Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

Nature Biotechnology - Tập 22 Số 1 - Trang 55-61 - 2004
Frank W. Larimer1, Patrick Chain2, Loren Hauser1, Jane E. Lamerdin2, Stephanie Malfatti2, Long Do2, Miriam Land1, Dale A. Pelletier2, J. Thomas Beatty3, Andrew S. Lang3, F. Robert Tabita4, Janet L. Gibson4, Thomas E. Hanson4, Cedric E. Bobst4, Janelle L. Torres y Torres5, Caroline Peres5, Faith H. Harrison5, Jan Kuever4, Caroline S. Harwood5
1Genome Analysis and Systems Modeling, Oak Ridge National Laboratory, One Bethel Valley Rd., Oak Ridge, 37831, Tennessee, USA
2Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, 94598, California, USA
3Department of Microbiology and Immunology, The University of British Columbia, 6174 University Blvd., Vancouver, V6T 1Z3, British Columbia, Canada
4Department of Microbiology, The Ohio State University, 484 West 12th Ave., Columbus, 43210, Ohio, USA
5Department of Microbiology, 3-432 Bowen Science Bldg., The University of Iowa, Iowa City, 52242, Iowa, USA

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Barbosa, M.J., Rocha, J.M., Tramper, J. & Wijffels, R.H. Acetate as a carbon source for hydrogen production by photosynthetic bacteria. J. Biotechnol. 85, 25–33 (2001).

Sasikala, C. & Ramana, C.V. Biodegradation and metabolism of unusual carbon compounds by anoxygenic phototrophic bacteria. Adv. Microb. Physiol. 39, 339–377 (1998).

Philippot, L. Denitrifying genes in bacterial and archaeal genomes. Biochim. Biophys. Acta. 1577, 355–376 (2002).

Hu, X., Ritz, T., Damjanovic, A., Autenrieth, F. & Schulten, K. Photosynthetic apparatus of purple bacteria. Q. Rev. Biophys. 35, 1–62 (2002).

Giraud, E., Hannibal, L., Fardoux, J., Vermeglio, A. & Dreyfus, B. Effect of Bradyrhizobium photosynthesis on stem nodulation of Aeschynomene sensitiva. Proc. Natl. Acad. Sci. USA 97, 14795–14800 (2000).

Boivin, C. et al. Stem nodulation in legumes: diversity, mechanisms, and unusual characteristics. Crit. Rev. Plant Sci. 16, 1–30 (1997).

Giraud, E. et al. Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417, 202–205 (2002).

van Berkum, P. et al. Discordant pylogenies within the rrn loci of Rhizobia. J. Bacteriol. 185, 2988–2998 (2003).

Cogdell, R.J. et al. How photosynthetic bacteria harvest solar energy. J. Bacteriol. 181, 3869–3879 (1999).

Gall, A. & Robert, B. Characterization of the different peripheral light-harvesting complexes from high- and low-light grown cells from Rhodopseudomonas palustris. Biochemistry 38, 5185–5190 (1999).

Johnson, C.H. & Golden, S.S. Circadian programs in cyanobacteria: adaptiveness and mechanism. Annu. Rev. Microbiol. 53, 389–409 (1999).

Tabita, F.R. Microbial ribulose–1,5–bisphosphate carboxylase/oxygenase: a different perspective. Photosynthesis Res. 60, 1–28 (1999).

Friedrich, C.G., Rother, D., Bardischewsky, F., Quentmeier, A. & Fischer, J. Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl. Environ. Microbiol. 67, 2873–2882 (2001).

Rolls, J.P. & Lindstrom, E.S. Effect of thiosulfate on the photosynthetic growth of Rhodopseudomonas palustris. J. Bacteriol. 94, 860–869 (1967).

Hanson, T.E. & Tabita, F.R. A ribulose–1,5–bisphosphate carboxylase/oxygenase (RubisCO)–like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc. Natl. Acad. Sci. USA 98, 4397–4402 (2001).

Hanson, T.E. & Tabita, F.R. Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RubisCO-like protein. Photosynthesis Res. 78, 231–248 (2003).

Do, Y.S. et al. Role of Rhodobacter sp. strain PS9, a purple non-sulfur photosynthetic bacterium isolated from an anaerobic swine waste lagoon, in odor remediation. Appl. Environ. Microbiol. 69, 1710–1720 (2003).

Kobayashi, M. & Kobayashi, M. in Anoxygenic Photosynthetic Bacteria (eds. Blankenship, R.E., Madigan, M.T. & Bauer, C.E.) 1269–1282 (Kluwer Academic Publishers, Dordrecht, The Netherlands, 1995).

