Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data

Biochimie

Volumn 91, Issue 2, 2009, Pages 192-203

  Weiss, Stéphanie ^a   Carapito, Christine ^b   Cleiss, Jessica ^a   Koechler, Sandrine ^a   Turlin, Evelyne ^c   Coppee, Jean Yves ^c   Heymann, Michaël ^a   Kugler, Valérie ^a   Stauffert, Magalie ^a   Cruveiller, Stéphane ^d,e   Médigue, Claudine ^d,e   Van Dorsselaer, Alain ^b   Bertin, Philippe N ^a   Arsène Ploetze, Florence ^a  

^a Université de Strasbourg   (France)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c INSTITUT PASTEUR   (France)

^d UniversitCrossed D Sign Paris Saclay   (France)

^e DIF   (France)

Author keywords

Arsenic; Genome annotation; Herminiimonas arsenicoxydans; Proteomic

Indexed keywords

HERMINIIMONAS;

EID: 58849166475     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2008.07.013     Document Type: Article

References (31)

1. Oremland R.S., and Stolz J.F. The ecology of arsenic. Science 300 (2003) 939-944
2. Mukhopadhyay R., Rosen B.P., Phung L.T., and Silver S. Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiol. Rev. 26 (2002) 311-325
3. Smith A.H., Lopipero P.A., Bates M.N., and Steinmaus C.M. Public health: enhanced: arsenic epidemiology and drinking water standards. Science 296 (2002) 2145-2146
4. Muller D., Simeonova D.D., Riegel P., et al. Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium. Int. J. Syst. Evol. Microbiol. 56 (2006) 1765-1769
5. Muller D., Médigue C., Koechler S., et al. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet. 3 (2007) e53
6. Muller D., Lièvremont D., Simeonova D.D., Hubert J.-C., and Lett M.-C. Arsenite oxidase aox genes from a metal-resistant β-proteobacterium. J. Bacteriol. 185 (2003) 135-141
7. Sarma A.D., and Emerich D.W. Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics. Proteomics 5 (2005) 4170-4184
8. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proc. Natl. Acad. Sci. 103 (2006) 17921-17926
9. Markert S., Arndt C., Felbeck H., et al. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315 (2007) 247-250
10. Carapito C., Muller D., Turlin E., et al. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant β-proteobacterium with an unsequenced genome. Biochimie 88 (2006) 595-606
11. Weeger W., Lièvremont D., Perret M., et al. Oxidation of arsenite to arsenate by a bacterium isolated from an aquatic environment. BioMetals 12 (1999) 141-149
12. Rabilloud T., Valette C., and Lawrence J. Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension. Electrophoresis 15 (1994) 1552-1558
13. Carr S., Aebersold R., Baldwin M., Burlingame A., Clauser K., and Nesvizhskii A. The need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and protein identification data. Mol. Cell. Proteomics 3 (2004) 531-533
14. Wilkins M.R., Appel R.D., Eyk J.E.V., et al. Guidelines for the next 10 years of proteomics. Proteomics 6 (2006) 4-8
15. Gardy J.L., Laird M.R., Chen F., et al. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21 (2005) 617-623
16. Smyth G.K., and Speed T.P. Normalization of cDNA microarray data. Methods 31 (2003) 265-273
17. Delmar P., Robin S., Tronik-LeRoux D., and Daudin J.-J. Mixture model on the variance for the analysis of gene expression data. J.R. Stat. Soc. C. 54 (2005) 31-50
18. Benjamini Y., and Yekutieli D. The control of the false discovery rate in multiple hypothesis testing under dependency. Ann. Stat. 29 (2001) 1165-1188
19. Tebbe A., Klein C., Bisle B., et al. Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics 5 (2005) 168-179
20. Maillet I., Berndt P., Malo C., et al. From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach. Proteomics 7 (2007) 1097-1106
21. Lèvine A., Vannier F., Absalon C., et al. Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6 (2006) 2157-2173
22. Morandell S., Stasyk T., Grosstessner-Hain K., et al. Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 6 (2006) 4047-4056
23. Pethe K., Bifani P., Drobecq H., et al. Mycobacterial heparin-binding hemagglutinin and laminin-binding protein share antigenic methyllysines that confer resistance to proteolysis. Proc. Natl. Acad. Sci. 99 (2002) 10759-10764
24. Tatutov R.L., Natale D.A., Garkavtsev I.V., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (2001) 22-28
25. Sharp P.M., and Li W.-H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
26. Li S., and Waters R. Escherichia coli strains lacking protein HU are UV sensitive due to a role for HU in homologous recombination. J. Bacteriol. 180 (1998) 3750-3756
27. Bernardini G., Renzone G., Comanducci M., et al. Proteome analysis of Neisseria meningitidis serogroup A. Proteomics 4 (2004) 2893-2926
28. Hansmeier N., Chao T.C., Daschkey S., et al. A comprehensive proteome map of the lipid-requiring nosocomial pathogen Corynebacterium jeikeium K411. Proteomics 7 (2007) 1076-1096
29. Meng Y.L., Liu Z., and Rosen B.P. As(III) and Sb(III) uptake by GlpF and efflux by ArsB in Escherichia coli. J. Biol. Chem. 279 (2004) 18334-18341
30. Oden K.L., Gladysheva T.B., and Rosen B.P. Arsenate reduction mediated by the plasmid-encoded ArsC protein is coupled to glutathione. Mol. Microbiol. 12 (1994) 301-306
31. Bertin P.N., Medigue C., and Normand P. Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. Microbiol. 154 (2008) 347-359