Think pink: Photosynthesis, plasmids and the Roseobacter clade

Environmental Microbiology

Volumn 14, Issue 10, 2012, Pages 2661-2672

  Petersen, Jörn ^a   Brinkmann, Henner ^b   Bunk, Boyke ^a   Michael, Victoria ^a   Päuker, Orsola ^a   Pradella, Silke ^a  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^b Universite de Montreal   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PIGMENT;

ARTICLE; CLASSIFICATION; DNA REPLICATION; GENE ORDER; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PHOTOSYNTHESIS; PHYLOGENY; PLASMID; REPLICON; ROSEOBACTER;

DNA REPLICATION; GENE ORDER; MOLECULAR SEQUENCE DATA; OPERON; PHOTOSYNTHESIS; PHYLOGENY; PIGMENTS, BIOLOGICAL; PLASMIDS; REPLICON; ROSEOBACTER;

ROSEOBACTER; ROSEOBACTER LITORALIS; SULFITOBACTER;

EID: 84867213928     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02806.x     Document Type: Article

References (47)

1. Bartosik, D., Baj, J., Sochacka, M., Piechucka, E., and Wlodarczyk, M. (2002) Molecular characterization of functional modules of plasmid pWKS1 of Paracoccus pantotrophus DSM 11072. Microbiology 148: 2847-2856.
2. Béjà, O., Suzuki, M.T., Heidelberg, J.F., Nelson, W.C., Preston, C.M., Hamada, T., etal. (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.
3. Brinkhoff, T., Giebel, H.A., and Simon, M. (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 189: 531-539.
4. Buchan, A., González, J.M., and Moran, M.A. (2005) Overview of the marine roseobacter lineage. Appl Environ Microbiol 71: 5665-5677.
5. Carver, T., Harris, S.R., Berriman, M., Parkhill, J., and McQuillan, J.A. (2012) Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28: 464-469.
6. Dubey, G.P., and Ben-Yehuda, S. (2011) Intercellular nanotubes mediate bacterial communication. Cell 144: 590-600.
7. Fuchs, B.M., Spring, S., Teeling, H., Quast, C., Wulf, J., Schattenhofer, M., etal. (2007) Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc Natl Acad Sci USA 104: 2891-2896.
8. González, V., Santamaría, R.I., Bustos, P., Hernández-González, I., Medrano-Soto, A., Moreno-Hagelsieb, G., etal. (2006) The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 103: 3834-3839.
9. Inui, M., Nakata, K., Roh, J.H., Vertès, A.A., and Yukawa, H. (2003) Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus. Appl Environ Microbiol 69: 725-733.
10. Ivanova, E.P., Mitik-Dineva, N., Wang, J., Pham, D.K., Wright, J.P., Nicolau, D.V., etal. (2008) Staleya guttiformis attachment on poly(tert-butylmethacrylate) polymeric surfaces. Micron 39: 1197-1204.
11. Jiao, N., Zhang, F., and Hong, N. (2010) Significant roles of bacteriochlorophyll a supplemental to chlorophyll a in the ocean. ISME J 4: 595-597.
12. Kalhoefer, D., Thole, S., Voget, S., Lehmann, R., Liesegang, H., Wollher, A., etal. (2011) Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics 12: 324.
13. King, J.D., Kocíncová, D., Westman, E.L., and Lam, J.S. (2009) Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa. Innate Immun 15: 261-312.
14. Labrenz, M., Tindall, B.J., Lawson, P.A., Collins, M.D., Schumann, P., and Hirsch, P. (2000) Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., alpha-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake. Int J Syst Evol Microbiol 50: 303-313.
15. Laus, M.C., Logman, T.J., Lamers, G.E., Van Brussel, A.A., Carlson, R.W., and Kijne, J.W. (2006) A novel polar surface polysaccharide from Rhizobium leguminosarum binds host plant lectin. Mol Microbiol 59: 1704-1713.
16. Le, S.Q., and Gascuel, O. (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25: 1307-1320.
17. Makarova, K.S., Aravind, L., Galperin, M.Y., Grishin, N.V., Tatusov, R.L., Wolf, Y.I., and Koonin, E.V. (1999) Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9: 608-628.
18. Moran, M.A., Belas, R., Schell, M.A., González, J.M., Sun, F., Sun, S., etal. (2007) Ecological genomics of marine Roseobacters. Appl Environ Microbiol 73: 4559-4569.
19. Naylor, G.W., Addlesee, H.A., Gibson, L.C.D., and Hunter, C.N. (1999) The photosynthesis gene cluster of Rhodobacter sphaeroides. Photosynth Res 62: 121-139.
20. Néron, B., Ménager, H., Maufrais, C., Joly, N., Maupetit, J., Letort, S., etal. (2009) Mobyle: a new full web bioinformatics framework. Bioinformatics 25: 3005-3011.
