The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism

Journal of Bacteriology

Volumn 189, Issue 3, 2007, Pages 683-690

  Swingley, Wesley D ^a,f   Sadekar, Sumedha ^b   Mastrian, Stephen D ^c   Matthies, Heather J ^d   Hao, Jicheng ^c   Ramos, Hector ^b   Acharya, Chaitanya R ^b,g   Conrad, Amber L ^c   Taylor, Heather L ^c   Dejesa, Liza C ^c   Shah, Maulik K ^c   O'Huallachain, Maeve E ^c   Lince, Michael T ^d   Blankenship, Robert E ^d   Beatty, J Thomas ^e   Touchman, Jeffrey W ^a,c  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^f HOKKAIDO UNIVERSITY   (Japan)

^g DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHORIBULOKINASE; RIBULOSEBISPHOSPHATE CARBOXYLASE; SEA WATER;

ALPHAPROTEOBACTERIA; ARTICLE; AUTOTROPHY; BACTERIAL GENE; BACTERIAL GROWTH; CARBON DIOXIDE FIXATION; CARBON FIXATION; GENE SEQUENCE; GREENHOUSE GAS; MICROBIAL GROWTH; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PHOTOSYNTHESIS; PHOTOTROPHIC BACTERIUM; PHYLOGENY; PRIORITY JOURNAL; PURPLE AEROBIC ANOXYGENIC PHOTOTROPH; REGULATORY MECHANISM; ROSEOBACTER; ROSEOBACTER DENITRIFICANS; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; PHOTOSYNTHESIS; PHYLOGENY; ROSEOBACTER; SEQUENCE ANALYSIS, DNA;

PROTEOBACTERIA; ROSEOBACTER DENITRIFICANS;

EID: 33846592314     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01390-06     Document Type: Article

References (41)

