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Volumn 4, Issue FEB, 2013, Pages

The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer

Author keywords

Marine nitrogen cycle; Nitrification; Nitrite oxidation; Nitrite oxidoreductase; Nitrite oxidizing bacteria; Nitrospina

Indexed keywords

BACTERIA (MICROORGANISMS); NITROSPINA; NITROSPINA GRACILIS; NITROSPIRA;

EID: 84875875462     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2013.00027     Document Type: Article
Times cited : (201)

References (136)
  • 1
    • 34547320510 scopus 로고    scopus 로고
    • Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic
    • Alawi, M., Lipski, A., Sanders, T., Pfeiffer, E. M.,and Spieck,E. (2007). Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. ISME J. 1, 256-264.
    • (2007) ISME J , vol.1 , pp. 256-264
    • Alawi, M.1    Lipski, A.2    Sanders, T.3    Pfeiffer, E.M.4    Spieck, E.5
  • 3
    • 64749109757 scopus 로고    scopus 로고
    • Periplasmic c cytochromes and chlorate reduction in Ideonella dechloratans
    • Bäcklund, A. S., Bohlin, J., Gustavsson, N., and Nilsson, T. (2009). Periplasmic c cytochromes and chlorate reduction in Ideonella dechloratans. Appl. Environ. Microbiol. 75, 2439-2445.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 2439-2445
    • Bäcklund, A.S.1    Bohlin, J.2    Gustavsson, N.3    Nilsson, T.4
  • 5
    • 0036051360 scopus 로고    scopus 로고
    • Immunological detection of Nitrospira-like bacteria in various soils
    • Bartosch, S., Hartwig, C., Spieck, E., and Bock, E. (2002). Immunological detection of Nitrospira-like bacteria in various soils. Microb. Ecol. 43, 26-33.
    • (2002) Microb. Ecol. , vol.43 , pp. 26-33
    • Bartosch, S.1    Hartwig, C.2    Spieck, E.3    Bock, E.4
  • 6
    • 0032828417 scopus 로고    scopus 로고
    • Identification of Nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase
    • Bartosch, S., Wolgast, I., Spieck, E., and Bock, E. (1999). Identification of Nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase. Appl. Environ. Microbiol. 65, 4126-4133.
    • (1999) Appl. Environ. Microbiol. , vol.65 , pp. 4126-4133
    • Bartosch, S.1    Wolgast, I.2    Spieck, E.3    Bock, E.4
  • 7
    • 79958144635 scopus 로고    scopus 로고
    • Diverse functions of cationic Mn(III) N-substituted pyridylporphyrins, recognized as SOD mimics
    • Batinic-Haberle, I., Rajic, Z., Tovmasyan, A., Reboucas, J. S., Ye, X., Leong, K. W., et al. (2011). Diverse functions of cationic Mn(III) N-substituted pyridylporphyrins, recognized as SOD mimics. Free Radic. Biol. Med. 51, 1035-1053.
    • (2011) Free Radic. Biol. Med. , vol.51 , pp. 1035-1053
    • Batinic-Haberle, I.1    Rajic, Z.2    Tovmasyan, A.3    Reboucas, J.S.4    Ye, X.5    Leong, K.W.6
  • 9
    • 78149247216 scopus 로고    scopus 로고
    • Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase
    • Biegel, E., and Müller, V. (2010). Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. Proc. Natl. Acad. Sci. U.S.A. 107, 18138-18142.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 18138-18142
    • Biegel, E.1    Müller, V.2
  • 11
    • 33746329868 scopus 로고    scopus 로고
    • Energy converting NADH:quinone oxidoreductase (complex I)
    • Brandt, U. (2006). Energy converting NADH:quinone oxidoreductase (complex I). Annu. Rev. Biochem. 75, 69-92.
    • (2006) Annu. Rev. Biochem. , vol.75 , pp. 69-92
    • Brandt, U.1
  • 12
    • 84871712835 scopus 로고    scopus 로고
    • Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation
    • Buckel, W., and Thauer, R. K. (2013). Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827, 94-113.
    • (2013) Biochim. Biophys. Acta , vol.1827 , pp. 94-113
    • Buckel, W.1    Thauer, R.K.2
  • 13
    • 77954809358 scopus 로고    scopus 로고
    • The structure of cbb3 cytochrome oxidase provides insights into proton pumping
    • Buschmann, S., Warkentin, E., Xie, H., Langer, J. D., Ermler, U., and Michel, H. (2010). The structure of cbb3 cytochrome oxidase provides insights into proton pumping. Science 329, 327-330.
    • (2010) Science , vol.329 , pp. 327-330
    • Buschmann, S.1    Warkentin, E.2    Xie, H.3    Langer, J.D.4    Ermler, U.5    Michel, H.6
  • 14
    • 33846349924 scopus 로고    scopus 로고
    • Rooting the tree of life by transition analyses
    • Cavalier-Smith, T. (2006). Rooting the tree of life by transition analyses. Biol. Direct 1, 19.
    • (2006) Biol. Direct , vol.1 , pp. 19
    • Cavalier-Smith, T.1
  • 16
    • 0037418252 scopus 로고    scopus 로고
    • Polyamines protect Escherichia coli cells from the toxic effect of oxygen
    • Chattopadhyay, M. K., Tabor, C. W., and Tabor,H. (2003). Polyamines protect Escherichia coli cells from the toxic effect of oxygen. Proc. Natl.Acad. Sci. U.S.A. 100, 2261-2265.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 2261-2265
    • Chattopadhyay, M.K.1    Tabor, C.W.2    Tabor, H.3
  • 17
    • 1242269905 scopus 로고    scopus 로고
    • Genomics of the ccoNOQP-encoded cbb3 oxidase complex in bacteria
    • Cosseau, C., and Batut, J. (2004). Genomics of the ccoNOQP-encoded cbb3 oxidase complex in bacteria. Arch. Microbiol. 181, 89-96.
    • (2004) Arch. Microbiol. , vol.181 , pp. 89-96
    • Cosseau, C.1    Batut, J.2
  • 18
    • 0035512205 scopus 로고    scopus 로고
    • In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants
    • Daims, H., Nielsen, J. L., Nielsen, P. H., Schleifer, K. H., and Wagner, M. (2001). In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl. Environ. Microbiol. 67, 5273-5284.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 5273-5284
    • Daims, H.1    Nielsen, J.L.2    Nielsen, P.H.3    Schleifer, K.H.4    Wagner, M.5
  • 19
    • 71149110185 scopus 로고    scopus 로고
    • Bacterial variability within an iron-silica-manganese-rich hydrothermal mound located offaxis at the cleft segment
    • Juan de Fuca Ridge.
    • Davis, R. E., Stakes, D. S., Wheat, C. G., and Moyer, C. L. (2009). Bacterial variability within an iron-silica-manganese-rich hydrothermal mound located offaxis at the cleft segment, Juan de Fuca Ridge. Geomicrobiol. J. 26, 570-580.
