Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

PLoS Genetics

Volumn 8, Issue 9, 2012, Pages

  Dufour, Yann S ^a,c   Imam, Saheed ^a   Koo, Byoung Mo ^b   Green, Heather A ^a   Donohue, Timothy J ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REACTIVE OXYGEN METABOLITE; RNA POLYMERASE; SINGLET OXYGEN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR RPOH 1; TRANSCRIPTION FACTOR RPOH 2; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BINDING SITE; DNA REPAIR; DNA SEQUENCE; GENE DUPLICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HEAT SHOCK; NONHUMAN; OXIDATIVE STRESS; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN MOTIF; REGULON; RHODOBACTER SPHAEROIDES; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION;

BASE SEQUENCE; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; HEAT-SHOCK PROTEINS; HEAT-SHOCK RESPONSE; HOT TEMPERATURE; OXIDATIVE STRESS; PROMOTER REGIONS, GENETIC; REACTIVE OXYGEN SPECIES; RHODOBACTER SPHAEROIDES; SIGMA FACTOR; SINGLET OXYGEN; TRANSCRIPTION, GENETIC;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); RHODOBACTER SPHAEROIDES;

EID: 84866951830     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002929     Document Type: Article

References (53)

1. Staron A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, et al. (2009) The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Mol Microbiol.
2. Paget M, Helmann J, (2003) The σ70 family of sigma factors. Genome Biology 4: 203.201-203.206.
3. Guisbert E, Yura T, Rhodius VA, Gross CA, (2008) Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the Escherichia coli Heat Shock Response. Microbiol Mol Biol Rev 72: 545-554.
4. Arsene F, Tomoyasu T, Mogk A, Schirra C, Schulze-Specking A, et al. (1999) Role of region C in regulation of the heat shock gene-specific sigma factor of Escherichia coli, σ32. J Bacteriol 181: 3552-3561.
5. Joo DM, Nolte A, Calendar R, Zhou YN, Jin DJ, (1998) Multiple regions on the Escherichia coli heat shock transcription factor σ32 determine core RNA polymerase binding specificity. J Bacteriol 180: 1095-1102.
6. Wosten M, (1998) Eubacterial sigma-factors. FEMS Microbiology Reviews 22: 127-150.
7. Koo BM, Rhodius VA, Campbell EA, Gross CA, (2009) Dissection of recognition determinants of Escherichia coli σ32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element. Mol Microbiol 72: 815-829.
8. Delory M, Hallez R, Letesson JJ, De Bolle X, (2006) An RpoH-like heat shock sigma factor is involved in stress response and virulence in Brucella melitensis 16 M. J Bacteriol 188: 7707-7710.
9. Ono Y, Mitsui H, Sato T, Minamisawa K, (2001) Two RpoH homologs responsible for the expression of heat shock protein genes in Sinorhizobium meliloti. Molecular and General Genetics 264: 902-912.
10. Oke V, Rushing BG, Fisher EJ, Moghadam-Tabrizi M, Long SR, (2001) Identification of the heat-shock sigma factor RpoH and a second RpoH-like protein in Sinorhizobium meliloti. Microbiology-Sgm 147: 2399-2408.
11. Narberhaus F, Krummenacher P, Fischer HM, Hennecke H, (1997) Three disparately regulated genes for σ32-like transcription factors in Bradyrhizobium japonicum. Molecular Microbiology 24: 93-104.
12. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9: 189-197.
13. Martinez-Salazar JM, Sandoval-Calderon M, Guo XW, Castillo-Ramirez S, Reyes A, et al. (2009) The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses. Microbiology-Sgm 155: 386-397.
14. Green HA, Donohue TJ, (2006) Activity of Rhodobacter sphaeroides RpoHII, a second member of the heat shock sigma factor family. J Bacteriol 188: 5712-5721.
15. Green H (2007) The function of two alternate sigma factors, RpoHI and RpoHII, in Rhodobacter sphaeroides [3278859]. United States - Wisconsin: The University of Wisconsin- Madison. 157 p.
16. Karls RK, Brooks J, Rossmeissl P, Luedke J, Donohue TJ, (1998) Metabolic roles of a Rhodobacter sphaeroides member of the σ2 family. J Bacteriol 180: 10-19.
17. Nuss AM, Glaeser J, Klug G, (2009) RpoHII activates oxidative-stress defense systems and is controlled by RpoE in the singlet oxygen-dependent response in Rhodobacter sphaeroides. J Bacteriol 191: 220-230.
18. Anthony JR, Warczak KL, Donohue TJ, (2005) A transcriptional response to singlet oxygen, a toxic byproduct of photosynthesis. Proc Natl Acad Sci U S A 102: 6502-6507.
19. Dufour YS, Landick R, Donohue TJ, (2008) Organization and evolution of the biological response to singlet oxygen stress. J Mol Biol 383: 713-730.
20. Nuss AM, Glaeser J, Berghoff BA, Klug G, (2010) Overlapping alternative sigma factor regulons in the response to singlet oxygen in Rhodobacter sphaeroides. J Bacteriol.
