Denitrifying genes in bacterial and Archaeal genomes

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1577, Issue 3, 2002, Pages 355-376

  Philippot, Laurent ^a  

^a CEMAGREF   (France)

Author keywords

Denitrification; Microbial genome; Nitrate reductase; Nitric oxide reductase; Nitrite reductase; Nitrous oxide reductase

Indexed keywords

NITRIC OXIDE REDUCTASE; NITRITE; NITROUS OXIDE; OXIDOREDUCTASE;

ARCHAEBACTERIUM; ATMOSPHERE; BACTERIAL GENOME; DENITRIFICATION; GENE CLUSTER; GENE STRUCTURE; GENETIC CODE; GENETIC ORGANIZATION; MICROBIAL GENETICS; MICROORGANISM; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REDUCTION; REVIEW; SOIL; UNINDEXED SEQUENCE;

GENES, ARCHAEAL; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NITRATE REDUCTASE; NITRATE REDUCTASES; NITRITE REDUCTASES; OXIDOREDUCTASES; PHYLOGENY;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 0037184270     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4781(02)00420-7     Document Type: Review

References (136)

1. Lashof D.A., Ahuja D.R. Relative contributions of greenhouse gas emissions to global warming. Nature. 3:1990;529-531.
2. Waibel A.E., Peter T., Carslaw K.S., Oelhaf H., Wetzel G., Crutzen P.J., Poschl U., Tsias A., Reimer E., Fischer H. Arctic ozone loss due to denitrification. Science. 283:1999;2064-2069.
3. Gamble T.N., Betlach H.R., Tiedje J.M. Numerically dominant denitrifying bacteria from world soils. App. Environ. Microbiol. 33:1977;926-939.
4. Tiedje J.M. Page A.L., Miller R.M., Keeny D.R. Methods of Soil Analysis Part 2. 2nd edn. 1982;1011-1026 Soil Science Society of America and American Society of Agronomy, Madison, WI.
5. Tiedje J.M. Ecology of denitrification and dissimilatory nitrate reduction to ammonium. Zehnder A.J.B. Biology of Anaerobic Microorganisms. 1988;179-244 Wiley, New York.
6. Zumft W.G. Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61:1997;533-536.
7. Knowles R. Soil Biochemistry. Ladd E.A., Paul J.N. 1981;323-369 Marcel Dekker, New York.
8. Cheneby D., Philippot L., Hartmann A., Henault C., Germon J.C. 16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils. FEMS Microbiol. Ecol. 1176:2000;1-8.
9. Bothe H., Jost G., Schloter M., Ward B.B., Witzel K. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol. Rev. 24:2000;673-690.
10. Arai H., Igarashi Y., Kodama T. The structural genes for nitric oxide reductase from Pseudomonas aeruginosa. Biochim. Biophys. Acta. 1261(2):1995;279-284.
11. Silvestrini M.C., Galeotti C.L., Gervais M., Schinina E., Barra D., Bossa F., Brunori M. Nitrite reductase from Pseudomonas aeruginosa: sequence of the gene and the protein. FEBS Lett. 254:1989;33-38.
12. Stover C.K., Pham X.Q., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., Brinkman F.S., Hufnagle W.O., Kowalik D.J., Lagrou M., Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y., Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R., Smith K., Spencer D., Wong G.K., Wu Z., Paulsen I.T. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature. 406:2000;959-964.
13. 1. Gene. 167:1995;87-91.
14. Jungst A., Braun C., Zumft W.G. The nirSTBM region coding for cytochrome cd1-dependent nitrite respiration of Pseudomonas stutzeri consists of a cluster of mono-, di- and tetraheme proteins. FEBS Lett. 279:1991;205-209.
15. Hartig E., Schiek U., Vollack K.U., Zumft W.G. Nitrate and nitrite control of respiratory nitrate reduction in denitrifying Pseudomonas stutzeri by a two-component regulatory system homologous to NarXL of Escherichia coli. J. Bacteriol. 181:1999;3658-3665.