21. Newton, R.J., Griffin, L.E., Bowles, K.M., Meile, C., Gifford, S., Givens, C.E., etal. (2010) Genome characteristics of a generalist marine bacterial lineage. ISME J 4: 784-798.
22. Petersen, J. (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193: 313-321.
23. Petersen, J., Brinkmann, H., and Pradella, S. (2009) Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 11: 2627-2638.
24. Petersen, J., Brinkmann, H., Berger, M., Brinkhoff, T., Päuker, O., and Pradella, S. (2011) Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol 28: 1229-1240.
25. Philippe, H. (1993) MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21: 5264-5272.
26. Porsby, C.H., Nielsen, K.F., and Gram, L. (2008) Phaeobacter and Ruegeria species of the Roseobacter clade colonize separate niches in a Danish Turbot (Scophthalmus maximus)-rearing farm and antagonize Vibrio anguillarum under different growth conditions. Appl Environ Microbiol 74: 7356-7364.
27. Pradella, S., Allgaier, M., Hoch, C., Päuker, O., Stackebrandt, E., and Wagner-Döbler, I. (2004) Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 70: 3360-3369.
28. Pradella, S., Päuker, O., and Petersen, J. (2010) Genome organization of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 192: 115-126.
29. Rao, D., Webb, J.S., Holmström, C., Case, R., Low, A., Steinberg, P., and Kjelleberg, S. (2007) Low densities of epiphytic bacteria from the marine alga Ulva australis inhibit settlement of fouling organisms. Appl Environ Microbiol 73: 7844-7852.
30. Rooney-Varga, J.N., Giewat, M.W., Savin, M.C., Sood, S., LeGresley, M., and Martin, J.L. (2005) Links between phytoplankton and bacterial community dynamics in a coastal marine environment. Microb Ecol 49: 163-175.
31. Sattley, W.M., Madigan, M.T., Swingley, W.D., Cheung, P.C., Clocksin, K.M., Conrad, A.L., etal. (2008) The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol 190: 4687-4696.
32. Seyedsayamdost, M.R., Case, R.J., Kolter, R., and Clardy, J. (2011) The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. Nat Chem 3: 331-335.
33. Shiba, T. (1991) Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst. Appl Microbiol 14: 140-145.
34. Stackebrandt, E., Rainey, F.A., and Ward-Rainey, N. (1996) Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives. Arch Microbiol 166: 211-223.
35. Stamatakis, A., and Alachiotis, N. (2010) Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinformatics 26: i132-i139.
36. Swingley, W.D., Sadekar, S., Mastrian, S.D., Matthies, H.J., Hao, J., Ramos, H., etal. (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189: 683-690.
37. 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.
38. Tang, K., Zong, R., Zhang, F., Xiao, N., and Jiao, N. (2010) Characterization of the photosynthetic apparatus and proteome of Roseobacter denitrificans. Curr Microbiol 60: 124-133.
39. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
40. Tomasch, J., Gohl, R., Bunk, B., Diez, M.S., and Wagner-Döbler, I. (2011) Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. ISME J 5: 1957-1968.
41. Wagner-Döbler, I., and Biebl, H. (2006) Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol 60: 255-280.
42. Wagner-Döbler, I., Ballhausen, B., Berger, M., Brinkhoff, T., Buchholz, I., Bunk, B., etal. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae - a hitchhiker's guide to life in the sea. ISME J 4: 61-77.
43. Yoon, J.H., Kang, S.J., Lee, M.H., and Oh, T.K. (2007) Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz etal. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter. Int J Syst Evol Microbiol 57: 1788-1792.
44. Yurkov, V.V., and Beatty, J.T. (1998) Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62: 695-724.
45. Zech, H., Thole, S., Schreiber, K., Kalhöfer, D., Voget, S., Brinkhoff, T., etal. (2009) Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 9: 3677-3697.
46. Zhong, Z., Caspi, R., Helinski, D., Knauf, V., Sykes, S., O'Byrne, C., etal. (2003) Nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium Ruegeria isolate PR1b. Plasmid 49: 233-252.
47. Zielenkiewicz, U., and Ceglowski, P. (2001) Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochim Pol 48: 1003-1023.