbon-carbon bonds for the generation of energy. Finally, obligate methanotrophs (a subset of methylotrophs) are those obligate methylotrophs that have the distinctive ability to oxidize methane.

[0166] Facultative methylotrophic bacteria are found in many environments, but are isolated most commonly from soil, landfill and waste treatment sites. Many facultative methylotrophs are members of the β, and γ subgroups of the Proteobacteria (Hanson et al., Microb. Growth C1 Compounds., [Int. Symp.], 7th (1993), 285-302. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK; Madigan et al., Brock Biology of Microorganisms, 8th edition, Prentice Hall, UpperSaddle River, N.J. (1997)). Facultative methylotrophic bacteria suitable in the present invention include, but are not limited to: Methylophilus, Methylobacillus, Methylobacterium, Hyphomicrobium, Xanthobacter, Bacillus, Paracoccus, Nocardia, Arthrobacter, Rhodopseudomonas, and Pseudomonas.

[0167] Those methylotrophs having the additional ability to utilize methane are referred to as methanotrophs. Of particular interest in the present invention are those obligate methanotrophs which are methane utilizers but which are obliged to use organic compounds lacking carbon-carbon bonds. Exemplary organisms included in this classification of obligate methanotrophs that utilize C1 compounds are the genera Methylomonas, Methylobacter, Mehtylococcus, Methylosinus, Methylocyctis, Methylomicrobium, and Methanomonas, although this is not intended to be limiting.

[0168] 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 that make it particularly useful for carbon flux manipulation (WO 02/20728). This particular strain possessing an energetically favorable carbon flux pathway served as the host organism from which SEQ ID NOs:1-18 were isolated and is known as Methylomonas 16a (ATCC PTA 2402).

[0169] Industrial Production

[0170] Where expression of a suitable coding region of interest is desired using an inducible promoter of the instant invention (selected from SEQ ID NOs:3, 6, 9, 12, 15, and 18) for commercial production of a product, a variety of culture methodologies may be applied. For example, large-scale production of a specific product made possible by chimeric gene expression in a recombinant microbial host may be accomplished by both batch and continuous culture methodologies.

[0171] 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 external 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.

[0172] 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 CO2. 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.

[0173] Commercial production of a product of interest in a C1 metabolizing bacteria, using the methodology and promoters of the present invention, may also be accomplished with a continuous culture. Continuous cultures are open systems 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, and 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.

[0174] 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.

[0175] Regulated Expression of Suitable Coding Regions of Interest

[0176] The promoters of the present invention may be used to effect the regulated expression of chimeric genes in various C1 metabolizing bacteria under specific induction conditions. Useful chimeric genes will include the promoter region of any one of the inducible genes defined herein (SEQ ID NOs:1, 4, 7, 10, 13, and 16), operably linked to a suitable coding region of interest to be expressed in a C1 metabolizing bacterial host. These promoter regions are identified as SEQ ID NOs:3, 6, 9, 12, 15, and 18. Any host that is capable of accommodating the promoter region is suitable including, but not limited to: Methylomonas, Methylobacter, Mehtylococcus, Methylosinus, Methylocyctis, Methylomicrobium, Methanomonas, Methylophilus, Methylobacillus, Methylobacterium, Hyphomicrobium, Xanthobacter, Bacillus, Paracoccus, Nocardia, Arthrobacter, Rhodopseudomonas, and Pseudomonas.

[0177] Coding regions of interest to be expressed as a chimeric gene in a recombinant C1 metabolizing bacterial host may be either endogenous to the host or heterologous and must be compatible with the host organism. Sequences encoding proteins of commercial value are particularly suitable for expression. For example, suitable coding regions of interest may include, but are not limited to those encoding viral, bacterial, fungal, plant, insect, or vertebrate proteins of interest, including mammalian polypeptides. Further, these coding regions of interest may be, for example, structural proteins, enzymes, or peptides. A particularly preferred, but non-limiting list includes:

[0178] 1) coding regions for enzymes involved in the central carbon pathway, such as transaldolase, fructose bisphosphate aldolase, keto deoxy phosphogluconate aldolase, phosphoglucomutase, glucose-6-phosphate isomerase, phosphofructokinase, 6-phosphogluconate dehydratase, 6-phosphogluconate-6-phosphate-1 dehydrogenase, and the like;

[0179] 2) coding regions for enzymes involved in the production of isoprenoid molecules, such as 1-deoxyxylulose-5-phosphate synthase (dxs), 1-deoxyxylulose-5-phosphate reductoisomerase (dxr), geranyltransferase or farnesyl diphosphate synthase (ispA), 2C-methyl-D-erythritol cytidyltransferase (ispD), to 4-diphosphocytidyl-2-C-methylerythritol kinase (ispE), 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (ispF), and geranylgeranyl pyrophosphate synthase (crtE);

[0180] 3) coding regions for carotenoid pathway enzymes such as zeaxanthin glucosyl transferase (crtX), lycopene cyclase (crtY), phytoene dehydrogenase (crtZ), phytoene synthase (crtB), beta-carotene hydroxylase (crtZ), phytoene desaturase (crtD), beta-carotene ketolase (crtO, crtW), and the like, which would enable the production of carotenoids such as antheraxanthin, astaxanthin, canthaxanthin, α-carotene, β-carotene, ε-carotene, γ-carotene, ζ-carotene, alpha-cryptoxanthin, diatoxanthin, 7,8-didehydroastaxanthin, fucoxanthin, fucoxanthinol, lactucaxanthin, lutein, lycopene, neoxanthin, neurosporene, peridinin, phytoene, rhodopin, rhodopin glucoside, siphonaxanthin, spheroidene, spheroidenone, spirilloxanthin, uriolide, uriolide acetate, violaxanthin, and zeaxanthin;