    • (2009) Geomicrobiol. J. , vol.26 , pp. 570-580
    • Davis, R.E.1    Stakes, D.S.2    Wheat, C.G.3    Moyer, C.L.4
  • 20
    • 79551491148 scopus 로고    scopus 로고
    • Proteins and protein complexes involved in the biochemical reactions of anaerobic ammonium-oxidizing bacteria
    • de Almeida, N. M., Maalcke, W. J., Keltjens, J. T., Jetten, M. S. M., and Kartal, B. (2011). Proteins and protein complexes involved in the biochemical reactions of anaerobic ammonium-oxidizing bacteria. Biochem. Soc. Trans. 39, 303.
    • (2011) Biochem. Soc. Trans. , vol.39 , pp. 303
    • De Almeida, N.M.1    Maalcke, W.J.2    Keltjens, J.T.3    Jetten, M.S.M.4    Kartal, B.5
  • 21
    • 31544483932 scopus 로고    scopus 로고
    • Community genomics among stratified microbial assemblages in the ocean's interior
    • DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N.-U., et al. (2006). Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496-503.
    • (2006) Science , vol.311 , pp. 496-503
    • DeLong, E.F.1    Preston, C.M.2    Mincer, T.3    Rich, V.4    Hallam, S.J.5    Frigaard, N.-U.6
  • 22
    • 0021749661 scopus 로고
    • Carboxylation of pyruvate and acetyl coenzyme A by reversal of the sodium pumps oxaloacetate decarboxylase and methylmalonyl-CoA decarboxylase
    • Dimroth, P., and Hilpert, W. (1984). Carboxylation of pyruvate and acetyl coenzyme A by reversal of the sodium pumps oxaloacetate decarboxylase and methylmalonyl-CoA decarboxylase. Biochemistry 23, 5360-5366.
    • (1984) Biochemistry , vol.23 , pp. 5360-5366
    • Dimroth, P.1    Hilpert, W.2
  • 23
    • 0029121005 scopus 로고
    • A new obligately chemolithoautotrophic, nitriteoxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship
    • Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W., and Bock, E. (1995). A new obligately chemolithoautotrophic, nitriteoxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164, 16-23.
    • (1995) Arch. Microbiol. , vol.164 , pp. 16-23
    • Ehrich, S.1    Behrens, D.2    Lebedeva, E.3    Ludwig, W.4    Bock, E.5
  • 24
    • 0034123440 scopus 로고    scopus 로고
    • First evidence for existence of an uphill electron transfer through the bc1 and NADH-Q oxidoreductase complexes of the acidophilic obligate chemolithotrophic ferrous ionoxidizing bacterium Thiobacillus ferrooxidans
    • Elbehti, A., Brasseur, G., and Lemesle-Meunier, D. (2000). First evidence for existence of an uphill electron transfer through the bc1 and NADH-Q oxidoreductase complexes of the acidophilic obligate chemolithotrophic ferrous ionoxidizing bacterium Thiobacillus ferrooxidans. J. Bacteriol. 182, 3602-3606.
    • (2000) J. Bacteriol. , vol.182 , pp. 3602-3606
    • Elbehti, A.1    Brasseur, G.2    Lemesle-Meunier, D.3
  • 28
    • 25444499441 scopus 로고    scopus 로고
    • Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants
    • Forzi, L., Koch, J., Guss, A. M., Radosevich, C. G., Metcalf, W. W., and Hedderich,R. (2005). Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants. FEBS J. 272, 4741-4753.
    • (2005) FEBS J , vol.272 , pp. 4741-4753
    • Forzi, L.1    Koch, J.2    Guss, A.M.3    Radosevich, C.G.4    Metcalf, W.W.5    Hedderich, R.6
  • 29
    • 0025156760 scopus 로고
    • Energy conservation in Nitrobacter
    • Freitag, A., and Bock, E. (1990). Energy conservation in Nitrobacter. FEMS Microbiol. Lett. 66, 157-162.
    • (1990) FEMS Microbiol. Lett. , vol.66 , pp. 157-162
    • Freitag, A.1    Bock, E.2
  • 30
    • 29144506348 scopus 로고    scopus 로고
    • Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils
    • Freitag, T. E., Chang, L., Clegg, C. D., and Prosser, J. I. (2005). Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl. Environ. Microbiol. 71, 8323-8334.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 8323-8334
    • Freitag, T.E.1    Chang, L.2    Clegg, C.D.3    Prosser, J.I.4
  • 31
    • 4944233611 scopus 로고    scopus 로고
    • PhyloGenie: automated phylome generation and analysis
    • Frickey,T.,and Lupas,A.N. (2004). PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res. 32, 5231-5238.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5231-5238
    • Frickey, T.1    Lupas, A.N.2
  • 32
    • 21244464827 scopus 로고    scopus 로고
    • Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea
    • Fuchs, B. M., Woebken, D., Zubkov, M. V., Burkill, P., and Amann, R. (2005). Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquat. Microb. Ecol. 39, 145-157.
    • (2005) Aquat. Microb. Ecol. , vol.39 , pp. 145-157
    • Fuchs, B.M.1    Woebken, D.2    Zubkov, M.V.3    Burkill, P.4    Amann, R.5
  • 33
    • 81155125185 scopus 로고    scopus 로고
    • Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone
    • Fuchsman, C. A., Kirkpatrick, J. B., Brazelton, W. J., Murray, J. W., and Staley, J. T. (2011). Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone. FEMS Microbiol. Ecol. 78, 586-603.
    • (2011) FEMS Microbiol. Ecol. , vol.78 , pp. 586-603
    • Fuchsman, C.A.1    Kirkpatrick, J.B.2    Brazelton, W.J.3    Murray, J.W.4    Staley, J.T.5
  • 35
    • 33646193540 scopus 로고    scopus 로고
    • Nitrospinaceae fam. nov
    • eds D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey, and K.-H. Schleifer (New York: Springer)
    • Garrity, G. M., Bell, J. A., and Lilburn, T. (2005). "Nitrospinaceae fam. nov.," in Bergey's Manual® of Systematic Bacteriology, eds D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey, and K.-H. Schleifer (New York: Springer), 999.
    • (2005) Bergey's Manual® of Systematic Bacteriology , pp. 999
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3
  • 36
    • 0032941787 scopus 로고    scopus 로고
    • The unusual iron sulfur composition of the Acidianus ambivalens succinate dehydrogenase complex
    • Gomes, C. M., Lemos, R. S., Teixeira, M., Kletzin, A., Huber, H., Stetter, K. O., et al. (1999). The unusual iron sulfur composition of the Acidianus ambivalens succinate dehydrogenase complex. Biochim. Biophys. Acta 1411, 134-141.
