Advertisement

Molecular Genetics and Genomics

, Volume 281, Issue 1, pp 19–33 | Cite as

Control of RpoS in global gene expression of Escherichia coli in minimal media

  • Tao Dong
  • Herb E. SchellhornEmail author
Original Paper

Abstract

RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. coli grown in glucose minimal media using microarray analyses. The expression of over 200 genes was altered by loss of RpoS in exponential and stationary phases, with only 48 genes common to both conditions. The nature of the RpoS-controlled regulon in minimal media was substantially different from that expressed in rich media. Specifically, the expression of many genes encoding regulatory factors (e.g., hfq, csrA, and rpoE) and genes in metabolic pathways (e.g., lysA, lysC, and hisD) were regulated by RpoS in minimal media. In early exponential phase, protein levels of RpoS in minimal media were much higher than that in Luria-Bertani media, which may at least partly account for the observed difference in the expression of RpoS-controlled genes. Expression of genes required for flagellar function and chemotaxis was elevated in the rpoS mutant. Western blot analyses show that the flagella sigma factor FliA was expressed much higher in rpoS mutants than in WT in all phase of growth. Consistent with this, the motility of rpoS mutants was enhanced relative to WT. In conclusion, RpoS and its controlled regulators form a complex regulatory network that mediates the expression of a large regulon in minimal media.

Keywords

Microarray RpoS RpoS regulon Stress response 

Notes

Acknowledgments

This work was supported by a research operating grant from the Canadian Institutes of Health Research (CIHR) to H.E. Schellhorn. We thank C. Joyce and S. Chiang for reviewing the manuscript and R. Yu for technical assistance.

Supplementary material

438_2008_389_MOESM1_ESM.xls (3.4 mb)
Suppmental Table. Transcriptome expression of E. coli wild type and rpoS mutants in exponential phase (OD600 = 0.3) and stationary phase (OD600 = 1.5) in glucose (0.2%) M63 minimal media. StdE: Standard Error (XLS 3508 kb)

