Proteomic insights into the lifestyle of an environmentally relevant marine bacterium

ISME Journal

Volumn 6, Issue 1, 2012, Pages 124-135

  Christie Oleza, Joseph Alexander ^a   Fernandez, Bernard ^a   Nogales, Balbina ^b   Bosch, Rafael ^b   Armengaud, Jean ^a  

^a CEA Marcoule   (France)

^b UNIVERSITAT DE LES ILLES BALEARS   (Spain)

Author keywords

core proteome; functional genomics; generalist; proteomics; Roseobacters; specialist

Indexed keywords

BACTERIAL PROTEIN; PROTEOME; SEA WATER;

ADAPTATION; ANTHROPOGENIC EFFECT; BACTERIUM; COASTAL WATER; GENE EXPRESSION; GENOMICS; HETEROGENEITY; LIFESTYLE; MARINE ECOSYSTEM; MICROBIAL COMMUNITY; OLIGOTROPHIC ENVIRONMENT; ORGANIC MATTER; PHYSIOLOGICAL RESPONSE; PROTEOMICS; SPECIALIST;

ARTICLE; GENETICS; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; RHODOBACTERACEAE;

BACTERIAL PROTEINS; PHYLOGENY; PROTEOME; RHODOBACTERACEAE; SEAWATER;

BACTERIA (MICROORGANISMS); ROSEOBACTER; RUEGERIA;

EID: 84355166729     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.86     Document Type: Article

References (41)

1. Baudet M, Ortet P, Gaillard JC, Fernandez B, Guerin P, Enjalbal C et al. (2010). Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics 9: 415-426.
2. Biers EJ, Sun S, Howard EC. (2009). Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome. Appl Environ Microbiol 75: 2221-2229.
3. Buchan A, Gonzalez JM, Moran MA. (2005). Overview of the marine roseobacter lineage. Appl Environ Microbiol 71: 5665-5677. (Pubitemid 41456854)
4. Burgmann H, Howard EC, Ye W, Sun F, Sun S, Napierala S et al. (2007). Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP). Environ Microbiol 9: 2742-2755. (Pubitemid 47547542)
5. Carvalho PC, Fischer JS, Chen EI, Yates JR, Barbosa VC. (2008). PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 9: 316.
6. Christie-Oleza JA, Armengaud J. (2010). In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study. Mar Drugs 8: 2223-2239.
7. Clair G, Roussi S, Armengaud J, Duport C. (2010). Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol Cell Proteomics 9: 1486-1498.
8. de Groot A, Dulermo R, Ortet P, Blanchard L, Guerin P, Fernandez B et al. (2009). Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet 5: e1000434.
9. DeLong EF. (2009). The microbial ocean from genomes to biomes. Nature 459: 200-206.
10. Fuhrman JA. (2009). Microbial community structure and its functional implications. Nature 459: 193-199.
11. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D et al. (2005). Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245. (Pubitemid 41170917)
12. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M et al. (2006). Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103: 425-430. (Pubitemid 43122417)
13. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I et al. (2008). Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res 18: 1133-1142. (Pubitemid 351931164)
14. Gustavsson N, Diez A, Nystrom T. (2002). The universal stress protein paralogues of Escherichia coli are coordinately regulated and co-operate in the defence against DNA damage. Mol Microbiol 43: 107-117. (Pubitemid 34212194)
15. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J et al. (2004). The complete genome and proteome of Mycoplasma mobile. Genome Res 14: 1447-1461. (Pubitemid 39193397)
16. Kato JY, Funa N, Watanabe H, Ohnishi Y, Horinouchi S. (2007). Biosynthesis of gamma-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc Natl Acad Sci USA 104: 2378-2383. (Pubitemid 46391405)
17. Keller M, Hettich R. (2009). Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73: 62-70.
18. Koonin EV, Wolf YI. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688-6719.
19. Lanfranconi MP, Bosch R, Nogales B. (2010). Short-term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution. Microbial Biotechnol 3: 607-621.
20. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S et al. (2009). The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA 106: 15527-15533.
21. Liu H, Sadygov RG, Yates 3rd JR. (2004). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201. (Pubitemid 38943698)
22. Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP et al. (2004). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910-913. (Pubitemid 40037153)
23. Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S et al. (2007). Ecological genomics of marine Roseobacters. Appl Environ Microbiol 73: 4559-4569. (Pubitemid 47122601)
24. Mou X, Sun S, Edwards RA, Hodson RE, Moran MA. (2008). Bacterial carbon processing by generalist species in the coastal ocean. Nature 451: 708-711. (Pubitemid 351220564)
25. Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE et al. (2010). Genome characteristics of a generalist marine bacterial lineage. ISME J 4: 784-798.
26. Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC et al. (2006). Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci USA 103: 18928-18933. (Pubitemid 350002805)
27. Polz MF, Hunt DE, Preheim SP, Weinreich DM. (2006). Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philosophical Transactions of the Royal Society B-Biological Sciences 361: 2009-2021. (Pubitemid 44787035)
28. Ramos JL, Gallegos MT, Marques S, Ramos-Gonzalez MI, Espinosa-Urgel M, Segura A. (2001). Responses of Gram-negative bacteria to certain environmental stressors. Curr Opin Microbiol 4: 166-171. (Pubitemid 32294418)
29. Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR et al. (2009). Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73: 249-299.
30. Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A et al. (2011). The genomic potential of Marinobacter aquaeolei-A biogeochemical opportunitroph. Appl Environ Microbiol 77: 2763-2771.
31. Sowell SM, Norbeck AD, Lipton MS, Nicora CD, Callister SJ, Smith RD et al. (2008). Proteomic analysis of stationary phase in the marine bacterium 'Candidatus Pelagibacter ubique'. Appl Environ Microbiol 74: 4091-4100. (Pubitemid 351962435)
32. Strom SL. (2008). Microbial ecology of ocean biogeochemistry: a community perspective. Science 320: 1043-1045. (Pubitemid 351929520)
33. Tang K, Huang H, Jiao N, Wu CH. (2010). Phylogenomic analysis of marine Roseobacters. PLoS One 5: e11604.
34. Ting L, Cowley MJ, Hoon SL, Guilhaus M, Raftery MJ, Cavicchioli R. (2009). Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling. Mol Cell Proteomics 8: 2227-2242.
35. VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. (2009). Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 7: 196-205.
36. Wagner-Dobler I, Biebl H. (2006). Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol 60: 255-280. (Pubitemid 44627949)
37. Wegener KM, Singh AK, Jacobs JM, Elvitigala TR, Welsh EA, Keren N et al. (2010). Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations. Mol Cell Proteomics 9: 2678-2689.
38. Wilmes P, Bond PL. (2006). Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92-97. (Pubitemid 43190739)
39. Wilmes P, Bond PL. (2009). Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles. Curr Opin Microbiol 12: 310-317.
40. York GM, Junker BH, Stubbe J, Sinskey AJ. (2001). Accumulation of the PhaP phasin of Ralstonia eutropha is dependent on production of polyhydroxybutyrate in cells. J Bacteriol 183: 4217-4226. (Pubitemid 32568073)
41. Zech H, Thole S, Schreiber K, Kalhofer D, Voget S, Brinkhoff T et al. (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.