16. Glockner A.B., Zumft W.G. Sequence analysis of an internal 9.72 kb segment from the 30-kb denitrification gene cluster of Pseudomonas stutzeri. Biochim. Biophys. Acta. 1277:1996;6-12.
17. Philippot L., Clays-Josserand A., Lensi R., Trinsoutrot I., Normand P., Potier P. Purification of the dissimilative nitrate reductase of Pseudomonas fluorescens and the cloning and the sequencing of its corresponding genes. Biochim. Biophys. Acta. 1350:1997;272-276.
18. Philippot L., Mirleau P., Mazurier S., Siblot S., Hartmann A., Lemanceau P., Germon J.C. Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes. Biochim. Biophys. Acta. 1517:2001;436-440.
19. Berks B.C., Ferguson S.J., Moir J.W.B., Richardson D.J.D. Enzymes and associated electron transports systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim. Biophys. Acta. 1232:1995;97-173.
20. Philippot L., Hojberg O. Dissimilatory nitrate reductases in bacteria. Biochim. Biophys. Acta. 1446:1999;1-23.
21. Cutruzzola F. Bacterial nitric oxide synthesis. Biochim. Biophys. Acta. 1411:1999;231-249.
22. Hendriks J., Oubrie A., Castresana J., Urbani A., Gemeinhardt S., Saraste M. Nitric oxide reductases in bacteria. Biochim. Biophys. Acta. 1459:2000;266-273.
23. Watmough N.J., Butland G., Cheesman M.R., Moir J.W., Richardson D.J., Spiro S.S. Nitric oxide in bacteria: synthesis and consumption. Biochim. Biophys. Acta. 1411(2-3):1999;456-474.
24. Richardson D.J., Berks B.C., Russel D.A., Spiro S., Taylor C.J. Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell. Mol. Life Sci. 58:2001;165-178.
25. Blasco F., Iobbi C., Giordano G., Chippaux M., Bonnefoy V. Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the α and β subunits in iron binding and electron transfer. Mol. Gen. Genet. 218:1989;249-256.
26. Hoffmann T., Troup B., Szabo A., Hungerer C., Jahn D. The anaerobic life of Bacillus subtilis: cloning of the genes encoding the respiratory nitrate reductase system. FEMS Microbiol. Lett. 131:1995;219-225.
27. Palmer T., Santini C.L., Iobbi-Nivol C., Eaves D.J., Boxer D.H., Giordano G. Involvement of the narJ and mob gene products in distinct steps in the biosynthesis of the molybdoenzyme nitrate reductase in Escherichia coli. Mol. Microbiol. 20:1996.
28. Liu X., DeMoss J.A. Characterization of NarJ; a system-specific chaperone required for nitrate reductase biogenesis in Escherichia coli. J. Biol. Chem. 272:1997;24266-24271.
29. Blasco F., Santos J.P.D., Magalon A., Frixon C., Guigliarelli B., Santini C.L., Giordano G. NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli. Mol. Microbiol. 28:1998;435-447.
30. Marger M.D., Saier M.H. A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport. Trends Biochem. Sci. 18:1993;13-20.
31. Noji S., Nohno T., Saito T., Taniguchi S. The narK gene product participates in nitrate transport induced in Escherichia coli nitrate-respiring cells. FEBS Lett. 252:1989;139-143.
32. DeMoss J.A., Hsu P.Y. NarK enhances nitrate uptake and nitrite excretion in Escherichia coli. J. Bacteriol. 173:1991;3303-3310.
33. Moir J.W.B., Wood N.J. Nitrate and nitrite transport in bacteria. Cell. Mol. Life Sci. 58:2001;215-224.
34. Bonnefoy V., Demoss J.A. Nitrate reductases in Escherichia coli. Antonie van Leeuwenhoek. 66:1994;47-56.
35. Bates D.M., Lazazzera B.A., Kiley P.J. Characterization of FNR* mutant protein indicates two distinct mechanisms for altering oxygen regulation of the Escherichia coli transcription factor FNR. J. Bacteriol. 177:1995;3972-3978.