[0181] 4) coding regions for cyclic terpenoid synthases (e.g., limonene synthase) for the production of terpenoids, and the like;

[0182] 5) coding regions for enzymes involved in the production of exopolysaccharides, such as UDP-glucose pyrophosphorylase (ugp), glycosyltransferase (gumD), polysaccharide export proteins (wza, espB), polysaccharide biosynthesis (espM), glycosyltransferase (waaE), sugar transferase (espV), galactosyltransferase (gumH), and glycosyltransferase genes and the like;

[0183] 6) coding regions for enzymes involved in the production of aromatic amino acids, such as 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (aroG), 3-dehydroquinate synthase (aroB), 3-dehydroquinase or 3 dehydroquinate dehydratase (aroQ), 5-shikimic acid dehydrogenase (aroE), shikimic acid kinase (aroK), 5-enolpyruvylshikimate-3-phosphate synthase, chorismate synthase (aroC), anthranilate synthase (trpE), anthranilate phosphoribosyltransferase (trpD), indole 3-glycerol phosphate synthase (trpC), tryptophan synthetase (trpB), chorismate mutase or prephenate dehydratase (pheA), and prephenate dehydrogenase (tyrAc); and

[0184] 7) coding regions of pds, phaC, phaE, efe, pdc, and adh genes and genes encoding pinene synthase, bornyl synthase, phellandrene synthase, cineole synthase, sabinene synthase, and taxadiene synthase.

EXAMPLES

[0185] 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.

[0186] General Methods

[0187] Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (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).

[0188] The meaning of abbreviations is as follows: “hr” means hour(s), “min” means minute(s), “sec” means second(s), “d” means day(s), “mL” means milliliter(s), “μL” means microliter(s), “nL” means nanoliter(s), “ag” means microgram(s), “ng” means nanogram(s), “mM” means millimole(s), “μM” means micromole(s), “OD” means optical density.

[0189] Molecular Biology Techniques:

[0190] Methods for agarose gel electrophoresis were performed as described in Maniatis (supra). Polymerase Chain Reactions (PCR) techniques were found in White, B., PCR Protocols: Current Methods and Applications, Volume 15 (1993) Humana Press, Inc., Totowa, N.J.

[0191] Media and Culture Conditions:

[0192] General materials and methods suitable for the maintenance and growth of bacterial cultures are found in: Experiments in Molecular Genetics (Jeffrey H. Miller), Cold Spring Harbor Laboratory Press (1972); Manual of Methods for General Bacteriology (Phillip Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds), pp. 210-213, American Society for Microbiology, Washington, D.C.; or, Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass. All reagents and materials used for the growth and maintenance of bacterial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), Gibco/BRL Life Technologies (Gaithersburg, Md.), or Sigma Chemical Company (St. Louis, Mo.) unless otherwise specified.

[0193] HPLC Analysis of Carotenoid Content

[0194] Cell pellets were extracted with 1 ml acetone by vortexing for 1 min and intermittent vortexing over the next 30 min. Cell debris was removed by centrifugation at 14,000×g for 10 min and the supernatants was collected and passed through a 0.45 μM filter. A Beckman System Gold® HPLC with Beckman Gold Nouveau Software (Columbia, Md.) was used for the study. The crude extraction (0.1 mL) was loaded onto a 125×4 mm RP8 (5 μm particles) column with corresponding guard column (Hewlett-Packard, San Fernando, Calif.). The flow rate was 1 mL/min, while the solvent program used was: 0-11.5 min 40% water/60% methanol; 11.5-20 min 100% methanol; 20-30 min 40% water/60% methanol. The spectral data was collected by a Beckman photodiode array detector (model 168).

Example 1

Growth of Methylomonas 16a

[0195] Example 1 summarizes the standard conditions used for growth of Methylomonas sp. 16a (ATCC# PTA-2402), as described in WO02/20728.

[0196] Methylomonas Strain and Culture Media.

[0197] The growth conditions described below were used throughout the experimental Examples for treatment of Methylomonas 16a, unless conditions were specifically mentioned to be otherwise.

[0198] Methylomonas 16a was grown in serum stoppered Wheaton bottles (Wheaton Scientific, Wheaton, Ill.) using a gas/liquid ratio of at least 8:1 (i.e. 20 mL of Nitrate liquid “BTZ-3” medium in 160 mL total volume). The standard gas phase for cultivation contained 25% methane in air, although methane concentrations could vary ranging from about 5-50% by volume of the culture headspace. These conditions comprise growth conditions and the cells are referred to as growing cells. In all cases, the cultures were grown at 30° C. with constant shaking in a Lab-Line rotary shaker unless otherwise specified.

[0199] Nitrate medium for Methylomonas 16a

[0200] Methylomonas 16a was grown in a defined medium comprised of only minimal salts; no organic additions such as yeast extract or vitamins were required to achieve growth. This defined medium, also referred to herein as “nitrate liquid medium”, or “BTZ-3” medium, was comprised of various salts mixed with Solution 1 as indicated below (Tables 2 and 3) or where specified the nitrate was replaced with 15 mM ammonium chloride. Solution 1 provides the composition for a 100 fold concentrated stock solution of trace minerals.