1. Ashida, H., A. Danchin, and A. Yokota. 2005. Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism? Res. Microbiol. 156:611-618.
2. Bauer, C. E. 2004. Regulation of photosystem synthesis in Rhodobacter capsulatus. Photosynth. Res. 80:353-360.
3. Bauer, C. E., S. Elsen, L. R. Swem, D. L. Swem, and S. Masuda. 2003. Redox and light regulation of gene expression in photosynthetic prokaryotes. Philos. Trans. R. Soc. Lond. B 358:147-154.
4. Beatty, J. T. 1995. Organization of photosynthesis gene transcripts, p. 1209-1219. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria, vol. 2. Kluwer Academic Publishers, Dordrecht, The Netherlands.
5. Braatsch, S., M. Gomelsky, S. Kuphal, and G. Klug. 2002. A single flavoprotein, AppA, integrates both redox and light signals in Rhodobacter sphaeroides. Mol. Microbiol. 45:827-836.
6. Buchan, A., J. Gonzalez, and M. A. Moran. 2005. Overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71:5665-5677.
7. Buggy, J. J., M. W. Sganga, and C. E. Bauer. 1994. Characterization of a light-responding trans-activator responsible for differentially controlling reaction center and light-harvesting-I gene expression in Rhodobacter capsulatus. J. Bacteriol. 176:6936-6943.
8. Candela, M., E. Zaccherini, and D. Zannoni. 2001. Respiratory electron transport and light-induced energy transduction in membranes from the aerobic photosynthetic bacterium Roseobacter denitrificans. Arch. Microbiol. 175:168-177.
9. Elsen, S., M. Jaubert, D. Pignol, and E. Giraud. 2005. PpsR: a multifaceted regulator of photosynthesis gene expression in purple bacteria. Mol. Microbiol. 57:17-26.
10. Giraud, E., J. Fardoux, N. Fourrier, L. Hannibal, B. Genty, P. Bouyer, B. Dreyfus, and A. Vermeglio. 2002. Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria. Nature 417:202-205.
11. Giraud, E., S. Zappa, L. Vuillet, J. M. Adriano, L. Hannibal, J. Fardoux, C. Berthomieu, P. Bouyer, D. Pignol, and A. Vermeglio. 2005. A new type of bacteriophytochrome acts in tandem with a classical bacteriophytochrome to control the antennae synthesis in Rhodopseudomonas palustris. J. Biol. Chem. 280:32389-32397.
12. Gomelsky, L., J. Sram, O. V. Moskvin, I. M. Horne, H. N. Dodd, J. M. Pemberton, A. G. McEwan, S. Kaplan, and M. Gomelsky. 2003. Identification and in vivo characterization of PpaA, a regulator of photosystem formation in Rhodobacter sphaeroides. Microbiology 149:377-388.
13. Gomelsky, M., and S. Kaplan. 1995. Genetic evidence that PpsR from Rhodobacter sphaeroides 2.4.1 functions as a repressor of puc and bchF expression. J. Bacteriol. 177:1634-1637.
14. Gomelsky, M., and G. Klug. 2002. BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem. Sci. 27:497-500.
15. Gonzalez, J. M., R. P. Kiene, and M. A. Moran. 1999. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65:3810-3819.
16. Goodner, B., G. Hinkle, S. Gattung, N. Miller, M. Blanchard, B. Qurollo, B. S. Goldman, Y. Cao, M. Askenazi, C. Halling, L. Mullin, K. Houmiel, J. Gordon, M. Vaudin, O. Iartchouk, A. Epp, F. Liu, C. Wollam, M. Allinger, D. Doughty, C. Scott, C. Lappas, B. Markelz, C. Flanagan, C. Crowell, J. Gurson, C. Lomo, C. Sear, G. Strub, C. Cielo, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328.
17. Huang, J., Z. Su, and Y. Xu. 2005. The evolution of microbial phosphonate degradative pathways. J. Mol. Evol. V 61:682-690.
18. Igarashi, N., J. Harada, S. Nagashima, K. Matsuura, K. Shimada, and K. V. P. Nagashima. 2001. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J. Mol. Evol. 52:333-341.
19. Jaubert, M., S. Zappa, J. Fardoux, J.-M. Adriano, L. Hannibal, S. Elsen, J. Lavergne, A. Verroeglio, E. Giraud, and D. Pignol. 2004. Light and redox control of photosynthesis gene expression in Bradyrhizobium. Dual roles of two PpsR. J. Biol. Chem. 279:44407-44416.
20. Kaneko, T., Y. Nakamura, S. Sato, K. Minamisawa, T. Ichiumi, S. Sasamoto, A. Watanabe, K. Idesawa, M. Iriguchi, K. Kawashima, M. Kohara, M. Matsumoto, S. Shimpo, H. Tsuruoka, T. Wada, M. Yamada, and S. Tabata. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9:189-197.
21. King, G. M. 2003. Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. Appl. Environ. Microbiol. 69:7257-7265.
22. Kolber, Z. S., F. G. Plumley, A. S. Lang, J. T. Beatty, R. E. Blankenship, C. L. VanDover, C. Vetriani, M. Koblizek, C. Rathgeber, and P. G. Falkowski. 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492-2495.
