PATENT ASSIGNEE'S COUNTRY | USA |
UPDATE | 10.00 |
PATENT NUMBER | This data is not available for free |
PATENT GRANT DATE | 24.10.00 |
PATENT TITLE |
Genes encoding denitrification reactions |
PATENT ABSTRACT |
This invention relates to the isolation of nucleic acid fragments from Pseudomonas sp. strain G-179 that encode periplasmic nitrate reductase and nitric oxide reductase enzymes. The enzymes are useful in denitrification reactions and for the identification of other denitrifying bacteria. In addition, this invention also relates to the construction of chimeric genes encoding all or a substantial portion of a bacterial nitric oxide reductase or a bacterial periplasmic nitrate reductase enzymes, in sense or antisense orientation, wherein the expression of the chimeric genes results in production of altered levels of the nitric oxide reductase or periplasmic nitrate reductase in a transformed host cell. |
PATENT INVENTORS | This data is not available for free |
PATENT ASSIGNEE | This data is not available for free |
PATENT FILE DATE | 15.07.99 |
PATENT REFERENCES CITED |
Ye et al., Appl. Environ. Microbiol 60: 1053-1058 (1994). Zumft et al., Microbiol. Mol. Biol. Rev. 61: 533-616 (1997). Bartnikas et al., J. Bacteriol. 179:3534-3540 (1997). de Boer et al., Eur. J. Biochem. 242:592-600 (1996). Berks et al., Biochem J., (1995)309:983-992. Reyes et al., Biochem. J., (1998)331:897-904. Groves et al., Mol. Microbiol. 19:467-481(1996). Zumft et al., Eur. J. Biochem. 219: 481-490 (1994). Bell et al., FEBS lett. 265:85-87 (1990). Kastrau et al., Eur. J. Biochem. 222:293-303 (1994). Tyson et al., Arch. Microbiol. 168: 403-411 (1997). Bell et al., (1993) J. of General Microbiology, vol. 139:pp. 3205-3214. Reyes, F et al., Mol. Microbiol. 19: 1307-1318 (1996). Sakurai, N. et al., Biochem. Biophys. Res. Commun. 243 (2):400-406 (1998). |
PATENT PARENT CASE TEXT | This data is not available for free |
PATENT CLAIMS |
What is claimed is: 1. An isolated nucleic acid fragment encoding a bacterial nitric oxide reductase gene product, wherein said gene product functions to produce a bacterial nitric oxide reductase selected from the group consisting of: (a) An isolated nucleic acid fragment encoding all or a portion of the amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 and SEQ ID NO: 8; (b) an isolated nucleic acid fragment having at least 90% identity with the nucleic acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5 and SEQ ID NO: 7; (c) an isolated nucleic acid fragment that hybridizes with SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5 and SEQ ID NO: 7 under the following hybridization conditions: 0.1X SSC, 0.1% SDS, 65.degree. C.; and (d) an isolated nucleic acid fragment that is complementary to (a), (b) or (c). 2. The isolated nucleic acid fragment of claim 1 selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5 and SEQ ID NO: 7. 3. A chimeric gene comprising the isolated nucleic acid fragment of claim 1 operably linked to suitable regulatory sequences. 4. A transformed host cell comprising the chimeric gene of claim 3. 5. The transformed host cell of claim 4 wherein the host cell is selected from the group consisting of bacteria, yeast and filamentous fungi. 6. The transformed host cell of claim 4 wherein the host cell is selected from the group consisting of Escherichia, Bacillus, yeast and denitrifying bacteria. 7. A nucleic acid fragment encoding all or a portion of the amino acid sequence encoding a bacterial nitric oxide reductase obtained by the method comprising: (a) probing a genomic library with the nucleic acid fragment of claim 1; (b) identifying a DNA clone that hybridizes under stringent conditions of 0.1X SSC, 0.1% SDS, at 65.degree. C. with the nucleic acid fragment of claim 1; and (c) sequencing the genomic fragment that comprises the clone identified in step (b), wherein the sequenced genomic fragment encodes a bacterial nitric oxide reductase gene product, wherein said gene product functions to produce a bacterial nitric oxide reductase. |
PATENT DESCRIPTION |