3TABLE 2Solution 1*Conc.MW(mM)g per LNitriloacetic acid191.166.912.8CuCl2 × 2H2O170.480.150.0254FeCl2 × 4H2O198.811.50.3MnCl2 × 4H2O197.910.50.1CoCl2 × 6H2O237.91.310.312ZnCl2136.290.730.1H3BO361.830.160.01Na2MoO4 × 2H2O241.950.040.01NiCl2 × 6H2O237.70.770.184*Mix the gram amounts designated above in 900 mL of H2O, adjust to pH = 7, and add H2O to a final volume of 1 L. Keep refrigerated.

[0201]

4

TABLE 3

Nitrate liquid medium (BTZ-3)**

Conc.

MW
(mM)
g per L

NaNO3
84.99
10
0.85

KH2PO4
136.09
3.67
0.5

Na2SO4
142.04
3.52
0.5

MgCl2 × 6H2O
203.3
0.98
0.2

CaCl2 × 2H2O
147.02
0.68
0.1

1 M HEPES (pH 7)
238.3

50 mL

Solution 1

10 mL

**Dissolve in 900 mL H2O. Adjust to pH = 7, and add H2O to give 1 L.

For agar plates: Add 15 g of agarose in 1 L of medium, autoclave, let cool down to 50° C., mix, and pour plates.

[0202] Assessment of Microbial Growth and Conditions for Harvesting Cells

[0203] Cells grown to maximum optical density had an OD660 of ˜1.0. Cells were harvested by centrifugation in a Sorval RC-5B centrifuge using an SS-34 rotor at 6000 rpm for 20 min. The cell pellets were resuspended in 50 mM HEPES buffer, pH 7. These cell suspensions were referred to as washed, resting cells.

[0204] Microbial growth was assessed by measuring the optical density of the culture at 660 nm in an Ultrospec 2000 UV/Vis is spectrophotometer (Pharmacia Biotech, Cambridge, England) using a 1 cm light path cuvet. Alternatively, microbial growth was assessed by harvesting cells from the culture medium by centrifugation as described above and resuspending the cells in distilled water with a second centrifugation to remove medium salts. The washed cells were then dried at 105° C. overnight in a drying oven for dry weight determination.

Example 2

Construction of a DNA Microarray of the Methylomonas Genome

[0205] Example 2 describes the multi-step procedure required to create a DNA microarray of the Methylomonas genome. This array comprised 3750 ORFs, representing approximately 93% of the total genome of the organism. Also described are procedures for preparing probes, hybridizing probes to microarrays, and collecting the data generated.

[0206] Amplification of DNA Regions for the Construction of DNA Microarrays

[0207] Specific primer pairs were used in PCR reactions to amplify the DNA sequence of each protein encoding ORF of Methylomonas sp. 16a. Primers were designed based on the 5′ and 3′ sequences of each ORF by methods well known by one skilled in the art. Genomic DNA (10-30 ng) was used as the template. Genomic DNA was prepared using the Fast DNA Kit (Bio 101; Carlsbad, Calif.). The PCR reactions were performed in the presence of HotStart Taq™ DNA polymerase (Qiagen, Valencia, Calif.) and the dNTPs (Gibco/BRL). Thirty-five cycles of denaturation at 95° C. for 30 sec, annealing at 55° C. for 30 sec and polymerization at 72° C. for 2 min were conducted. PCR products were visualized following electrophresis on 1% argarose gels. The PCR amplified DNA samples were purified by the high-throughput PCR purification kit from Qiagen (Valencia, Calif.).

[0208] Arraying amplified ORFs

[0209] Before arraying, for each samp[le, an equal volume of DMSO (10 μL) and DNA (10 μL; about 50 ng/μL)sample was mixed in 384-well microtiter plates. A generation II DNA spotter (Molecular Dynamics, Sunnyvale, Calif.) was used to array the samples onto coated glass slides (Telechem, Sunnyvale, Calif.). Each PCR product was arrayed in duplicate on each slide. After cross-linking by UV light, the slides were stored under vacuum in a desiccator at room temperature until use.

[0210] RNA Isolation

[0211] Methylomonas 16a was cultured in nitrate liquid medium with ammonium or nitrate (10 mM) as the nitrogen source under 25% methane in air as described in Example 1. Samples of the culture (typically 20 mL) were harvested when the OD660 reached 0.3 (exponential phase). Cell cultures were harvested quickly and ruptured in RLT buffer (Qiagen RNeasy Mini Kit, Valencia, Calif.) with a beads-beater (Bio101, Vista, Calif.). Debris was pelleted by centrifugation for 3 min at 14,000×g at 4° C. RNA isolation was completed using the protocol supplied with this kit. After on-column DNAase treatment, the RNA product was eluted with 50-100 μL RNAase-free distilled water. RNA preparations were stored frozen at either −20° C. or −80° C.