    • (1999) Biochim. Biophys. Acta , vol.1411 , pp. 134-141
    • Gomes, C.M.1    Lemos, R.S.2    Teixeira, M.3    Kletzin, A.4    Huber, H.5    Stetter, K.O.6
  • 37
    • 84882884095 scopus 로고    scopus 로고
    • The Marine Nitrogen Cycle: Overview and Challenges
    • 2nd Edn, eds D. G. Capone, D. A. Bronk, M. R. Mulholland, and E. J. Carpenter (San Diego: Academic Press)
    • Gruber, N. (2008). "The Marine Nitrogen Cycle: Overview and Challenges," in Nitrogen in the Marine Environment, 2nd Edn, eds D. G. Capone, D. A. Bronk, M. R. Mulholland, and E. J. Carpenter (San Diego: Academic Press), 1-50.
    • (2008) Nitrogen in the Marine Environment , pp. 1-50
    • Gruber, N.1
  • 38
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S., and Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 39
    • 0033823160 scopus 로고    scopus 로고
    • The phylogeny of Proteobacteria:relationships to other eubacterial phyla and eukaryotes
    • Gupta, R. S. (2000). The phylogeny of Proteobacteria:relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol. Rev. 24, 367-402.
    • (2000) FEMS Microbiol. Rev. , vol.24 , pp. 367-402
    • Gupta, R.S.1
  • 40
    • 0035756272 scopus 로고    scopus 로고
    • The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins
    • Gupta, R. S. (2001). The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int. Microbiol. 4, 187-202.
    • (2001) Int. Microbiol. , vol.4 , pp. 187-202
    • Gupta, R.S.1
  • 41
    • 0036597701 scopus 로고    scopus 로고
    • Critical issues in bacterial phylogeny
    • Gupta, R. S., and Griffiths, E. (2002). Critical issues in bacterial phylogeny. Theor. Popul. Biol. 61, 423-434.
    • (2002) Theor. Popul. Biol. , vol.61 , pp. 423-434
    • Gupta, R.S.1    Griffiths, E.2
  • 42
    • 67349267351 scopus 로고    scopus 로고
    • A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12
    • Guymer, D., Maillard, J., and Sargent, F. (2009). A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12. Arch. Microbiol. 191, 519-528.
    • (2009) Arch. Microbiol. , vol.191 , pp. 519-528
    • Guymer, D.1    Maillard, J.2    Sargent, F.3
  • 43
    • 79251593880 scopus 로고    scopus 로고
    • A screen for potential ferredoxin electron transfer partners uncovers new, redox dependent interactions
    • Hanke, G. T., Satomi, Y., Shinmura, K., Takao, T., and Hase, T. (2011). A screen for potential ferredoxin electron transfer partners uncovers new, redox dependent interactions. Biochim. Biophys. Acta 1814, 366-374.
    • (2011) Biochim. Biophys. Acta , vol.1814 , pp. 366-374
    • Hanke, G.T.1    Satomi, Y.2    Shinmura, K.3    Takao, T.4    Hase, T.5
  • 44
    • 38649143651 scopus 로고    scopus 로고
    • Energy conservation via electron-transferring flavoprotein in anaerobic bacteria
    • Herrmann, G., Jayamani, E., Mai, G., and Buckel, W. (2008). Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J. Bacteriol. 190, 784-791.
    • (2008) J. Bacteriol. , vol.190 , pp. 784-791
    • Herrmann, G.1    Jayamani, E.2    Mai, G.3    Buckel, W.4
  • 45
    • 33846109956 scopus 로고    scopus 로고
    • 2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage
    • 2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage. Environ. Microbiol. 9, 81-92.
    • (2007) Environ. Microbiol , vol.9 , pp. 81-92
    • Hügler, M.1    Huber, H.2    Molyneaux, S.J.3    Vetriani, C.4    Sievert, S.M.5
  • 46
    • 33748769754 scopus 로고    scopus 로고
    • Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments
    • Hunter, E. M., Mills, H. J., and Kostka, J. E. (2006). Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl. Environ. Microbiol. 72, 5689-5701.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 5689-5701
    • Hunter, E.M.1    Mills, H.J.2    Kostka, J.E.3
  • 47
    • 29244479524 scopus 로고    scopus 로고
    • Anabolic five subunittype pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6
    • Ikeda, T., Ochiai, T., Morita, S., Nishiyama, A., Yamada, E., Arai, H., et al. (2006). Anabolic five subunittype pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6. Biochem. Biophys. Res. Commun. 340, 76-82.
    • (2006) Biochem. Biophys. Res. Commun. , vol.340 , pp. 76-82
    • Ikeda, T.1    Ochiai, T.2    Morita, S.3    Nishiyama, A.4    Yamada, E.5    Arai, H.6
  • 48
    • 84871715093 scopus 로고    scopus 로고
    • Insight into the evolution of the iron oxidation pathways
    • doi:10.1016/j.bbabio.2012.1010.1001. [Epub ahead of print]
    • Ilbert, M., and Bonnefoy, V. (2012). Insight into the evolution of the iron oxidation pathways. Biochim. Biophys. Acta. doi:10.1016/j.bbabio.2012.1010.1001. [Epub ahead of print].
    • (2012) Biochim. Biophys. Acta.
    • Ilbert, M.1    Bonnefoy, V.2
  • 49
    • 0037131179 scopus 로고    scopus 로고
    • Novel [2Fe-2S]-type redox center C in SdhC of archaeal respiratory complex II from Sulfolobus tokodaii strain 7
    • Iwasaki, T., Kounosu, A., Aoshima, M., Ohmori, D., Imai, T., Urushiyama, A., et al. (2002). Novel [2Fe-2S]-type redox center C in SdhC of archaeal respiratory complex II from Sulfolobus tokodaii strain 7. J. Biol. Chem. 277, 39642-39648.
    • (2002) J. Biol. Chem. , vol.277 , pp. 39642-39648
    • Iwasaki, T.1    Kounosu, A.2    Aoshima, M.3    Ohmori, D.4    Imai, T.5    Urushiyama, A.6
  • 50
    • 1842332148 scopus 로고    scopus 로고
    • A succinate dehydrogenase with novel structure and properties from the hyperthermophilic archaeon Sulfolobus acidocaldarius: genetic and biophysical characterization
    • Janssen, S., Schafer, G., Anemuller, S., and Moll, R. (1997). A succinate dehydrogenase with novel structure and properties from the hyperthermophilic archaeon Sulfolobus acidocaldarius: genetic and biophysical characterization. J. Bacteriol. 179, 5560-5569.
    • (1997) J. Bacteriol. , vol.179 , pp. 5560-5569
    • Janssen, S.1    Schafer, G.2    Anemuller, S.3    Moll, R.4
  • 52
    • 0026640112 scopus 로고
    • Reduction of arsenate to arsenite by the ArsC protein of the arsenic resistance operon of Staphylococcus aureus plasmid pI258
    • Ji, G., and Silver, S. (1992). Reduction of arsenate to arsenite by the ArsC protein of the arsenic resistance operon of Staphylococcus aureus plasmid pI258. Proc. Natl. Acad. Sci. U.S.A. 89, 9474-9478.
