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EcoSal Plus

Domain 5:

Responding to the Environment

Stationary-Phase Gene Regulation in  §

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  • Author: Regine Hengge1
  • Editor: James M. Slauch2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Institut für Biologie—Mikrobiologie, Freie Universität Berlin, 14195 Berlin, Germany.; 2: The Schoold of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL
  • Received 12 May 2011 Accepted 30 August 2011 Published 16 December 2011
  • Address correspondence to Regine HenngeRhenggea@zedat.fu-berlin.de
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  • Abstract:

    In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in depends on the σ (RpoS) subunit of RNA polymerase. σ is closely related to the vegetative sigma factor σ (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σ is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σ levels, which mainly rely on the rapid inhibition of σ proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σ directly or indirectly activates more than 500 genes. Additional signal input is integrated by σ cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σ. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σ is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σ to specific environmental niches.

  • Citation: Hengge R. 2011. Stationary-Phase Gene Regulation in  §, EcoSal Plus 2011; doi:10.1128/ecosalplus.5.6.3

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References

1. Hengge-Aronis R. 1993. Survival of hunger and stress: the role of rpoS in stationary phase gene regulation in Escherichia coli. Cell 72:165–168. [PubMed][CrossRef]
2. Kolter R, Siegele DA, Tormo A. 1993. The stationary phase of the bacterial life cycle. Annu Rev Microbiol 47:855–874. [PubMed][CrossRef]
3. Nyström T. 2004. Stationary-phase physiology. Annu Rev Microbiol 58:161–181. [PubMed][CrossRef]
4. Finkel SE. 2006. Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol 4:113–120. [PubMed][CrossRef]
5. Storz G, Hengge R (ed). 2011. Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
6. Hengge R. 2011. The general stress response in Gram-negative bacteria, p 251–289. In Storz G and Hengge R (ed), Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
7. Hengge-Aronis R. 1996. Regulation of gene expression during entry into stationary phase, p 1497–1512. In Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, and Umbarger HE (ed), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. ASM Press, Washington, DC.
8. Hengge-Aronis R. 2000. The general stress response in Escherichia coli, p 161–178. In Storz G and Hengge-Aronis R (ed), Bacterial Stress Responses. ASM Press, Washington, DC.
9. Jenkins DE, Schultz JE, Matin A. 1988. Starvation-induced cross-protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol 170:3910–3914.[PubMed]
10. Jenkins DE, Chaisson SA, Matin A. 1990. Starvation-induced cross-protection against osmotic challenge in Escherichia coli. J Bacteriol 172:2779–2781.[PubMed]
11. Lange R, Hengge-Aronis R. 1991. Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol 5:49–59. [PubMed][CrossRef]
12. 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 173:4188–4194.[PubMed]
13. Hengge-Aronis R. 1996. Back to log phase: σS as a global regulator in the osmotic control of gene expression in Escherichia coli. Mol Microbiol 21:887–893. [PubMed][CrossRef]
14. Fischer D, Teich A, Neubauer P, Hengge-Aronis R. 1998. The general stress sigma factor σS of Escherichia coli is induced during diauxic shift from glucose to lactose. J Bacteriol 180:6203–6206.[PubMed]
15. Monod J. 1947. The phenomenon of enzymatic adaptation. Growth 11:223–289.
16. 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 103:2374–2379. [PubMed][CrossRef]
17. Price CW. 2011. General stress response in Bacillus subtilis and related Gram-positive bacteria, p 301–318. In Storz G and Hengge R (ed), Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
18. Francez-Charlot A, Frunzke J, Vorholt JA. 2011. The general stress response in alpha-proteobacteria, p 291–300. In Storz G and Hengge R (ed), Bacterial Stress Responses. ASM Press, Washington, DC.
19. Kaper JB, Nataro JP, Mobley HLT. 2004. Pathogenic Escherichia coli. Nat Rev Microbiol 2:123–140. [PubMed][CrossRef]
