Nitrate reduction and the nitrogen cycle in archaea

Microbiology

Volumn 150, Issue 11, 2004, Pages 3527-3546

  Cabello, Purificación ^a   Roldán, M Dolores ^a   Moreno Vivián, Conrado ^a  

^a UNIVERSITY OF CÓRDOBA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; AMMONIA; BACTERIAL ENZYME; GLUTAMATE AMMONIA LIGASE; GLUTAMATE DEHYDROGENASE; GLUTAMATE SYNTHASE; INORGANIC COMPOUND; NITRATE; NITRATE REDUCTASE; NITRATE TRANSPORTER; NITRIC OXIDE; NITROGEN;

ARCHAEBACTERIUM; ARCHAEOGLOBUS FULGIDUS; BACTERIAL GENOME; BACTERIAL METABOLISM; BIOCHEMISTRY; CRENARCHAEOTA; DENITRIFICATION; ENZYME REGULATION; ENZYME STRUCTURE; EUBACTERIUM; GENE SEQUENCE; HALOBACTERIUM; METABOLIC REGULATION; METHANOBACTERIUM; MICROBIAL RESPIRATION; MOLECULAR EVOLUTION; NITROGEN CYCLE; NITROGEN FIXATION; NITROGEN METABOLISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PYROCOCCUS; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; REDUCTION; REVIEW; SULFOLOBUS; SULFOLOBUS SOLFATARICUS; THERMOPLASMA; THERMOPLASMA ACIDOPHILUM;

ARCHAEA; NITRATES; NITROGEN; NITROGEN COMPOUNDS; NITROGEN FIXATION; OXIDATION-REDUCTION;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; PROKARYOTA;

EID: 9144223171     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.27303-0     Document Type: Review

References (151)

1. Afshar, S., Kim, C., Monbouquette, H. G. & Schröder, I. (1998). Effect of tungstate on nitrate reduction by the hyperthermophilic archaeon Pyrobaculum aerophilum. Appl Environ Microbiol 64, 3004-3008.
2. Afshar, S., Johnson, E., de Vries, S. & Schröder, I. (2001). Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon Pyrobaculum aerophilum. J Bacteriol 183, 5491-5495.
3. Álvarez-Ossorio, M. C., Muriana, F. J. G., de la Rosa, F. F. & Relimpio, A. M. (1992). Purification and characterization of nitrate reductase from the halophile archaebacterium Haloferax mediterranei. Z Naturforsch 47C, 670-676.
4. Antipov, A. N., Lyalikova, N. N., Khijniak, T. V. & L'vov, N. P. (1998). Molybdenum-free nitrate reductases from vanadate-reducing bacteria. FEBS Lett 441, 257-260.
5. Antipov, A. N., Sorokin, D. Y., L'vov, N. P. & Kuenen, J. G. (2003). New enzyme belonging to the family of molybdenum-free nitrate reductases. Biochem J 369, 185-189.
6. II signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol Mol Biol Rev 65, 80-105.
7. Belay, N., Sparling, R. & Daniels, L. (1984). Dinitrogen fixation by a thermophilic methanogenic bacterium. Nature 312, 286-288.
8. Bell, S. D. & Jackson, S. P. (2001). Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4, 208-213.
9. Berks, B. C., Ferguson, S. J., Moir, J. W. B. & Richardson, D. J. (1995). Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochem Biophys Acta 1232, 97-173.
10. Berks, B. C., Sargent, F. & Palmer, T. (2000). The Tat protein export pathway. Mol Microbiol 35, 260-274.
11. Berman-Frank, I., Lundgren, P. & Falkowski, P. (2003). Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res Microbiol 154, 157-164.
12. Bertero, M. G., Rothery, R. A., Palak, M., Hou, C., Lim, D., Blasco, F., Weiner, J. H. & Strynadka, N. C. (2003). Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol 10, 681-687.
13. Bhatnagar, L., Zeikus, J. G. & Aubert, J. P. (1986). Purification and characterization of glutamine synthetase from the archaebacterium Methanobacterium ivanovi. J Bacteriol 165, 638-643.
14. Bhuiya, M. W., Sakuraba, H., Kujo, C., Nunoura-Kominato, N., Kawaraba, Y., Kikuchi, H. & Ohshima, T. (2000). Glutamate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications. Extremophiles 4, 333-341.