References

  1. Ades SE, Connolly LE, Alba BM, Gross CA (1999) The Escherichia coli sigma(E)-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor. Genes Dev 13:2449–2461PubMedCrossRefGoogle Scholar
  2. Baldi P, Hatfield GW (2002) DNA microarrays and gene expression: from experiments to data analysis and modeling. Cambridge University Press, CambridgeGoogle Scholar
  3. Becker G, Klauck E, Hengge-Aronis R (1999) Regulation of RpoS proteolysis in Escherichia coli: the response regulator RssB is a recognition factor that interacts with the turnover element in RpoS. Proc Natl Acad Sci USA 96:6439–6444PubMedCrossRefGoogle Scholar
  4. Bergholz TM, Wick LM, Qi W, Riordan JT, Ouellette LM, Whittam TS (2007) Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium. BMC Microbiol 7:97PubMedCrossRefGoogle Scholar
  5. Bougdour A, Gottesman S (2007) ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc Natl Acad Sci USA 104:12896–12901PubMedCrossRefGoogle Scholar
  6. Costanzo A, Ades SE (2006) Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE, by guanosine 3′, 5′-bispyrophosphate (ppGpp). J Bacteriol 188:4627–4634PubMedCrossRefGoogle Scholar
  7. De Las PA, Connolly L, Gross CA (1997) SigmaE is an essential sigma factor in Escherichia coli. J Bacteriol 179:6862–6864Google Scholar
  8. Dong T, Kirchhof MG, Schellhorn HE (2008) RpoS regulation of gene expression during exponential growth of Escherichia coli K12. Mol Genet Genomics 279:267–277PubMedCrossRefGoogle Scholar
  9. Foster PL (2007) Stress-induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 42:373–397PubMedCrossRefGoogle Scholar
  10. Groat RG, Schultz JE, Zychlinsky E, Bockman A, Matin A (1986) Starvation proteins in Escherichia coli: kinetics of synthesis and role in starvation survival. J Bacteriol 168:486–493PubMedGoogle Scholar
  11. Haugen BJ, Pellett S, Redford P, Hamilton HL, Roesch PL, Welch RA (2007) In vivo gene expression analysis identifies genes required for enhanced colonization of the mouse urinary tract by uropathogenic Escherichia coli strain CFT073 dsdA. Infect Immun 75:278–289PubMedCrossRefGoogle Scholar
  12. Hengge-Aronis R (1993) Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in Escherichia coli. Cell 72:165–168PubMedCrossRefGoogle Scholar
  13. Hengge-Aronis R (2002) Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373–95PubMedCrossRefGoogle Scholar
  14. Ishihama A (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54:499–518PubMedCrossRefGoogle Scholar
  15. Jishage M, Ishihama A (1995) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38. J Bacteriol 177:6832–6835PubMedGoogle Scholar
  16. Kabir MS, Yamashita D, Koyama S, Oshima T, Kurokawa K, Maeda M, Tsunedomi R, Murata M, Wada C, Mori H, Yamada M (2005) Cell lysis directed by sigmaE in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli. Microbiology 151:2721–2735PubMedCrossRefGoogle Scholar
  17. Kanehara K, Ito K, Akiyama Y (2002) YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev 16:2147–2155PubMedCrossRefGoogle Scholar
  18. Karp PD, Paley S, Romero P (2002) The Pathway Tools software. Bioinformatics 18(Suppl 1):S225–S232PubMedGoogle Scholar
  19. Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Bonavides-Martinez C, Ingraham J (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35:7577–7590PubMedCrossRefGoogle Scholar
  20. King T, Ferenci T (2005) Divergent roles of RpoS in Escherichia coli under aerobic and anaerobic conditions. FEMS Microbiol Lett 244:323–327PubMedCrossRefGoogle Scholar
  21. Kobayashi A, Hirakawa H, Hirata T, Nishino K, Yamaguchi A (2006) Growth phase-dependent expression of drug exporters in Escherichia coli and its contribution to drug tolerance. J Bacteriol 188:5693–5703PubMedCrossRefGoogle Scholar
  22. Lacour S, Landini P (2004) SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences. J Bacteriol 186:7186–7195PubMedCrossRefGoogle Scholar
  23. Lange R, Hengge-Aronis R (1991) Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol 5:49–59PubMedCrossRefGoogle Scholar
  24. Lange R, Hengge-Aronis R (1994) The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. Genes Dev 8:1600–1612PubMedCrossRefGoogle Scholar
  25. Lelong C, Aguiluz K, Luche S, Kuhn L, Garin J, Rabilloud T, Geiselmann J (2007) The Crl-RpoS regulon of Escherichia coli. Mol Cell Proteomics 6:648–659PubMedCrossRefGoogle Scholar
  26. Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31–36PubMedCrossRefGoogle Scholar
  27. Liu M, Durfee T, Cabrera JE, Zhao K, Jin DJ, Blattner FR (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280:15921–15927PubMedCrossRefGoogle Scholar
  28. Ma Z, Richard H, Tucker DL, Conway T, Foster JW (2002) Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J Bacteriol 184:7001–7012PubMedCrossRefGoogle Scholar
  29. Mandel MJ, Silhavy TJ (2005) Starvation for different nutrients in Escherichia coli results in differential modulation of RpoS levels and stability. J Bacteriol 187:434–442PubMedCrossRefGoogle Scholar
  30. Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472PubMedCrossRefGoogle Scholar
  31. Masuda N, Church GM (2003) Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol 48:699–712PubMedCrossRefGoogle Scholar