23. Kyndt, J. A., T. E. Meyer, and M. A. Cusanovich. 2004. Photoactive yellow protein, bacteriophytochrome, and sensory rhodopsin in purple phototrophic bacteria. Photochem. Photobiol. Sci. 3:519-530.
24. Larimer, F. W., P. Chain, L. Hauser, J. Lamerdin, S. Malfatti, L. Do, M. L. Land, D. A. Pelletier, J. T. Beatty, A. S. Lang, F. R. Tabita, J. L. Gibson, T. E. Hanson, C. Bobst, J. L. Torres y Torres, C. Peres, F. H. Harrison, J. Gibson, and C. S. Harwood. 2004. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat. Biotechnol. 22:55-61.
25. Li, H., M. R. Sawaya, F. R. Tabita, and D. Eisenberg. 2005. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 13:779-789.
26. Masuda, S., and C. E. Bauer. 2002. AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell 110:613-623.
27. Masuda, S., Y. Matsumoto, K. V. P. Nagashima, K. Shimada, K. Inoue, C. E. Bauer, and K. Matsuura. 1999. Structural and functional analyses of photosynthetic regulatory genes regA and regB from Rhodovulum sulfidophilum, Roseobacter denitrificans, and Rhodobacter capsulatus. J. Bacteriol. 181:4205-4215.
28. Moran, M. A., A. Buchan, J. M. Gonzalez, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D. A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, and N. Ward. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
29. Moskvin, O. V., L. Gomelsky, and M. Gomelsky. 2005. Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development. J. Bacteriol. 187:2148-2156.
30. Ponnampalam, S. N., J. J. Buggy, and C. E. Bauer. 1995. Characterization of an aerobic repressor that coordinately regulates bacteriochlorophyll, carotenoid, and light harvesting-II expression in Rhodobacter capsulatus. J. Bacteriol. 177:2990-2997.
31. 2 fixation. Crit. Rev. Biochem. Mol. Biol. 26:261-300.
32. Sauer, U., and B. J. Eikmanns. 2005. The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol. Rev. 29:765-794.
33. Smart, J. L., J. W. Willett, and C. E. Bauer. 2004. Regulation of hem gene expression in Rhodobacter capsulatus by redox and photosystem regulators RegA, CrtJ, FnrL, and AerR. J. Mol. Biol. 342:1171-1186.
34. Steunou, A. S., C. Astier, and S. Ouchane. 2004. Regulation of photosynthesis genes in Rubrivivax gelatinosus: transcription factor PpsR is involved in both negative and positive control. J. Bacteriol. 186:3133-3142.
35. Stothard, P., and D. S. Wishart. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.
36. Ternan, N. G., J. W. McGrath, G. McMullan, and J. P. Quinn. 1998. Organophosphonates: occurrence, synthesis and biodegradation by microorganisms. World J. Microbiol. Biotechnol. V 14:635-647.
37. Thomas, J. W., J. W. Touchman, R. W. Blakesley, G. G. Bouffard, S. M. Beckstrom-Sternberg, E. H. Margulies, M. Blanchette, A. C. Siepel, P. J. Thomas, J. C. McDowell, B. Masken, N. F. Hansen, M. S. Schwartz, R. J. Weber, W. J. Kent, D. Karolchik, T. C. Bruen, R. Bevan, D. J. Cutler, S. Schwartz, L. Elnitski, J. R. Idol, A. B. Prasad, S. Q. Lee-Lin, V. V. B. Maduro, T. J. Summers, M. E. Portnoy, N. L. Dietrich, N. Akhter, K. Ayele, B. Benjamin, K. Cariaga, C. P. Brinkley, S. Y. Brooks, S. Granite, X. Guan, J. Gupta, P. Haghighi, S. L. Ho, M. C. Huang, E. Karlins, P. L. Laric, R. Legaspi, M. J. Lim, Q. L. Maduro, C. A. Masiello, S. D. Mastrian, J. C. McCloskey, R. Pearson, S. Stantripop, E. E. Tiongson, J. T. Tran, C. Tsurgeon, J. L. Vogt, M. A. Walker, K. D. Wetherby, L. S. Wiggins, A. C. Young, L. H. Zhang, K. Osoegawa, B. Zhu, B. Zhao, C. L. Shu, P. J. De Jong, C. E. Lawrence, A. F. Smit, A. Chakravarti, D. Haussler, P. Green, W. Miller, and E. D. Green. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788-793.
38. Wood, H. G., C. H. Werkman, A. Hemingway, and A. O. Nier. 1941. The position of carbon dioxide in succinic acid synthesized by heterotrophic bacteria. J. Biol. Chem. 139:377-381.
39. Yurkov, V. V., and J. T. Beatty. 1998. Aerobic anoxygenic phototrophic bacteria. Microbiol. Mol. Biol. Rev. 62:695-724.
40. Yutin, N., and O. Beja. 2005. Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. Environ. Microbiol. 7:2027-2033.
41. Zupan, J., T. R. Muth, O. Draper, and P. Zambryski. 2000. The transfer of DNA from Agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J. 23:11-28.