Molecular Genetics and Genomics

, Volume 279, Issue 3, pp 267–277 | Cite as

RpoS regulation of gene expression during exponential growth of Escherichia coli K12

Original Paper


RpoS is a major regulator of genes required for adaptation to stationary phase in E. coli. However, the exponential phase expression of some genes is affected by rpoS mutation, suggesting RpoS may also have an important physiological role in growing cells. To test this hypothesis, we examined the regulatory role of RpoS in exponential phase using both genomic and biochemical approaches. Microarray expression data revealed that, in the rpoS mutant, the expression of 268 genes was attenuated while the expression of 24 genes was enhanced. Genes responsible for carbon source transport (the mal operon for maltose), protein folding (dnaK and mopAB), and iron acquisition (fepBD, entCBA, fecI, and exbBD) were positively controlled by RpoS. The importance of RpoS-mediated control of iron acquisition was confirmed by cellular metal analysis which revealed that the intracellular iron content of wild type cells was two-fold higher than in rpoS mutant cells. Surprisingly, many previously identified RpoS stationary-phase dependent genes were not controlled by RpoS in exponential phase and several genes were RpoS-regulated only in exponential phase, suggesting the involvement of other regulators. The expression of RpoS-dependent genes osmY, tnaA and malK was controlled by Crl, a transcriptional regulator that modulates RpoS activity. In summary, the identification of a group of exponential phase genes controlled by RpoS reveals a novel aspect of RpoS function.


Regulation RpoS Microarray Stress response Exponential phase 



This work was supported by a research operating grant from the Canadian Institutes of Health Research (CIHR) to H.E.S. We thank Z. Yu, X.W. Wang and C. Lu for technical support and S.M. Chiang and C. Joyce for critically reviewing this manuscript. The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, and are accessible through GEO Series accession number GSE9814.

Supplementary material

438_2007_311_MOESM1_ESM.doc (148 kb)
(DOC 148 kb)
438_2007_311_MOESM2_ESM.xls (124 kb)
(XLS 124 kb)