    • (1992) Proc. Natl. Acad. Sci. U. S. A. , vol.89 , pp. 9474-9478
    • Ji, G.1    Silver, S.2
  • 53
    • 84867638141 scopus 로고    scopus 로고
    • Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic MidOcean Ridge
    • Jorgensen, S. L., Hannisdal, B., Lanzen, A.,Baumberger,T.,Flesland,K.,Fonseca, R., et al. (2012). Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic MidOcean Ridge. Proc. Natl. Acad. Sci. U.S.A. 109, E2846-E2855.
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109
    • Jorgensen, S.L.1    Hannisdal, B.2    Lanzen, A.3    Baumberger, T.4    Flesland, K.5    Fonseca, R.6
  • 54
    • 1642370336 scopus 로고    scopus 로고
    • Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes
    • Jormakka, M., Richardson, D., Byrne, B., and Iwata, S. (2004). Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes. Structure 12, 95-104.
    • (2004) Structure , vol.12 , pp. 95-104
    • Jormakka, M.1    Richardson, D.2    Byrne, B.3    Iwata, S.4
  • 55
    • 34547584314 scopus 로고    scopus 로고
    • Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server
    • Käll, L., Krogh, A., and Sonnhammer, E. L. L. (2007). Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 35, W429-W432.
    • (2007) Nucleic Acids Res , vol.35
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 56
    • 55749098824 scopus 로고    scopus 로고
    • The cyanate utilization capacity of marine unicellular cyanobacteria
    • Kamennaya, N. A., Chernihovsky, M., and Anton, F. P. (2008). The cyanate utilization capacity of marine unicellular cyanobacteria. Limnol. Oceanogr. 53, 2485-2494.
    • (2008) Limnol. Oceanogr. , vol.53 , pp. 2485-2494
    • Kamennaya, N.A.1    Chernihovsky, M.2    Anton, F.P.3
  • 57
    • 0034836201 scopus 로고    scopus 로고
    • ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products
    • Kanao, T., Fukui, T., Atomi, H., and Imanaka,T. (2001).ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products. Eur. J. Biochem. 268, 1670-1678.
    • (2001) Eur. J. Biochem. , vol.268 , pp. 1670-1678
    • Kanao, T.1    Fukui, T.2    Atomi, H.3    Imanaka, T.4
  • 58
    • 0034607799 scopus 로고    scopus 로고
    • Sulfite:cytochrome c Oxidoreductase from Thiobacillus novellus: purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family
    • Kappler, U., Bennett, B., Rethmeier, J., Schwarz, G., Deutzmann, R., McEwan, A. G., et al. (2000). Sulfite:cytochrome c Oxidoreductase from Thiobacillus novellus: purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J. Biol. Chem. 275, 13202-13212.
    • (2000) J. Biol. Chem. , vol.275 , pp. 13202-13212
    • Kappler, U.1    Bennett, B.2    Rethmeier, J.3    Schwarz, G.4    Deutzmann, R.5    McEwan, A.G.6
  • 59
    • 0035877588 scopus 로고    scopus 로고
    • Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme
    • Kniemeyer, O., and Heider, J. (2001). Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J. Biol. Chem. 276, 21381-21386.
    • (2001) J. Biol. Chem. , vol.276 , pp. 21381-21386
    • Kniemeyer, O.1    Heider, J.2
  • 60
    • 0036499057 scopus 로고    scopus 로고
    • SHOT: a web server for the construction of genome phylogenies
    • Korbel, J. O., Snel, B., Huynen, M. A., and Bork, P. (2002). SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18, 158-162.
    • (2002) Trends Genet , vol.18 , pp. 158-162
    • Korbel, J.O.1    Snel, B.2    Huynen, M.A.3    Bork, P.4
  • 61
    • 33644907541 scopus 로고    scopus 로고
    • Dichotomy of major bacterial phyla inferred from gene arrangement comparisons
    • Kunisawa, T. (2006). Dichotomy of major bacterial phyla inferred from gene arrangement comparisons. J. Theor. Biol. 239, 367-375.
    • (2006) J. Theor. Biol. , vol.239 , pp. 367-375
    • Kunisawa, T.1
  • 62
    • 77952724095 scopus 로고    scopus 로고
    • Evaluation of the phylogenetic position of the sulfatereducing bacterium Thermodesul fovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes
    • Kunisawa, T. (2010). Evaluation of the phylogenetic position of the sulfatereducing bacterium Thermodesul fovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes. Int. J. Syst. Evol. Microbiol. 60, 1090-1102.
    • (2010) Int. J. Syst. Evol. Microbiol. , vol.60 , pp. 1090-1102
    • Kunisawa, T.1
  • 63
    • 79952439176 scopus 로고    scopus 로고
    • Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison
    • Kunisawa, T. (2011). Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison. Antonie Van Leeuwenhoek 99, 417-422.
    • (2011) Antonie Van Leeuwenhoek , vol.99 , pp. 417-422
    • Kunisawa, T.1
  • 64
    • 33847723418 scopus 로고    scopus 로고
    • Distribution of abundant prokaryotic organisms in the water column of the central Baltic Sea with an oxic-anoxic interface
    • Labrenz, M., Jost, G., and Jurgens, K. (2007). Distribution of abundant prokaryotic organisms in the water column of the central Baltic Sea with an oxic-anoxic interface. Aquat. Microb. Ecol. 46, 177-190.
    • (2007) Aquat. Microb. Ecol. , vol.46 , pp. 177-190
    • Labrenz, M.1    Jost, G.2    Jurgens, K.3
  • 65
    • 0023388022 scopus 로고
    • Nucleotide sequence and expression of the mercurial-resistance operon from Staphylococcus aureus plasmid pI258
    • Laddaga, R. A., Chu, L., Misra, T. K., and Silver, S. (1987). Nucleotide sequence and expression of the mercurial-resistance operon from Staphylococcus aureus plasmid pI258. Proc. Natl. Acad. Sci. U.S.A. 84, 5106-5110.
    • (1987) Proc. Natl. Acad. Sci. U. S. A. , vol.84 , pp. 5106-5110
    • Laddaga, R.A.1    Chu, L.2    Misra, T.K.3    Silver, S.4
  • 66
    • 53849112973 scopus 로고    scopus 로고
    • Electroneutral and electrogenic catalysis by dihaem-containing succinate:quinone oxidoreductases
    • Lancaster, C. R. D., Herzog, E., Juhnke, H. D., Madej, M. G., Müller, F. G., Paul, R., et al. (2008). Electroneutral and electrogenic catalysis by dihaem-containing succinate:quinone oxidoreductases. Biochem. Soc. Trans. 36, 996-1000.
    • (2008) Biochem. Soc. Trans. , vol.36 , pp. 996-1000
    • Lancaster, C.R.D.1    Herzog, E.2    Juhnke, H.D.3    Madej, M.G.4    Müller, F.G.5    Paul, R.6
  • 67
    • 0037122940 scopus 로고    scopus 로고
    • Succinate:quinone oxidoreductases from Epsilonproteobacteria
    • Lancaster,C. R. D.,and Simon,J. (2002). Succinate:quinone oxidoreductases from Epsilonproteobacteria. Biochim. Biophys. Acta 1553, 84-101.