FIELD OF THE INVENTION This invention is in the field of microbial denitrification. More specifically, this invention pertains to nucleic acid fragments encoding new bacterial nitric oxide reductase and bacterial periplasmic nitrate reductase enzymes. BACKGROUND OF THE INVENTION The complete pathway for microbial denitrification has been established as: NO.sub.3.sup.- .fwdarw.NO.sub.2.sup.- .fwdarw.NO.fwdarw.N.sub.2 O.fwdarw.N.sub.2 (Ye et al., Appl. Environ. Microbiol. 60:1053-1058(1994); Zumft et al., Microbiol. Mol. Biol. Rev. 61:533-616 (1997)). In the natural environment, denitrification plays a major role in completing the nitrogen cycle by converting nitrate (NO.sub.3.sup.-) or nitrite (NO.sub.2.sup.-) to nitrogen gas (N.sub.2). Bacteria attempt to maintain the balance necessary between fixed nitrogen and atmospheric nitrogen. In the denitrification process, the soil bacteria use nitrate, rather than oxygen, as the ultimate electron acceptor in a series of reactions to generate a transmembrane proton gradient that is used to synthesize ATP. In practical applications, microbial denitrification has been widely used for water purification (Mateju et al., Enzyme Microb. Technol. 14:172-183 (1992)). On the other hand, nitrous oxide (N.sub.2 O) has been shown to have detrimental effect on the stratospheric ozone layer (de Boer et al., Eur. J. Biochem. 242:592-600 (1996)). NOx, along with carbon monoxide and hydrocarbons can lead to an increase in the amount of stratospheric ozone. Thus, the production of N.sub.2 O and nitric oxide (NO) due to incomplete denitrification is of concern. It will be useful therefore to devise new and better methods for denitrification of industrial waste streams to effect complete denitrification. The identification of genes encoding proteins responsible for key denitrification reactions will be essential for the development of improved denitrification methods. Two of the essential genes in the bacterial denitrification pathway are those encoding nitric oxide reductase (nor) and nitrate reductase (nap). Genes encoding these enzymes have been identified in both denitrifying bacteria as well as non-denitrifyers. For example, Bartnikas et al., J. Bacteriol. 179:3534-3540 (1997) teach the identification and sequencing of a gene cluster required for the expression of nitric oxide reductase in Rhodobacter sphaeroidesi and de Boer et al., (Eur. J. Biochem. 242:592-600 (1996)) describe a nor gene cluster isolated from Paracoccus denitrificans. Genes encoding periplasmic nitrate reductase have been characterized from Thiosphaera pantotropha (Berks et al., Biochem J., (1995), 309, 983) and from Rhodobacter sphaeroides (Reyes et al., Biochem J, (1998), 331, 897). Finally Grove et al., (Mol. Microbiol. 19:467-481 (1996)) describe the identification of a gene encoding a periplasmic nitrate reductase from the non-denitrifying E. coli K-12. The utility in being able to manipulate the nor and nap genes to modify bacterial denitrification is clear from the interplay of these enzymes with the genes encoding nitrite reductase (nir) in the bacterial denitrification process. In bacterial denitrification, NO is produced from NO.sub.3.sup.- in two consecutive reactions catalyzed by the two metalloenzymes nitrate reductase and nitrite reductase, and then is decomposed into N.sub.2 O by nitric oxide reductase. The key step of denitrification is the reduction of NO.sub.2.sup.- by nitrite reductases. These quintessential enzymes catalyze the conversion of a mineral form of nitrogen to a gaseous form. It is well recognized that gaseous forms of nitrogen compounds are no longer easily available for assimilation by the biomass. The product of nitrite reduction, NO, is only present in trace amount due to its efficient removal by nitric oxide reductase. However, it has been observed that mutations in the NO step render the cells incapable of using nitrate and nitrite as the alternative electron acceptors due to NO toxicity. In addition, mutations in the nitric oxide reductase (nor) region have shown a negative impact on the activity or expression level of nitrite reductase (nir) in Pseudomonas stutzeri and Paracoccus denitrificans (Grove et al., Mol. Microbiol. 19:467-481 (1996); Zumft et al., Eur. J. Biochem. 219:481-490 (1994)). Nonetheless, in Rhodobacter sphaeroides, promoter activity for the nitrite reductase gene nirK was higher in nor mutants (Bartnikas et al., J. Bacteriol. 179:3534-3540 (1997)). Activities of these two steps are commonly controlled by the proteins NnrU, NirQ, and NnrR (Bell et al., FEBS Lett. 265:85-87 (1990); Kastrau et al., Eur. J. Biochem. 222:293-303 (1994); Tyson et al., Arch. Microbiol. 168:403-411 (1997)), depending on the organism studied. This evidence distinctly suggests that reduction of nitrite and nitric oxide is highly interdependent. Prior to the identification of role of the nitrate reductases in the periplasmic space, the principal nitrate reductase activity in bacterial denitrification has been attributed to those associated with membrane (Bell et al, 1993, J. of General Microbiology, Vol. 139, p. 3205-3214). Applicant has discovered new genes isolated from Pseudomonas sp. encoding a periplasmic nitrate reductase and nitric oxide reductase. The genes are may be expressed in recombinant systems effect bacterial denitrification and the genes or portions thereof may be used to identify other denitrifying bacterial strains. Further, it has been demonstrate