[0212] Synthesis of Fluorescent cDNA from Total RNA

[0213] RNA samples (7 to 15 μg) and random hexamer primers (6 μg; Gibco/BRL) were mixed and brought to a volume of 25 μL with RNAase-free water. Each sample was denatured at 70° C. for 10 min and then chilled on ice for 30 sec. After adding 14 μL of labeling mixture, annealing was accomplished by incubation at room temperature for 10 min. The labeling mixture contained 8 μL of 5× enzyme buffer, 4 μL DTT (0.1 M), and 2 μL of 20× dye mixture. The dye mixture consisted of 2 mM of each dATP, dGTP, and dTTP, 1 mM dCTP, and 1 mM of Cy3-dCTP or Cy5-dCTP. After adding 1 to 1.5 μL of SuperScript II reverse transcriptase (200 units/mL, Life Technologies Inc., Gaithersburg, Md.), cDNA synthesis was allowed to proceed at 42° C. for 2 hr. The RNA was removed by adding 2 μL NaOH (2.5 N) to the reaction. After 10 min of incubation at 37° C., the pH was adjusted with 10 μL of HEPES (2 M). The labeled cDNA was then purified with a PCR purification kit (Qiagen, Valencia, Calif.). Labeling efficiency was monitored using either A550 for Cy3 incorporation, or A650 for Cy5.

[0214] Fluorescent Labeling of Genomic DNA

[0215] Methylomonas sp. 16a genomic DNA, prepared as described above, was nebulized to approximately 2 kb pair fragments. The fragmented genomic DNA (0.5 to 1 μg) was mixed with 6 μg of random hexamers primers (Gibco/BRL) in 15 μL of water. The mix was denatured by placement in boiling water for 5 min. Then, the reaction was annealed on ice for 30 sec before being transferred to room temperature. Subsequently, 2 μL of 5× Buffer 2 (Gibco/BRL) and 2 ul dye mixture were added. The components of the dye mixture and the labeling procedure were the same as described above for RNA labeling, except that the Klenow fragment of DNA polymerase 1 (5 μg/μL, Gibco/BRL) was used as the enzyme. After incubation at 37° C. for 2 hr, the labeled DNA probe was purified using a PCR purification kit (Qiagen, Valencia, Calif.).

[0216] Hybridization and Washing

[0217] Slides were first incubated with prehybridization solution containing 3.5×SSC (Gibco/BRL), 0.1% SDS, 1% bovine serum albumin (BSA, Fraction V, Sigma) for 30 min at 37° C. After prehybridization, hybridization solutions (Molecular Dynamics, Sunnyvale, Calif.) containing 100 picomol of dye (Cy3 or Cy5) incorporated into the labeled probes, described in the Examples to follow, were added to the slides which were then covered with cover slips. Slides were placed in a humidified chamber in a 42° C. incubator. After overnight incubation, slides were initially washed for 5 min at room temperature with a solution containing 0.1×SSC and 0.1% SDS. Slides were then washed at 65° C. for 10 min with the same solution three times. After washing, the slides were rinsed quickly in distilled water and dried with a stream of nitrogen gas.

[0218] Data Collection and Analysis

[0219] The signal generated from each slide was quantified with a laser scanner (Molecular Dynamics, Sunnyvale, Calif.). The images were analyzed with ArrayVision 4.0 software (Imaging Research, Inc., Ontario, Canada). The raw fluorescent intensity for each spot was adjusted by subtracting the background. These readings were exported to spreadsheets for further analysis.

Example 3

Identification of Nitrate Induced DNA Regions in Methylomonas

[0220] Using a Methylomonas DNA microarray prepared according to the methods described in Example 2, Applicants identified two nitrate inducible genes. The promoters of these genes can be employed for directing chimeric gene expression in Methylomonas and other C1 metabolizing bacteria, in response to nitrate. This Example describes the identification of these nitrate inducible genes and their deduced promoter regions.

[0221] Specifically, Methylomonas sp. 16a was grown at 30° C. in BTZ-3 medium with either 10 mM ammonium chloride or 10 mM sodium nitrate as the nitrogen source. Cultures (typically 20 ml)at exponential phase (OD660=0.3) were harvested for RNA isolation. Total RNA was isolated, labeled with fluorescent dyes, and used as probe on microarrays as described in Example 2. To identify genes specifically induced in the presence of nitrate, microarray hybridization experiments using probes made from RNA samples from these two growth conditions were compared. The ratio of spot intensities for each gene between nitrate and ammonia samples was used to identify two genes that were induced in the presence of nitrate (Table 4).

5TABLE 4Induction of Genes Involved In NitrateUtilization In MethylomonasGeneDescriptionFold of Induction*nrtAnitrogen transporter64glnBnitrogen regulator protein26*Units in fold induction (in the presence of nitrate) vs. control (in the presence of ammonia).

[0222] Table 5 is a description of the nitrate induced genes discovered from Methylomonas 16a. More specifically, Table 5 illustrates the relationship of the amino acid sequences encoded by these genes to known sequences in the art. All sequences were compared by conducting BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol. 215:403-410 (1993) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant 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 nitrate induced gene 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 BLASTX algorithm (Gish, W. and States, D. J. Nature Genetics 3:266-272 (1993)) provided by the NCBI. The results of the BLASTX comparison are given below in Table 5, which gives the known protein sequence to which the amino acid sequence encoded by each of the induced genes has the most identity and similarity. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected by chance in a search of a database of this size.