    • (2002) Biochim. Biophys. Acta , vol.1553 , pp. 84-101
    • Lancaster, C.R.D.1    Simon, J.2
  • 69
    • 0037122944 scopus 로고    scopus 로고
    • Quinol:fumarate oxidoreductases and succinate:quinone oxidoreductases: phylogenetic relationships, metal centres and membrane attachment
    • Lemos, R. S., Fernandes, A. S., Pereira, M. M., Gomes, C. M., and Teixeira, M. (2002). Quinol:fumarate oxidoreductases and succinate:quinone oxidoreductases: phylogenetic relationships, metal centres and membrane attachment. Biochim. Biophys. Acta 1553, 158-170.
    • (2002) Biochim. Biophys. Acta , vol.1553 , pp. 158-170
    • Lemos, R.S.1    Fernandes, A.S.2    Pereira, M.M.3    Gomes, C.M.4    Teixeira, M.5
  • 70
    • 0034810204 scopus 로고    scopus 로고
    • Acidianus ambivalens complex II typifies a novel family of succinate dehydrogenases
    • Lemos,R. S.,Gomes,C. M.,and Teixeira, M. (2001). Acidianus ambivalens complex II typifies a novel family of succinate dehydrogenases. Biochem. Biophys. Res. Commun. 281, 141-150.
    • (2001) Biochem. Biophys. Res. Commun. , vol.281 , pp. 141-150
    • Lemos, R.S.1    Gomes, C.M.2    Teixeira, M.3
  • 71
    • 58049183225 scopus 로고    scopus 로고
    • Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations
    • doi:10.1186/1471-2164-9-581
    • Levican, G., Ugalde, J. A., Ehrenfeld, N., Maass, A., and Parada, P. (2008). Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9:581. doi:10.1186/1471-2164-9-581
    • (2008) BMC Genomics , vol.9 , pp. 581
    • Levican, G.1    Ugalde, J.A.2    Ehrenfeld, N.3    Maass, A.4    Parada, P.5
  • 72
    • 37349033588 scopus 로고    scopus 로고
    • Swiveling domain mechanism in pyruvate phosphate dikinase
    • Lim, K., Read, R. J., Chen, C. C. H., Tempczyk, A., Wei, M., Ye, D., et al. (2007). Swiveling domain mechanism in pyruvate phosphate dikinase. Biochemistry 46, 14845-14853.
    • (2007) Biochemistry , vol.46 , pp. 14845-14853
    • Lim, K.1    Read, R.J.2    Chen, C.C.H.3    Tempczyk, A.4    Wei, M.5    Ye, D.6
  • 73
    • 77953297724 scopus 로고    scopus 로고
    • Quinol-cytochrome c oxidoreductase and cytochrome c4 mediate electron transfer during selenate respiration in Thauera selenatis
    • Lowe, E. C., Bydder, S., Hartshorne, R. S., Tape, H. L. U., Dridge, E. J., Debieux, C. M., et al. (2010). Quinol-cytochrome c oxidoreductase and cytochrome c4 mediate electron transfer during selenate respiration in Thauera selenatis. J. Biol. Chem. 285, 18433-18442.
    • (2010) J. Biol. Chem. , vol.285 , pp. 18433-18442
    • Lowe, E.C.1    Bydder, S.2    Hartshorne, R.S.3    Tape, H.L.U.4    Dridge, E.J.5    Debieux, C.M.6
  • 74
    • 77955791222 scopus 로고    scopus 로고
    • A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
    • Lücker, S., Wagner, M., Maixner, F., Pelletier, E., Koch, H., Vacherie, B., et al. (2010). A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci. U.S.A. 107, 13479-13484.
    • (2010) Proc. Natl. Acad. Sci. U. S. A , vol.107 , pp. 13479-13484
    • Lücker, S.1    Wagner, M.2    Maixner, F.3    Pelletier, E.4    Koch, H.5    Vacherie, B.6
  • 75
    • 2542523843 scopus 로고    scopus 로고
    • ARB: a software environment for sequence data
    • Ludwig, W. (2004). ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363-1371.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1363-1371
    • Ludwig, W.1
  • 76
    • 77956874467 scopus 로고    scopus 로고
    • Molecular phylogeny of microorganisms: is rRNA still a useful marker?
    • eds A. Oren and R. T. Papke (Norfolk: Caister Academic Press)
    • Ludwig, W. (2010). "Molecular phylogeny of microorganisms: is rRNA still a useful marker?," in Molecular Phylogeny of Microorganisms, eds A. Oren and R. T. Papke (Norfolk: Caister Academic Press), 65-84.
    • (2010) Molecular Phylogeny of Microorganisms , pp. 65-84
    • Ludwig, W.1
  • 77
    • 0034065733 scopus 로고    scopus 로고
    • Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction
    • Ma, K., Weiss, R., and Adams, M. W. (2000). Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J. Bacteriol. 182, 1864-1871.
    • (2000) J. Bacteriol. , vol.182 , pp. 1864-1871
    • Ma, K.1    Weiss, R.2    Adams, M.W.3
  • 78
    • 0031766842 scopus 로고    scopus 로고
    • Anaerobic expression of Escherichia coli succinate dehydrogenase: functional replacement of fumarate reductase in the respiratory chain during anaerobic growth
    • Maklashina, E., Berthold, D. A., and Cecchini, G. (1998). Anaerobic expression of Escherichia coli succinate dehydrogenase: functional replacement of fumarate reductase in the respiratory chain during anaerobic growth. J. Bacteriol. 180, 5989-5996.
    • (1998) J. Bacteriol. , vol.180 , pp. 5989-5996
    • Maklashina, E.1    Berthold, D.A.2    Cecchini, G.3
  • 79
    • 35448931242 scopus 로고    scopus 로고
    • Look on the positive side! The orientation, identification and bioenergetics of Archaeal membrane-bound nitrate reductases
    • Martinez-Espinosa, R. M., Dridge, E. J., Bonete, M. J., Butt, J. N., Butler, C. S., Sargent, F., et al. (2007). Look on the positive side! The orientation, identification and bioenergetics of 'Archaeal' membrane-bound nitrate reductases. FEMS Microbiol. Lett. 276, 129-139.
    • (2007) FEMS Microbiol. Lett. , vol.276 , pp. 129-139
    • Martinez-Espinosa, R.M.1    Dridge, E.J.2    Bonete, M.J.3    Butt, J.N.4    Butler, C.S.5    Sargent, F.6
  • 80
    • 0036016822 scopus 로고    scopus 로고
    • Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin containing enzymes
    • McDevitt, C. A., Hugenholtz, P., Hanson, G. R., and McEwan, A. G. (2002). Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin containing enzymes. Mol. Microbiol. 44, 1575-1587.