36. Kiley P.J., Reznikoff W.S. Fnr mutants that activate gene expression in the presence of oxygen. J. Bacteriol. 173:1991;16-22.
37. Spiro S., Guest J.R. FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol. Rev. 75:1990;399-428.
38. Spiro S., Guest J.R. Activation of the lac operon of Escherichia coli by a mutant FNR protein. Mol. Microbiol. 1:1987;53-58.
39. Eiglmeier K., Honoré N., Luchi S., Lin E.C.C., Cole S.T. Molecular genetic analysis of FNR-dependent promoters. Mol. Microbiol. 3:1989;869-878.
40. 2-dependent gene regulation in facultatively anaerobic bacteria. Arch. Microbiol. 164:1995;81-90.
41. Unden G., Becker S., Bongaerts J., Schirawski J., Six S. Oxygen regulated gene expression in facultatively anaerobic bacteria. Antonie van Leeuwenhoek. 66:1994;3-23.
42. Spiro S. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek. 66:1994;23-36.
43. Zimmermann A., Reimmann C., Galimand M., Haas D. Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr; a regulatory gene homologous with fnr of Escherichia coli. Mol. Microbiol. 5:1991;1483-1490.
44. Haas D., Gamper M., Zimmermann A. Silver S., Witholt B., Galli E. Pseudomonas 1991. Molecular Biology and Biotechnology. 1992;177-187 American Society for Microbiology, Washington, DC.
45. Galimand M., Gamper M., Zimmermann A., Haas D. Positive FNR-like control of anaerobic arginine degradation and nitrate respiration in Pseudomonas aeruginosa. J. Bacteriol. 173:1991;1598-1606.
46. Sawers R.G. Identification and molecular characterization of a transcriptional regulator from Pseudomonas aeruginosa PAO1 exhibiting structural and functional similarity to the FNR protein of Escherichia coli. Mol. Microbiol. 5:1991;1469-1481.
47. Ye R.W., Haas D., Ka J.O., Krishnapillai V., Zimmermann A., Baird C., Tiedje J.M. Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr; an analog of Fnr. J. Bacteriol. 177:1995;3606-3609.
48. Wood N.J., Alizadeh T., Bennett S., Pearce J., Ferguson S., Richardson D., Moir J.W.B. Maximal expression of membrane-bound nitrate reductase in Paracoccus is induced by nitrate via a third FNR-like regulator named NarR. J. Bacteriol. 183:2001;3606-3613.
49. Walker M.S., DeMoss J.A. NarL-phosphate must bind to multiple upstream sites to activate transcription from the narG promoter of Escherichia coli. Mol. Microbiol. 14:1994;633-641.
50. Dong X.R., Li S.F., DeMoss J.A. Upstream sequence elements required for NarL-mediated activation of transcription from the narGHJI promoter of Escherichia coli. J. Biol. Chem. 267:1992;14122-14128.
51. Stewart V., Parales J. Identification and expression of genes narL and narX of the nar nitrate reductase locus in Escherichia coli K-12. J. Bacteriol. 170:1988;1589-1597.
52. Nohno T., Noji S., Taniguchiand S., Saito T. The narX and narL genes encoding the nitrate-sensing regulators of Escherichia coli are homologous to a family of prokaryotic two component regulatory genes. Nucleic Acids Res. 17:1989;2947-2957.
53. Chiang R.C., Cavicchioli R., Gunsalus R.P. Identification and characterization of narQ; a second nitrate sensor for nitrate dependent gene regulation in Escherichia coli. Mol. Microbiol. 6:1992;1913-1923.
54. Siddiqui R.A., Warnecke-Eberz U., Hengsberger A., Schneider B., Friedrich B. Structure and function of a periplasmic nitrate reductase in Alcaligenes eutrophus H16. J. Bacteriol. 175:1993;5867-5876.
55. Berks B.C., Richardson D.J., Reilly A., Willis A.C., Ferguson S.J. The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha. Biochem. J. 309:1995;983-992.
56. Reyes F., Gavira M., Castillo F., Moreno-Vivian C. Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster. Biochem. J. 331:1998;897-904.