6TABLE 5Nitrate Induced Genes Identified From Methylomonas 16aSEQGeneSimilarityID%%NameIdentifiedNOsIdentityaSimilaritybE-valuecCitationnrtANITRATE1, 234499e−56Frias, J. E., et al.,TRANSPORT“Nitrate assimilationPROTEIN NRTAgene cluster from theemb|CAA68041.2|heterocyst-forming(X99709) mutationcyanobacteriumof nrtA impairsAnabaena sp. strainactive nitrate/nitritePCC 7120”, J. Bacteriol.transport179 (2): 477-486[Anabaena sp.(1997).glnBgb|AAC46397.1|4, 576892e−46Meletzus, D., et al.,(U91902) PII-“Characterization of theproteinglnK-amtB operon of[AzotobacterAzotobacter vinelandii”,vinelandii]J. Bacteriol. 180 (12):3260-3264 (1998).a% Identity is defined as percentage of amino acids that are identical between the two proteins. b% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. cExpect value. 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.

[0223] Following the identification of these nitrate induced genes, the genomic DNA sequence surrounding the coding region ATG start site for each gene was analyzed by PSI-BLAST (Altschul, S. F. et al., Nucleic Acids Res. 25:3389-340 (1997)) to identify other ORFs in the proximity. It was determined that there was no ORF in the same orientation located upstream of either coding region, indicating that each coding region was not iternal to an operon and therefore each gene included a promoter region. For the nrtA gene, the nucleotide region spanning from 408 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:1) to 143 bases downstream of the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:3.

[0224] For the nitrogen regulating PII-protein (glnB) gene, the nucleotide region spanning from 444 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:4) to 107 bases downstream of the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:6.

Example 4

Identification of a pH Induced DNA Region in Methylomonas

[0225] Using a Methylomonas DNA microarray prepared according to the methods described in Example 2, Applicants identified one pH inducible gene. The promoter of this gene can be employed for directing chimeric gene expression in Methylomonas and other C1 metabolizing bacteria, in response to low pH. This Example describes the identification of the gene encoding glyoxalase 11 and its deduced promoter region.

[0226] Specifically, Methylomonas sp. 16a was grown at 30° C. in BTZ-3 medium without nitrate and with 5 mM ammonium chloride. The pH in the medium was adjusted with HCl to 5.5 when the cell density reached exponential phase (OD660=0.3). After 45 min of treatment the culture was harvested, and total RNA was isolated labeled with fluorescent dyes, and used as probe on microarrays as described in Example 2. To identify genes induced by lowering the pH, microarray hybridization experiments using probes made from RNA samples prepared from treated (pH 5.5) and untreated (pH 7.0) cultures were compared. The ratio of spot intensities for each gene between treated and untreated samples was used to identify a gene that was induced in response to a change in pH (Table 6).

7TABLE 6Gene Induced in Response to pH ModificationIn MethylomonasGeneDescriptionFold of Induction*glyoxIIputative glyoxalase II35*Units in fold induction (pH 5.5) vs. control (pH 7.0).

[0227] Table 7 is a description of the pH induced gene discovered from Methylomonas 16a. More specifically, Table 7 illustrates the relationship of the aminio acid sequence encoded by this gene to known sequences in the art. The sequence was analyzed by conducting BLAST searches, as described in Example 3.

8TABLE 7pH Induced Genes Identified From Methylomonas 16aSEQGeneSimilarityID%%E-NameIdentifiedNOsIdentityaSimilaritybvaluecCitationglyox II>gb|AAB17995.1|7, 851684e−59ACCESSION H96575(U74610)Theologis, A., et al,glyoxalase IISequence and analysis[Arabidopsisof chromosome 1 of thethaliana]plant ArabidopsisthalianaNature 408 (6814), 816-820(2000)a% Identity is defined as percentage of amino acids that are identical between the two proteins. b% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. cExpect value. 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.

[0228] Following the identification of this pH induced gene, the genomic DNA sequence surrounding the coding region ATG start site was analyzed by PSI-BLAST (Altschul, S. F. et al., Nucleic Acids Res. 25:3389-340 (1997)) to identify other ORFs in the proximity. It was determined that there was no ORF in the same orientation located upstream of the this coding region, indicating that a promoter region was located upstream of this ORF. Thus, the nucleotide region spanning from −423 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:7) to 156 bases downstream of the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:9.

Example 5

Identification of Temperature Induced DNA Region in Methylomonas

[0229] Using a Methylomonas DNA microarray prepared according to the methods described in Example 2, Applicants identified one temperature inducible gene. The promoter of this gene can be employed for directing chimeric gene expression in Methylomonas and other C1 metabolizing bacteria, when temperature is modified as an inducing condition. This Example describes the identification of htpg and its deduced promoter region.

[0230] Specifically, Methylomonas sp. 16a was grown at 30° C. in BTZ-3 medium with 5 mM ammonium chloride. The temperature of the culture was shifted to 42° C. when the cell density reached exponential phase (OD660=0.3). After 45 min of treatment the culture was harvested and total RNA was isolated, labeled with fluorescent dyes, and used as a probe on microarrays as described in Example 2. To identify genes induced by increasing the temperature, microarray hybridization experiments using probes made from RNA samples from treated and untreated cultures were compared. The ratio of spot intensities for each gene between treated and untreated samples was used to identify those that were induced at higher temperature (Table 8).

9TABLE 8Gene Induced in Response to TemperatureModification In MethylomonasGeneDescriptionFold of Induction*htpgHeat shock protein16*Units in fold induction (t = 42° C.) vs. control (t = 30° C.).

[0231] Table 9 is a description of the temperature induced gene discovered from Methylomonas 16a. More specifically, Table 9 illustrates the relationship of the amino acid sequence encoded by this gene to known protein sequences in the art. The sequence was analyzed by conducting BLASTX searches, as described in Example 3.

