The genome of the ammonia-oxidizing candidatus nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations

Environmental Microbiology

Volumn 14, Issue 12, 2012, Pages 3122-3145

  Spang, Anja ^a,e   Poehlein, Anja ^b,e   Offre, Pierre ^b   Zumbrägel, Sabine ^c   Haider, Susanne ^a   Rychlik, Nicolas ^a   Nowka, Boris ^a   Schmeisser, Christel ^a   Lebedeva, Elena V ^d   Rattei, Thomas ^a   Böhm, Christoph ^a   Schmid, Markus ^a   Galushko, Alexander ^a   Hatzenpichler, Roland ^a   Weinmaier, Thomas ^a   Daniel, Rolf ^b   Schleper, Christa ^a   Spieck, Eva ^c   Streit, Wolfgang ^c   Wagner, Michael ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY OF HAMBURG   (Germany)

^d WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

^e CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; CARBON; HEAVY METAL;

ADAPTATION; ARTICLE; BACTERIAL GENOME; CHEMOTAXIS; ECOSYSTEM; ENERGY METABOLISM; EURYARCHAEOTA; EVOLUTION; GENETICS; METABOLISM; OXIDATION REDUCTION REACTION; PHYLOGENY; PHYSIOLOGY; TRANSPORT AT THE CELLULAR LEVEL; ULTRASTRUCTURE;

ADAPTATION, BIOLOGICAL; AMMONIA; BIOLOGICAL EVOLUTION; BIOLOGICAL TRANSPORT; CARBON; CHEMOTAXIS; ECOSYSTEM; ENERGY METABOLISM; EURYARCHAEOTA; GENOME, BACTERIAL; METALS, HEAVY; OXIDATION-REDUCTION; PHYLOGENY;

ARCHAEA; BACTERIA (MICROORGANISMS); CANDIDATUS NITROSOPUMILUS; EURYARCHAEOTA;

EID: 84870486180     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02893.x     Document Type: Article

References (196)

1. Ajon, M., Fröls, S., van Wolferen, M., Stoecker, K., Teichmann, D., Driessen, A.J.M., etal. (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol 82: 807-817.
2. Akita, M., Adachi, A., Takemura, K., Yamagami, T., Matsunaga, F., and Ishino, Y. (2010) Cdc6/Orc1 from Pyrococcus furiosus may act as the origin recognition protein and Mcm helicase recruiter. Genes Cells 15: 537-552.
3. Al-Attar, S., Westra, E.R., van der Oost, J., and Brouns, S.J.J. (2011) Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 392: 277-289.
4. Albers, S.V., and Pohlschröder, M. (2009) Diversity of archaeal type IV pilin-like structures. Extremophiles 13: 403-410.
5. Albers, S.V., Szabó, Z., and Driessen, A.J.M. (2003) Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity. J Bacteriol 185: 3918-3925.
6. Albers, S.V., Konings, W.N., and Driessen, A.J. (2007) Solute transport. In Archaea: Molecular and Cellular Biology. Cavicchioli, R. (ed.). Washington, DC, USA: American Society for Microbiology, pp. 354-368.
7. Anderson, A.J., and Dawes, E.A. (1990) Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev 54: 450-472.
8. Andrade, S.L.A., and Einsle, O. (2007) The Amt/Mep/Rh family of ammonium transport proteins. Mol Membr Biol 24: 357-365.
9. Arp, D.J., Chain, P.S.G., and Klotz, M.G. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu Rev Microbiol 61: 503-528.
10. Ashby, M.K. (2006) Distribution, structure and diversity of 'bacterial' genes encoding two-component proteins in the Euryarchaeota. Archaea 2: 11-30.
11. Avery, S.V. (1995) Caesium accumulation by microorganisms: uptake mechanisms, cation competition, compartmentalization and toxicity. J Ind Microbiol 14: 76-84.
12. Bandeiras, T.M., Salgueiro, C., Kletzin, A., Gomes, C.M., and Teixeira, M. (2002) Acidianus ambivalens type-II NADH dehydrogenase: genetic characterisation and identification of the flavin moiety as FMN. FEBS Lett 531: 273-277.
13. Bardy, S.L., Ng, S.Y.M., and Jarrell, K.F. (2004) Recent advances in the structure and assembly of the archaeal flagellum. J Mol Microbiol Biotechnol 7: 41-51.
