Salt stress in Desulfovibrio vulgaris hildenborough: An integrated genomics approach

Journal of Bacteriology

Volumn 188, Issue 11, 2006, Pages 4068-4078

  Mukhopadhyay, Aindrila ^a   He, Zhili ^a,b   Alm, Eric J ^a   Arkin, Adam P ^a,e   Baidoo, Edward E ^a   Borglin, Sharon C ^a   Chen, Wenqiong ^a,d   Hazen, Terry C ^a   He, Qiang ^a,b   Holman, Hoi Ying ^a   Huang, Katherine ^a   Huang, Rick ^a   Joyner, Dominique C ^a   Katz, Natalie ^a   Keller, Martin ^a,d   Oeller, Paul ^a,d   Redding, Alyssa ^a,e   Sun, Jun ^a,d   Wall, Judy ^a,c   Wei, Jing ^a,d   Yang, Zamin ^a,b   Yen, Huei Che ^a,c   Zhou, Jizhong ^a,b   Keasling, Jay D ^a,e,f   more..

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c University of Missouri   (United States)

^d DIVERSA CORPORATION   (United States)

^e University of California   (United States)

^f Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ADENOSINE TRIPHOSPHATE; BETAINE; ECTOINE; GLYCINE; HELICASE; LACTIC ACID; NUCLEIC ACID BASE; PERMEASE; POTASSIUM CHLORIDE; RNA HELICASE; SODIUM CHLORIDE;

ARTICLE; BACTERIAL CELL; BACTERIAL FLAGELLUM; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIUM CULTURE; BASE PAIRING; CHEMOTAXIS; CONTROLLED STUDY; DESULFOVIBRIO VULGARIS; DOWN REGULATION; ELECTRON MICROSCOPY; GENE CONTROL; HABITAT STRUCTURE; LIQUID CULTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; PROTEIN TRANSPORT; PROTEOMICS; RADIOACTIVE WASTE; REDUCTION; SALINITY; SALT STRESS; TRANSCRIPTOMICS; UPREGULATION;

BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CULTURE MEDIA; DESULFOVIBRIO VULGARIS; GENOME, BACTERIAL; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPERON; SODIUM CHLORIDE;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH;

EID: 33744776637     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01921-05     Document Type: Article

References (62)