57. Potter L.C., Cole J.A. Essential roles for the products of the napABCD genes, but not napFGH, in periplasmic nitrate reduction by Escherichia coli K-12. Biochem. J. 344(1):1999;69-76.
58. Liu H.P., Takio S., Satoh T., Yamamoto I. Involvement in denitrification of the napKEFDABC genes encoding the periplasmic nitrate reductase system in the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans. Biosci. Biotechnol. Biochem. 63:1999;530-536.
59. Castillo F., Dobao M.M., Reyes F., Blaso R., Roldan M.D., Gavira M., Caballero F.J., Moreno-Vivian C., Martinez-luque M. Molecular and regulatory properties of the nitrate reducing systems of Rhodobacter. Curr. Microbiol. 33:1996;341-346.
60. Bedzyk L., Wang T., Ye R.W. The periplasmic nitrate reductase in Pseudomonas sp. strain G-179 catalyzes the first step of denitrification. J. Bacteriol. 181(9):1999;2802-2806.
61. Glockner A.B., Jungst A., Zumft W.G. Copper-containing nitrite reductase from Pseudomonas aurofaciens is functional in a mutationally cytochrome cd1 free background (NirS-) of Pseudomonas stutzeri. Arch. Microbiol. 160:1993;18-26.
62. Boer A.P.d., Reijnders W.N., Kuenen J.G., Stouthamer A.H., Spanning R.J.v. Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans. Antonie van Leeuwenhoek. 66:1994;111-127.
63. Palmedo G., Seither P., Korner H., Matthews J.C., Burkhalter R.S., Timkovich R., Zumft W.G. Resolution of the nirD locus for heme d1 synthesis of cytochrome cd1 (respiratory nitrite reductase) from Pseudomonas stutzeri. Eur. J. Biochem. 232(3):1995;737-746.
64. 1 biosynthesis. J. Bacteriol. 179:1997;235-242.
65. Arai H., Sanbongi Y., Igarashi Y., Kodama T. Cloning and sequencing of the gene encoding cytochrome c-551 from Pseudomonas aeruginosa. FEBS Lett. 261:1990;196-198.
66. Zumft W.G., Dölher K., Körner H., Löchelt S., Viebrock A., Frunzke K. Defects in cytochrome cd1-dependent nitrite respiration of transposon Tn5-induced mutants from Pseudomonas stutzeri. Arch. Microbiol. 149:1988;492-498.
67. Arai H., Igarashi Y., Kodama T. Nitrite activates the transcription of the Pseudomonas aeruginosa nitrite reductase and cytochrome c-551 operon under anaerobic conditions. FEBS Lett. 288:1991;227-228.
68. 1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification: evidence for a denitrification-specific nitrate- and nitrite-responsive regulatory system. J. Bacteriol. 181:1999;161-166.
69. Arai H., Igarashi Y., Kodama T. Structure and ANR-dependent transcription of the nir genes for denitrification from Pseudomonas aeruginosa. Biosci. Biotechnol. Biochem. 58:1994;1286-1291.
70. Spanning R.J.V., Boer A.P.D., Reijnders W.N., Spiro S., Westerhoff H.V., Stouthamer A.H., Oost J.V.d. Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators. FEBS Lett. 27:1995;151-154.
71. Vollack K.U., Hartig E., Korner H., Zumft W.G. Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. Mol. Microbiol. 31:1999;1681-1694.
72. Arai H., Igarashi Y., Kodama T. Expression of nir and nor genes of denitrification of Pseudomonas aeruginosa requires a novel CRP/FNR-related transcriptional regulator; DNR, in addition to ANR. FEBS Lett. 371:1995;73-76.
73. Spanning R.J.V., Boer A.P.D., Reijnders W.N., Westerhoff H.V., Stouthamer A.H., Oost J.V.D. FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation. Mol. Microbiol. 23:1997;893-907.
74. Hutchings M.I., Shearer N., Wastell S., Spanning R.J.v., Spiro S. Heterologous NNR-mediated nitric oxide signaling in Escherichia coli. J. Bacteriol. 182:2000;6434-6439.
