SEARCH

SEARCH BY CITATION

References

  • Alexeyev, M.F. (1999) The pKNOCK series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria. Biotechniques 26: 824828.
  • Arkhipova, O.V., and Akimenko, V.K. (2005) Unsaturated organic acids as terminal electron acceptors for reductase chains of anaerobic bacteria. Microbiology 74: 629639.
  • Backiel, J., Juárez, O., Zagorevski, D.V., Wang, Z., Nilges, M.J., and Barquera, B. (2008) Covalent binding of flavins to RnfG and RnfD in the Rnf complex from Vibrio cholerae. Biochemistry 47: 1127311284.
  • Barquera, B., Häse, C.C., and Gennis, R.B. (2001) Expression and mutagenesis of the NqrC subunit of the NQR respiratory Na+ pump from Vibrio cholerae with covalently attached FMN. FEBS Lett 492: 4549.
  • Barquera, B., Hellwig, P., Zhou, W., Morgan, J.E., Häse, C.C., Gosink, K.K., et al. (2002) Purification and characterization of the recombinant Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae. Biochemistry 41: 37813789.
  • Bender, R.A. (2012) Regulation of the histidine utilization (hut) system in bacteria. Microbiol Mol Biol Rev 76: 565584.
  • Bogachev, A.V., Bertsova, Y.V., Bloch, D.A., and Verkhovsky, M.I. (2006) Thermodynamic properties of the redox centers of Na+-translocating NADH:quinone oxidoreductase. Biochemistry 45: 34213428.
  • Bogachev, A.V., Bloch, D.A., Bertsova, Y.V., and Verkhovsky, M.I. (2009) Redox properties of the prosthetic groups of Na+-translocating NADH:quinone oxidoreductase. 2. Study of the enzyme by optical spectroscopy. Biochemistry 48: 62996304.
  • Casutt, M.S., Wendelspiess, S., Steuber, J., and Fritz, G. (2010) Crystallization of the Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae. Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 16771679.
  • Claverie, J.M. (2005) Fewer genes, more noncoding RNA. Science 309: 15291530.
  • Dobbin, P.S., Butt, J.N., Powell, A.K., Reid, G.A., and Richardson, D.J. (1999) Characterization of a flavocytochrome that is induced during the anaerobic respiration of Fe3+ by Shewanella frigidimarina NCIMB400. Biochem J 342: 439448.
  • Ells, A.H. (1959) A colorimetric method for the assay of soluble succinic dehydogenase and pyridinenucleotide-linked dehydrogenases. Arch Biochem Biophys 85: 561562.
  • Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.-y., et al. (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics 15: 5.6.15.6.30.
  • Fadeeva, M.S., Bertsova, Y.V., Verkhovsky, M.I., and Bogachev, A.V. (2008) Site-directed mutagenesis of conserved cysteine residues in NqrD and NqrE subunits of Na+-translocating NADH:quinone oxidoreductase. Biochemistry (Mosc) 73: 123129.
  • Gao, H., Barua, S., Liang, Y., Wu, L., Dong, Y., Reed, S., et al. (2010) Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microb Biotechnol 3: 455466.
  • Hayashi, M., Nakayama, Y., Yasui, M., Maeda, M., Furuishi, K., and Unemoto, T. (2001) FMN is covalently attached to a threonine residue in the NqrB and NqrC subunits of Na+-translocating NADH-quinone reductase from Vibrio alginolyticus. FEBS Lett 488: 58.
  • Heidelberg, J.F., Paulsen, I.T., Nelson, K.E., Gaidos, E.J., Nelson, W.C., Read, T.D., et al. (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol 20: 11181123.
  • Hunt, K.A., Flynn, J.M., Naranjo, B., Shikhare, I.D., and Gralnick, J.A. (2010) Substrate-level phosphorylation is the primary source of energy conservation during anaerobic respiration of Shewanella oneidensis strain MR-1. J Bacteriol 192: 33453351.
  • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567580.
  • Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860921.
  • Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 29472948.
  • Lawrence, J. (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr Opin Genet Dev 9: 642648.
  • Leys, D., Tsapin, A.S., Nealson, K.H., Meyer, T.E., Cusanovich, M.A., and Van Beeumen, J.J. (1999) Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1. Nat Struct Biol 6: 11131117.
  • Lukk, T., Sakai, A., Kalyanaraman, C., Brown, S.D., Imker, H.J., Song, L., et al. (2012) Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci USA 109: 41224127.
  • MacDonald, M.J., and D'Cunha, G.B. (2007) A modern view of phenylalanine ammonia lyase. Biochem Cell Biol 85: 273282.