    • (2002) Mol. Microbiol. , vol.44 , pp. 1575-1587
    • McDevitt, C.A.1    Hugenholtz, P.2    Hanson, G.R.3    McEwan, A.G.4
  • 81
    • 34247847886 scopus 로고    scopus 로고
    • Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre
    • Mincer, T. J., Church, M. J., Taylor, L. T., Preston, C., Karl, D. M., and Delong, E. F. (2007). Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 9, 1162-1175.
    • (2007) Environ. Microbiol. , vol.9 , pp. 1162-1175
    • Mincer, T.J.1    Church, M.J.2    Taylor, L.T.3    Preston, C.4    Karl, D.M.5    Delong, E.F.6
  • 82
    • 78649703098 scopus 로고    scopus 로고
    • Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria
    • Park, B.-J., Park, S.-J., Yoon, D.-N., Schouten,S.,Sinninghe Damste,J. S., and Rhee, S.-K. (2010). Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl. Environ. Microbiol. 76, 7575-7587.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 7575-7587
    • Park, B.-J.1    Park, S.-J.2    Yoon, D.-N.3    Schouten, S.4    Sinninghe Damste, J.S.5    Rhee, S.-K.6
  • 83
    • 10644233687 scopus 로고    scopus 로고
    • Manganese(III) binding to a pyoverdine siderophore produced by a manganese(II)-oxidizing bacterium
    • Parker,D. L.,Sposito,G.,and Tebo,B. M. (2004). Manganese(III) binding to a pyoverdine siderophore produced by a manganese(II)-oxidizing bacterium. Geochim. Cosmochim. Acta 68, 4809-4820.
    • (2004) Geochim. Cosmochim. Acta , vol.68 , pp. 4809-4820
    • Parker, D.L.1    Sposito, G.2    Tebo, B.M.3
  • 84
    • 52149101801 scopus 로고    scopus 로고
    • A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes
    • Peplies, J., Kottmann, R., Ludwig, W., and Glöckner, F. O. (2008). A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 31, 251-257.
    • (2008) Syst. Appl. Microbiol. , vol.31 , pp. 251-257
    • Peplies, J.1    Kottmann, R.2    Ludwig, W.3    Glöckner, F.O.4
  • 85
    • 0035371783 scopus 로고    scopus 로고
    • A novel scenario for the evolution of haem-copper oxygen reductases
    • Pereira, M. M., Santana, M., and Teixeira, M. (2001). A novel scenario for the evolution of haem-copper oxygen reductases. Biochim. Biophys. Acta 1505, 185-208.
    • (2001) Biochim. Biophys. Acta , vol.1505 , pp. 185-208
    • Pereira, M.M.1    Santana, M.2    Teixeira, M.3
  • 86
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • Petersen, T. N., Brunak, S., Von Heijne, G., and Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786.
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 87
    • 0035916384 scopus 로고    scopus 로고
    • Energy model and metabolic flux analysis for autotrophic nitrifiers
    • Poughon, L., Dussap, C. G., and Gros, J. B. (2001). Energy model and metabolic flux analysis for autotrophic nitrifiers. Biotechnol. Bioeng. 72, 416-433.
    • (2001) Biotechnol. Bioeng. , vol.72 , pp. 416-433
    • Poughon, L.1    Dussap, C.G.2    Gros, J.B.3
  • 88
    • 33144476849 scopus 로고    scopus 로고
    • Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals
    • Radeva, G., and Selenska-Pobell, S. (2005). Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals. Can. J. Microbiol. 51, 910-923.
    • (2005) Can. J. Microbiol. , vol.51 , pp. 910-923
    • Radeva, G.1    Selenska-Pobell, S.2
  • 89
    • 0242365676 scopus 로고    scopus 로고
    • Genomescale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., Williams, B. L., King, N., and Carroll, S. B. (2003). Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 90
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F., and Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 91
    • 50049103112 scopus 로고    scopus 로고
    • The prokaryotic complex iron-sulfur molybdoenzyme family
    • Rothery, R. A., Workun, G. J., and Weiner, J. H. (2008). The prokaryotic complex iron-sulfur molybdoenzyme family. Biochim. Biophys. Acta 1778, 1897-1929.
    • (2008) Biochim. Biophys. Acta , vol.1778 , pp. 1897-1929
    • Rothery, R.A.1    Workun, G.J.2    Weiner, J.H.3
  • 92
    • 78049432317 scopus 로고    scopus 로고
    • Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current
    • Santoro,A. E.,Casciotti,K. L.,and Francis, C. A. (2010). Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environ. Microbiol. 12, 1989-2006.
    • (2010) Environ. Microbiol. , vol.12 , pp. 1989-2006
    • Santoro, A.E.1    Casciotti, K.L.2    Francis, C.A.3
  • 94
    • 33644872938 scopus 로고    scopus 로고
    • Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
    • Sazanov, L. A., and Hinchliffe, P. (2006). Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science 311, 1430-1436.
    • (2006) Science , vol.311 , pp. 1430-1436
    • Sazanov, L.A.1    Hinchliffe, P.2
  • 95
    • 0032189445 scopus 로고    scopus 로고
    • Menaquinone-dependent succinate dehydrogenase of bacteria catalyzes reversed electron transport driven by the proton potential
    • Schirawski, J., and Unden, G. (1998). Menaquinone-dependent succinate dehydrogenase of bacteria catalyzes reversed electron transport driven by the proton potential. Eur. J. Biochem. 257, 210-215.
    • (1998) Eur. J. Biochem. , vol.257 , pp. 210-215
    • Schirawski, J.1    Unden, G.2
  • 97
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., Strimmer, K., Vingron, M., and Von Haeseler, A. (2002). TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 98
    • 0034819978 scopus 로고    scopus 로고
    • Generation of a proton potential by succinate dehydrogenase of Bacillus subtilis functioning as a fumarate reductase
    • Schnorpfeil, M., Janausch, I. G., Biel, S., Kröger, A., and Unden, G. (2001). Generation of a proton potential by succinate dehydrogenase of Bacillus subtilis functioning as a fumarate reductase. Eur. J. Biochem. 268, 3069-3074.
    • (2001) Eur. J. Biochem. , vol.268 , pp. 3069-3074
    • Schnorpfeil, M.1    Janausch, I.G.2    Biel, S.3    Kröger, A.4    Unden, G.5
  • 99
    • 77955372800 scopus 로고    scopus 로고
    • Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17
    • Schott, J., Griffin, B. M., and Schink, B. (2010). Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17. Microbiology 156, 2428-2437.
    • (2010) Microbiology , vol.156 , pp. 2428-2437
    • Schott, J.1    Griffin, B.M.2    Schink, B.3
  • 100
    • 0032812283 scopus 로고    scopus 로고
    • Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors
    • Schramm, A., De Beer, D., Van Den Heuvel, J. C., Ottengraf, S., and Amann, R. (1999). Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol. 65, 3690-3696.