75. Vollack K.U., Zumft W.G. Nitric oxide signaling and transcriptional control of denitrification genes in Pseudomonas stutzeri. J. Bacteriol. 183:2001;2516-2526.
76. Iwasaki H., Matsubara T. A nitrite reductase from Achromobacter cycloclastes. FEBS Lett. 291:1972;41-44.
77. Dispirito A.A., Taaffe L.R., Lipscomb J.D., Hooper A.B. A blue copper oxidase from Nitrosomonas europaea. Biochim. Biophys. Acta. 827:1985;320-326.
78. Sawada E., Satoh T., Kitamura H. Purification and properties of a dissimilatory nitrite reductase of a denitrifying phototrophic bacterium. Plant Cell Physiol. 19:1978;1339-1351.
79. Denariaz G., Payne W.J., Legall J. The denitrifying nitrite reductase of Bacillus halodenitrificans. Biochim. Biophys. Acta. 1056:1991;225-232.
80. Inatomi K., Hochstein L.I. The purification and properties of a copper nitrite reductase from Haloferax denitrificans. Curr. Microbiol. 32:1996;72-76.
81. Ichiki H., Tanaka Y., Mochizuki K., Yoshimatsu K., Sakurai T., Fujiwara T. Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. J. Bacteriol. 183(14):2001;4149-4156.
82. Hoehn G.T., Clark V.L. Isolation and nucleotide sequence of the gene (aniA) encoding the major anaerobically induced outer membrane protein of Neisseria gonorrhoeae. Infect. Immun. 60(11):1992;4695-4703.
83. Householder T.C., Bell W.A., Lissenden S., Cole J.A., Clark V.L. Cis and trans acting elements involved in regulation of aniA, the gene encoding the major anaerobically induced outer membrane protein in Neisseria gonorrhoeae. J. Bacteriol. 181:1999;541-551.
84. Mellies J., Jose J., Meyer T.F. Neisseria gonorrhoeae gene aniA encodes an inducible nitrite reductase. Mol. Gen. Genet. 256:1997;523-532.
85. Tosques I.E., Kwiatkowski A.V., Shi J., Shapleigh J.P. Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3. J. Bacteriol. 179(4):1997;1090-1095.
86. Bartnikas T.B., Tosques I.E., Laratta W.P., Shi J., Shapleigh J.P. Characterization of the nitric oxide reductase-encoding region in Rhodobacter sphaeroides 2.4.3. J. Bacteriol. 179(11):1997;3534-3540.
87. Zumft W.G., Braun C., Cuypers H. Nitric oxide reductase from Pseudomonas stutzeri. Primary structure and gene organization of a novel bacterial cytochrome bc complex. Eur. J. Biochem. 219:1994;481-490.
88. Sakurai N., Sakurai T. Genomic DNA cloning of the region encoding nitric oxide reductase in Paracoccus halodenitrificans and a structure model relevant to cytochrome oxidase. Biochem. Biophys. Res. Commun. 243:1998;400-406.
89. Cramm R., Siddiqui R.A., Friedrich B. Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16. J. Bacteriol. 179(21):1997;6769-6777.
90. Pohlmann A., Cramm R., Schmelz K., Friedrich B.A. A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha. Mol. Microbiol. 38(3):2000;626-638.
91. Boer A.P.d., Oost J.v.d., Reijnders W.N., Westerhoff H.V., Stouthamer A.H., Spanning R.J.v. Mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from Paracoccus denitrificans. Eur. J. Biochem. 242:1996;592-600.
92. Kukimoto M., Nishiyama M., Tanokura M., Horinouchi S. Gene organization for nitric oxide reduction in Alcaligenes faecalis S-6. Biosci. Biotechnol. Biochem. 64(4):2000;852-857.
93. Suharti S., Strampraad M.J., Schroder I., Vries S.d. A novel copper A containing menaquinol NO reductase from Bacillus azotoformans. Biochemistry. 40:2001;2632-2639.