14. Bartossek, R., Nicol, G.W., Lanzen, A., Klenk, H.-P., and Schleper, C. (2010) Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiol 12: 1075-1088.
15. Bartossek, R., Spang, A., Weidler, G., Lanzen, A., and Schleper, C. (2012) Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group. Front Microbiol 3: 208.
16. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. (2011) GenBank. Nucleic Acids Res 39: D32-D37.
17. 2 fixation pathways. Appl Environ Microbiol 77: 1925-1936.
18. Berg, I.A., Kockelkorn, D., Buckel, W., and Fuchs, G. (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318: 1782-1786.
19. Berg, I.A., Kockelkorn, D., Ramos-Vera, W.H., Say, R.F., Zarzycki, J., Hügler, M., etal. (2010a) Autotrophic carbon fixation in archaea. Nat Rev Microbiol 8: 447-460.
20. 2 fixation cycles in Crenarchaeota. Microbiology 156: 256-269.
21. Blainey, P.C., Mosier, A.C., Potanina, A., Francis, C.A., and Quake, S.R. (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6: e16626.
22. Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252.
23. Brochier-Armanet, C., Gribaldo, S., and Forterre, P. (2012) Spotlight on the Thaumarchaeota. ISME J 6: 227-230.
24. Burroughs, A.M., Allen, K.N., Dunaway-Mariano, D., and Aravind, L. (2006) Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 361: 1003-1034.
25. Busch, W., and Saier, M.H., Jr (2002) The transporter classification (TC) system, 2002. Crit Rev Biochem Mol Biol 37: 287-337.
26. Chan, H., Babayan, V., Blyumin, E., Gandhi, C., Hak, K., Harake, D., etal. (2010) The p-type ATPase superfamily. J Mol Microbiol Biotechnol 19: 5-104.
27. Claudel-Renard, C., Chevalet, C., Faraut, T., and Kahn, D. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res 31: 6633-6639.
28. Cochrane, G., Akhtar, R., Bonfield, J., Bower, L., Demiralp, F., Faruque, N., etal. (2009) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 37: D19-D25.
29. Craig, L., and Li, J. (2008) Type IV pili: paradoxes in form and function. Curr Opin Struct Biol 18: 267-277.
30. Czyzewski, B.K., and Wang, D.-N. (2012) Identification and characterization of a bacterial hydrosulphide ion channel. Nature 483: 494-497.
31. Deppenmeier, U. (2002) Redox-driven proton translocation in methanogenic Archaea. Cell Mol Life Sci 59: 1513-1533.
32. Desmond, E., Brochier-Armanet, C., and Gribaldo, S. (2007) Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol Biol 7: 106.
33. Ellen, A.F., Zolghadr, B., Driessen, A.M.J., and Albers, S.-V. (2010) Shaping the archaeal cell envelope. Archaea 2010: 608243.
34. Empadinhas, N., and da Costa, M.S. (2006) Diversity and biosynthesis of compatible solutes in hyper/thermophiles. Int Microbiol 9: 199-206.
35. Empadinhas, N., and da Costa, M.S. (2008) Osmoadaptation mechanisms in prokaryotes: distribution of compatible solutes. Int Microbiol 11: 151-161.
36. Empadinhas, N., and da Costa, M.S. (2011) Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 13: 2056-2077.
37. Empadinhas, N., Marugg, J.D., Borges, N., Santos, H., and Costa, M.S. (2001) Pathway for the synthesis of mannosylglycerate in the hyperthermophilic archaeon Pyrococcus horikoshii. Biochemical and genetic characterization of key enzymes. J Biol Chem 276: 43580-43588.
38. Estelmann, S., Hügler, M., Eisenreich, W., Werner, K., Berg, I.A., Ramos-Vera, W.H., etal. (2011) Labeling and enzyme studies of the central carbon metabolism in Metallosphaera sedula. J Bacteriol 193: 1191-1200.
39. Faguy, D.M., Bayley, D.P., Kostyukova, A.S., Thomas, N.A., and Jarrell, K.F. (1996) Isolation and characterization of flagella and flagellin proteins from the Thermoacidophilic archaea Thermoplasma volcanium and Sulfolobus shibatae. J Bacteriol 178: 902-905.
40. Filée, J., Siguier, P., and Chandler, M. (2007) Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 71: 121-157.
41. Fong, R.N., Kim, K.-S., Yoshihara, C., Inwood, W.B., and Kustu, S. (2007) The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion. Proc Natl Acad Sci USA 104: 18706-18711.
42. Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E., and Oakley, B.B. (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688.
43. French, E., Kozlowski, J.A., Mukherjee, M., Bullerjahn, G., and Bollmann, A. (2012) Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 78: 5773-5780.
44. Fröls, S., Ajon, M., Wagner, M., Teichmann, D., Zolghadr, B., Folea, M., etal. (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol 70: 938-952.
45. Fuchs, G. (2011) Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu Rev Microbiol 65: 631-658.
46. Fukuda, E., and Wakagi, T. (2002) Substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from Sulfolobus sp. strain 7. Biochim Biophys Acta 1597: 74-80.
47. Furumoto, T., Yamaguchi, T., Ohshima-Ichie, Y., Nakamura, M., Tsuchida-Iwata, Y., Shimamura, M., etal. (2011) A plastidial sodium-dependent pyruvate transporter. Nature 476: 472-475.
48. Gelder, J.D., Willemse-Erix, D., Scholtes, M.J., Sanchez, J.I., Maquelin, K., Vandenabeele, P., etal. (2008) Monitoring poly(3-hydroxybutyrate) production in Cupriavidus necator DSM 428 (H16) with raman spectroscopy. Anal Chem 80: 2155-2160.
49. Ghosh, A., and Albers, S.-V. (2011) Assembly and function of the archaeal flagellum. Biochem Soc Trans 39: 64-69.
50. 2+ transport system. Mol Microbiol 5: 2753-2762.
51. Gomes, C.M., Bandeiras, T.M., and Teixeira, M. (2001) A new type-II NADH dehydrogenase from the Archaeon Acidianus ambivalens: characterization and in vitro reconstitution of the respiratory chain. J Bioenerg Biomembr 33: 1-8.
52. Goujon, M., McWilliam, H., Li, W., Valentin, F., Squizzato, S., Paern, J., and Lopez, R. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38: W695-W699.
53. Grage, K., Jahns, A.C., Parlane, N., Palanisamy, R., Rasiah, I.A., Atwood, J.A., and Rehm, B.H.A. (2009) Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications. Biomacromolecules 10: 660-669.
54. Grissa, I., Vergnaud, G., and Pourcel, C. (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-W57.
55. Gubry-Rangin, C., Hai, B., Quince, C., Engel, M., Thomson, B.C., James, P., etal. (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA 108: 21206-21211.
56. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
57. Hall, T.A. (1999) BioEdit: a user-friendly tbiological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
58. Hallam, S.J., Konstantinidis, K.T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., etal. (2006a) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103: 18296-18301.
59. Hallam, S.J., Mincer, T.J., Schleper, C., Preston, C.M., Roberts, K., Richardson, P.M., and DeLong, E.F. (2006b) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4: e95.
60. Han, J., Hou, J., Liu, H., Cai, S., Feng, B., Zhou, J., and Xiang, H. (2010) Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases. Appl Environ Microbiol 76: 7811-7819.
61. Hansen, T., Oehlmann, M., and Schönheit, P. (2001) Novel type of glucose-6-phosphate isomerase in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 183: 3428-3435.
62. Hansen, T., Schlichting, B., Felgendreher, M., and Schönheit, P. (2005) Cupin-type phosphoglucose isomerases (Cupin-PGIs) constitute a novel metal-dependent PGI family representing a convergent line of PGI evolution. J Bacteriol 187: 1621-1631.
63. Hasan, M.R., Rahman, M., Jaques, S., Purwantini, E., and Daniels, L. (2010) Glucose 6-phosphate accumulation in mycobacteria: implications for a novel F420-dependent anti-oxidant defense system. J Biol Chem 285: 19135-19144.
64. Hatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., and Wagner, M. (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci USA 105: 2134-2139.
65. Hollibaugh, J.T., Gifford, S., Sharma, S., Bano, N., and Moran, M.A. (2011) Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. ISME J 5: 866-878.
66. Hommes, N.G., Kurth, E.G., Sayavedra-Soto, L.A., and Arp, D.J. (2006) Disruption of sucA, which encodes the E1 subunit of alpha-ketoglutarate dehydrogenase, affects the survival of Nitrosomonas europaea in stationary phase. J Bacteriol 188: 343-347.