21. Dufour YS, Kiley PJ, Donohue TJ, (2010) Reconstruction of the core and extended regulons of global transcription factors. PLoS Genet 6: e1001027 doi:10.1371/journal.pgen.1001027.
22. Ind AC, Porter SL, Brown MT, Byles ED, de Beyer JA, et al. (2009) Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl Environ Microbiol 75: 6613-6615.
23. Comolli J, Carl A, Hall C, Donohue TJ, (2002) Transcriptional activation of the Rhodobacter sphaeroides cytochrome c2 gene P2 promoter by the response regulator PrrA. J Bacteriol 184: 390-399.
24. El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M, (2005) Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A 102: 2736-2741.
25. Einhauer A, Jungbauer A, (2001) The FLAG peptide, a versatile fusion tag for the purification of recombinant proteins. J Biochem Biophys Methods 49: 455-465.
26. Price MN, Huang KH, Alm EJ, Arkin AP, (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33: 880-892.
27. MacGregor BJ, Karls RK, Donohue TJ, (1998) Transcription of the Rhodobacter sphaeroides cycA P1 promoter by alternate RNA polymerase holoenzymes. J Bacteriol 180: 1-9.
28. Kourennaia OV, Tsujikawa L, Dehaseth PL, (2005) Mutational analysis of Escherichia coli heat shock transcription factor σ32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition. J Bacteriol 187: 6762-6769.
29. Tittabutr P, Payakapong W, Teaumroong N, Boonkerd N, Singleton PW, et al. (2006) The alternative sigma factor RpoH2 is required for salt tolerance in Sinorhizobium sp. strain BL3. Res Microbiol 157: 811-818.
30. Kaufusi PH, Forsberg LS, Tittabutr P, Borthakur D, (2004) Regulation of exopolysaccharide synthesis in Rhizobium sp. strain TAL1145 involves an alternative sigma factor gene, rpoH2. Microbiology 150: 3473-3482.
31. Hecker M, Pane-Farre J, Volker U, (2007) SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria. Annual Review of Microbiology 61: 215-236.
32. Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R, (2005) Genome-wide analysis of the general stress response network in Escherichia coli: σS-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology 187: 1591-1603.
33. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, et al. (2009) The integrated microbial genomes system: an expanding comparative analysis resource. Nucl Acids Res pp. gkp887.
34. Touati D, (2000) Iron and oxidative stress in bacteria. Arch Biochem Biophys 373: 1-6.
35. Carmel-Harel O, Storz G, (2000) Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. Annual Review of Microbiology 54: 439-461.
36. McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, et al. (2007) High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 25: 584-592.
37. Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA, (2006) Regulon and promoter analysis of the E. coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress. Genes Dev 20: 1776-1789.
38. Sambrook J, Russell DW (2006) The condensed protocols from Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. v, 800 p. p.
39. Sistrom WR, (1960) A requirement for sodium in the growth of Rhodopseudomonas sphaeroides. J Gen Microbiol 22: 778-785.
40. Tavano CL, Podevels AM, Donohue TJ, (2005) Identification of genes required for recycling reducing power during photosynthetic growth. J Bacteriol 187: 5249-5258.
41. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. Vienna, Austria.
42. Bolstad BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Berkeley: University of California- Berkeley.
43. Brettschneider J, Collin F, Bolstad BM, Speed TP, (2008) Quality Assessment for Short Oligonucleotide Microarray Data. Technometrics 50: 241-264.
44. Gentleman R (2005) Bioinformatics and computational biology solutions using R and Bioconductor. New York: Springer. xix, 473 p. p.
45. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
46. Smyth GK (2005) Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer. pp. 397-420.
47. Kuan PF, Chun H, Keles S, (2008) CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput pp. 515-526.
48. Liu X, Brutlag DL, Liu JS, (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput pp. 127-138.
49. Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
50. Crooks GE, Hon G, Chandonia JM, Brenner SE, (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
51. Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
52. Schilke BA, Donohue TJ, (1995) ChrR positively regulates transcription of the Rhodobacter sphaeroides cytochrome c2 gene. J Bacteriol 177: 1929-1937.
53. Heckman KL, Pease LR, (2007) Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc 2: 924-932.