  • Maier, T.M., Myers, J.M., and Myers, C.R. (2003) Identification of the gene encoding the sole physiological fumarate reductase in Shewanella oneidensis MR-1. J Basic Microbiol 43: 312327.
  • Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A., and Ronchi, S. (1999) Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Structure 7: 745756.
  • Mehler, A.H., and Tabor, H. (1953) Deamination of histidine to form urocanic acid in liver. J Biol Chem 201: 775784.
  • Mikoulinskaia, O., Akimenko, V., Galouchko, A., Thauer, R.K., and Hedderich, R. (1999) Cytochrome c-dependent methacrylate reductase from Geobacter sulfurreducens AM-1. Eur J Biochem 263: 346352.
  • Morris, C.J., Black, A.C., Pealing, S.L., Manson, F.D.C., Chapman, S.K., Reid, G.A., et al. (1994) Purification and properties of a novel cytochrome: flavocytochrome c from Shewanella putrefaciens. Biochem J 302: 587593.
  • Myers, J.M., and Myers, C.R. (2000) Role of the tetraheme cytochrome CymA in anaerobic electron transport in cells of Shewanella putrefaciens MR-1 with normal levels of menaquinone. J Bacteriol 182: 6775.
  • Pankhurst, K.L., Mowat, C.G., Rothery, E.L., Hudson, J.M., Jones, A.K., Miles, C.S., et al. (2006) A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina. J Biol Chem 281: 2058920597.
  • Pennisi, E. (2003) Bioinformatics. Gene counters struggle to get the right answer. Science 301: 10401041.
  • Petersen, T.N., Brunak, S., von Heijne, G., and Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785786.
  • Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., et al. (2012) The Pfam protein families database. Nucleic Acids Res 40(D1): D290D301.
  • Rahman, O., Cummings, S.P., Harrington, D.J., and Sutcliffe, I.C. (2008) Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria. World J Microbiol Biotechnol 24: 23772382.
  • Ramazzina, I., Cendron, L., Folli, C., Berni, R., Monteverdi, D., Zanotti, G., and Percudani, R. (2008) Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 283: 2329523304.
  • Reid, G.A., Miles, C.S., Moysey, R.K., Pankhurst, K.L., and Chapman, S.K. (2000) Catalysis in fumarate reductase. Biochim Biophys Acta 1459: 310315.
  • Rentzsch, R., and Orengo, C.A. (2009) Protein function prediction – the power of multiplicity. Trends Biotechnol 27: 210219.
  • Sato, K., Nishina, Y., Setoyama, C., Miura, R., and Shiga, K. (1999) Unusually high standard redox potential of acrylyl-CoA/propionyl-CoA couple among enoyl-CoA/acyl-CoA couples: a reason for the distinct metabolic pathway of propionyl-CoA from longer acyl-CoAs. J Biochem 126: 668675.
  • Schweikert, G., Behr, J., Zien, A., Zeller, G., Ong, C.S., Sonnenburg, S., et al. (2009) mGene.web: a web service for accurate computational gene finding. Nucleic Acids Res 37: W312W316.
  • Sen, N.P., McGeer, P.L., and Paul, R.M. (1962) Imidazolepropionic acid as a urinary metabolite of L-histidine. Biochem Biophys Res Commun 9: 257261.
  • Sucheta, A., Ackrell, B.A., Cochran, B., and Armstrong, F.A. (1992) Diode-like behavior of a mitochondrial electron-transport enzyme. Nature 356: 361362.
  • Thompson, D.K., Beliaev, A.S., Giometti, C.S., Tollaksen, S.L., Khare, T., Lies, D.P., et al. (2002) Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol 68: 881892.
  • Turner, K.L., Doherty, M.K., Heering, H.A., Armstrong, F.A., Reid, G.A., and Chapman, S.K. (1999) Redox properties of flavocytochrome c3 from Shewanella frigidimarina NCIMB400. Biochemistry 38: 33023309.
  • Verkhovsky, M.I., and Bogachev, A.V. (2010) Sodium-translocating NADH:quinone oxidoreductase as a redox-driven ion pump. Biochim Biophys Acta 1797: 738746.
  • Watanabe, T., and Honda, K. (1982) Measurement of the extinction coefficient of the methyl viologen cation radical and the efficiency of its formation by semiconductor photocatalysis. J Phys Chem 86: 26172619.
  • Yeats, C., Bentley, S., and Bateman, A. (2003) New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol 3: ARTN 3.
  • Yu, N.Y., Wagner, J.R., Laird, M.R., Melli, G., Rey, S., Lo, R., et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26: 16081615.
  • Zhou, W., Bertsova, Y.V., Feng, B., Tsatsos, P., Verkhovskaya, M.L., Gennis, R.B., et al. (1999) Sequencing and preliminary characterization of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio harveyi. Biochemistry 38: 1624616252.