67. Horvath, P., and Barrangou, R. (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167-170.
68. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., etal. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-D215.
69. + antiporter in Escherichia coli. Biol Pharm Bull 17: 395-398.
70. Izumi, C.M.S., and Temperini, M.L.A. (2010) FT-Raman investigation of biodegradable polymers: poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate). Vib Spectrosc 54: 127-132.
71. Jeong, J.-J., Fushinobu, S., Ito, S., Jeon, B.-S., Shoun, H., and Wakagi, T. (2003) Characterization of the cupin-type phosphoglucose isomerase from the hyperthermophilic archaeon Thermococcus litoralis. FEBS Lett 535: 200-204.
72. Jung, M.-Y., Park, S.-J., Min, D., Kim, J.-S., Rijpstra, W.I.C., Sinninghe Damsté, J.S., etal. (2011) Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil. Appl Environ Microbiol 77: 8635-8647.
73. Kelman, L.M., and Kelman, Z. (2004) Multiple origins of replication in archaea. Trends Microbiol 12: 399-401.
74. Kerscher, L., and Oesterhelt, D. (1981) Purification and properties of two 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. Eur J Biochem 116: 587-594.
75. Kim, B.K., Jung, M.-Y., Yu, D.S., Park, S.-J., Oh, T.K., Rhee, S.-K., and Kim, J.F. (2011) Genome sequence of an ammonia-oxidizing soil archaeon, 'Candidatus Nitrosoarchaeum koreensis' MY1. J Bacteriol 193: 5539-5540.
76. Kim, J.-G., Jung, M.-Y., Park, S.-J., Rijpstra, W.I.C., Sinninghe Damsté, J.S., Madsen, E.L., etal. (2012) Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 14: 1528-1543.
77. Klotz, M.G., and Stein, L.Y. (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278: 146-156.
78. Klunker, D., Haas, B., Hirtreiter, A., Figueiredo, L., Naylor, D.J., Pfeifer, G., etal. (2003) Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei. J Biol Chem 278: 33256-33267.
79. Könneke, M., Bernhard, A.E., Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
80. Koshiishi, I., Mamura, Y., and Imanari, T. (1997) Cyanate causes depletion of ascorbate in organisms. Biochim Biophys Acta 1336: 566-574.
81. Kraus, L.M., and Kraus, A.P., Jr (1998) The search for the uremic toxin: the case for carbamoylation of amino acids and proteins. Wien Klin Wochenschr 110: 521-530.
82. Kristensen, D.M., Kannan, L., Coleman, M.K., Wolf, Y.I., Sorokin, A., Koonin, E.V., and Mushegian, A. (2010) A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26: 1481-1487.
83. Krupovic, M., Spang, A., Gribaldo, S., Forterre, P., and Schleper, C. (2011) A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea. Biochem Soc Trans 39: 82-88.
84. Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., and Salzberg, S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
85. Large, A.T., Goldberg, M.D., and Lund, P.A. (2009) Chaperones and protein folding in the archaea. Biochem Soc Trans 37: 46-51.
86. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., etal. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
87. Lebedeva, E.V., Alawi, M., Fiencke, C., Namsaraev, B., Bock, E., and Spieck, E. (2005) Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone. FEMS Microbiol Ecol 54: 297-306.
88. Lee, S.M., Grass, G., Rensing, C., Barrett, S.R., Yates, C.J.D., Stoyanov, J.V., and Brown, N.L. (2002) The Pco proteins are involved in periplasmic copper handling in Escherichia coli. Biochem Biophys Res Commun 295: 616-620.
89. Lehtovirta-Morley, L.E., Stoecker, K., Vilcinskas, A., Prosser, J.I., and Nicol, G.W. (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA 108: 15892-15897.
90. Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., etal. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
91. Levin, E.J., Quick, M., and Zhou, M. (2009) Crystal structure of a bacterial homologue of the kidney urea transporter. Nature 462: 757-761.
92. Li, N., and Cannon, M.C. (1998) Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli. J Bacteriol 180: 2450-2458.
93. Lima, T., Auchincloss, A.H., Coudert, E., Keller, G., Michoud, K., Rivoire, C., etal. (2009) HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 37: D471-D478.
94. Lin, X.L., and White, R.H. (1986) Occurrence of coenzyme F420 and its gamma-monoglutamyl derivative in nonmethanogenic archaebacteria. J Bacteriol 168: 444-448.