20. Anderson KL, Whitlock JE, Harwood VJ. 2005. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl Environ Microbiol 71:3041–3048. [PubMed][CrossRef]
21. Davies CM, Long JA, Donald M, Ashbolt NJ. 1995. Survival of fecal microorganisms in marine and freshwater sediments. Appl Environ Microbiol 61:1888–1896.[PubMed]
22. Desmarais TR, Solo-Gabriele HM, Palmer CJ. 2002. Influence of soil on fecal indicator organisms in a tidally influenced subtropical environmental. Appl Environ Microbiol 68:1165–1172. [PubMed][CrossRef]
23. Munro PM, Flatau GN, Clement RL, Gauthier MJ. 1995. Influence of the RpoS (KatF) sigma factor on maintenance of viability and culturability of Escherichia coli and Salmonella typhimurium in seawater. Appl Environ Microbiol 61:1853–1858.[PubMed]
24. Chevance FFV, Hughes KT. 2008. Coordinating assembly of a bacterial macromolecular machine. Nat Rev Microbiol 6:455–465. [PubMed][CrossRef]
25. Costanzo A, Ades S. 2006. Growth phase-dependent regulation of the extracytoplasmic stress factor, sigmaE by guanosine 3′,5′-bispyrophosphate (ppGpp). J Bacteriol 188:4627–4634. [PubMed][CrossRef]
26. Dong T, Yu R, Schellhorn HE. 2011. Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli. Mol Microbiol 79:375–386. [PubMed][CrossRef]
27. Gruber TM, Bryant DA. 1997. Molecular systematic studies of eubacteria, using σ70-type sigma factors of group 1 and 2. J Bacteriol 179:1734–1747.[PubMed]
28. Hengge-Aronis R. 2002. Signal transduction and regulatory mechanisms involved in control of the σS subunit of RNA polymerase in Escherichia coli. Microbiol Mol Biol Rev 66:373–395. [PubMed][CrossRef]
29. Soutourina O, Kolb A, Krin E, Laurent-Winter C, Rimsky S, Danchin A, Bertin P. 1999. Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon. J Bacteriol 181:7500–7508.[PubMed]
30. Wang S, Fleming RT, Westbrook EM, Matsumura P, McKay DB. 2006. Structure of the Escherichia coli FlhDC complex, a prokaryotic heteromeric regulator of transcription. J Mol Biol 355:798–808. [PubMed][CrossRef]
31. Botsford JL, Harman JG. 1992. Cyclic AMP in prokaryotes. Microbiol Rev 56:100–122.[PubMed]
32. Magnusson LU, Farewell A, Nyström T. 2005. ppGpp: a global regulator in Escherichia coli. Trends Microbiol 13:236–242. [PubMed][CrossRef]
33. Pesavento C, Hengge R. 2009. Bacterial nucleotide-based second messengers. Curr Opin Microbiol 12:170–176. [PubMed][CrossRef]
34. Potrykus K, Cashel M. 2008. (p)ppGpp: still magical? Annu Rev Microbiol 62:35–51. [PubMed][CrossRef]
35. Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama A. 1999. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181:6361–6370.[PubMed]
36. Blot N, Mavathur R, Geertz M, Travers A, Muskhelisvili G. 2006. Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep 7:710–715. [PubMed][CrossRef]
37. Barne KA, Bown JA, Busby SJW, Minchin SD. 1997. Region 2.5. of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the “extended” motif at promoters. EMBO J 16:4034–4040. [PubMed][CrossRef]
38. Laurie AD, Bernardo LM, Sze CC, Skarfstad E, Szalewska-Palasz A, Nyström T, Shingler V. 2002. The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase. J Biol Chem 278:1494–1503. [PubMed][CrossRef]
39. Hengge R. 2010. Role of cyclic Di-GMP in the regulatory networks of Escherichia coli, p 230--252. In Wolfe AJ and Visick KL (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC.
40. Jin DJ, Cabrera JE. 2006. Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli. J Struct Biol 156:284–291. [PubMed][CrossRef]
41. Sezonov G, Joseleau-Petit D, D’Ari R. 2007. Escherichia coli physiology in Luria-Bertani broth. J Bacteriol 189:8746–8749. [PubMed][CrossRef]
42. Ferenci T. 2001. Hungry bacteria—definition and properties of a nutritional state. Environ Microbiol 3:605–611. [PubMed][CrossRef]
43. Traxler MF, Zacharia VM, Marquardt S, Summers SM, Nguyen HT, Stark SE, Conway T. 2011. Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the “feast to famine” gradient in Escherichia coli. Mol Microbiol 79:830–845. [PubMed][CrossRef]
44. Holland K, Busby SJ, Lloyd GS. 2007. New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome. FEMS Microbiol Lett 274:89–94. [PubMed][CrossRef]
45. 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 280:15921–15927. [PubMed][CrossRef]
46. Barembruch C, Hengge R. 2007. Cellular levels and activity of the flagellar sigma factor FliA of Escherichia coli are controlled by FlgM-modulated proteolysis. Mol Microbiol 65:76–89. [PubMed][CrossRef]