15. Bhuiya, M. W., Sakuraba, H. & Ohshima, T. (2002a). Temperature dependence of kinetic parameters for hyperthermophilic glutamate dehydrogenase from Aeropyrum pernix K1. Biosci Biotechnol Biochem 66, 873-876.
16. Bhuiya, M. W., Tsuge, H., Sakuraba, H., Yoneda, K., Katunuma, N. & Ohshima, T. (2002b). Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1. Acta Crystallogr D Biol Crystallogr 58, 1338-1339.
17. Bickel-Sandkötter, S. & Ufer, M. (1995). Properties of a dissimilatory nitrate reductase from the halophilic archaeon Haloferax volcanii. Z Naturforsch 50C, 365-372.
18. Blakey, D., Leech, A., Thomas, G. H., Coutts, G., Findlay, K. & Merrick, M. (2002). Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochem J 364, 527-535.
19. Bonete, M. J., Camacho, M. L. & Cadenas, E. (1987). A new glutamate dehydrogenase from Halobacterium halobium with different coenzyme specificity. Int J Biochem 19, 1149-1155.
20. Bonete, M. J., Pérez-Pomares, F., Ferrer, J. & Camacho, M. L. (1996). NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids. Biochim Biophys Acta 1289, 14-24.
21. Brown, J. R. & Doolittle, W. F. (1997). Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev 61, 456-502.
22. Brown, J. R., Masuchi, Y., Robb, F. T. & Doolittle, W. F. (1994). Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J Mol Evol 38, 566-576.
23. 2O) reductase. Evidence of a bridging inorganic sulfur. J Biol Chem 275, 41133-41136.
24. Buc, J., Santini, C. L., Giordani, R., Czjzek, M., Wu, L. F. & Giordano, G. (1999). Enzymatic and physiological properties of the tungsten-substituted molybdenum TMAO reductase from Escherichia coli. Mol Microbiol 32, 159-168.
25. Bult, C. J., White, O., Olsen, G. J. & 20 other authors (1996). Complete genome sequence ofthe methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.
26. Campbell, W. H. (2001). Structure and function of eukaryotic NAD(P)H: nitrate reductase. Cell Mol Life Sci 58, 194-204.
27. Castillo, F., Dobao, M. M., Reyes, F., Blasco, R., Roldán, M. D., Gavira, M., Caballero, F. J., Moreno-Viviá n, C. & Martínez-Luque, M. (1996). Molecular and regulatory properties of the nitrate reducing systems of Rhodobacter. Curr Microbiol 33, 341-346.
28. Castresana, J. & Moreira, D. (1999). Respiratory chains in the last common ancestor of living organisms. J Mol Evol 49, 453-460.
29. Chèneby, D., Hallet, S., Mondon, M., Martín-Laurent, F., Germon, J. C. & Philippot, L. (2003). Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis. Microb Ecol 46, 113-121.
30. Chien, Y. T. & Zinder, S. H. (1996). Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol 178, 143-148.
31. 2- and ammonium-grown cells of the archaeon Methanosarcina barkeri 227. J Bacteriol 180, 2723-2728.
32. Chien, Y. T., Auerbuch, V., Brabban, A. D. & Zinder, S. H. (2000). Analysis of genes encoding an alternative nitrogenase in the archaeon Methanosarcina barkeri 227. J Bacteriol 182, 3247-3253.
33. Cohen-Kupiec, R., Marx, C. J. & Leigh, J. A. (1999). Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis. J Bacteriol 181, 256-261.
34. Coutts, G., Thomas, G., Blakey, D. & Merrick, M. (2002). Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J 21, 536-545.
35. 2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422, 606-608.
36. de Boer, W. & Kowalchuk, G. A. (2001). Nitrification in acid soils: microorganisms and mechanisms. Soil Biol Biochem 33, 853-866.
37. Deppenmeier, U., Lienard, T. & Gottschalk, G. (1999). Novel reactions involved in energy conservation by methanogenic archaea. FEBS Lett 457, 291-297.
38. Deppenmeier, U., Johann, A., Hartsch, T. & 19 other authors (2002). The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4, 453-461.
39. de Vries, S. & Schröder, I. (2002). Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. Biochem Soc Trans 30, 662-667.