95. + antiporter from the soda Lake Haloalkaliphile Alkalimonas amylolytica is adaptive for the extreme environment. J Bacteriol 187: 7589-7595.
96. Loqué, D., Lalonde, S., Looger, L.L., von Wirén, N., and Frommer, W.B. (2007) A cytosolic trans-activation domain essential for ammonium uptake. Nature 446: 195-198.
97. Lorenz, M.C., and Heitman, J. (1998) The MEP2 ammonium permease regulates pseudohyphal differentiation in Saccharomyces cerevisiae. EMBO J 17: 1236-1247.
98. Lu, Q., Han, J., Zhou, L., Zhou, J., and Xiang, H. (2008) Genetic and biochemical characterization of the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthase in Haloferax mediterranei. J Bacteriol 190: 4173-4180.
99. Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., etal. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107: 13479-13484.
100. Macario, A.J.L., Malz, M., and de Macario, E. (2004) Evolution of assisted protein folding: the distribution of the main chaperoning systems within the phylogenetic domain archaea. Front Biosci 9: 1318-1332.
101. Magrane, M., and UniProt Consortium (2011) UniProt Knowledgebase: a hub of integrated protein data. Database bar009.
102. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J.J., Charpentier, E., Horvath, P., etal. (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9: 467-477.
103. Mansour, N.M., Sawhney, M., Tamang, D.G., Vogl, C., and Saier, M.H., Jr (2007) The bile/arsenite/riboflavin transporter (BART) superfamily. FEBS J 274: 612-629.
104. Martens-Habbena, W., Berube, P.M., Urakawa, H., De La Torre, J.R., and Stahl, D.A. (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-979.
105. Mechold, U., Ogryzko, V., Ngo, S., and Danchin, A. (2006) Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells. Nucleic Acids Res 34: 2364-2373.
106. Melo, A.M.P., Bandeiras, T.M., and Teixeira, M. (2004) New insights into type II NAD(P)H:quinone oxidoreductases. Microbiol Mol Biol Rev 68: 603-616.
107. Moparthi, V.K., and Hägerhäll, C. (2011) The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. J Mol Evol 72: 484-497.
108. Mosier, A.C., Allen, E.E., Kim, M., Ferriera, S., and Francis, C.A. (2012a) Genome sequence of 'Candidatus Nitrosopumilus salaria' BD31, an ammonia-oxidizing archaeon from the San Francisco Bay Estuary. J Bacteriol 194: 2121-2122.
109. Mosier, A.C., Lund, M.B., and Francis, C.A. (2012b) Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. Microb Ecol. doi:10.007/s00248-012-0075-1.
110. Mosier, A.C., Allen, E.E., Kim, M., Ferriera, S., and Francis, C.A. (2012c) Genome sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay Estuary. J Bacteriol 194: 2119-2120.
111. Murakami, R., Sato, H., Dybal, J., Iwata, T., and Ozaki, Y. (2007) Formation and stability of β-structure in biodegradable ultra-high-molecular-weight poly(3-hydroxybutyrate) by infrared, Raman, and quantum chemical calculation studies. Polymer 48: 2672-2680.
112. 3 selectivities of AQP1, AQP4, AQP5, AmtB, and RhAG. Proc Natl Acad Sci USA 106: 5406-5411.
113. Mußmann, M., Brito, I., Pitcher, A., Sinninghe Damsté, J.S., Hatzenpichler, R., Richter, A., etal. (2011) Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc Natl Acad Sci USA 108: 16771-16776.
114. Neves, C., da Costa, M.S., and Santos, H. (2005) Compatible solutes of the hyperthermophile Palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales. Appl Environ Microbiol 71: 8091-8098.
115. Norais, C., Hawkins, M., Hartman, A.L., Eisen, J.A., Myllykallio, H., and Allers, T. (2007) Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet 3: e77.
116. Norton, J.M., Alzerreca, J.J., Suwa, Y., and Klotz, M.G. (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177: 139-149.
117. Nowakowska, M., Sterzel, M., and Szczubialłka, K. (2006) Photosensitized oxidation of cyanide in aqueous solutions of photoactive modified hydroxyethylcellulose. J Polym Environ 14: 59-64.
118. Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., etal. (2011) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39: 3204-3223.
119. Offner, S., Hofacker, A., Wanner, G., and Pfeifer, F. (2000) Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea. J Bacteriol 182: 4328-4336.
120. Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G., Selkov, E., Jr, etal. (2003) The ERGO genome analysis and discovery system. Nucleic Acids Res 31: 164-171.
121. Park, Y.-J., Yoo, C.-B., Choi, S.Y., and Lee, H.-B. (2006) Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1. J Biochem Mol Biol 39: 46-54.
122. Patridge, E.V., and Ferry, J.G. (2006) WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase. J Bacteriol 188: 3498-3506.
123. Paulsen, I.T., Nguyen, L., Sliwinski, M.K., Rabus, R., and Saier, M.H., Jr (2000) Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes. J Mol Biol 301: 75-100.
124. Peiser, G.D., Wang, T.-T., Hoffman, N.E., Yang, S.F., Liu, H., and Walsh, C.T. (1984) Formation of cyanide from carbon 1 of 1-aminocyclopropane-1-carboxylic acid during its conversion to ethylene. Proc Natl Acad Sci USA 81: 3059-3063.
125. Pereira, M.M., Bandeiras, T.M., Fernandes, A.S., Lemos, R.S., Melo, A.M., and Teixeira, M. (2004) Respiratory chains from aerobic thermophilic prokaryotes. J Bioenerg Biomembr 36: 93-105.
126. + concentration on caesium toxicity and accumulation in Escherichia coli and Bacillus subtilis. J Ind Microbiol 14: 218-225.
127. Perrière, G., and Gouy, M. (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369.
128. Pester, M., Schleper, C., and Wagner, M. (2011) The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 14: 300-306.
129. Pester, M., Rattei, T., Flechl, S., Gröngröft, A., Richter, A., Overmann, J., etal. (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14: 525-539.
130. Pfeifer, F. (2006) Gas vesicles of archaea and bacteria. In Complex Intracellular Structures in Prokaryotes. Shively, J.M. (ed.). Heidelberg, Germany: Springer-Verlag, pp. 115-140.
131. Pitcher, A., Rychlik, N., Hopmans, E.C., Spieck, E., Rijpstra, W.I.C., Ossebaar, J., etal. (2010) Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic group I.1b Archaeon. ISME J 4: 542-552.
132. Pohlschroder, M., Ghosh, A., Tripepi, M., and Albers, S.-V. (2011) Archaeal type IV pilus-like structures-evolutionarily conserved prokaryotic surface organelles. Curr Opin Microbiol 14: 357-363.
133. Poli, A., Di Donato, P., Abbamondi, G.R., and Nicolaus, B. (2011) Synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by archaea. Archaea 2011: 693253.
134. Prosser, J.I. (1989) Autotrophic nitrification in bacteria. Adv Microb Physiol 30: 125-181.
135. Pruitt, K.D., Tatusova, T., Brown, G.R., and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130-D135.
136. Purwantini, E., and Daniels, L. (1996) Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis. J Bacteriol 178: 2861-2866.
137. 2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage. Proc Natl Acad Sci USA 106: 6333-6338.
138. Purwantini, E., Gillis, T.P., and Daniels, L. (1997) Presence of F420-dependent glucose-6-phosphate dehydrogenase in Mycobacterium and Nocardia species, but absence from Streptomyces and Corynebacterium species and methanogenic Archaea. FEMS Microbiol Lett 146: 129-134.
139. Quaiser, A., Ochsenreiter, T., Klenk, H., Kletzin, A., Treusch, A.H., Meurer, G., etal. (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4: 603-611.
140. Radax, R., Rattei, T., Lanzen, A., Bayer, C., Rapp, H.T., Urich, T., and Schleper, C. (2012) Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol 14: 1308-1324.
141. Ramírez-Díaz, M.I., Díaz-Pérez, C., Vargas, E., Riveros-Rosas, H., Campos-García, J., and Cervantes, C. (2008) Mechanisms of bacterial resistance to chromium compounds. Biometals 21: 321-332.
142. Rattei, T., Tischler, P., Götz, S., Jehl, M.-A., Hoser, J., Arnold, R., etal. (2010) SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res 38: D223-D226.
143. Rehm, B.H., and Steinbüchel, A. (1999) Biochemical and genetic analysis of PHA synthases and other proteins required for PHA synthesis. Int J Biol Macromol 25: 3-19.
144. Ren, Q., Kang, K.H., and Paulsen, I.T. (2004) TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res 32: D284-D288.