47. Kalir S, Alon U. 2004. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell 117:713–720. [PubMed][CrossRef]
48. Zhao K, Liu M, Burgess RR. 2007. Adaptation in bacterial flagellar and motility systems: from regulon members to “foraging”-like behavior in E. coli. Nucleic Acids Res 35:4441–4452. [PubMed][CrossRef]
49. Bouveret E, Battesti A. 2011. The stringent response, p 231–250. In Storz G and Hengge R (ed), Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
50. Gentry DR, Hernandez VJ, Nguyen LH, Jensen DB, Cashel M. 1993. Synthesis of the stationary-phase sigma factor sS is positively regulated by ppGpp. J Bacteriol 175:7982–7989.[PubMed]
51. Hirsch M, Elliott T. 2002. Role of ppGpp in rpoS stationary phase regulation in Escherichia coli. J Bacteriol 184:5077–5087. [PubMed][CrossRef]
52. 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 sS subunit of RNA-polymerase in Escherichia coli. J Bacteriol 177:4676–4680.[PubMed]
53. Frye J, Karlinsey JE, Felise HR, Marzolf B, Dowidar N, McClelland M, Hughes KT. 2006. Identification of new flagellar genes of Salmonella enterica serovar typhimurium. J Bacteriol 188:2233–2243. [PubMed][CrossRef]
54. Girgis HS, Liu Y, Ryu WS, Tavazoie S. 2007. A comprehensive genetic characterization of bacterial motility. PLoS Genet 3:e154. [CrossRef]
55. Ohnishi K, Kutsukake K, Suzuki H, Iino T. 1990. Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium. Mol Gen Genet 221:139–147. [PubMed][CrossRef]
56. Pesavento C, Becker G, Sommerfeldt N, Possling A, Tschowri N, Mehlis A, Hengge R. 2008. Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev 22:2434–2446. [PubMed][CrossRef]
57. Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ. 2006. LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli. J Bacteriol 188:3175–3181. [PubMed][CrossRef]
58. Lange R, Hengge-Aronis R. 1994. The cellular concentration of the σS subunit of RNA-polymerase in Escherichia coli is controlled at the levels of transcription, translation and protein stability. Genes Dev 8:1600–1612. [PubMed][CrossRef]
59. 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 279:19540–19550. [PubMed][CrossRef]
60. England P, Westblade LF, Karimova G, Robbe-Saule V, Norel F, Kolb A. 2008. Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery. J Biol Chem 283:33455–33464. [PubMed][CrossRef]
61. Monteil V, Kolb A, Mayer C, Hoos S, England P, Norel F. 2010. Crl binds to domain 2 of σS and confers a competitive advantage on a natural rpoS mutant of Salmonella enterica serovar Typhi. J Bacteriol 192:6401–6410. [PubMed][CrossRef]
62. Pratt LA, Silhavy TJ. 1998. Crl stimulates RpoS activity during stationary phase. Mol Microbiol 29:1225–1236. [PubMed][CrossRef]
63. Typas A, Barembruch C, Hengge R. 2007. Stationary phase reorganisation of the E.coli transcription machinery by Crl protein, a fine-tuner of σS activity and levels. EMBO J 26:1569–1578. [PubMed][CrossRef]
64. 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 95:4953–4958. [PubMed][CrossRef]
65. Jishage M, Ishihama A. 1999. Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D. J Bacteriol 181:3768–3776.[PubMed]
66. Mitchell JE, Oshima T, Piper SE, Webster CL, Westblade LF, Karimova G, Ladant D, Kolb A, Hobman JL, Busby SJ, Lee DJ. 2007. The Escherichia coli regulator of σ70 protein, Rsd, canup-regulate some stress-dependent promoters by sequestering σ70. J Bacteriol 189:3489–3495. [PubMed][CrossRef]
67. Piper SE, Mitchell JE, Lee DJ, Busby SJ. 2009. A global view of Escherichia coli Rsd protein and its interaction. Mol Biosyst 5:1934–1947. [CrossRef]
68. Jishage M, Kvint K, Shingler V, Nyström T. 2002. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270. [PubMed][CrossRef]
69. Grigorova IR, Phleger NJ, Mutalik VK, Gross CA. 2006. Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA. Proc Natl Acad Sci USA 103:5332–5337. [PubMed][CrossRef]
70. Gruber T, Gross CA. 2003. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57:441–466. [PubMed][CrossRef]
71. Maeda H, Fujita N, Ishihama A. 2000. Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res 28:3497–3503. [PubMed][CrossRef]
72. Notley L, Ferenci T. 1996. Induction of RpoS-dependent functions in glucose-limited continuous culture: what level of nutrient limitation induces the stationary phase of Escherichia coli. J Bacteriol 178:1465–1468.[PubMed]
