SEARCH

SEARCH BY CITATION

References

  • Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zheng, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST – a new generation of protein database search programs. Nucleic Acids Res 25: 33893402.
  • Baar, C., Eppinger, M., Raddatz, G., Simon, J., Lanz, C., Klimmek, O., et al. (2003) Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci USA 100: 1169011695.
  • Beliaev, A.S., Klingeman, D.M., Klappenbach, J.A., Wu, L., Romine, M.F., Tiedje, J.M., et al. (2005) Global transcription analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J Bacteriol 187: 71387145.
  • Bergmann, D.J., Hooper, A.B., and Klotz, M.G. (2005) Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. Appl Environ Microbiol 71: 53715382.
  • Bode, C., Goebell, H., and Stähler, E. (1968) Zur Eliminierung von Trübungsfehlern bei der Eiweißbestimmung mit der Biuretmethode. Z Klin Chem Klin Biochem 6: 418422.
  • Burns, J.L., and DiChristina, T.J. (2009) Anaerobic respiration of elemental sulphur and thiosulfate by Shewanella oneidensis MR-1 requires psrA, a homolog of the phs gene of Salmonella enterica serovar typhimurium LT2. Appl Environ Microbiol 75: 52095217.
  • Clarke, T.A., Hemmings, A.M., Burlat, B., Butt, J.N., Cole, J.A., and Richardson, D.J. (2006) Comparison of the structural and kinetic properties of the cytochrome c nitrite reductases from Escherichia coli, Wolinella succinogenes, Sulfurospirillum deleyianum and Desulfovibrio desulfuricans. Biochem Soc Trans 34: 143145.
  • Clarke, T.A., Cole, J.A., Richardson, D.J., and Hemmings, A.M. (2007) The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA. Biochem J 406: 1930.
  • Cordova, C.D., Schicklberger, F.R., Yu, Y., and Spormann, A.M. (2011) Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1. J Bacteriol 193: 23232321.
  • Crane, B.R., and Getzoff, E.D. (1996) The relationship between structure and function for the sulfite reductases. Curr Opin Struct Biol 6: 744756.
  • Dahl, C., and Friedrich, C.G. (2008) Microbial Sulfur Metabolism. Berlin: Springer.
  • Dietrich, W., and Klimmek, O. (2002) The function of methyl-menaquinone-6 and polysulfide reductase membrane anchor (PsrC) in polysulfide respiration of Wolinella succinogenes. Eur J Biochem 269: 10861095.
  • Drummond, A., and Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
  • Einsle, O., Stach, P., Messerschmidt, A., Simon, J., Kröger, A., Huber, R., and Kroneck, P.M.H. (2000) Cytochrome c nitrite reductase from Wolinella succinogenes: structure at 1.6 Å resolution, inhibitor binding, and heme-packing motifs. J Biol Chem 275: 3960839616.
  • Francis, R.T., and Becker, R.R. (1984) Specific indication of hemoproteins in polyacrylamide gels using a double-staining process. Anal Biochem 136: 509514.
  • Gross, R., Pisa, R., Sänger, M., Lancaster, C.R.D., and Simon, J. (2004) Characterization of the menaquinone reduction site in the diheme cytochrome b membrane anchor of Wolinella succinogenes Ni/Fe-hydrogenase. J Biol Chem 279: 274281.
  • Gross, R., Eichler, R., and Simon, J. (2005) Site-directed modifications indicate differences in axial haem c iron ligation between the related NrfH and NapC families of multihaem c-type cytochromes. Biochem J 390: 689693.
  • Hartshorne, R.S., Kern, M., Meyer, B., Clarke, T.A., Karas, M., Richardson, D.J., and Simon, J. (2007) A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding. Mol Microbiol 64: 10491060.
  • Hartshorne, S., Richardson, D.J., and Simon, J. (2006) Multiple haem lyase genes indicate substrate specificity in cytochrome c biogenesis. Biochem Soc Trans 34: 146149.