  1. Alteri CJ, Mobley HL (2007) Quantitative profile of the uropathogenic Escherichia coli outer membrane proteome during growth in human urine. Infect Immun 75:2679–2688PubMedCrossRefGoogle Scholar
  2. Baev MV, Baev D, Radek AJ, Campbell JW (2006) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols, and organic acids with transcriptional microarrays. Appl Microbiol Biotechnol 71:310–316PubMedCrossRefGoogle Scholar
  3. Barnard TJ, Watson ME Jr, McIntosh MA (2001) Mutations in the Escherichia coli receptor FepA reveal residues involved in ligand binding and transport. Mol Microbiol 41:527–536PubMedCrossRefGoogle Scholar
  4. Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11:774–784PubMedCrossRefGoogle Scholar
  5. Boos W, Shuman H (1998) Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol Mol Biol Rev 62:204–229PubMedGoogle Scholar
  6. Bougdour A, Lelong C, Geiselmann J (2004) Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase. J Biol Chem 279:19540–19550PubMedCrossRefGoogle Scholar
  7. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254PubMedCrossRefGoogle Scholar
  8. Chen G, Patten CL, Schellhorn HE (2004) Positive selection for loss of RpoS function in Escherichia coli. Mutat Res 554:193–203PubMedGoogle Scholar
  9. Cheung KJ, Badarinarayana V, Selinger DW, Janse D, Church GM (2003) A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res 13:206–215PubMedCrossRefGoogle Scholar
  10. Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J Biol Chem 281:4802–4815PubMedCrossRefGoogle Scholar
  11. 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
  12. Dahl MK, Manson MD (1985) Interspecific reconstitution of maltose transport and chemotaxis in Escherichia coli with maltose-binding protein from various enteric bacteria. J Bacteriol 164:1057–1063PubMedGoogle Scholar
  13. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640–6645PubMedCrossRefGoogle Scholar
  14. Dippel R, Bergmiller T, Bohm A, Boos W (2005) The maltodextrin system of Escherichia coli: glycogen-derived endogenous induction and osmoregulation. J Bacteriol 187:8332–8339PubMedCrossRefGoogle Scholar
  15. Farewell A, Kvint K, Nystrom T (1998) Negative regulation by RpoS: a case of sigma factor competition. Mol Microbiol 29:1039–1051PubMedCrossRefGoogle Scholar
  16. Fayet O, Ziegelhoffer T, Georgopoulos C (1989) The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures. J Bacteriol 171:1379–1385PubMedGoogle Scholar
  17. Ferguson AD, Hofmann E, Coulton JW, Diederichs K, Welte W (1998a) Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. Science 282:2215–2220PubMedCrossRefGoogle Scholar
  18. Ferguson GP, Creighton RI, Nikolaev Y, Booth IR (1998b) Importance of RpoS and Dps in survival of exposure of both exponential- and stationary-phase Escherichia coli cells to the electrophile N-ethylmaleimide. J Bacteriol 180:1030–1036PubMedGoogle Scholar
  19. Gaal T, Mandel MJ, Silhavy TJ, Gourse RL (2006) Crl facilitates RNA polymerase holoenzyme formation. J Bacteriol 188:7966–7970PubMedCrossRefGoogle Scholar
  20. Gragerov A, Nudler E, Komissarova N, Gaitanaris GA, Gottesman ME, Nikiforov V (1992) Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. Proc Natl Acad Sci USA 89:10341–10344PubMedCrossRefGoogle Scholar
  21. Gyaneshwar P, Paliy O, McAuliffe J, Jones A, Jordan MI, Kustu S (2005) Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. Proc Natl Acad Sci USA 102:3453–3458PubMedCrossRefGoogle Scholar
  22. Hansen UM, McClure WR (1980) Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J Biol Chem 255:9564–9570PubMedGoogle Scholar
  23. Hantash FM, Ammerlaan M, Earhart CF (1997) Enterobactin synthase polypeptides of Escherichia coli are present in an osmotic-shock-sensitive cytoplasmic locality. Microbiology 143(Pt 1):147–156PubMedGoogle Scholar
  24. Hantke K (1990) Dihydroxybenzoylserine–a siderophore for E. coli. FEMS Microbiol Lett 55:5–8PubMedGoogle Scholar
  25. Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852–1858PubMedCrossRefGoogle Scholar
  26. Heitzer A, Mason CA, Snozzi M, Hamer G (1990) Some effects of growth conditions on steady state and heat shock induced htpG gene expression in continuous cultures of Escherichia coli. Arch Microbiol 155:7–12PubMedCrossRefGoogle Scholar
  27. Hengge-Aronis R (1996) Back to log phase: sigma S as a global regulator in the osmotic control of gene expression in Escherichia coli. Mol Microbiol 21:887–893PubMedCrossRefGoogle Scholar
  28. 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
  29. Heyde M, Portalier R (1990) Acid shock proteins of Escherichia coli. FEMS Microbiol Lett 57:19–26PubMedCrossRefGoogle Scholar
  30. Hirsch M, Elliott T (2005) Stationary-phase regulation of RpoS translation in Escherichia coli. J Bacteriol 187:7204–7213PubMedCrossRefGoogle Scholar
  31. Horwich AL, Low KB, Fenton WA, Hirshfield IN, Furtak K (1993) Folding in vivo of bacterial cytoplasmic proteins: role of GroEL. Cell 74:909–917PubMedCrossRefGoogle Scholar
  32. 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
  33. Jishage M, Ishihama A (1998) A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc Natl Acad Sci USA 95:4953–4958PubMedCrossRefGoogle Scholar
  34. Jishage M, Iwata A, Ueda S, Ishihama A (1996) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J Bacteriol 178:5447–5451PubMedGoogle Scholar
  35. Jishage M, Kvint K, Shingler V, Nystrom T (2002) Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270PubMedCrossRefGoogle Scholar
  36. 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 187:1135–1160PubMedCrossRefGoogle Scholar