    • (1999) Appl. Environ. Microbiol. , vol.65 , pp. 3690-3696
    • Schramm, A.1    De Beer, D.2    Van Den Heuvel, J.C.3    Ottengraf, S.4    Amann, R.5
  • 102
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • doi: 10.1038/msb.2011.75
    • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539. doi: 10.1038/msb.2011.75
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3    Gibson, T.J.4    Karplus, K.5    Li, W.6
  • 104
    • 0028917560 scopus 로고
    • Thermophilic Bacilli have split cytochrome b genes for cytochrome b6 and subunit IV
    • Sone, N., Sawa, G., Sone, T., and Noguchi, S. (1995). Thermophilic Bacilli have split cytochrome b genes for cytochrome b6 and subunit IV. J. Biol. Chem. 270, 10612-10617.
    • (1995) J. Biol. Chem , vol.270 , pp. 10612-10617
    • Sone, N.1    Sawa, G.2    Sone, T.3    Noguchi, S.4
  • 105
    • 84871326069 scopus 로고    scopus 로고
    • Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi
    • Sorokin, D. Y., Lücker, S., Vejmelkova, D., Kostrikina, N. A., Kleerebezem, R., Rijpstra, W. I., et al. (2012). Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 6, 2245-2256.
    • (2012) ISME J , vol.6 , pp. 2245-2256
    • Sorokin, D.Y.1    Lücker, S.2    Vejmelkova, D.3    Kostrikina, N.A.4    Kleerebezem, R.5    Rijpstra, W.I.6
  • 106
    • 34547339831 scopus 로고    scopus 로고
    • The lithoautotrophic nitrite-oxidizing bacteria
    • eds D. J. Brenner, N. R. Krieg, J. T. Staley, and G. M. Garrity (New York: Springer)
    • Spieck, E., and Bock, E. (2005a). "The lithoautotrophic nitrite-oxidizing bacteria," in Bergey's Manual® of Systematic Bacteriology, eds D. J. Brenner, N. R. Krieg, J. T. Staley, and G. M. Garrity (New York: Springer), 149-153.
    • (2005) Bergey's Manual® of Systematic Bacteriology , pp. 149-153
    • Spieck, E.1    Bock, E.2
  • 107
    • 84875905920 scopus 로고    scopus 로고
    • Nitrospina Watson and Waterbury 1971, 225AL
    • eds D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey, and K.-H. Schleifer. (New York: Springer)
    • Spieck, E., and Bock, E. (2005b)."Nitrospina Watson and Waterbury 1971, 225AL," in Bergey's Manual® of Systematic Bacteriology, eds D. J. Brenner, N. R. Krieg, G. M. Garrity, J. T. Staley, D. R. Boone, P. Vos, M. Goodfellow, F. A. Rainey, and K.-H. Schleifer. (New York: Springer), 999-1003.
    • (2005) Bergey's Manual( of Systematic Bacteriology , pp. 999-1003
    • Spieck, E.1    Bock, E.2
  • 108
    • 0031951770 scopus 로고    scopus 로고
    • Isolation and immunocytochemical location of the nitrite-oxidizing system in Nitrospira moscoviensis
    • Spieck, E., Ehrich, S., Aamand, J., and Bock, E. (1998). Isolation and immunocytochemical location of the nitrite-oxidizing system in Nitrospira moscoviensis. Arch. Microbiol. 169, 225-230.
    • (1998) Arch. Microbiol. , vol.169 , pp. 225-230
    • Spieck, E.1    Ehrich, S.2    Aamand, J.3    Bock, E.4
  • 110
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: a fast program for maximum likelihoodbased inference of large phylogenetic trees
    • Stamatakis, A., Ludwig, T., and Meier, H. (2005). RAxML-III: a fast program for maximum likelihoodbased inference of large phylogenetic trees. Bioinformatics 21, 456-463.
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 111
    • 52949130583 scopus 로고    scopus 로고
    • Expression of a putative nitrite reductase and the reversible inhibition of nitritedependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255
    • Starkenburg, S. R., Arp, D. J., and Bottomley, P. J. (2008). Expression of a putative nitrite reductase and the reversible inhibition of nitritedependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255. Environ. Microbiol. 10, 3036-3042.
    • (2008) Environ. Microbiol. , vol.10 , pp. 3036-3042
    • Starkenburg, S.R.1    Arp, D.J.2    Bottomley, P.J.3
  • 112
    • 33645741019 scopus 로고    scopus 로고
    • Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    • Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M. W., et al. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440, 790-794.
    • (2006) Nature , vol.440 , pp. 790-794
    • Strous, M.1    Pelletier, E.2    Mangenot, S.3    Rattei, T.4    Lehner, A.5    Taylor, M.W.6
  • 113
    • 0021686081 scopus 로고
    • Membrane-bound nitrite oxidoreductase of Nitrobacter: evidence for a nitrate reductase system
    • Sundermeyer-Klinger, H., Meyer, W., Warninghoff, B., and Bock, E. (1984). Membrane-bound nitrite oxidoreductase of Nitrobacter: evidence for a nitrate reductase system. Arch. Microbiol. 140,153-158.
    • (1984) Arch. Microbiol. , vol.140 , pp. 153-158
    • Sundermeyer-Klinger, H.1    Meyer, W.2    Warninghoff, B.3    Bock, E.4
  • 114
    • 34247874630 scopus 로고    scopus 로고
    • Catalytic properties of Staphylococcus aureus and Bacillus members of the secondary cation/proton antiporter-3 (Mrp) family are revealed by an optimized assay in an Escherichia coli host
    • Swartz, T. H., Ito, M., Ohira, T., Natsui, S., Hicks, D. B., and Krulwich, T. A. (2007). Catalytic properties of Staphylococcus aureus and Bacillus members of the secondary cation/proton antiporter-3 (Mrp) family are revealed by an optimized assay in an Escherichia coli host. J. Bacteriol. 189, 3081-3090.
    • (2007) J. Bacteriol. , vol.189 , pp. 3081-3090
    • Swartz, T.H.1    Ito, M.2    Ohira, T.3    Natsui, S.4    Hicks, D.B.5    Krulwich, T.A.6
  • 115
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577.
    • (2007) Syst. Biol. , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 118
    • 0028079873 scopus 로고
    • Evolutionary relationships among ammonia and nitriteoxidizing bacteria
    • Teske, A., Alm, E., Regan, J. M., Toze, S., Rittmann, B. E., and Stahl, D. A. (1994). Evolutionary relationships among ammonia and nitriteoxidizing bacteria. J. Bacteriol. 176, 6623-6630.
    • (1994) J. Bacteriol. , vol.176 , pp. 6623-6630
    • Teske, A.1    Alm, E.2    Regan, J.M.3    Toze, S.4    Rittmann, B.E.5    Stahl, D.A.6
  • 119
    • 84859794545 scopus 로고    scopus 로고
    • Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific
    • Thamdrup, B., Dalsgaard, T., and Revsbech, N. P. (2012). Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific. Deep Sea Res. Part 1 Oceanogr. Res. Pap. 65, 36-45.