94. Unden G., Trageser M. Oxygen regulated gene expression in Escherichia coli: control of anaerobic respiration by the FNR protein. Antonie van Leeuwenhoek. 59:1991;65-76.
95. 2O reductase contains CuA-type sites. Proc. Natl. Acad. Sci. U. S. A. 86(11):1989;4082-4086.
96. SooHoo C.K., Hollocher T.C. Purification and characterization of nitrous oxide reductase from Pseudomonas aeruginosa strain P2. J. Biol. Chem. 266(4):1991;2203-2209.
97. Hoeren F.U., Berks B.C., Ferguson S.J., McCarthy J.E.G. Sequence and expression of the gene encoding the respiratory nitrous-oxide reductase from Paracoccus denitrificans. New and conserved structural and regulatory motifs. Eur. J. Biochem. 218(1):1993;49-57.
98. Holloway P., McCormick W., Watson R.J., Chan Y.-K. Identification and analysis of the dissimilatory nitrous oxide reductase genes, nosRZDFY, of Rhizobium meliloti. J. Bacteriol. 178:1996;1505-1514.
99. Chan Y.K., McCormick W.A., Watson R.J. A new nos gene downstream from nosDFY is essential for dissimilatory reduction of nitrous oxide by Rhizobium (Sinorhizobium) meliloti. Microbiology. 143:1997;2817-2824.
100. Scala D.J., Kerkhof L.J. Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 65:1999;1681-1687.
101. Berks B.C. A common export pathway for proteins binding complex redox cofactors? Mol. Microbiol. 22:1996;393-404.
102. Weiner J.H., Bilous P.T., Shaw G.M., Lubitz S.P., Frost L., Thomas G.H., Cole J.A., Turner R.J. A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins. Cell. 93:1998;93-101.
103. Cuypers H., Viebrock-Sambale A., Zumft W.G. NosR, a membrane-bound regulatory component necessary for expression of nitrous oxide reductase in denitrifying Pseudomonas stutzeri. J. Bacteriol. 174(16):1992;5332-5339.
104. Zumft W.G., Viebrock-Sambale A., Braun C. Nitrous oxide reductase from denitrifying Pseudomonas stutzeri: genes for copper-processing and properties of the deduced products, including a new member of the family of ATP/GTP-binding proteins. Eur. J. Biochem. 192:1990;591-599.
105. McGuirl M., Nelson L.K., Bollinger J.A., Chan Y.-K., Dooley D.M. The nos (nitrous oxide reductase) gene cluster from the soils bacterium Achromobacter cycloclastes: cloning, sequence analysis and expression. J. Inorg. Biochem. 70:1998;155-169.
106. McGuirl M.A., Bollinger J.A., Cosper N., Scott R.A., Dooley D.M. Expression, purification, and characterization of NosL, a novel Cu(I) protein of the nitrous oxide reductase (nos) gene cluster. J. Biol. Inorg. Chem. 6(2):2001;189-195.
107. Saunders N.F.W., Hornberg J.J., Reijnders W.N.M., Westerhoff H.V., Vries S.d., Spanning R.J.M.v. The NosX and NirX proteins of Paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase. J. Bacteriol. 182:2000;5211-5217.
108. Cuypers H., Berghofer J., Zumft W.G. Multiple nosZ promoters and anaerobic expression of nos genes necessary for Pseudomonas stutzeri nitrous oxide reductase and assembly of its copper centers. Biochim. Biophys. Acta. 1264:1995;183-190.
109. Tamames J. Evolution of gene order conservation in prokaryotes. Genome Biol. 2(6):2001;1-11.
110. Lathe W.C., Snel P., Bork P. Gene context conservation of a higher order than operons. TIBS. 25:2000;474-479.
111. Mushegian A.R., Koonin E.V. Gene order is not conserved in bacterial evolution. TIG. 12:1996;289-290.
112. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
113. Besemer J., Borodovsky M. Heuristic approach to deriving models for gene finding. NAR. 27(19):1999;3911-3920.
114. Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S., Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Kikuchi H. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6(2):1999;83-101.