  • Hooper, A.B., Arciero, D.M., Bergmann, D., and Hendrich, M.P. (2005) The oxidation of ammonia as an energy source in bacteria in respiration. In Respiration in Archaea and Bacteria. Zannoni, D. (ed.). Dordrecht: Springer, pp. 121147.
  • Hsieh, Y.C., Liu, M.Y., Wang, V.C., Chiang, Y.L., Liu, E.H., Wu, W.G., et al. (2010) Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from Desulfovibrio gigas. Mol Microbiol 78: 11011106.
  • Huang, C.J., and Barrett, E.L. (1990) Identification and cloning of genes involved in anaerobic sulfite reduction by Salmonella typhimurium. J Bacteriol 172: 41004102.
  • Johnson, E.F., and Mukhopadhyay, B. (2005) A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. J Biol Chem 280: 3877638786.
  • Jormakka, M., Yokoyama, K., Yano, T., Tamakoshi, M., Akimoto, S., Shimamura, T., et al. (2008) Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol 15: 730737.
  • Kemp, G.L., Clarke, T.A., Marritt, S.J., Lockwood, C., Poock, S.R., Hemmings, A.M., et al. (2010) Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. Biochem J 431: 7380.
  • Kern, M., and Simon, J. (2008) Characterization of the NapGH quinol dehydrogenase complex involved in Wolinella succinogenes nitrate respiration. Mol Microbiol 69: 11371152.
  • Kern, M., and Simon, J. (2009a) Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria. Biochim Biophys Acta 1787: 646656.
  • Kern, M., and Simon, J. (2009b) Periplasmic nitrate reduction in Wolinella succinogenes: cytoplasmic NapF facilitates NapA maturation and requires the menaquinol dehydrogenase NapH for membrane attachment. Microbiology 155: 27842794.
  • Kern, M., and Simon, J. (2011) Production of recombinant multiheme cytochromes c in Wolinella succinogenes. Methods Enzymol 486: 429446.
  • Kern, M., Mager, A., and Simon, J. (2007) Role of individual nap gene cluster products in NapC-independent nitrate respiration of Wolinella succinogenes. Microbiology 153: 37393747.
  • Kern, M., Eisel, F., Scheithauer, J., Kranz, R.G., and Simon, J. (2010a) Substrate specificity of three cytochrome c haem lyase isoenzymes from Wolinella succinogenes: unconventional haem c binding motifs are not sufficient for haem c attachment by NrfI and CcsA1. Mol Microbiol 75: 122137.
  • Kern, M., Scheithauer, J., Kranz, R.G., and Simon, J. (2010b) Essential histidine pairs indicate conserved haem binding in epsilonproteobacterial cytochrome c haem lyases. Microbiology 156: 37733781.
  • Kern, M., Volz, J., and Simon, J. (2011) The oxidative and nitrosative stress defence network of Wolinella succinogenes: cytochrome c nitrite reductase mediates the stress response to nitrite, nitric oxide, hydroxylamine and hydrogen peroxide. Environ Microbiol 13: 24782494.
  • King, T.E., and Morris, R.O. (1967) Determination of acid-labile sulfide and sulfhydryl groups. Methods Enzymol 10: 634641.
  • Klimmek, O., Dietrich, W., Dancea, F., Lin, Y.-J., Pfeiffer, S., Löhr, F., et al. (2004) Sulfur respiration. In Respiration in Bacteria and Archaea. Zannoni, D. (ed.). Dordrecht: Springer, pp. 217232.
  • Klotz, M.G., and Stein, L.Y. (2011) Genomics of ammonia-oxidizing bacteria and insights into their evolution. In Nitrification. Ward, B.B., Klotz, M.G., and Arp, D.J. (eds). Washington, DC: ASM Press, pp. 5794.
  • Klotz, M.G., Schmid, M.C., Strous, M., Op den Camp, H.J.M., Jetten, M.S.M., and Hooper, A.B. (2008) Evolution of an octaheme cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 10: 31503163.
  • Kostera, J., Youngblut, M.D., Slosarczyk, J.M., and Pacheco, A.A. (2008) Kinetic and product distribution analysis of NO· reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase. J Biol Inorg Chem 13: 10731083.