145. Ren, Q., Chen, K., and Paulsen, I.T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35: D274-D279.
146. Robinson, N.P., and Bell, S.D. (2007) Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc Natl Acad Sci USA 104: 5806-5811.
147. Robinson, N.P., Dionne, I., Lundgren, M., Marsh, V.L., Bernander, R., and Bell, S.D. (2004) Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116: 25-38.
148. Saier, M.H., Jr, Tran, C.V., and Barabote, R.D. (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 34: D181-D186.
149. Saier, M.H., Jr, Yen, M.R., Noto, K., Tamang, D.G., and Elkan, C. (2009) The Transporter Classification Database: recent advances. Nucleic Acids Res 37: D274-D278.
150. Sambrook, J., and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. New York, NY, USA: Cold Spring Harbor Laboratory Press.
151. Say, R.F., and Fuchs, G. (2010) Fructose 1, 6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464: 1077-1081.
152. Schäfer, G., Purschke, W., and Schmidt, C.L. (1996) On the origin of respiration: electron transport proteins from archaea to man. FEMS Microbiol Rev 18: 173-188.
153. Schäfer, G., Engelhard, M., and Müller, V. (1999) Bioenergetics of the archaea. Microbiol Mol Biol Rev 63: 570-620.
154. Schiex, T., Gouzy, J., Moisan, A., and de Oliveira, Y. (2003) FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res 31: 3738-3741.
155. Schleper, C., and Nicol, G.W. (2010) Ammonia-oxidising archaea - physiology, ecology and evolution. Adv Microb Physiol 57: 1-41.
156. Schleper, C., Jurgens, G., and Jonuscheit, M. (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3: 479-488.
157. Schmeisser, C., Liesegang, H., Krysciak, D., Bakkou, N., Le Quéré, A., Wollherr, A., etal. (2009) Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems. Appl Environ Microbiol 75: 4035-4045.
158. Schröder, I., Johnson, E., and de Vries, S. (2003) Microbial ferric iron reductases. FEMS Microbiol Rev 27: 427-447.
159. Selengut, J.D., and Haft, D.H. (2010) Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. J Bacteriol 192: 5788-5798.
160. + exchanger CAX1. J Biol Chem 280: 30136-30142.
161. Siebers, B., and Schönheit, P. (2005) Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol 8: 695-705.
162. Sigrist, C.J.A., Cerutti, L., de Castro, E., Langendijk-Genevaux, P.S., Bulliard, V., Bairoch, A., and Hulo, N. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38: D161-D166.
163. Silver, S., and Ji, G. (1994) Newer systems for bacterial resistances to toxic heavy metals. Environ Health Perspect 102: 107-113.
164. Soderberg, T. (2005) Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes. Archaea 1: 347-352.
165. Soderberg, T., and Alver, R.C. (2004) Transaldolase of Methanocaldococcus jannaschii. Archaea 1: 255-262.
166. Sorek, R., Kunin, V., and Hugenholtz, P. (2008) CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6: 181-186.
167. Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., etal. (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
168. Spieck, E., and Lipski, A. (2011) Cultivation, growth physiology and chemotaxonomy of nitrite-oxidizing bacteria. In Methods of Enzymology, Vol. 486, Part A, Microbial Nitrification and Related Processes. Klotz, M.G. (ed.). Oxford, UK: Academic Press/Elsevier, pp. 109-130.
169. Stewart, F.J., Ulloa, O., and DeLong, E.F. (2012) Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol 14: 23-40.
170. Szabó, Z., Stahl, A.O., Albers, S.V., Kissinger, J.C., Driessen, A.J.M., and Pohlschröder, M. (2007a) Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases. J Bacteriol 189: 772-778.
171. Szabó, Z., Sani, M., Groeneveld, M., Zolghadr, B., Schelert, J., Albers, S.V., etal. (2007b) Flagellar motility and structure in the hyperthermoacidophilic archaeon Sulfolobus solfataricus. J Bacteriol 189: 4305-4309.
172. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. (1997) A genomic perspective on protein families. Science 278: 631-637.
173. Tech, M., and Merkl, R. (2003) YACOP: enhanced gene prediction obtained by a combination of existing methods. In Silico Biol 3: 441-451.
174. Thomas, N.A., Bardy, S.L., and Jarrell, K.F. (2001) The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol Rev 25: 147-174.