that the instant periplasmic nitrate reductase is the penultimate nitrate reductase in the denitrification pathway as compared with the cytoplasmic variety of the enzyme in Pseudomonas sp. SUMMARY OF THE INVENTION This invention relates to isolated nucleic acid fragments encoding a bacterial nitric oxide reductase selected from the group consisting of: (a) an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8; (b) an isolated nucleic acid fragment that is substantially similar to an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8; (c) an isolated nucleic acid fragment encoding a polypeptide having at least a 73% identity with the amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8; (d) an isolated nucleic acid molecule that hybridizes with SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5 or SEQ ID NO:7 under the following hybridization conditions: 40% formamide, with 5X or 6X SSC; and (e) an isolated nucleic acid fragment that is complementary to (a), (b), (c) or (d). The present invention further provides isolated nucleic acid fragments encoding a bacterial periplasmic nitrate reductase selected from the group consisting of: (a) an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14; (b) an isolated nucleic acid fragment that is substantially similar to an isolated nucleic acid fragment encoding all or a substantial portion of the amino acid sequence selected from the group consisting of SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14; (c) an isolated nucleic acid fragment encoding a polypeptide having at least a 76% identity with the amino acid sequence selected from the group consisting of SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14; (d) an isolated nucleic acid molecule that hybridizes with SEQ ID NO:9, SEQ ID NO:11 or SEQ ID NO:13 under the following hybridization conditions: 40% formamide, with 5X or 6X SSC.; and (e) an isolated nucleic acid fragment that is complementary to (a), (b), (c) or (d). In another embodiment, the instant invention relates to chimeric genes encoding a bacterial nitric oxide reductase or bacterial periplasmic nitrate reductase or to chimeric genes that comprise nucleic acid fragments as described above, the chimeric genes operably linked to suitable regulatory sequences, wherein expression of the chimeric genes results in transformation of the respective enzyme substrates. The present invention further provides a transformed host cell comprising the above described chimeric genes. The transformed host cells can be of eucaryotic or procaryotic origin. In an alternate embodiment, the present invention provides methods of obtaining a nucleic acid fragment encoding all or substantially all of the amino acid sequence encoding a bacterial nitric oxide reductase comprising either hybridization or primer-directed amplification methods known in the art and using the above described nucleic acid fragment. Primer-directed amplification methods use all or a part of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5 and SEQ ID NO:7. The product of these methods is also provided by the invention. Similarly, the invention provides methods of obtaining a nucleic acid fragment encoding all or substantially all of the amino acid sequence encoding a bacterial periplasmic nitrate reductase comprising either hybridization or primer-directed amplification methods known in the art and using the above described nucleic acid fragments. Primer-directed amplification methods use all of a part of SEQ ID NO:9, SEQ ID NO:11 and SEQ ID NO:13. The product of these methods is also provided by the invention. Finally the invention provides methods for bacterial denitrification incorporating recombinant hosts expressing the present nitrate reductase and nitric oxide reductase enzymes. BRIEF DESCRIPTION OF THE DRAWINGS, Sequence Descriptions FIG. 1 is a diagram showing the confirmation of the open reading frames encoding the nir, nap and nor genes. The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions which form a part of this application. Applicant(s) have provided 14 sequences in conformity 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 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 Adminstrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. .sctn.1.822. SEQ ID NO:1 is the nucleotide sequence of the norB gene encoding the large subunit of the nitric oxide reductase gene isolated from Pseudomonas sp. strain G-179. SEQ ID NO:2 is the deduced amino acid sequence of the NorB large subunit of the nitric oxide reductase enzyme isolated from Pseudomonas sp. strain G-179. SEQ ID NO:3 is the nucleotide sequence of the norC gene encoding the small subunit of the nitric oxide reductase gene isolated from Pseudomonas sp. strain G-179. SEQ ID NO:4 is the deduced amino acid sequence of the NorC small subunit of the nitric oxide reductase enzyme isolated from Pseudomonas sp. strain G-179. SEQ ID NO:5 is the nucleotide sequence of the norQ gene encoding a nitric oxide reductase assembly protein isolated from Pseudomonas sp. strain G-179. SEQ ID NO:6 is the deduced amino acid sequence of the NorQ nitric oxide reductase assembly protein isolated from Pseudomonas sp. strain G-179. SEQ ID NO:7 is the nucleotide sequence of the norD gene encoding a nitric oxide reductase assembly protein isolated from Pseudomonas sp. strain G-179. SEQ ID NO:8 is the deduced amino acid sequence of the NorD nitric oxide reductase assembly protein isolated from Pseudomonas sp. strain G-179. SEQ ID NO:9 is the nucleotide sequence of the napA gene encoding the large subunit of the periplasmic nitrate reductase gene isolated from Pseudomonas sp. strain G-179. SEQ ID NO:10 is the deduced amino acid sequence of the NapA large subunit of the periplasmic nitrate reductase enzyme isolated from Pseudomonas sp. strain G-179. SEQ ID NO:11 is the nucleotide sequence of the napB gene encoding the small subunit of the periplasmic nitrate reductase gene isolated from Pseudomonas sp. strain G-179. SEQ ID NO:12 is the deduced amino acid sequence of the NapB small subunit of the periplasmic nitrate reductase enzyme isolated from Pseudomonas sp. strain G-179. SEQ ID NO:13 is the nucleotide sequence of the napC gene encoding an electron transport protein that complements the function of the periplasmic nitrate reductase gene isolated from Pseudomonas sp. strain G-179. SEQ ID NO:14 is the deduced amino acid sequence of the NapC electron transport protein that complements the function of the periplasmic nitrate reductase enzyme isolated from Pseudomonas sp. strain G-179. DETAILED DESCRIPTION OF THE INVENTION The present invention provides new sequences encoding bacterial nitric oxide reductase and bacterial periplasmic nitrate reductase enzymes. The genes and their expression products are useful for the creation of recombinant organisms that have the ability to denitrify toxic waste substances, for the identification of new denitrifying species of bacteria and for fermentation processes in the absence or presence of oxygen. Nucleic acid fragments encoding at least a portion of several of the above mentioned reductase enzymes have been isolated and identified by comparison to public databases containing nucleotide and protein sequences using the BLAST algorithms well known to those skilled in the art. The supergene cluster containing genes involved in the reduction of nitrate, nitrite, nitric oxide and anaerobic heme biosynthesis was isolated from a denitrifying bacterium Pseudomonas sp. strain G-179 containing a Cu-type nitrate reductase. The nir gene region required for nitrite reduction contained the nitrite reductase structural gene nirU, an unknown nirV, and a regulatory component nnrR. Upstream from the nir region was the napDEFABC gene cluster for the function of periplasmic nitrate reductase. The hemN gene encoding oxygen-independent copropophyringogen III oxidase was located further downstream from the nap region. The next gene cluster was norEFBCQD involved in nitric oxide reduction. The nor region was also linked to another gene cluster that may be involved in uptake or transport function. Mutations in the nor region not only render the strain incapable of using nitrate, nitrite and nitric oxide as the alternative electron acceptor, but also alter its ability to grow on nitrous oxide. This evidence suggests that reduction of nitric oxide and nitrous oxide is functionally linked, and indicates that manipulation of the nor and nir gene cluster will be effective in controlling denitrification. Furthermore a mutation in the nap region abolished the capability for nitrate reduction suggesting that the periplasmic nitrate reductase plays an essential role in denitrification. In this disclosure, a number of terms and abbreviations are used. The following definitions are provided. "Open reading frame" is abbreviated ORF. "Polymerase chain reaction" is abbreviated PCR. "Cytochrome c oxidase polypetide III" is abbreviated Cox3. As used herein, "denitrification" refers to the reduction of nitrate (NO.sub.3.sup.-) to gaseous intermediates, principally nitrogen gas. The term "denitrifying bacteria" refers to any bacteria capable of "denitrification". "Nitric oxide reductase" refers to an integral membrane enzyme of the anaerobic respiratory chain of Pseudomonas sp. strain G-179 that is involved in the denitrification process and specifically catalyzes the reduction of nitric oxide (NO) to nitrous oxide (N.sub.2 O). "NorB" and "norB" will refer to the protein and corresponding gene encoding the large subunit of the nitric oxide reductase enzyme. "NorQ and "norQ" and "NorD" and "norD" will refer to the protein and genes encoding two open reading frames flanking the large and small subunits of the nitric oxide reductase gene, believed to have and effect on the assembly of the Nor proteins. The term "periplasmic nitrate reductase" refers to an enzyme involved in the denitrification process that catalyzes the reduction of nitrate (NO.sub.3.sup.