40. Dias, J. M., Than, M. E., Humm, A. & 10 other authors (1999). Crystal structure of the first dissimilatory nitrate reductase at 1.9 Å solved by MAD methods. Structure 7, 65-79.
41. DiRuggiero, J. & Robb, F. T. (1995). Expression and in vitro assembly of recombinant glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 61, 159-164.
42. DiRuggiero, J. & Robb, F. T. (1996). Enzymes of central nitrogen metabolism from hyperthermophiles: characterization, thermostability, and genetics. Adv Protein Chem 48, 311-339.
43. DiRuggiero, J., Dunn, D., Maeder, D. L., Holley-Shanks, R., Chatard, J., Horlacher, R., Robb, F. T., Boos, W. & Weiss, R. B. (2000). Evidence of recent lateral gene transfer among hyperthermoplilic archaea. Mol Microbiol 38, 684-693.
44. Eady, R. R. (1996). Structure-function relationships of alternative nitrogenases. Chem Rev 96, 3013-3030.
45. Eisenberg, D., Gill, H. S., Pfluegl, G. M. U. & Rotstein, S. H. (2000). Structure-function relationships of glutamine synthetases. Biochim Biophys Acta 1477, 122-145.
46. Ellington, M. J. K., Richardson, D. J. & Ferguson, S. J. (2003). Rhodobacter capsulatus gains a competitive advantage from respiratory nitrate reduction during light-dark transitions. Microbiology 149, 941-948.
47. Fani, R., Gallo, R. & Liò, P. (2000). Molecular evolution of nitrogen fixation: the evolutionary history of the nijD, nifK, nifE, and nifN genes. J Mol Evol 51, 1-11.
48. Ferguson, S. J. (1998). Nitrogen cycle enzymology. Curr Opin Chem Biol 2, 182-193.
49. Ferrer, J., Pérez-Pomares, F. & Bonete, M. J. (1996). NADP-glutamate dehydrogenase from the halophilic archaeon Haloferax mediterranei: enzyme purification, N-terminal sequence and stability. FEMS Microbiol Lett 141, 59-63.
50. Fitz-Gibbon, S. T., Ladner, H., Kim, U. J., Stetter, K. O., Simon, M. I. & Miller, J. H. (2002). Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A 99, 984-989.
51. Galagan, J. E., Nusbaum, C., Roy, A. & 52 other authors (2002). The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12, 532-542.
52. Gates, A. J., Hughes, R. O., Sharp, S. R. & 7 other authors (2003). Properties of the periplasmic nitrate reductases from Paracoccus pantotrophus and Escherichia coli after growth in tungsten-supplemented media. FEMS Microbiol Lett 220, 261-269.
53. Gavira, M., Roldán, M. D., Castillo, F. & Moreno-Vivián, C. (2002). Regulation of nap gene expression and periplasmic nitrate reductase activity in the phototrophic bacterium Rhodobacter sphaeroides DSM158. J Bacteriol 184, 1693-1702.
54. Gomes, C. M., Giuffrè, A., Forte, E., Vicente, J., Saraiva, L., Brunori, M. & Teixeira, M. (2002). A novel type of nitric-oxide reductase: Escherichia coli flavorubredoxin. J Biol Chem 277, 25273-25276.
55. Gregory, L. G., Bond, P. L., Richardson, D. J. & Spiro, S. (2003). Characterization of a nitrate-respiring bacterial community using the nitrate reductase gene (narG) as a functional marker. Microbiology 149, 229-237.
56. Halbleib, C. M. & Ludden, P. W. (2000). Regulation of biological nitrogen fixation. J Nutr 130, 1081-1084.
57. +-dependent glutamate dehydrogensase. FEMS Microbiol Lett 211, 37-41.
58. Helianti, I., Morita, Y., Yamamura, A., Murakami, Y., Yokoyama, K. & Tamiya, E. (2001). Characterization of native glutamate dehydrogenase from an aerobic hyperthermophilic archaeon Aeropyrum pernix KI. Appl Microbiol Biotechnol 56, 388-394.
59. Helianti, I., Morita, Y., Murakami, Y., Yokoyama, K. & Tamiya, E. (2002). Expression of two kinds of recombinant glutamate dehydrogenase from Aeropyrum pernix with different N-terminal sequence length in Escherichia coli. Appl Microbiol Biotechnol 59, 462-466.
