Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris hildenborough

Applied and Environmental Microbiology

Volumn 78, Issue 4, 2012, Pages 1168-1177

  Zhou, Aifen ^a,g   Chen, Yunyu I ^a,g   Zane, Grant M ^b,g   He, Zhili ^a,g   Hemme, Christopher L ^a,g   Joachimiak, Marcin P ^c,g   Baumohl, Jason K ^c,g   He, Qiang ^d,g   Fields, Matthew W ^e,g   Arkin, Adam P ^c,g   Wall, Judy D ^b,g   Hazen, Terry C ^c,g   Zhou, Jizhong ^a,c,f,g  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d University of Tennessee   (United States)

^e MONTANA STATE UNIVERSITY   (United States)

^f TSINGHUA UNIVERSITY   (China)

^g Virtual Institute for Microbial Stress and Survivalh   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CR REDUCTIONS; DELETION MUTANTS; DESULFOVIBRIO VULGARIS; DETRENDED CORRESPONDENCE ANALYSIS; ENVIRONMENTAL CHANGE; FUNCTIONAL CHARACTERIZATION; GENE TRANSCRIPTIONS; GROWTH CONDITIONS; KNOCKOUT MUTANT; METABOLIC PATHWAYS; MULTIPLE STRESS CONDITIONS; PARALOGS; PHYSIOLOGICAL DIFFERENCES; STRESS CONDITION; STRESS RESPONSE; SULFATE REDUCTION; SYSTEMATIC STUDY; TRANSCRIPTIONAL PROFILING; TRANSCRIPTIONAL REGULATOR; VULGARIS;

BIOINFORMATICS; CHROMATES; GENES; HEALTH; PHYSIOLOGY; PLANTS (BOTANY); SODIUM CHLORIDE; STRAIN RATE; TRANSCRIPTION;

PHYSIOLOGICAL MODELS;

BACTERIAL DNA; BACTERIAL PROTEIN; CHROMIC ACID; CYCLIC AMP BINDING PROTEIN; NITRITE; SODIUM CHLORIDE; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

BIOINFORMATICS; CHROMIUM; CORRESPONDENCE ANALYSIS; ENVIRONMENTAL CHANGE; ENVIRONMENTAL STRESS; FITNESS; GENE EXPRESSION; GENETIC ANALYSIS; GROWTH RATE; HOMOLOGY; MUTATION; NITRITE; PHYSIOLOGY; SODIUM CHLORIDE; SULFATE-REDUCING BACTERIUM;

AIR; ARTICLE; BIOLOGY; CHEMISTRY; DESULFOVIBRIO VULGARIS; DNA SEQUENCE; GENE DELETION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGICAL STRESS; PHYSIOLOGY;

AIR; BACTERIAL PROTEINS; CHROMATES; COMPUTATIONAL BIOLOGY; CYCLIC AMP RECEPTOR PROTEIN; DESULFOVIBRIO VULGARIS; DNA, BACTERIAL; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; NITRITES; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH;

EID: 84863142624     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.05666-11     Document Type: Article

References (53)