10TABLE 9Temperature Induced Genes identified From Methylomonas 16aSEQGeneSimilarityID%%E-NameIdentifiedNOsIdentityaSimilaritybvaluecCitationhtpg>sp|P10413|10, 1157740.0Bardwell J. C. A., Craig E. A.;HTPG_ECOLI heat“Eukaryotic Mr 83,000shock proteinheat shock protein hasHTPG (higha homologue intemperatureEscherichia coil”, Proc.protein G) (heatNati. Acad. Sci. U.S.A.shock protein84: 5177-5181 (1987).C62.5)a% Identity is defined as percentage of amino acids that are identical between the two proteins. b% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. cExpect value. 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.

[0232] Following the identification of this temperature induced gene, the genomic DNA sequence surrounding the coding region ATG start site was analyzed by PSI-BLAST (Altschul, S. F. et al., Nucleic Acids Res. 25:3389-340 (1997)) to identify other ORFs in the proximity. It was determined that there was no ORF in the same orientation located upstream of the coding region, indicating that it was not internal to an operon and therefore the gene included a promoter region. The nucleotide region spanning from 540 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:10) to 110 bases downstream of the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:12.

Example 6

Identification of Constitutively Expressed Genes when Methane and Methanol were Used as the Carbon Sources in Methylomonas

[0233] Using a Methylomonas DNA microarray prepared according to the methods described in Example 2, Applicants identified methane and methanol induced genes. The promoters of these genes can be employed for directing chimeric gene expression in Methylomonas and other C1 metabolizing bacteria, when cultures are grown in the presence of methane and/or methanol. This Example describes the identification of genes that are highly expressed when grown on methane and methanol and their deduced promoter regions.

[0234] Identification of these genes takes advantage of the capability of DNA microarray experiments to estimate gene expression levels. Methylomonas sp. 16a cultures were grown in BTZ-3 medium with 25% methane in air or 80 mM methanol. Cultures at exponential phase were harvested, RNA was isolated and each sample was labeled with Cy5 fluorescent dye. Methylomonas sp. 16a genomic DNA was labeled with Cy3 dye as described in Example 2. The genomic DNA probe was combined with each RNA-derived probe separately. The two mixed probe samples were hybridized to separate slides. After quantification, the ratio between the RNA (Cy5) and DNA probes (Cy3) was calculated for each spot on the two microarrays. The mRNA abundance for each gene was estimated based on the ratio of an individual gene divided by the sum of all ratios as described in Wei Y., et al. (J. Bacteriol. 183(2):545-56 (2001)). Subsequently, the expression level for each gene was ranked according to its mRNA abundance. Two genes with high levels of expression when grown on methane or methanol were identified (Table 10). The moxF gene involved in methanol metabolism was ranked #3 when grown on methane and was ranked #22 when grown on methanol. The hps gene was ranked #14 when grown on methane and was ranked #57 when grown on methanol.

11TABLE 10Ranking of highly expressed genes of Methylomonaswhen grown on methane or methanolGeneDescriptionMethaneMethanolmoxFMethanol dehydrogenase subunit322hpsHexulose-6-phosphate synthase1457

[0235] Table 11 is a more detailed description of these two genes discovered from Methylomonas 16a. More specifically, Table 11 illustrates the relationships of the amino acid sequences encoded by these genes to known protein sequences in the art. All sequences were analyzed by conducting BLASTX searches, as described in Example 3.

12TABLE 11Proteins Encoded by Highly Expressed Genes of Methylomonas whenGrown on Methane or MethanolSEQGeneSimilarityID%%E-NameIdentifiedNOsIdentityaSimilaritybvaluecCitationmoxFpir||A47120 alcohol13, 1460761e−12Waechter-Brulla, D., et al.,dehydrogenase“Methanol(acceptor) (ECoxidation genes in the1.1.99.8) largemarine methanotrophchain MoxFMethylomonas sp.precursor -strain A4”, J. Bacteriol.Methylomonas sp.175 (12):(fragment)3767-3775 (1993).gb|AAA25302.1|(L11308) methanoldehydrogenase[Methylomonas sp.]hpsgb|AAG29505.1|AF19, 2055643e−55GeneBank accession294615_1number: AAG29505(AF294615) 3-hexulose-6-phosphatesynthase[Aminomonasaminovorusa% Identity is defined as percentage of amino acids that are identical between the two proteins. b% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. cExpect value. 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.

[0236] Following the identification of these genes, the genomic DNA sequence surrounding the coding region ATG start site for each gene was analyzed by PSI-BLAST (Altschul, S. F. et al., Nucleic Acids Res. 25:3389-340 (1997)) to identify other ORFs in the proximity. It was determined that there was no ORF in the same orientation located upstream of each coding region, indicating that they were not internal to operons and therefore the genes included promoter regions. For the moxF gene, the nucleotide region spanning from 500 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:13) to 196 bases downstream of the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:15.

[0237] For the hps gene, the nucleotide region spanning from 520 bases upstream of the ATG start site (ATG at nucleotide=1 of SEQ ID NO:16) to the ATG start site was selected as being sufficient to contain the promoter region. This region of DNA is provided as SEQ ID NO:18.