  • Kranz, R.G., Richard-Fogal, C., Taylor, J.S., and Frawley, E.R. (2009) Cytochrome c biogenesis: mechanisms for covalent modifications and trafficking of heme and for heme-iron redox control. Microbiol Mol Biol Rev 73: 510528.
  • Kröger, A., Geisler, V., and Duchêne, A. (1994) Isolation of Wolinella succinogenes hydrogenase, Chromatofocusing. In A Practical Guide to Membrane Protein Purification. von Jagow, G., and Schägger, H. (eds). London: Academic Press, pp. 141147.
  • Kröger, A., Biel, S., Simon, J., Gross, R., Unden, G., and Lancaster, C.R.D. (2002) Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism. Biochim Biophys Acta 1553: 2338.
  • Lorenzen, J.P., Kröger, A., and Unden, G. (1993) Regulation of anaerobic respiratory pathways in Wolinella succinogenes by the presence of electron acceptors. Arch Microbiol 159: 477483.
  • Lukat, P., Rudolf, M., Stach, P., Messerschmidt, A., Kroneck, P.M.H., Simon, J., and Einsle, O. (2008) Binding and reduction of sulfite by cytochrome c nitrite reductase. Biochemistry 47: 20802086.
  • Macy, J.M., Schröder, I., Thauer, R.K., and Kröger, A. (1986) Growth of Wolinella succinogenes on H2S plus fumarate and on formate plus sulfur as energy sources. Arch Microbiol 144: 147150.
  • Mileni, M., MacMillan, F., Tziatzios, C., Zwicker, K., Haas, A.H., Mäntele, W., et al. (2006) Heterologous production in Wolinella succinogenes and characterization of the quinol:fumarate reductase enzymes from Helicobacter pylori and Campylobacter jejuni. Biochem J 395: 191201.
  • Myers, J.D., and Kelly, D.J. (2005) A sulphite respiration system in the chemoheterotrophic human pathogen Campylobacter jejuni. Microbiology 151: 233242.
  • Oliveira, T.F., Vonrhein, C., Matias, P.M., Venceslau, S.S., Pereira, I.A.C., and Archer, M. (2008) The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration. J Biol Chem 283: 3414134149.
  • Oliveira, T.F., Franklin, E., Afonso, J.P., Khan, A.R., Oldham, N.J., Pereira, I.A.C., and Archer, M. (2011) Structural insights into dissimilatory sulfite reductases: structure of desulforubidin from Desulfomicrobium norvegicum. Front Microbiol 2: 71. doi: 10.3389/fmicb.2011.00071.
  • Pachmayer, F. (1960) Vorkommen und Bestimmung von Schwefelverbindungen in Mineralwasser. PhD thesis, Ludwig Maximilians Universität, Munich, Germany.
  • Parey, K., Warkentin, E., Kroneck, P.M.H., and Ermler, U. (2010) Reaction cycle of the dissimilatory sulfite reductase from Archaeoglobus fulgidus. Biochemistry 49: 89128921.
  • Pereira, I.A.C., Ramos, A.R., Grein, F., Marques, M.C., da Silva, S.M., and Venceslau, S.S. (2011) A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2: 69. doi: 10.3389/fmicb.2011.00069.
  • Pereira, I.C., Abreu, I.A., Xavier, A.V., LeGall, J., and Teixeira, M. (1996) Nitrite reductase from Desulfovibrio desulfuricans (ATCC 27774) – a heterooligomer heme protein with sulfite reductase activity. Biochem Biophys Res Commun 224: 611618.
  • Pfennig, N., and Trüper, H.G. (1981) Isolation of members of the families chromatiaceae and chlorobiaceae. In The Prokaryotes. vol. 1. Starr, M.P. (ed.). Berlin: Springer, pp. 279289.
  • Pisa, R., Stein, T., Eichler, R., Gross, R., and Simon, J. (2002) The nrfI gene is essential for the attachment of the active site haem group of Wolinella succinogenes cytochrome c nitrite reductase. Mol Microbiol 43: 763770.