1. Aono S, Nakajima H, Saito K, Okada M. 1996. A novel heme protein that acts as a carbon monoxide-dependent transcriptional activator in Rhodospirillum rubrum. Biochem. Biophys. Res. Commun. 228:752-756.
2. Bender KS, et al. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 73: 5389-5400.
3. Borenstein SB. 1994. Microbiologically influenced corrosion handbook. Industrial Press Inc, New York, NY.
4. Botsford JL, Harman JG. 1992. Cyclic AMP in prokaryotes. Microbiol. Mol. Biol. Rev. 56:100-122.
5. Busby S, Ebright RH. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
6. Chae HZ, et al. 1994. Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiolspecific antioxidant define a large family of antioxidant enzymes. Proc. Natl. Acad. Sci. U. S. A. 91:7017-7021.
7. Chhabra SR, et al. 2006. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 188:1817-1828.
8. Dispensa M, et al. 1992. Anaerobic growth of Rhodopseudomonas palustris on 4-hydroxybenzoate is dependent on AadR, a member of the cyclic AMP receptor protein family of transcriptional regulators. J. Bacteriol. 174:5803-5813.
9. Dufour YS, Kiley PJ, Donohue TJ. 2010. Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet. 6:e1001027.
10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Egland PG, Harwood CS. 2000. HbaR, a 4-hydroxybenzoate sensor and FNR-CRP superfamily member, regulates anaerobic 4-hydroxybenzoate degradation by Rhodopseudomonas palustris. J. Bacteriol. 182:100-106.
12. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
13. Galimand M, Gamper M, Zimmermann A, Haas D. 1991. Positive FNR-like control of anaerobic arginine degradation and nitrate respiration in Pseudomonas aeruginosa. J. Bacteriol. 173:1598-1606.
14. Gibson J, Dispensa M, Fogg GC, Evans DT, Harwood CS. 1994. 4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas palustris: purification, gene sequence, and role in anaerobic degradation. J. Bacteriol. 176:634-641.
15. He Q, et al. 2010. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. ISME J. 4:1386-1397.
16. He Q, et al. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72:4370-4381.
17. He Y, Shelver D, Kerby RL, Roberts GP. 1996. Characterization of a CO-responsive transcriptional activator from Rhodospirillum rubrum. J. Biol. Chem. 271:120-123.
18. He Z, et al. 2010. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris Hildenborough to salt adaptation. Appl. Environ. Microbiol. 76:1574-1586.
19. Heidelberg JF, et al. 2004. The genome sequence of the anaerobic, sulfatereducing bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol. 22:554-559.
20. Joachimiak M, Weisman J, May B. 2006. JColorGrid: software for the visualization of biological measurements. BMC Bioinformatics 7:225.
21. Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR. 2005. Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J. Bacteriol. 187:1135-1160.
22. Keller KL, Bender KS, Wall JD. 2009. Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency. Appl. Environ. Microbiol. 75:7682-7691.
23. Kiley PJ, Beinert H. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol. Rev. 22:341-352.
24. Kiley PJ, Reznikoff WS. 1991. Fnr mutants that activate gene expression in the presence of oxygen. J. Bacteriol. 173:16-22.
25. Kolb A, Busby S, Buc H, Garges S, Adhya S. 1993. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62: 749-797.
26. Körner H, Sofia HJ, Zumft WG. 2003. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol. Rev. 27:559-592.
27. Lawson CL, et al. 2004. Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struct. Biol. 14:10-20.
28. Letunic I, Bork P. 2007. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128.
29. Li B, Wing H, Lee D, Wu H-C, Busby S. 1998. Transcription activation by Escherichia coli FNR protein: similarities to, and differences from, the CRP paradigm. Nucleic Acids Res. 26:2075-2081.
30. Li X, Krumholz LR. 2009. Thioredoxin is involved in U(VI) and Cr(VI) reduction in Desulfovibrio desulfuricans G20. J. Bacteriol. 191:4924-4933.
31. Lopez O, et al. 2001. Regulation of gene expression in response to oxygen in Rhizobium etli: role of FnrN in fixNOQP expression and in symbiotic nitrogen fixation. J. Bacteriol. 183:6999-7006.
32. Lovley DR, Phillips EJP. 1994. Reduction of chromate by Desulfovibrio vulgaris and its c3 cytochrome. Appl. Environ. Microbiol. 60:726-728.
33. Markowitz VM, et al. 2010. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38:D382-D390.
34. McKay DB, Steitz TA. 1981. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature 290: 744-749.
35. Mesa S, Hennecke H, Fischer HM. 2006. A multitude of CRP/FNR-like transcription proteins in Bradyrhizobium japonicum. Biochem. Soc. Trans. 34:156-159.
36. Mukhopadhyay A, et al. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J. Bacteriol. 188:4068-4078.
37. Mukhopadhyay A, et al. 2007. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 189:5996-6010.
38. Nakajima H, et al. 2001. Redox properties and coordination structure of the heme in the CO-sensing transcriptional activator CooA. J. Biol. Chem. 276:7055-7061.
39. Oh J-I, Eraso JM, Kaplan S. 2000. Interacting regulatory circuits involved in orderly control of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J. Bacteriol. 182:3081-3087.
40. Ouattara AS, Jacq VA. 1992. Characterization of sulfate-reducing bacteria isolated from Senegal ricefields. FEMS Microbiol. Ecol. 101:217-228.
41. Poole RK, et al. 1996. Nitric oxide, nitrite, and Fnr regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12. J. Bacteriol. 178:5487-5492.
42. Poole RK, Hughes MN. 2000. New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress. Mol. Microbiol. 36:775-783.
43. Rodionov D, Dubchak I, Arkin A, Alm E, Gelfand M. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing deltaproteobacteria. Genome Biol. 5:R90.
44. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
45. Schultz JE, Matin A. 1991. Molecular and functional characterization of a carbon starvation gene of Escherichia coli. J. Mol. Biol. 218:129-140.
46. Spring S, et al. 2009. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T). Stand. Genomic Sci. 1:242-253.
47. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
48. Thompson DK, et al. 2002. Transcriptional and proteomic analysis of a ferric uptake regulator (Fur) mutant of Shewanella oneidensis: possible involvement of Fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl. Environ. Microbiol. 68:881-892.
49. Viamajala S, Peyton BM, Apel WA, Petersen JN. 2002. Chromate/nitrite interactions in Shewanella oneidensis MR-1: evidence for multiple hexavalent chromium [Cr(VI)] reduction mechanisms dependent on physiological growth conditions. Biotechnol. Bioeng. 78:770-778.
50. Vollack K-U, Härtig E, Körner H, Zumft WG. 1999. Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. Mol. Microbiol. 31:1681-1694.
51. Zhou A, et al. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ. Microbiol. 12: 2645-2657.
52. Zhou J, et al. 2011. How sulfate reducing microorganisms cope with stress: lessons from systems biology. Nat. Rev. Microbiol. 9:452-466.
53. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins, p 97-166. In Bryson V, Vogel HJ (ed), Evolving genes and proteins. Academic Press, New York, NY.