  37. Khil PP, Camerini-Otero RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol Microbiol 44:89–105PubMedCrossRefGoogle Scholar
  38. Kluck CJ, Patzelt H, Genevaux P, Brehmer D, Rist W, Schneider-Mergener J, Bukau B, Mayer MP (2002) Structure-function analysis of HscC, the Escherichia coli member of a novel subfamily of specialized Hsp70 chaperones. J Biol Chem 277:41060–41069PubMedCrossRefGoogle Scholar
  39. 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
  40. 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
  41. Lange R, Fischer D, Hengge-Aronis R (1995) Identification of transcriptional start sites and the role of ppGpp in the expression of rpoS, the structural gene for the sigma S subunit of RNA polymerase in Escherichia coli. J Bacteriol 177:4676–4680PubMedGoogle Scholar
  42. Lange R, Hengge-Aronis R (1994a) 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
  43. Lange R, Hengge-Aronis R (1994b) The nlpD gene is located in an operon with rpoS on the Escherichia coli chromosome and encodes a novel lipoprotein with a potential function in cell wall formation. Mol Microbiol 13:733–743PubMedCrossRefGoogle Scholar
  44. Lee HJ, Park KJ, Lee AY, Park SG, Park BC, Lee KH, Park SJ (2003) Regulation of fur expression by RpoS and fur in Vibrio vulnificus. J Bacteriol 185:5891–5896PubMedCrossRefGoogle Scholar
  45. 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
  46. 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
  47. Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, Moras D (1998) Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell 95:771–778PubMedCrossRefGoogle Scholar
  48. Lombardo MJ, Aponyi I, Rosenberg SM (2004) General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics 166:669–680PubMedCrossRefGoogle Scholar
  49. Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472PubMedCrossRefGoogle Scholar
  50. Mason CA, Dunner J, Indra P, Colangelo T (1999) Heat-induced expression and chemically induced expression of the Escherichia coli stress protein HtpG are affected by the growth environment. Appl Environ Microbiol 65:3433–3440PubMedGoogle Scholar
  51. Nunoshiba T, Obata F, Boss AC, Oikawa S, Mori T, Kawanishi S, Yamamoto K (1999) Role of iron and superoxide for generation of hydroxyl radical, oxidative DNA lesions, and mutagenesis in Escherichia coli. J Biol Chem 274:34832–34837PubMedCrossRefGoogle Scholar
  52. Nystrom T (2004) Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 54:855–862PubMedCrossRefGoogle Scholar
  53. 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
  54. Pease AJ, Roa BR, Luo W, Winkler ME (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J Bacteriol 184:1359–1369PubMedCrossRefGoogle Scholar
  55. 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
  56. Robbe-Saule V, Lopes MD, Kolb A, Norel F (2007) Physiological effects of Crl in Salmonella are modulated by sigmaS level and promoter specificity. J Bacteriol 189:2976–2987PubMedCrossRefGoogle Scholar
  57. Sammartano LJ, Tuveson RW, Davenport R (1986) Control of sensitivity to inactivation by H2O2 and broad-spectrum near-UV radiation by the Escherichia coli katF (rpoS) locus. J Bacteriol 168:13–21PubMedGoogle Scholar
  58. Schellhorn HE, Audia JP, Wei LI, Chang L (1998) Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli. J Bacteriol 180:6283–6291PubMedGoogle Scholar
  59. Schellhorn HE, Stones VL (1992) Regulation of katF (rpoS) and katE in Escherichia coli K-12 by weak acids. J Bacteriol 174:4769–4776PubMedGoogle Scholar
  60. Schembri MA, Kjaergaard K, Klemm P (2003) Global gene expression in Escherichia coli biofilms. Mol Microbiol 48:253–267PubMedCrossRefGoogle Scholar
  61. Schweder T, Lee KH, Lomovskaya O, Matin A (1996) Regulation of Escherichia coli starvation sigma factor (sigmaS) by ClpXP protease. J Bacteriol 178:470–476PubMedGoogle Scholar
  62. Seputiene V, Daugelavicius A, Suziedelis K, Suziedeliene E (2006) Acid response of exponentially growing Escherichia coli K-12. Microbiol Res 161:65–74PubMedCrossRefGoogle Scholar
  63. Shea CM, McIntosh MA (1991) Nucleotide sequence and genetic organization of the ferric enterobactin transport system: homology to other periplasmic binding protein-dependent systems in Escherichia coli. Mol Microbiol 5:1415–1428PubMedCrossRefGoogle Scholar
  64. Torres AG, Redford P, Welch RA, Payne SM (2001) TonB-dependent systems of uropathogenic Escherichia coli: aerobactin and heme transport and TonB are required for virulence in the mouse. Infect Immun 69:6179–6185PubMedCrossRefGoogle Scholar
  65. 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
  66. Typas A, Barembruch C, Possling A, Hengge R (2007) Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels. EMBO J 26:1569–1578PubMedCrossRefGoogle Scholar
  67. Van Hove B, Staudenmaier H, Braun V (1990) Novel two-component transmembrane transcription control: regulation of iron dicitrate transport in Escherichia coli K-12. J Bacteriol 172:6749–6758PubMedGoogle Scholar
  68. 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
  69. Wassarman KM, Storz G (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell 101:613–623PubMedCrossRefGoogle Scholar
  70. 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

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Tao Dong
    • 1
  • Mark G. Kirchhof
    • 2
  • Herb E. Schellhorn
    • 1
  1. 1.Department of BiologyMcMaster UniversityHamiltonCanada
  2. 2.Robarts Research Institute, Departments of Microbiology and Immunology, and Medicine, The FOCIS Center for Clinical Immunology and ImmunotherapeuticsUniversity of Western OntarioLondonCanada

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