-) to nitrite (NO.sub.2.sup.-). "NapA, NapB and NapC" and "napA, napB and napC" refers to the protein and corresponding genes encoding the large subunit, the small subunit and the electron transport protein, respectively, of the periplasmic nitrate reductase enzyme. The term "hydropathy" refers to a measurement that shows regions of hydrophobicity or polarity of a protein. 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. There term "gene cluster" or "super gene cluster" will mean genes organized in a single expression unit. As used herein, "substantially similar" refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. "Substantially similar" also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. "Substantially similar" also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotide bases that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary sequences. For example, it is well known in the art that alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein are common. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue (such as glycine) or a more hydrophobic residue (such as valine, leucine, or isoleucine). Similarly, changes which result in substitution of one negatively charged residue for another (such as aspartic acid for glutamic acid) or one positively charged residue for another (such as lysine for arginine) can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to hybridize, under stringent conditions (0.1X SSC, 0.1% SDS, 65.degree. C.), with the sequences exemplified herein. Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are at least 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are at least 90% identical to the identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are at least 95% identical to the DNA sequence of the nucleic acid fragments reported herein. A "substantial portion" of an amino acid or nucleotide sequence comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a "substantial portion" of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular fungal proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above. The term "complementary" is used to describe the relationship between nucleotide bases that are capable to hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences. 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. 215:403-410 (1990), and DNASTAR (DNASTAR, Inc. 1228 S. Park St. Madison, Wis. 53715 USA). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the "default values" of the program referenced, unless otherwise specified. As used herein "default vales" will mean any set of values or parameters which originally load with the software when first initialized. 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, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (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, New York (1991). Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, the GCG Pileup program found in the GCG program package, as used in the instant invention, using the Needleman and Wunsch algorithm with their standard default values of gap creation penalty=12 and gap extension penalty=4 (Devereux et al., Nucleic Acids Res. 12:387-395 (1984)), BLASTP, BLASTN, and FASTA (Pearson et al., Proc. Natl. Acad. Sci. US.A. 85:2444-2448 (1988). The BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul et al., Natl. Cent. Biotechnol. Inf., Natl. Library Med. (NCBI NLM) NIH, Bethesda, Md. 20894; Altschul et al., J. Mol. Biol. 215:403-410 (1990)). Another preferred method to determine percent identity, is by the method of DNASTAR protein alignment protocol using the Jotun-Hein algorithm (Hein et al., Methods Enzymol. 183:626-645 (1990)). Default parameters for the Jotun-Hein method for alignments are: for multiple alignments, gap penalty=11, gap length penalty=3; for pairwise alignments ktuple=6. As an illustration, by a polynucleotide having a nucleotide sequence having at least, for example, 95% "identity" to a reference nucleotide sequence of SEQ ID NO: 1 it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence of SEQ ID NO:1. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence. Analogously, by a polypeptide having an amino acid sequence having at least, for example, 95% identity to a reference amino acid sequence of SEQ ID NO:2 is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of SEQ ID NO: 2. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence. "Codon degeneracy" refers to divergence 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 bacterial reductase enzymes as set forth in SEQ ID NOs: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14. 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. A nucleic acid molecule is "hybridizable" to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989), (hereinafter Maniatis) 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. For preliminary screening for homologous nucleic acids, low stringency hybridization conditions, corresponding to a Tm of 55.degree., can be used, e.g., 5X SSC, 0.1% SDS, 0.25% milk, and no formamide; or 30% formamide, 5X SSC, 0.5% SDS. Moderate stringency hybridization conditions correspond to a higher Tm, e.g., 40% formamide, with 5X or 6X SSC. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Maniatis 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 Maniatis supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe. "Synthetic genes" can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. "Chemically synthesized", as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available. "Gene" refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5' non-coding sequences) and following (3' non-coding sequences) the coding sequence. "Native gene" refers to a gene as found in nature with its own regulatory sequences. "Chimeric gene" refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. "Endogenous gene" refers to a native gene in its natural location in the genome of an organism. A "foreign" gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A "transgene" is a gene that has been introduced into the genome by a transformation procedure. "Coding sequence" refers to a DNA sequence that codes for a specific amino acid sequence. "Suitable regulatory sequences" refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences. "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 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. "RNA transcript" refers to the product resulting from RNA polymerasecatalyzed 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 posttranscriptional processing of the primary transcript and is referred to as the mature RNA. "Messenger RNA (mRNA)" refers to the RNA that is without introns and that can be translated into protein by the cell. "cDNA" refers to a double-stranded DNA that is complementary to and derived from mRNA. "Sense" RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. "Antisense RNA" refers to 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). 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, introns, 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. The term "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation. The term "expression", as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide. "Mature" protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. "Precursor" protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals. "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. The terms "plasmid", "vector" and "cassette" refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3' untranslated sequence into a cell. "Transformation cassette" refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. "Expression cassette" refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host. 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 Cold Press 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). Genes encoding NapA, B and C proteins as well as NorB, C, Q and D proteins isolated from a denitrifying bacteria have been identified by comparison to the GenBank database using the BLAST algorithms well known to those skilled in the art. NapA showed the highest correlation at the amino acid level, having about 76% identity to to a similar Paracoccus denitrificans protein. NapB and NapC had even less identity with only 62% and 66% identity at the amino acid level to Rhodobacter sphaeroides and Paracoccus denitrificans proteins respectively. Of the nitric oxide reductase proteins, NorQ demonstrated the highest percent identity to a known protein, having 73% identity at the amino acid level to a Paracoccus halodenitrificans protein. NorB, Nor C and NorD showed only 66%, 64% and 43% identity respectively at the amino acid level to proteins isolated from Paracoccus denitrificans, and Rhodobacter sphaeroides. The nucleic acid fragments of the instant invention may be used to isolate cDNAs and genes encoding homologous enzymes from the same or other bacterial species. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g., polymerase chain reaction, ligase chain reaction). For example, genes encoding other nitric oxide reductase (nor) and periplasmic nitrate reductase enzymes (nap), either as cDNAs or genomic DNAs, could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired bacteria using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of or full-length of the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length cDNA or genomic fragments under conditions of appropriate stringency. In addition, two short segments of the instant nucleic acid fragments 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 plant genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., PNAS USA 85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3' or 5' end. Primers oriented in the 3' and 5' directions can be designed from the instant sequences. Using commercially available 3' RACE or 5' RACE systems (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)). Availability of the instant nucleotide and deduced amino acid sequences facilitates immunological screening cDNA expression libraries. Synthetic peptides representing portions of the instant amino acid sequences may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen cDNA expression libraries to isolate full-length cDNA clones of interest (Lerner, R. A. Adv. Immunol. 36:1 (1984); Maniatis). The instant nitric oxide reductase and periplasmic nitrate reductase enzymes produced in heterologous host cells, particularly in the cells of microbial hosts, can be used to prepare antibodies to the enzymes by methods well known to those skilled in the art. The antibodies are useful for detecting the enzymes in situ in cells or in vitro in cell extracts. Preferred heterologous host cells for production of the instant nitric oxide reductase and periplasmic nitrate reductase enzymes are microbial hosts. Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of the instant nitric oxide reductase and periplasmic nitrate reductase enzymes. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the enzymes. Additionally, chimeric genes will be effective in altering the denitrifying properties of the host bacteria. It is expected, for example, that introduction of chimeric nor or nap gene clusters under the control of the appropriate promoters, into a host cell comprising at least one copy of these genes will demonstrate increased denitrifying activity. It is contemplated that it will be useful to express the instant genes both in host cells having pre-existing denitrifying pathways as well as those hosts lacking such pathways. Introduction of nor and nap genes into denitrifying bacteria (such as Paracoccus denitrificans, Rhodobacter sphaeroides, Thiosphaera pantotropha and various Pseudomonas sp.) will result in elevated levels of nitric oxide reductase and nitrate reductase, improving the rate of denitrification. Additionally, the instant genes may also be introduced into non-denitrifying bacteria where there are advantages to convey denitrifying properties to a non-denitrifying organism. Vectors or cassettes useful for the transformation of suitable host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5' of the gene which harbors transcriptional initiation controls and a region 3' of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host. Initiation control regions or promoters, which are useful to drive expression of the genes encoding the nitric oxide reductase and periplasmic nitrate reductase enzymes in the desired host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, trp, 1P.sub.L, 1P.sub.R, T7, tac, and trc (useful for expression in Escherichia coli). Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary, however, it is most preferred if included. All or a portion of the nucleic acid fragments of the instant invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to expression of the instant enzymes. For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatis) of restriction-digested bacterial genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et at., Genomics 1:174-181 (1987)) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequence in the genetic map previously obtained using this population (Botstein et al., Am. J. Hum. Genet. 32:314-331 (1980)). A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the instant nucleic acid sequences. Examples include allele-specific amplification, polymorphism of PCR-amplified fragments (CAPS), allele-specific ligation, nucleotide extension reactions, Radiation Hybrid Mapping and Happy Mapping. For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, this is generally not necessary for mapping methods. Such information may be useful in plant breeding in order to develop lines with desired starch phenotypes. |
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