McGrath, J.E. & Harfoot, C.G. Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas. Appl. Environ. Microbiol. 63, 3333–3335 (1997).

Egland, P.G., Gibson, J. & Harwood, C.S. Reductive, coenzyme A–mediated pathway for 3–chlorobenzoate degradation in the phototrophic bacterium Rhodopseudomonas palustris. Appl. Environ. Microbiol. 67, 1396–1399 (2001).

Egland, P.G., Pelletier, D.A., Dispensa, M., Gibson J. & Harwood, C.S. A cluster of bacterial genes for anaerobic benzene ring biodegradation. Proc. Natl. Acad. Sci. USA 94, 6484–6489 (1997).

Noh, U., Heck, S., Giffhorn, F. & Kohring, G.W. Phototrophic transformation of phenol to 4-hydroxyphenylacetate by Rhodopseudomonas palustris. Appl. Microbiol. Biotechnol. 58, 830–835 (2002).

Masai, E. et al. Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether. J. Bacteriol. 185, 1768–1775 (2003).

Galperin, M.Y., Nikolskaya, A.N. & Koonin, E.V. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol. Lett. 203, 11–21 (2001).

Helmann, J.D. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46, 47–110 (2002).

Newman, J.D., Anthony, J.R. & Donohue, T.J. The importance of zinc-binding to the function of Rhodobacter sphaeroides ChrR as an anti-sigma factor. J. Mol. Biol. 313, 485–499 (2001).

Lang, A.S. & Beatty, J.T. The gene transfer agent of Rhodobacter capsulatus and “constitutive transduction” in prokaryotes. Arch. Microbiol. 175, 241–249 (2001).

Marketon, M.M., Glenn, S.A., Eberhard, A. & Gonzalez, J.E. Quorum sensing controls exopolysaccharide production in Sinorhizobium meliloti. J. Bacteriol. 185, 325–331 (2003).

Schaefer, A.L., Taylor, T.A., Beatty, J.T. & Greenberg, E.P. Long-chain acyl-homoserine lactone quorum-sensing regulation of Rhodobacter capsulatus gene transfer agent production. J. Bacteriol. 184, 6515–6521 (2002).

Paulson, I.T., Nguyen, L., Sliwinski, M.K., Rabus, R. & Saier, M.H. Jr. Microbial genome analysis: comparative transport capabilities in eighteen prokaryotes. J. Mol. Biol. 301, 75–100 (2000).

Saier, M.H. Jr. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64, 354–411 (2000).

Rosen, B.P. Transport and detoxification systems for transition metals, heavy metals and metalloids in eukaryotic and prokaryotic microbes. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 133, 689–693 (2002).

Cao, T.B. & Saier, M.H. Jr. Conjugal type IV macromolecular transfer systems of Gram–negative bacteria: organismal distribution, structural constraints and evolutionary conclusions. Microbiology 147, 3201–3214 (2001).

Saier, M.H. Jr. & Paulsen, I.T. Phylogeny of multidrug transporters. Semin. Cell Dev. Biol. 12, 205–213 (2001).

Kelly, D.J. & Thomas, G.H. The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. FEMS Microbiol. Rev. 25, 405–424 (2001).

Oda, Y. et al. Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments. Appl. Environ. Microbiol. 68, 3467–3477 (2002).

Lynch, D. et al. Genetic organization of the region encoding regulation, biosynthesis, and transport of rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti. J. Bacteriol. 183, 2576–2585 (2001).

Visca, P., Leoni, L., Wilson, M.J. & Lamont, I.L. Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas. Mol. Microbiol. 45, 1177–1190 (2002).

Sasikala, C. & Ramana, C.V. Biotechnological potentials of anoxygenic phototrophic bacteria. II. Biopolyesters, biopesticide, biofuel, and biofertilizer. Adv. Appl. Microbiol. 41, 227–278 (1995).

Eady, R.R. Structure–function relationships of alternative nitrogenases. Chem. Rev. 96, 3013–3030 (1996).

Fleischmann, R.D. et al. Whole genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).

Kim, U.J., Shizuya, H., deJong, P.J., Birren, B. & Simon, M.I. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 20, 1083–1085 (1992).

Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194 (1998).

Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998).

Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202 (1998).

Chain, P. et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185, 2759–2773 (2003).

Badger, J.H. & Olsen, G.J. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16, 512–524 (1999).

Delcher, A.L., Harmon, D., Kasif, S., White, O. & Salzberg, S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636–4641 (1999).