175. de la Torre, J.R., Walker, C.B., Ingalls, A.E., Könneke, M., and Stahl, D.A. (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810-818.
176. Tourna, M., Stieglmeier, M., Spang, A., Könneke, M., Schintlmeister, A., Urich, T., etal. (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci USA 108: 8420-8425.
177. Treusch, A.H., Leininger, S., Kletzin, A., Schuster, S.C., Klenk, H., and Schleper, C. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7: 1985-1995.
178. +-translocating NADH:quinone oxidoreductase from Vibrio cholerae: functional role of the NqrF subunit. J Biol Chem 279: 21349-21355.
179. Turkarslan, S., Reiss, D.J., Gibbins, G., Su, W.L., Pan, M., Bare, J.C., etal. (2011) Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol 7: 554.
180. Urakawa, H., Martens-Habbena, W., and Stahl, D.A. (2011) Physiology and genomics of ammonia-oxidizing archaea. In Nitrification. Ward, B.B., Arp, D.J., and Klotz, M.G. (eds). Washington, DC, USA: American Society for Microbiology, pp. 117-156.
181. Vallenet, D., Labarre, L., Rouy, Z., Barbe, V., Bocs, S., Cruveiller, S., etal. (2006) MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53-65.
182. Vallenet, D., Engelen, S., Mornico, D., Cruveiller, S., Fleury, L., Lajus, A., etal. (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database bap021.
183. Verhamme, D.T., Prosser, J.I., and Nicol, G.W. (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5: 1067-1071.
184. Verhees, C.H., Huynen, M.A., Ward, D.E., Schiltz, E., de Vos, W.M., and van der Oost, J. (2001) The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily. J Biol Chem 276: 40926-40932.
185. Verkhovsky, M.I., and Bogachev, A.V. (2010) Sodium-translocating NADH:quinone oxidoreductase as a redox-driven ion pump. Biochim Biophys Acta 1797: 738-746.
186. Walker, C.B., Torre, J.R., Klotz, M.G., Urakawa, H., Pinel, N., Arp, D.J., etal. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107: 8818-8823.
187. Walsh, M.A., Otwinowski, Z., Perrakis, A., Anderson, P.M., and Joachimiak, A. (2000) Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Structure 8: 505-514.
188. van de Werken, H.J.G., Brouns, S.J.J., and van der Oost, J. (2008) Pentose metabolism in archaea. In Archaea: New Models for Prokaryotic Biology. Blum, P. (ed.). Norfolk, UK: Caister Academic Press, pp. 71-94.
189. Wood, A.P., Aurikko, J.P., and Kelly, D.P. (2004) A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy? FEMS Microbiol Rev 28: 335-352.
190. +-induced nitrogenase switch-off and ADP-ribosylation in Rhodobacter capsulatus. J Bacteriol 184: 4081-4088.
191. Zhang, J.-Y., Zou, J., Bao, Q., Chen, W.-L., Wang, L., Yang, H., and Zhang, C.-C. (2006) A lithium-sensitive and sodium-tolerant 3′-phosphoadenosine-5′-phosphatase encoded by halA from the cyanobacterium Arthrospira platensis is closely related to its counterparts from yeasts and plants. Appl Environ Microbiol 72: 245-251.
192. Zhang, L., Zhang, L., Liu, Y., Yang, S., Gao, C., Gong, H., etal. (2009) Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase B1 and regulate its functions. Proc Natl Acad Sci USA 106: 7792-7797.
193. Zhang, Q., Iwasaki, T., Wakagi, T., and Oshima, T. (1996) 2-Oxoacid:ferredoxin oxidoreductase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Biochem 120: 587-599.
194. Zheng, L., Kostrewa, D., Bernèche, S., Winkler, F.K., and Li, X.-D. (2004) The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proc Natl Acad Sci USA 101: 17090-17095.
195. Zolghadr, B., Weber, S., Szabó, Z., Driessen, A.J.M., and Albers, S.-V. (2007) Identification of a system required for the functional surface localization of sugar binding proteins with class III signal peptides in Sulfolobus solfataricus. Mol Microbiol 64: 795-806.
196. Zolghadr, B., Klingl, A., Rachel, R., Driessen, A.J.M., and Albers, S.-V. (2011) The bindosome is a structural component of the Sulfolobus solfataricus cell envelope. Extremophiles 15: 235-244.