    • (2012) Deep Sea Res. Part 1 Oceanogr. Res. Pap. , vol.65 , pp. 36-45
    • Thamdrup, B.1    Dalsgaard, T.2    Revsbech, N.P.3
  • 120
    • 84858004545 scopus 로고    scopus 로고
    • Polyamines reduce oxidative stress in Escherichia coli cells exposed to bactericidal antibiotics
    • Tkachenko, A. G., Akhova, A. V., Shumkov, M. S., and Nesterova, L. Y. (2012). Polyamines reduce oxidative stress in Escherichia coli cells exposed to bactericidal antibiotics. Res. Microbiol. 163, 83-91.
    • (2012) Res. Microbiol. , vol.163 , pp. 83-91
    • Tkachenko, A.G.1    Akhova, A.V.2    Shumkov, M.S.3    Nesterova, L.Y.4
  • 122
    • 75549085348 scopus 로고    scopus 로고
    • MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
    • Uchiyama, I., Higuchi, T., and Kawai, M. (2010). MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. Nucleic Acids Res. 38, D361- D365.
    • (2010) Nucleic Acids Res , vol.38
    • Uchiyama, I.1    Higuchi, T.2    Kawai, M.3
  • 125
    • 0029888257 scopus 로고    scopus 로고
    • Identification and characterization of a gene cluster involved in manganese oxidation by spores of the marine Bacillus sp. strain SG-1
    • van Waasbergen, L. G., Hildebrand, M., and Tebo, B. M. (1996). Identification and characterization of a gene cluster involved in manganese oxidation by spores of the marine Bacillus sp. strain SG-1. J. Bacteriol. 178, 3517-3530.
    • (1996) J. Bacteriol. , vol.178 , pp. 3517-3530
    • Van Waasbergen, L.G.1    Hildebrand, M.2    Tebo, B.M.3
  • 126
    • 35748974830 scopus 로고    scopus 로고
    • Occurrence, classification, and biological function of hydrogenases: an overview
    • Vignais, P. M., and Billoud, B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107, 4206-4272.
    • (2007) Chem. Rev. , vol.107 , pp. 4206-4272
    • Vignais, P.M.1    Billoud, B.2
  • 128
    • 33846134052 scopus 로고    scopus 로고
    • Communities of Archaea and Bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota
    • Weidler, G. W., Dornmayr-Pfaffenhuemer, M., Gerbl, F. W., Heinen, W., and Stan-Lotter, H. (2007). Communities of Archaea and Bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps, and evidence of ammonia-oxidizing Crenarchaeota. Appl. Environ. Microbiol. 73, 259-270.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 259-270
    • Weidler, G.W.1    Dornmayr-Pfaffenhuemer, M.2    Gerbl, F.W.3    Heinen, W.4    Stan-Lotter, H.5
  • 129
    • 75149154830 scopus 로고    scopus 로고
    • Function of Ech hydrogenase in ferredoxin-dependent, membrane-bound electron transport in Methanosarcina mazei
    • Welte, C., Kallnik,V., Grapp, M., Bender, G., Ragsdale, S., and Deppenmeier, U. (2010). Function of Ech hydrogenase in ferredoxin-dependent, membrane-bound electron transport in Methanosarcina mazei. J. Bacteriol. 192, 674-678.
    • (2010) J. Bacteriol. , vol.192 , pp. 674-678
    • Welte, C.1    Kallnik, V.2    Grapp, M.3    Bender, G.4    Ragsdale, S.5    Deppenmeier, U.6
  • 130
    • 18744403681 scopus 로고    scopus 로고
    • Intramolecular electron transfer in nitrite reductases
    • Wherland, S., Farver, O., and Pecht, I. (2005). Intramolecular electron transfer in nitrite reductases. Chemphyschem 6, 805-812.
    • (2005) Chemphyschem , vol.6 , pp. 805-812
    • Wherland, S.1    Farver, O.2    Pecht, I.3
  • 131
    • 0000762497 scopus 로고
    • Recherches sur les organismes de la nitrification
    • Winogradsky, S. (1890). Recherches sur les organismes de la nitrification. Ann. Inst. Pasteur 4, 213-231.
    • (1890) Ann. Inst. Pasteur , vol.4 , pp. 213-231
    • Winogradsky, S.1
  • 132
    • 0033215197 scopus 로고    scopus 로고
    • Characterization of the putative 2x[4Fe-4S]-binding NQO9 subunit of the proton-translocating NADH-quinone oxidoreductase (NDH-1) of Paracoccus denitrificans. Expression, reconstitution, and EPR characterization
    • Yano, T., Magnitsky, S., Sled, V. D., Ohnishi, T., and Yagi, T. (1999). Characterization of the putative 2x[4Fe-4S]-binding NQO9 subunit of the proton-translocating NADH-quinone oxidoreductase (NDH-1) of Paracoccus denitrificans. Expression, reconstitution, and EPR characterization. J. Biol. Chem. 274, 28598-28605.
    • (1999) J. Biol. Chem. , vol.274 , pp. 28598-28605
    • Yano, T.1    Magnitsky, S.2    Sled, V.D.3    Ohnishi, T.4    Yagi, T.5
  • 133
    • 0029891269 scopus 로고    scopus 로고
    • Purification and characterization of 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter ther mophilus TK-6
    • Yoon, K. S., Ishii, M., Igarashi, Y., and Kodama, T. (1996). Purification and characterization of 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter ther mophilus TK-6. J. Bacteriol. 178, 3365-3368.
    • (1996) J. Bacteriol. , vol.178 , pp. 3365-3368
    • Yoon, K.S.1    Ishii, M.2    Igarashi, Y.3    Kodama, T.4
  • 134
    • 0030895852 scopus 로고    scopus 로고
    • Purification and characterization of pyruvate:ferredoxin oxidoreductase from Hydrogenobacterthermophilus TK-6
    • Yoon, K. S., Ishii, M., Kodama, T., and Igarashi, Y. (1997). Purification and characterization of pyruvate:ferredoxin oxidoreductase from Hydrogenobacterthermophilus TK-6. Arch. Microbiol. 167, 275-279.
    • (1997) Arch. Microbiol. , vol.167 , pp. 275-279
    • Yoon, K.S.1    Ishii, M.2    Kodama, T.3    Igarashi, Y.4
  • 135
    • 6044240910 scopus 로고    scopus 로고
    • The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis
    • Zamboni, N., Maaheimo, H., Szyperski, T., Hohmann, H.-P., and Sauer, U. (2004). The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis. Metab. Eng. 6, 277-284.
    • (2004) Metab. Eng. , vol.6 , pp. 277-284
    • Zamboni, N.1    Maaheimo, H.2    Szyperski, T.3    Hohmann, H.-P.4    Sauer, U.5
  • 136
    • 0034640504 scopus 로고    scopus 로고
    • Proton pumping by cytochrome oxidase: progress, problems and postulates
    • Zaslavsky, D., and Gennis, R. B. (2000). Proton pumping by cytochrome oxidase: progress, problems and postulates. Biochim. Biophys. Acta 1458, 164-179.
    • (2000) Biochim. Biophys. Acta , vol.1458 , pp. 164-179
    • Zaslavsky, D.1    Gennis, R.B.2


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