  32. Matin A (1991) The molecular basis of carbon-starvation-induced general resistance in Escherichia coli. Mol Microbiol 5:3–10PubMedCrossRefGoogle Scholar
  33. McCann MP, Kidwell JP, Matin A (1991) The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J Bacteriol 173:4188–4194PubMedGoogle Scholar
  34. Mecsas J, Rouviere PE, Erickson JW, Donohue TJ, Gross CA (1993) The activity of sigma E, an Escherichia coli heat-inducible sigma-factor, is modulated by expression of outer membrane proteins. Genes Dev 7:2618–2628PubMedCrossRefGoogle Scholar
  35. Miller JH (1992) A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  36. Missiakas D, Mayer MP, Lemaire M, Georgopoulos C, Raina S (1997) Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins. Mol Microbiol 24:355–371PubMedCrossRefGoogle Scholar
  37. Muffler A, Fischer D, Hengge-Aronis R (1996) The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev 10:1143–1151PubMedCrossRefGoogle Scholar
  38. Nitta T, Nagamitsu H, Murata M, Izu H, Yamada M (2000) Function of the sigma(E) regulon in dead-cell lysis in stationary-phase Escherichia coli. J Bacteriol 182:5231–5237PubMedCrossRefGoogle Scholar
  39. Nystrom T (2004) Stationary-phase physiology. Annu Rev Microbiol 58:161–181PubMedCrossRefGoogle Scholar
  40. Partridge JD, Scott C, Tang Y, Poole RK, Green J (2006) Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions. J Biol Chem 281:27806–27815PubMedCrossRefGoogle Scholar
  41. Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE (2004) Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics 272:580–591PubMedCrossRefGoogle Scholar
  42. Peterson CN, Mandel MJ, Silhavy TJ (2005) Escherichia coli starvation diets: essential nutrients weigh in distinctly. J Bacteriol 187:7549–7553PubMedCrossRefGoogle Scholar
  43. Phadtare S, Inouye M (2001) Role of CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli. J Bacteriol 183:1205–1214PubMedCrossRefGoogle Scholar
  44. Pratt LA, Silhavy TJ (1996) The response regulator SprE controls the stability of RpoS. Proc Natl Acad Sci USA 93:2488–2492PubMedCrossRefGoogle Scholar
  45. Rahman M, Hasan MR, Oba T, Shimizu K (2006) Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations. Biotechnol Bioeng 94:585–595PubMedCrossRefGoogle Scholar
  46. Romeo T (1998) Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB. Mol Microbiol 29:1321–1330PubMedCrossRefGoogle Scholar
  47. Rouviere PE, De Las PA, Mecsas J, Lu CZ, Rudd KE, Gross CA (1995) rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli. EMBO J 14:1032–1042PubMedGoogle Scholar
  48. Ruiz N, Silhavy TJ (2003) Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion. J Bacteriol 185:5984–5992PubMedCrossRefGoogle Scholar
  49. Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003) Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem 278:29837–29855PubMedCrossRefGoogle Scholar
  50. Sezonov G, Joseleau-Petit D, D’Ari R (2007) Escherichia coli physiology in Luria-Bertani broth. J Bacteriol 189:8746–8749PubMedCrossRefGoogle Scholar
  51. Simon R, Lam A, Li M-C, Ngan M, Menenzes S, Zhao Y (2007) Analysis of gene expression data using BRB-Array Tools. Cancer Inform 2:11–17Google Scholar
  52. Studemann A, Noirclerc-Savoye M, Klauck E, Becker G, Schneider D, Hengge R (2003) Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX. EMBO J 22:4111–4120PubMedCrossRefGoogle Scholar
  53. Tao H, Bausch C, Richmond C, Blattner FR, Conway T (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181:6425–6440PubMedGoogle Scholar
  54. Traxler MF, Chang DE, Conway T (2006) Guanosine 3′, 5′-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli. Proc Natl Acad Sci USA 103:2374–2379PubMedCrossRefGoogle Scholar
  55. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121PubMedCrossRefGoogle Scholar
  56. Typas A, Barembruch C, Possling A, Hengge R (2007) Stationary phase re organisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigma s activity and levels. EMBO J 26:1569–1578PubMedCrossRefGoogle Scholar
  57. Vijayakumar SR, Kirchhof MG, Patten CL, Schellhorn HE (2004) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis. J Bacteriol 186:8499–8507PubMedCrossRefGoogle Scholar
  58. Wang QP, Kaguni JM (1989) A novel sigma factor is involved in expression of the rpoH gene of Escherichia coli. J Bacteriol 171:4248–4253PubMedGoogle Scholar
  59. Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005) Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 187:1591–1603PubMedCrossRefGoogle Scholar
  60. Weichart D, Querfurth N, Dreger M, Hengge-Aronis R (2003) Global role for ClpP-containing proteases in stationary-phase adaptation of Escherichia coli. J Bacteriol 185:115–125PubMedCrossRefGoogle Scholar
  61. Wolfe AJ (2005) The acetate switch. Microbiol Mol Biol Rev 69:12–50PubMedCrossRefGoogle Scholar
  62. Wu Z, Irizarry RA (2004) Preprocessing of oligonucleotide array data. Nat Biotechnol 22:656–658PubMedCrossRefGoogle Scholar
  63. Zhou Y, Gottesman S (1998) Regulation of proteolysis of the stationary-phase sigma factor RpoS. J Bacteriol 180:1154–1158PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of BiologyMcMaster UniversityHamiltonCanada

Personalised recommendations