60. Hendriks, J., Oubrie, A., Castresana, J., Urbani, A., Gemeinhardt, S. & Saraste, M. (2000). Nitric oxide reductases in bacteria. Biochim Biophys Acta 1459, 266-273.
61. Hille, R. (2002). Molybdenum and tungsten in biology. Trends Biochem Sci 27, 360-367.
62. Hochstein, L. I. & Lang, F. (1991). Purification and properties of a dissimilatory nitrate reductase from Haloferax denitrificans. Arch Biochem Biophys 288, 380-385.
63. Howard, J. B. & Rees, D. C. (1996). Structural basis of biological nitrogen fixation. Chem Rev 96, 2965-2982.
64. Ichiki, H., Tanaka, Y., Mochizuki, K., Yoshimatsu, K, Sakurai, T. & Fujiwara, T. (2001). Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. J Bacteriol 183, 4149-4156.
65. Inatomi, K. & Hochstein, L. I. (1996). The purification and properties of a copper nitrite reductase from Haloferax denitrificans. Curr Microbiol 32, 72-76.
66. Javelle, A., Severi, E., Thornton, J. & Merrick, M. (2004). Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J Biol Chem 279, 8530-8538.
67. Jongsareejit, B., Rahman, R. N. Z. A., Fujiwara, S. & Imanaka, T. (1997). Gene cloning, sequencing and enzymatic properties of glutamate synthase from the hyperthermophilic archaeon Pyrococcus sp. KOD1. Mol Gen Genet 254, 635-642.
68. Jormakka, M., Byrne, B. & Iwata, S. (2003). Protonmotive force generation by a redox loop mechanism. FEBS Lett 545, 25-30.
69. Jormakka, M., Richardson, D. J., Byrne, B. & Iwata, S. (2004). Architecture of NarGH reveals a structural classification of MobisMGD enzymes. Structure 12, 95-104.
70. Kabayashi, T., Higuchi, S., Kimura, K., Kudo, T. & Horikoshi, K. (1995). Properties of glutamate dehydrogenase and its involvement in alanine production in a hyperthermophilic archaeon, Thermococcus profundus. J Biochem 118, 587-592.
71. Kawarabayasi, Y., Hino, Y., Horikawa, H. & 25 other authors (1999). Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix KI. DNA Res 6, 83-101.
72. Kawarabayasi, Y., Hino, Y., Horikawa, H. & 27 other authors (2001). Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 8, 123-140.
73. Kawashima, T., Amano, N., Koike, H. & 12 other authors (2000). Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci U S A 97, 14257-14262.
74. Kelman, L. M. & Kelman, Z. (2003). Archaea: an archetype for replication initiation studies? Mol Microbiol 48, 605-615.
75. Kessler, P. S. & Leigh, J. A. (1999). Genetics of nitrogen regulation in Methanococcus maripaludis. Genetics 152, 1343-1351.
76. Kessler, P. S., McLarnan, J. & Leigh, J. A. (1997). Nitrogenase phylogeny and the molybdenum dependence of nitrogen fixation in Methanococcus maripaludis. J Bacteriol 179, 541-543.
77. Kessler, P. S., Blank, C. & Leigh, J. A. (1998). The nif gene operon of the methanogenic archaeon Methanococcus maripaludis. J Bacteriol 180, 1504-1511.
78. 2. J Bacteriol 183, 882-889.
79. Klenk, H. P., Clayton, R. A., Tomb, J. F. & 48 other authors (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370.
80. Kowalchuk, G. A. & Stephen, J. R. (2001). Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55, 485-529.
81. Kuypers, M. M. M., Sliekers, A. O., Lavik, G., Schmid, M., Jorgensen, B. B., Kuenen, J. G., Damsté, J. S. S., Strous, M. & Jetten, M. S. M. (2003). Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422, 608-611.
82. Leigh, J. A. (2000). Nitrogen fixation in methanogens: the archaeal perspective. Curr Issues Mol Biol 2, 125-131.
83. Lie, T. J. & Leigh, J. A. (2003). A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol 47, 235-246.
84. Lobo, A. L. & Zinder, S. H. (1990). Nitrogenase in the archaebacterium Methanosarcina barkeri 227. J Bacteriol 172, 6789-6796.