  • Quentin, K.E., and Pachmayr, F. (1964) Bestimmung von Thiosulfat in schwefelhaltigen Mineralwässern. Fresenius J Anal Chem 200: 250256.
  • Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  • Schiffer, A., Parey, K., Warkentin, E., Diederichs, K., Huber, H., Stetter, K.O., et al. (2008) Structure of the dissimilatory sulfite reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus. J Mol Biol 379: 10631074.
  • Schumacher, W., Kroneck, P.M.H., and Pfennig, N. (1992) Comparative systematic study on ‘Spirillum’ 5175, Campylobacter and Wolinella species. Arch Microbiol 158: 287293.
  • Shirodkar, S., Reed, S., Romine, M., and Saffarini, D. (2011) The octahaem SirA catalyses dissimilatory sulfite reduction in Shewanella oneidensis MR-1. Environ Microbiol 13: 108115.
  • Simon, J. (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26: 285309.
  • Simon, J., and Hederstedt, L. (2011) Composition and function of cytochrome c biogenesis System II. FEBS J 278: 41794188.
  • Simon, J., and Kern, M. (2008) Quinone-reactive proteins devoid of haem b form widespread membrane-bound electron transport modules in bacterial respiration. Biochem Soc Trans 36: 10111016.
  • Simon, J., Gross, R., Ringel, M., Schmidt, E., and Kröger, A. (1998) Deletion and site-directed mutagenesis of the Wolinella succinogenes fumarate reductase operon. Eur J Biochem 251: 418426.
  • Simon, J., Gross, R., Einsle, O., Kroneck, P.M.H., Kröger, A., and Klimmek, O. (2000) A NapC/NirT-type cytochrome c (NrfH) is the mediator between the quinone pool and the cytochrome c nitrite reductase of Wolinella succinogenes. Mol Microbiol 35: 686696.
  • Simon, J., Pisa, R., Stein, T., Eichler, R., Klimmek, O., and Gross, R. (2001) The tetraheme cytochrome c NrfH is required to anchor the cytochrome c nitrite reductase in the membrane of Wolinella succinogenes. Eur J Biochem 268: 57765782.
  • Simon, J., Eichler, R., Pisa, R., Biel, S., and Gross, R. (2002) Modification of heme c binding motifs in the small subunit (NrfH) of the Wolinella succinogenes cytochrome c nitrite reductase complex. FEBS Lett 522: 8387.
  • Simon, J., Sänger, M., Schuster, S.C., and Gross, R. (2003) Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein. Mol Microbiol 49: 6979.
  • Simon, J., Einsle, O., Kroneck, P.M.H., and Zumft, W.G. (2004) The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase. FEBS Lett 569: 712.
  • Simon, J., van Spanning, R.J.M., and Richardson, D.J. (2008) The organization of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochim Biophys Acta 1777: 14801490.
  • Simon, J., Kern, M., Hermann, B., Einsle, O., and Butt, J.N. (2011) Physiological function and catalytic versatility of bacterial multihaem cytochromes c involved in nitrogen and sulfur cycling. Biochem Soc Trans 39: 18641870.
  • Stach, P., Einsle, O., Schumacher, W., Kurun, E., and Kroneck, P.M.H. (2000) Bacterial cytochrome c nitrite reductase: new structural and functional aspects. J Inorg Biochem 79: 381385.
  • Swofford, D.L. (1999) PAUP (Phylogenetic Analysis Using Parsimony)*. Sunderland, MA: Sinauer Associates.
  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 48764882.
  • Upadhyay, A.K., Hooper, A.B., and Hendrich, M.P. (2006) NO reductase activity of the tetraheme cytochrome c554 of Nitrosomonas europaea. J Am Chem Soc 128: 43304337.
  • Whelan, S., and Goldman, N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691699.
  • Zehnder, A.J.B., and Wuhrmann, K. (1976) Titanium (III) citrate as a nontoxic oxidation-reduction buggering system for the culture of obligate anaerobes. Science 194: 11651166.