1. Allakhverdiev, S. I., M. Kinoshita, M. Inaba, I. Suzuki, and N. Murata. 2001. Unsaturated fatty acids in membrane lipids protect the photosynthetic machinery against salt-induced damage in Synechococcus. Plant Physiol. 125: 1842-1853.
2. Aim, E. J., K. H. Huang, M. N. Price, R. P. Koche, K. Keller, I. L. Dubchak, and A. P. Arkin. 2005. The MicrobesOnline web site for comparative genomics. Genome Res. 15:1015-1022.
3. Baliga, N. S., M. Pan, Y. A. Goo, E. C. Yi, D. R. Goodlett, K. Dimitrov, P. Shannon, R. Aebersold, W. V. Ng, and L. Hood. 2002. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. USA 99:14913-14918.
4. Barron, A., G. May, E. Bremer, and M. Villarejo. 1986. Regulation of envelope protein composition during adaptation to osmotic stress in Escherichia coli. J. Bacteriol. 167:433-438.
5. Benbouzidrollet, N. D., M. Conte, J. Guezennec, and D. Prieur. 1991. Monitoring of a Vibrio natriegens and Desulfovibrio vulgaris marine aerobic biofilm on a stainless-steel surface in a laboratory tubular flow system. J. Appl. Bacteriol. 71:244-251.
6. Ben-David, E. A., P. J. Holden, D. J. Stone, B. D. Harch, and L. J. Foster. 2004. The use of phospholipid fatty acid analysis to measure impact of acid rock drainage on microbial communities in sediments. Microb. Ecol. 48:300-315.
7. Bhargava, S. 2005. The role of potassium as an ionic signal in the regulation of cyanobacterium Nostoc muscorum response to salinity and osmotic stress. J. Basic Microbiol. 45:171-181.
8. Blessing, T. C., B. W. Wielinga, M. J. Morra, and S. Fendorf. 2001. CoII-IEDTA reduction by Desulfovibrio vulgaris and propagation of reactions involving dissolved sulfide and polysulfides. Environ. Sci. Technol. 35:1599-1603.
9. Brandenburg, K., S. S. Funari, M. H. Koch, and U. Seydel. 1999. Investigation into the acyl chain packing of endotoxins and phospholipids under near physiological conditions by WAXS and FTIR spectroscopy. J. Struct. Biol. 128:175-186.
10. Brandis, A., and R. K. Thauer. 1981. Growth of Desulfovibrio species on hydrogen and sulphate as sole energy source. J. Gen. Microbiol. 126:249-252.
11. Bremer, R., and R. Kramer. 2000. Coping with osmotic challenges: osmo-regulation through accumulation and release of compatible solutes in bacteria. ASM Press, Washington, D.C.
12. Cheville, A. M., K. W. Arnold, C. Buchrieser, C. M. Cheng, and C. W. Kaspar. 1996. rpoS regulation of acid, heat, and salt tolerance in Escherichia coli O157:H7. Appl. Environ. Microbiol. 62:1822-1824.
13. Chhabra, S. R., Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A. P. Arkin, and A. K. Singh. 2006. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188:1817-1828.
14. Cypionka, H. 1995. Solute transport and cell energetics. Plenum, New York, NY.
15. Dimroth, P. 1990. Mechanisms of sodium transport in bacteria. Philos. Trans. R. Soc. Lond. B 326:465-477.
16. Dudoit, S., and J. Fridlyand. 2002. A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol. 3:25.
17. Edlund, A., P. D. Nichols, R. Roffey, and D. C. White. 1985. Extractable and lipopolysaccharide fatty acid and hydroxy acid profiles from Desulfovibrio species. J. Lipid Res. 26:982-988.
18. Fairman, M. E., P. A. Maroney, W. Wang, H. A. Bowers, P. Gollnick, T. W. Nilsen, and E. Jankowsky. 2004. Protein displacement by DExH/D "RNA helicases" without duplex unwinding. Science 304:730-734.
19. Funabashi, H., T. Haruyama, M. Mie, Y. Yanagida, E. Kobatake, and M. Aizawa. 2002. Non-destructive monitoring of rpoS promoter activity as stress marker for evaluating cellular physiological status. J. Biotechnol. 95:85-93.
20. Glaasker, E., F. S. Tjan, P. F. Ter Steeg, W. N. Konings, and B. Poolman. 1998. Physiological response of Lactobacillus plantarum to salt and nonelectrolyte stress. J. Bacteriol. 180:4718-4723.