85. Lubben, M. & Morand, K. (1994). Novel prenylated hemes as cofactors of cytochrome oxidases. Archaea have modified hemes a and O. J Biol Chem 269, 21473-21479.
86. Ludden, P. W. (1994). Reversible ADP-ribosylation as a mechanism of enzyme regulation in procaryotes. Mol Cell Biochem 138, 123-129.
87. Maeder, D. L., Weiss, R. B., Dunn, D. M., Cherry, J. L., Gonález, J. M., DiRuggiero, J. & Robb, F. T. (1999). Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics 152, 1299-1305.
88. Martínez-Espinosa, R. M., Marhuenda-Egea, F. C. & Bonete, M. J. (2001a). Purification and characterization of a possible assimilatory nitrite reductase from the halophile archaeon Haloferax mediterranei. FEMS Microbiol Lett 196, 113-118.
89. Martínez-Espinosa, R. M., Marhuenda-Egea, F. C. & Bonete, M. J. (2001b). Assimilatory nitrate reductase from the haloarchaeon Haloferax mediterranei: purification and characterization. FEMS Microbiol Lett 204, 381-385.
90. Martínez-Espinosa, R. M., Marhuenda-Egea, F. C., Donaire, A. & Bonete, M. J. (2003). NMR studies of a ferredoxin from Haloferax mediterranei and its physiological role in nitrate assimilatory pathway. Biochim Biophys Acta 1623, 47-51.
91. Mehta, M. P., Butterfield, D. A. & Baross, J. A. (2003). Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microbiol 69, 960-970.
92. Merrick, M. J. & Edwards, R. A. (1995). Nitrogen control in bacteria. Microbiol Rev 59, 604-622.
93. Moir, J. W. B. & Wood, N. J. (2001). Nitrate and nitrite transport in bacteria. Cell Mol Life Sci 58, 215-224.
94. Moreno-Vivián, C. & Ferguson, S. J. (1998). Definition and distinction between assimilatory, dissimilatory and respiratory pathways. Mol Microbiol 29, 664-666.
95. Moreno-Vivián, C., Schmehl, M., Masepohl, B., Arnold, W. & Klipp, W. (1989). DNA sequence and genetic analysis of the Rhodobacter capsulatus nifENX gene region: homology between NifX and NifB suggests involvement of NifX in processing of the iron-molybdenum cofactor. Mol Gen Genet 216, 353-363.
96. Moreno-Vivián, C., Cabello, P., Martínez-Luque, M., Blasco, R. & Castillo, F. (1999). Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 181, 6573-6584.
97. Murillo, M. F., Gugliuzza, T., Senko, J., Basu, P. & Stolz, J. F. (1999). A heme c-containing enzyme complex that exhibits nitrate and nitrite reductase activity from the dissimilatory iron-reducing bacterium Geobacter metallireducens. Arch Microbiol 172, 313-320.
98. Murray, P. A. & Zinder, S. H. (1984). Nitrogen fixation by a methanogenic archaebacterium. Nature 312, 284-286.
99. Nakahara, K., Tanimoto, T., Hatano, K, Usuda, K. & Shoun, H. (1993). Cytochrome P-450 55A1 (P-45OdNIR) acts as nitric oxide reductase employing NADH as the direct electron donor. J Biol Chem 268, 8350-8355.
100. Ng, W. V., Kennedy, S. P., Mahairas, G. G. & 40 other authors (2000). Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97, 12176-12181.
101. Ninfa, A. J. & Atkinson, M. R. (2000). PII signal transduction proteins. Trends Microbiol 8, 172-179.
102. Pesole, G., Gissi, C., Lanave, C. & Saccone, C. (1995). Glutamine synthetase gene evolution in bacteria. Mol Biol Evol 12, 189-197.
103. Petri, R. & Imhoff, J. F. (2000). The relationship of nitrate reducing bacteria on the basis of narH gene sequences and comparison of narH and 16S rDNA based phylogeny. Syst Appl Microbiol 23, 47-57.
104. Philippot, L. (2002). Denitrifying genes in bacterial and archaeal genomes. Biochim Biophys Acta 1577, 355-376.
105. Potter, L., Angove, H., Richardson, D. J. & Cole, J. A. (2001). Nitrate reduction in the periplasm of Gram-negative bacteria. Adv Microb Physiol 45, 51-112.