115. Ramirez S., Moreno R., Zafra O., Castan P., Valles C., Berenguer J. Two nitrate/nitrite transporters are encoded within the mobilizable plasmid for nitrate respiration of Thermus thermophilus HB8. J. Bacteriol. 182(8):2000;2179-2183.
116. Richardson D.J., Berks B.C., Russel D.A., Spiro S., Taylor C.J. Functional, biochemical and genetic diversity of prokaryotic nitrate reductase. Cell. Mol. Life Sci. 58:2001;165-178.
117. Nielsen H., Engelbrecht J., Brunak S., Heijne G.v. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1997;1-6.
118. Jain R., Shapleigh J.P. Characterization of nirV and a gene encoding a novel pseudoazurin in Rhodobacter sphaeroides 2.4.3. Microbiology. 147:2001;2505-2515.
119. Jungst A., Zumft W.G. Interdependence of respiratory NO reduction and nitrite reduction revealed by mutagenesis of nirQ, a novel gene in the denitrifying gene cluster of Pseudomonas stutzeri. FEBS. 314:1992;308-314.
120. Arai H., Kodama T., Igarashi Y. The role of the nirQOP genes in energy conservation during anaerobic growth of Pseudomonas aeruginosa. Biosci. Biotechnol. Biochem. 62:1998;1995-1999.
121. Ye R.W., Haas D., Ka J.O., Krishnapillai V., Zimmermann A., Baird C., Tiedje J.M. Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr; an analog of Fnr. J. Bacteriol. 177:1995;3606-3609.
122. Smith G.B., Tiedje J.M. Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria. Appl. Environ. Microbiol. 58:1992;376-384.
123. Ward B.B., Cockcroft A.R., Kilpatrick K.A. Antibody and DNA probes for detection of nitrite reductase in seawater. J. Gene Microbiol. 139:1993;2285-2293.
124. Braker G., Fesefeldt A., Witzel K.P. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64:1998;3769-3775.
125. Berg K.H.L.v., Bothe H. The distribution of denitrifying bacteria in soils monitored by DNA probing. FEMS Microbiol. Ecol. 86:1992;331-340.
126. 2-fixation and nitrification in bacteria isolated from different soils. Z. Naturforsch. 53(1-2):1998;69-81.
127. Michotey V., Mejean V., Bonin P. Comparison of methods for quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. Appl. Environ. Microbiol. 66(4):2000;1564-1571.
128. Mergel A., Schmitz O., Mallmann T., Bothe H. Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil. FEMS Microbiol. Ecol. 36:2001;33-42.
129. Gruntzig V., Nold S., Zhou J., Tiedje J.M. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real time PCR. Appl. Environ. Microbiol. 67:2001;760-768.
130. Flanagan D.A., Gregory L.G., Carter J.P., Karakas-Sen A., Richardson D.J., Spiro S. Detection of genes for periplasmic nitrate reductase in nitrate respiring bacteria and in community DNA. FEMS Microbiol. Lett. 177:1999;263-270.
131. Scala D.J., Kerkhof L.J. Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 162:1998;61-68.
132. Braker G., Zhou J., Wu L., Devol A.H., Tiedje J.M. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities. Appl. Environ. Microbiol. 66:2000;2096-2104.
133. Braker G., Ayala-Del-Rio H.L., Devol A.H., Fesefeldt A., Tiedje J.M. Community structure of pacific northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67:2001;1893-1901.
134. Gregory L.G., Karakas-Sen A., Richardson D.J., Spiro S. Detection of genes for membrane-bound nitrate reductase in nitrate-respiring bacteria and in community DNA. FEMS Microbiol Lett. 183(2):2000;275-279.
135. Weier K.L., Macrae I.C. Denitrifying bacteria in the profile of a brigalow clay soil beneath a permanent pasture and a cultivated crop. Soil Biol. Biochem. 24:1992;919-923.
136. Jones A.M., Hollocher T.C., Knowles R. Nitrous oxide reductase from Flexibacter canadensis: a unique membrane bound enzyme. FEMS Microbiol. Lett. 92:1992;205-209.