21. Griffin, T. J., S. P. Gygi, T. Ideker, B. Rist, J. Eng, L. Hood, and R. Aebersold. 2002. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics 1:323-333.
22. Griffin, T. J., D. K. Han, S. P. Gygi, B. Rist, H. Lee, R. Aebersold, and K. C. Parker. 2001. Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass Spectrom. 12:1238-1246.
23. Hadas, O., and R. Pinkas. 1995. Sulfate reduction processes in sediments at different sites in Lake Kinneret, Israel. Microb. Ecol. 30:55-66.
24. Hanash, S. M., M. P. Bobek, D. S. Rickman, T. Williams, J. M. Rouillard, R. Kuick, and E. Puravs. 2002. Integrating cancer genomics and proteomics in the post-genome era. Proteomics 2:69-75.
25. Heidelberg, J. F., R. Seshadri, S. A. Haveman, C. L. Hemme, I. T. Paulsen, J. F. Kolonay, J. A. Eisen, N. Ward, B. Methe, L. M. Brinkac, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, D. Fouts, D. H. Haft, J. Selengut, J. D. Peterson, T. M. Davidsen, N. Zafar, L. Zhou, D. Radune, G. Dimitrov, M. Hance, K. Tran, H. Khouri, J. Gill, T. R. Utterback, T. V. Feldblyum, J. D. Wall, G. Voordouw, and C. M. Fraser. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol. 22:554-559.
26. Hoffmann, T., A. Schutz, M. Brosius, A. Volker, U. Volker, and E. Bremer. 2002. High-salinity-induced iron limitation in Bacillus subtilis. J. Bacteriol. 184:718-727.
27. Holman, H. Y., K. A. Bjornstad, M. P. McNamara, M. C. Martin, W. R. McKinney, and E. A. Blakely. 2002. Synchrotron infrared spectromicroscopy as a novel bioanalytical microprobe for individual living cells: cytotoxicity considerations. J. Biomed. Opt. 7:417-424.
28. Jain, N., J. Thatte, T. Braciale, K. Ley, M. O'Connell, and J. K. Lee. 2003. Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics 19:1945-1951.
29. Jebbar, M., L. Sohn-Bosser, E. Bremer, T. Bernard, and C. Blanco. 2005. Ectoine-induced proteins in Sinorhizobium meliloti include an ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism. J. Bacteriol. 187:1293-1304.
30. Kaplan, D. L., and M. O'Donnell. 2004. Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes. Mol. Cell 15: 453-465.
31. Kates, M. 1986. Influence of salt concentration on the membrane lipids of halophilic bacteria. FEMS Microbiol. Rev. 39:95-101.
32. Keen, R. G., R. Fu, and G. Voordouw. 1997. Deletion of two downstream genes alters expression of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough. Arch. Microbiol. 167:376-383.
33. Ko, R., L. T. Smith, and G. M. Smith. 1994. Glycine betaine confers enhanced osmotolerance and cryotolerance on Listeria monocylogenes. J. Bacteriol. 176:426-431.
34. Li, X., Z. He, and J. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33:6114-6123.
35. Liu, H., R. G. Sadygov, and J. R. Yates, 3rd. 2004. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76:4193-4201.
36. Liu, Y., W. Gao, Y. Wang, L. Wu, X. Liu, T. Yan, E. Alm, A. Arkin, D. K. Thompson, M. W. Fields, and J. Zhou. 2005. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions. J. Bacteriol. 187:2501-2507.
37. Los, D. A., and N. Murata. 2004. Membrane fluidity and its roles in the perception of environmental signals. Biochim. Biophys. Acta 1666:142-157.
38. 3 cytochrome. Appl. Environ. Microbiol. 60:726-728.
39. Ma, D., D. N. Cook, M. Alberti, N. G. Pon, H. Nikaido, and J. E. Hearst. 1995. Genes acrA and acrB encode a stress-induced efflux system of Escherichia coli. Mol. Microbiol. 16:45-55.
40. MacKay, V. L., X. Li, M. R. Flory, E. Turcott, G. L. Law, K. A. Serikawa, X. L. Xu, H. Lee, D. R. Goodlett, R. Aebersold, L. P. Zhao, and D. R. Morris. 2004. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol. Cell Proteomics 3:478-489.