106. Rahman, R. N. Z. A., Jongsareejit, B., Fujiwara, S. & Imanaka, T. (1997). Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl Environ Microbiol 63, 2472-2476.
107. Ramírez, S., Moreno, R., Zafra, O., Castán, P., Vallés, C. & Berenguer, J. (2000). Two nitrate/nitrite transporters are encoded within the mobilizable plasmid for nitrate respiration of Thermus thermophilus HB8. J Bacteriol 182, 2179-2183.
108. Ramírez-Arcos, S., Fernández-Herrero, L. A. & Berenguer, J. (1998a). A thermophilic nitrate reductase is responsible for the strain specific anaerobic growth of Thermus thermophilus HB8. Biochim Biophys Acta 1396, 215-227.
109. Ramírez-Arcos, S., Fernández-Herrero, L. A., Marín, I. & Berenguer, J. (1998b). Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180, 3137-3143.
110. Rasmussen, T., Berks, B. C., Sanders-Loehr, J., Dooley, D. M., Zumft, W. G. & Thomson, A. J. (2000). The catalytic center in nitrous oxide reductase, CuZ, is a copper-sulfide cluster. Biochemistry 39, 12753-12756.
111. Rees, D. C. (2002). Great metalloclusters in enzymology. Annu Rev Biochem 71, 221-246.
112. Reeve, J. N. (2003). Archaeal chromatin and transcription. Mol Microbiol 48, 587-598.
113. Reyes, F., Roldán, M. D., Klipp, W., Castillo, F. & Moreno-Vivián, C. (1996). Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases. Mol Microbiol 19, 1307-1318.
114. Reyes, F., Gavira, M., Castillo, F. & Moreno-Vivián, C. (1998). Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster. Biochem J 331, 897-904.
115. Richardson, D. J. (2000). Bacterial respiration: a flexible process for a changing environment. Microbiology 146, 551-571.
116. Richardson, D. J. & Watmough, N. J. (1999). Inorganic nitrogen metabolism in bacteria. Curr Opin Chem Biol 3, 207-219.
117. Richardson, D. J., Berks, B. C., Russell, D. A., Spiro, S. & Taylor, C. J. (2001). Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 58, 165-178.
118. Ruepp, A., Graml, W., Santos-Martínez, M. L. & 7 other authors (2000). The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508-513.
119. Sapra, R., Bagramyan, K. & Adams, M. W. W. (2003). A simple energy-conserving system: proton reduction coupled to proton translocation. Proc Natl Acad Sci U S A 100, 7545-7550.
120. Saraste, M. (1994). Structure and evolution of cytochrome oxidase. Antonie Van Leeuwenhoek 65, 285-287.
121. Saraste, M. & Castresana, J. (1994). Cytochrome oxidase evolved by tinkering with denitrification enzymes. FEBS Lett 341, 1-4.
122. Scharf, B. & Engelhard, M. (1993). Halocyanin, an archaebacterial blue copper protein (type I) from Natronobacterium pharaonis. Biochemistry 32, 12894-12900.
123. Schütz, M., Brugna, M., Lebrun, E. & 9 other authors (2000). Early evolution of cytochrome bc complexes. J Mol Biol 300, 663-675.
124. She, Q., Singh, R. K, Confalonieri, F. & 28 other authors (2001). The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98, 7835-7840.
125. Shoun, H. & Tanimoto, T. (1991). Denitrification by the fungus Fusarium oxysporum and involvement of cytochrome P-450 in the respiratory nitrite reduction. J Biochem 266, 11078-11082.
126. Slesarev, A. I., Mezhevaya, K. V., Makarova, K. S. & 13 other authors (2002). The complete genome of hyperthermophile Methanopyrus kandleri-AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A 99, 4644-4649.
127. Smith, E. L., Austen, B. M., Blumenthal, K. M. & Nyc, J. F. (1975). Glutamate dehydrogenases. In The Enzymes, vol. XI, pp. 293-367. Edited by P. D. Boyer. New York: Academic Press.
128. Smith, D. R., Doucette-Stamm, L. A., Deloughery, C. & 34 other authors (1997). Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genomics. J Bacteriol 179, 7135-7155.
129. 3 bidirectionally. Proc Natl Acad Sci U S A 99, 3926-3931.