Example 7

Demonstration of Activity of moxF Promoter by Expressing a Marker Gene in Methylomonas

[0238] To show the promoter activity of the selected promoter sequence for the moxF gene, the promoter was used to express the β-galactosidase (lacZ) reporter gene. The promoter fragment was amplified by standard PCR procedures from Methylomonas sp. 16a genomic DNA using the primer pair:

13[SEQ ID NO:19]5′-CAGGATCCGCGCCGTATGCTTTCGAATCCGCC-3′[SEQ ID NO:20]5′-CAGGATCCTGGAGAGCTGTTCCAGCTCCTTGTTC-3′

[0239] The amplified promoter fragment was digested with BamHI and ligated to BamHI digested pTJS75LacZKam. Plasmid pTJS75LacZKam is the pTJS75 vector (Schmidhauser and Helinski, v164 #1 p46455 (1985)) to which a β-galactosidase (lacZ) coding region had been added (FIG. 1). Plasmid pTJS75 is a broad host range plasmid belonging to the lncP group. The resulting plasmid was transformed into Methylomonas sp. 16a and colonies containing the plasmid were grown on LB plates containing x-gal (5-bromo-3-indoyl-β-d-galactopyranoside). Visual inspection of the colonies revealed that some were blue in color, indicating that the x-gal substrate was converted by the β-galactosidase enzyme to the indigo derivative. Plasmid DNA from these colonies was analyzed by restriction enzyme digestion and showed that the moxF promoter fragment was oriented towards the lacZ coding region. Thus β-galactosidase enzyme was expressed, indicating that the moxF promoter region fragment had promoter activity in Methylomonas sp. 16a.

Example 8

Use of hps Promoter to Drive Foreign Gene Expression in Methylomonas sp. 16a and Escherichia coli

[0240] Example 8 demonstrates that the hps promoter is useful to drive foreign gene expression in Methyolomonas sp. 16a and E. coli. This was tested by amplifying an hmps promoter fragment from genomic DNA, cloning the promoter into a plasmid containing the carotenoid gene cluster crtEXYIBZ such that expression of the crtZ gene was driven by the hps promoter, transforming this plasmid into E. coli, and then detecting the presence of zeaxanthin glucosides. Transformation of the plasmid into Methyolomonas 16a via bacterial conjugation also resulted in detection of zeaxanthin glucosides. As the crtZ gene, encoding β-carotene hydroxylase, catalyses the hydroxylation reaction from β-carotene to zeaxanthin, the detection of zeaxanthin glucosides confirmed the ability of the hps promoter to drive the chimeric gene expression of crtZ.

[0241] Amplification of the hps Promoter

[0242] A 500 bp DNA fragment (SEQ ID NO:18) containing the hps promoter was amplified from Methylomonas 16a genomic DNA using the following primers in a PCR:

14[SEQ ID NO:21]5′-CCCATGGGTTCGGAATCCCTGA-3′[SEQ ID NO:22]5′-GGAATTCCTCCTCTCCGAAAGTTTTTAATTATTAG-3′

[0243] The thermocycler conditions were set for 30 cycles at 94° C. for 30 sec, 61° C. for 30 sec and 72° C. for 2 min, followed by a final extension at 72° C. for 5 min. The 500 bp PCR product was purified using a Qiagen PCR purification kit, digested with NcoI and EcoRI for 1 hr at 37° C. and then purified following gel electrophoresis in 1% (w/v) agarose. The NcoI/EcoRI-digested PCR product was ligated to NcoI/EcoRI-digested pBHR1 (MoBiTec, LLC, Marco Island, Fla.) and the ligated DNA was used to transform E. coli DH5α. Transformants were selected on LB agar containing kanamycin (50 μg/ml). Analysis of the plasmid DNA from one transformant by restriction enzyme digestion and gel electrophoresis confirmed the presence of the expected plasmid, designated pHPS (FIG. 2A).

[0244] The crtEXYIBZ gene cluster from Pantoea stweartii was obtained on a 6255 bp EcoRI fragment from pCRT1 (WO 02/18617). In this gene cluster, the crtZ coding region is in opposite orientation to the other coding regions in the cluster and must be transcribed from a separate promoter. The 6255 bp EcoRI fragment containing the crt EXYIBZ coding regions was ligated to pHPS that had been digested with EcoRI and dephosphorylated with calf intestinal alkaline phosphatase (Gibco/BRL). The ligated DNA was used to transform E. coli DH5a. Transformants were selected on LB agar containing kanamycin (50 μg/ml). Analysis of restriction enzyme digested plasmid DNA from one transformant demonstrating yellow colony color confirmed the presence of a plasmid with the EcoRI fragment oriented such that the chloramphenicol acetyltransferase gene promoter (CAT promoter) is adjacent to the crtEXYIB coding regions, which was designated pCRT18 FIG. 2B). The yellow color indicated that carotenoids were being produced. In pCRT18 expression of the crtZ gene, encoding β-carotene hydroxylase, is directed from the Methylomonas 16a hps promoter (FIG. 2B). If the crtZ gene were expressed, then one would expect a transconjugant containing pCRT18 to synthesize zeaxanthin glucosides since these are derived from β-carotene by the β-carotene hydroxylase activity encoded by crtZ.

[0245] Cells of this colony were grown and assayed by HPLC as described in the general methods. The HPLC analysis showed peaks that eluted at 10.767-11.300, consistent with the expected profile for the mono-and diglucosides of zeaxanthin (eluting earlier than zeaxanthin, which has a rentention time of approximately 13.5 min). Thus zeaxanthin glucosides were observed in E. coli containing pCRT18, indicating that the Methylomonas 16a hps promoter directed heterologous gene expression in a bacterial host other than Methylomonas.