41. + uptake Ktr system from the cyanobacterium Synechocystis sp. PCC 6803 and its role in the early phases of cell adaptation to hyperosmotic shock. J. Biol. Chem. 279:54952-54962.
42. Noguera, D. R., G. A. Brusseau, B. E. Rittmann, and D. A. Stahl. 1998. Unified model describing the role of hydrogen in the growth of Desulfovibrio vulgaris under different environmental conditions. Biotechnol. Bioeng. 59: 732-746.
43. Nunez, C, L. Adams, S. Childers, and D. R. Lovley. 2004. The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J. Bacteriol. 186:5543-5546.
44. Nyyssola, A., T. Reinikainen, and M. Leisola. 2001. Characterization of glycine sarcosine N-methyltransferase and sarcosine dimethylglycine N-methyltransferase. Appl. Environ. Microbiol. 67:2044-2050.
45. Ouattara, A. S., and V. A. Jacq. 1992. Characterization of sulfate-reducing bacteria isolated from Senegal ricefields. FEMS Microbiol. Ecol. 101:217-228.
46. Padan, E., and T. A. Krulwich. 2000. Sodium stress in bacterial stress response. ASM Press, Washington, D.C.
47. Paithoonrangsarid, K., M. A. Shoumskaya, Y. Kanesaki, S. Satoh, S. Tabata, D. A. Los, V. V. Zinchenko, H. Hayashi, M. Tanticharoen, I. Suzuki, and N. Murata. 2004. Five histidine kinases perceive osmotic stress and regulate distinct sets of genes in Synechocystis. J. Biol. Chem. 279:53078-53086.
48. Panepinto, J., L. Liu, J. Ramos, X. Zhu, T. Valyi-Nagy, S. Eksi, J. Fu, H. A. Jaffe, B. Wickes, and P. R. Williamson. 2005. The DEAD-box RNA helicase Vad1 regulates multiple virulence-associated genes in Cryptococcus neoformans. J. Clin. Investig. 115:632-641.
49. + pump. Biochemistry 35:6233-6242.
50. Postgate, J. R. 1984. The sulfate-reducing bacteria. Cambridge University Press, Cambridge, United Kingdom.
51. Rodionov, D. A., I. Dubchak, A. Arkin, E. Alm, and M. S. Gelfand. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 5:R90.
52. Sanan-Mishra, N., X. H. Pham, S. K. Sopory, and N. Tuteja. 2005. Pea DNA helicase 45 overexpression in tobacco confers high salinity tolerance without affecting yield. Proc. Natl. Acad. Sci. USA 102:509-514.
53. Shapiguzov, A., A. A. Lyukevich, S. I. Allakhverdiev, T. V. Sergeyenko, I. Suzuki, N. Murata, and D. A. Los. 2005. Osmotic shrinkage of cells of Synechocystis sp. PCC 6803 by water efflux via aquaporins regulates osmostress-inducible gene expression. Microbiology 151:447-455.
54. Sleator, R. D., and C. Hill. 2002. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol. Rev. 26:49-71.
55. Steil, L., T. Hoffmann, I. Budde, U. Volker, and E. Bremer. 2003. Genomewide transcriptional profiling analysis of adaptation of Bacillus subtilis to high salinity. J. Bacteriol. 185:6358-6370.
56. + translocation by complex I (NADH:quinone oxidoreductase) of Escherichia coli. Mol. Microbiol. 35:428-434.
57. Tabak, H. H., and R. Govind. 2003. Advances in biotreatment of acid mine drainage and biorecovery of metals. 2. Membrane bioreactor system for sulfate reduction. Biodegradation 14:437-452.
58. Wang, R., J. T. Prince, and E. M. Marcotte. 2005. Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 15:1118-1126.
59. Wei, J., J. Sun, W. Yu, A. Jones, P. Oeller, M. Keller, G. Woodnutt, and J. M. Short. 2005. Global proteome discovery using an online three-dimensional LC-MS/MS. J. Proteome Res. 4:801-808.
60. White, C., R. J. Bobbie, J. D. King, J. S. Nickels, and P. Amoe. 1979. Lipid analysis of sediments for microbial biomass and community structure. American Society of Testing and Materials, Philadelphia, PA.
61. Wolters, D. A., M. P. Washburn, and J. R. Yates, 3rd. 2001. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73:5683-5690.
62. Ye, Q., Y. Roh, S. L. Carroll, B. Blair, J. Zhou, C. L. Zhang, and M. W. Fields. 2004. Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl. Environ. Microbiol. 70:5595-5602.