130. Stolz, J. F. & Basu, P. (2002). Evolution of nitrate reductase: molecular and structural variations on a common function. Chembiochem 3, 198-206.
131. Studholme, D. J. & Pau, R. N. (2003). A DNA element recognized by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea. BMC Microbiology 3, 24-33.
132. Syntichaki, K. M., Loulakakis, K. A. & Roubelakis-Angelakis, K. A. (1996). The amino-acid sequence similarity of plant glutamate dehydrogenase to the extremophilic archaeal enzyme conforms to its stress-related function. Gene 168, 87-92.
133. Thomas, G., Coutts, G. & Merrick M. (2000). The glnKamtB operon: a conserved gene pair in prokaryotes. Trends Genet 16, 11-14.
134. Tiboni, O., Cammarano, P. & Sanangelantoni, A. M. (1993). Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences. J Bacteriol 175, 2961-2969.
135. Tomlinson, G. A., Jahnke, L. L. & Hochstein, L. I. (1986). Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium. Int J Syst Bacteriol 36, 66-70.
136. Trotta, P. P., Platzer, K. E. B., Haschemeyer, R. H. & Meister, A. (1974). Glutamine-binding subunit of glutamate synthase and partial reactions catalyzed by this glutamine amidotransferase. Proc Natl Acad Sci U S A 71, 4607-4611.
137. Völkl, P., Huber, R., Drobner, E., Rachel, R., Burggraf, S., Tricone, A. & Stetter, K. O. (1993). Pyrobaculum aerophilum sp. nov., a novel nitrate-reducing hyperthermophilic archaeum. Appl Environ Microbiol 59, 2918-2926.
138. 2O in Ferroglobus placidus. Arch Microbiol 167, 19-23.
139. Wang, S., Feng, Y., Zhang, Z., Zheng, B., Li, N., Cao, S., Matsui, I. & Kosugi, Y. (2003). Heat effect on the structure and activity of the recombinant glutamate dehydrogenase from a hyperthermophilic archaeon Pyrococcus horikoshii. Arch Biochem Biophys 411, 56-62.
140. Wenner, C. & Soppa, J. (1999). Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii. Genetics 152, 1417-1428.
141. Werber, M. M. & Mevarech, M. (1978). Induction of a dissimilatory reduction pathway of nitrate in Halobacterium of the Dead Sea. A possible role for the 2Fe-ferredoxin isolated from this organism. Arch Biochem Biophys 186, 60-65.
142. Williams, R. J. P. & Fraústo da Silva, J. J. R. (2002). The involvement of molybdenum in life. Biochem Biophys Res Comm 292, 293-299.
143. Woese, C. R., Kandler, O. & Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87, 4576-4579.
144. Wood, N. J., Alizadeh, T., Bennet, S., Pearce, J., Ferguson, S. J., Richardson, D. J. & Moir, J. W. (2001). Maximal expression of membrane-bound nitrate reductase in Paracoccus is induced by nitrate via a third FNR-like regulator named NarR. J Bacteriol 183, 3606-3613.
145. Wood, N. J., Alizadeh, T., Richardson, D. J., Ferguson, S. J. & Moir, J. W. (2002). Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol Microbiol 44, 157-170.
146. Yin, Z., Purschke, W. G., Schafer, G. & Schmidt, C. L. (1998). The glutamine synthetase from the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius: isolation, characterization and sequencing of the gene. Biol Chem 379, 1349-1354.
147. Yip, K. S., Stillman, T. J., Britton, K. L. & 7 other authors (1995). The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for iron-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3, 1147-1158.
148. Yoshimatsu, K., Sakurai, T. & Fujiwara, T. (2000). Purification and characterization of dissimilatory nitrate reductase from a denitrifying halophilic archaeon, Haloarcula marismortui. FEBS Lett 470, 216-220.
149. Yoshimatsu, K., Iwasaki, Y. & Fujiwara, T. (2002). Sequence and electron paramagnetic resonance analysis of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui. FEBS Lett 516, 145-150.
150. Zumft, W. G. (1997). Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61, 533-616.
151. Zumft, W. G. & Castillo, F. (1978). Regulatory properties of the nitrogenase from Rhodopseudomonas palustris. Arch Microbiol 117, 53-60.