[0246] Plasmid pCRT18 was transferred into Methylomonas 16a by tri-parental conjugal mating. The E. coli helper strain containing pRK2013 and the E. coli DH5α donor strain containing pCRT18 were each grown overnight in LB medium containing kanamycin (50 μg/mL), washed three times in LB, and resuspended in a volume of LB representing approximately a 60-fold concentration of the original culture volume. The Methylomonas 16a recipient was grown for 48 hr in Nitrate liquid “BTZ-3” medium in an atmosphere containing 25% (v/v) methane, washed three times in BTZ-3, and resuspended in a volume of BTZ-3 representing a 150-fold concentration of the original culture volume. The donor, helper, and recipient cell pastes were combined on the surface of BTZ-3 agar plates containing 0.5% (w/v) yeast extract in ratios of 1:1:2, respectively. Plates were maintained at 30° C. in 25% methane for 16-72 hr to allow conjugation to occur, after which the cell pastes were collected and resuspended in BTZ-3. Dilutions were plated on BTZ-3 agar containing kanamycin (50 μg/mL) and incubated at 30° C. in 25% methane for up to 1 week. Transconjugants were streaked onto BTZ-3 agar with kanamycin (50 μg/mL) for isolation. Analysis of the plasmid DNA isolated from these transconjugants by restriction enzyme digestion confirmed the presence of pCRT18.

[0247] For analysis of carotenoid composition, transconjugants were cultured in 25 ml BTZ-3 containing kanamycin (50 μg/mL) and incubated at 30° C. in 25% methane as the sole carbon source for up to 1 week. The cells were harvested by centrifugation and frozen at −20° C. After thawing, the pellets were extracted and carotenoid content was analyzed by HPLC according to the methodology of the General Methods above. HPLC analysis of extracts from Methylomonas 16a containing pCRT18 confirmed the synthesis of zeaxanthin glucosides (FIG. 2C). Specifically, peaks eluted at 10.767-11.300, consistent with the expected profile for the mono- and diglucosides of zeaxanthin (eluting earlier than zeaxanthin, which has a rentention time of approximately 13.5 min).

[0248] Since plasmid pCRT1, containing the same crtEXYIBZ gene cluster as pCRT18 but lacking the Methylomonas 16a hps promoter, only conferred upon Methylomonas 16a the ability to produce α-carotene (WO 02/18617), the appearance of zeaxanthin glucosides in Methylomonas 16a containing pCRT18 confirmed that crtZ was expressed from the hps promoter.

[0249] To eliminate the formation of zeaxanthin glucosides, the crtX gene encoding zeaxanthin glucosyl-transferase was deleted from pCRT18. The 5149 bp EcoRV (position 1107)/EcoRI (position 6256) fragment of pCRT18 was replaced with a 3870 bp EcoRV (position 1107)/EcoRI (position 4977) fragment from which the crtX gene was deleted. Using PCR-mediated overlap extension, the crtX gene was deleted from the crtEXYIBZ gene cluster in three PCR steps. Template DNA for the first two reactions was a plasmid named pCRT2, which contains the complete crtEXYIBZ gene cluster without a promoter. First, the crtE coding region was amplified with the primers TRCcrtEF and CrtYER (SEQ ID NO:23, 24), incorporating 23 bases of crtY homology on the reverse primer.

155′-CGGAATTCCCGCCCTGCCACTCATCGC-3′[SEQ ID NO:23]5′CCAGAATGAGATCATAGTGCGGTTGCATGCAGCATCCTTAA[SEQ ID NO:24]CTGACGGCAG-3′

[0250] The 1373 bp PCR product was gel purified and used as template in the third polymerase chain reaction.

[0251] Second, the crtYIB coding regions were amplified together with primers CrtEYF and CrtBR (SEQ ID NO:25, 26), incorporating 26 bases of crtE homology on the forward primer.

165′CTGCCGTCAGTTAAGGATGCTGCATGCAACCGCACTAT[SEQ ID NO:25]GATCTCATTCTGG5′-GCGAATTCGCTAGCGGCTAGATCGGGCGCTGCC-3′[SEQ ID NO:26]

[0252] The 3604 bp PCR product was gel purified and used as template in the third polymerase chain reaction.

[0253] In the third PCR step, the products of the first two reactions were combined, primed to each other via their 23 bases of perfect homology, and amplified with the two outermost primers, TRCcrtEF and CrtBR (SEQ ID NO:23, 26). The resulting 4952 bp product contained the gene cluster crtEYIB, excluding the crtX gene entirely. A 3870 bp EcoR1/EcoRV digestion fragment which includes crtE, crtY, crtI, and a portion of crtB was ligated into EcoRV and EcoRI digested pCRT18, replacing the 5149 bp EcoRV/EcoRI fragment. The resulting plasmid, pCRT24 (FIG. 3A), was transferred into Methylomonas 16a by tri-parental conjugal mating and the transconjugants were analyzed for their carotenoid composition by HPLC, as described in the General Methods.

[0254] Zeaxanthin (retention time 13.500 min) and cryptoxanthin (retention time 14.767 min) were produced in Methylomonas 16a containing pCRT24 (FIG. 3B) demonstrating the conversion of P-carotene (retention time 16.233 min) by the crtZ gene product, and thereby expression of the crtZ coding region from the hps promoter was confirmed.

Natural promoters for gene expression in C1 metabolizing bacteria

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