73. Notley-McRobb L, King T, Ferenci T. 2002. rpoS mutations and loss of general stress resistance in Escherichia coli populations as a consequence of conflict between competing stress responses. J Bacteriol 184:806–811. [PubMed][CrossRef]
74. Tomoyasu T, Ohkishi T, Ukyo Y, Tokumitsu A, Takaya A, Suzuki M, Sekiya K, Matsui H, Kutsukake K, Yamamoto T. 2002. The ClpXP ATP-dependent protease regulates flagellum synthesis in Salmonella enterica serovar typhimurium. J Bacteriol 184:645–653. [PubMed][CrossRef]
75. Tomoyasu T, Takaya A, Isogai E, Yamamoto T. 2003. Turnover of FlhD and FlhC, master regulator proteins for Salmonella flagellum biogenesis, by the ATP-dependent ClpXP protease. Mol Microbiol 48:443–452. [PubMed][CrossRef]
76. Chilcott GS, Hughes KT. 2000. Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol Mol Biol Rev 64:694–708. [CrossRef]
77. Adler J, Templeton B. 1967. The effect of environmental conditions on the motility of Escherichia coli. J Gen Microbiol 46:175–184.[PubMed]
78. Amsler CD, Cho M, Matsumura P. 1993. Multiple factors underlying the maximum motility of Escherichia coli as cultures enter post-exponential growth. J Bacteriol 175:6238–6244.[PubMed]
79. Boehm A, Kaiser M, Li H, Spangler C, KCA, Ackerman M, Kaever V, Sourjik V, Roth V, Jenal U. 2010. Second messenger-mediated adjustment of bacterial swimming velocity. Cell 141:107–116. [PubMed][CrossRef]
80. Lange R, Hengge-Aronis R. 1991. Growth phase-regulated expression of bolA and morphology of stationary phase Escherichia coli cells is controlled by the novel sigma factor σS (rpoS). J Bacteriol 173:4474–4481.[PubMed]
81. Santos JM, Lobo M, Matos AP, De Pedro MA, Arraiano CM. 2002. The gene bolA regulates dacA (PBP5), dacC (PBP6) and ampC (AmpC), promoting normal morphology in Escherichia coli. Mol Microbiol 45:1729–1740. [PubMed][CrossRef]
82. Santos JM, Freire P, Vicente M, Arraiano CM. 1999. The stationary-phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth. Mol Microbiol 32:789–798. [PubMed][CrossRef]
83. Patten CL, Kirchhhof MG, Schertzberg MR, Morton RA, Schellhorn HE. 2004. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics 272:580–591. [PubMed][CrossRef]
84. Weber H, Polen T, Heuveling J, Wendisch V, Hengge R. 2005. Genome-wide analysis of the general stress response network in Escherichia coli: σS-dependent genes, promoters and sigma factor selectivity. J Bacteriol 187:1591–1603. [PubMed][CrossRef]
85. Jung JU, Gutierrez C, Martin F, Ardourel M, Villarejo M. 1990. Transcription of osmB, a gene encoding an Escherichia coli lipoprotein, is regulated by dual signals. J Biol Chem 265:10574–10581.[PubMed]
86. Wang A-Y, Cronan JE Jr. 1994. The growth phase-dependent synthesis of cyclopropane fatty acids in Escherichia coli is the result of an RpoS (KatF)-dependent promoter plus enzyme instability. Mol Microbiol 11:1009–1017. [PubMed][CrossRef]
87. Hammar M, Arnquist A, Bian Z, Olsén A, Normark S. 1995. Expression of two csg operons is required for production of fibronectin- and Congo red-binding curli polymers in Escherichia coli K-12. Mol Microbiol 18:661–670. [PubMed][CrossRef]
88. Olsén A, Jonsson A, Normark S. 1989. Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli. Nature 338:652–655. [PubMed][CrossRef]
89. Prigent-Combaret C, Prensier G, Le Thi TT, Vidal Q, Lejeune P, Dorel C. 2000. Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid. Environ Microbiol 2:450–464. [PubMed][CrossRef]
90. Yang S, Lopez CR, Zechiedrich EL. 2006. Quorum sensing and multidrug transporters in Escherichia coli. Proc Natl Acad Sci USA 103:2386–2391. [PubMed][CrossRef]
91. Mandel MJ, Silhavy TJ. 2005. Starvation for different nutrients in Escherichia coli results in differential modulation of RpoS levels and stability. J Bacteriol 187:434–442. [PubMed][CrossRef]
92. Muffler A, Traulsen DD, Lange R, Hengge-Aronis R. 1996. Posttranscriptional osmotic regulation of the σS subunit of RNA polymerase in Escherichia coli. J Bacteriol 178:1607–1613.[PubMed]
93. Bearson SMD, Benjamin WH Jr, Swords WE, Foster JW. 1996. Acid shock induction of RpoS is mediated by the mouse virulence gene mviA of Salmonella typhimurium. J Bacteriol 178:2572–2579.[PubMed]
94. Heuveling J, Possling A, Hengge R. 2008. A role for Lon protease in the control of the acid resistance genes of Escherichia coli. Mol Microbiol 69:534–547. [PubMed][CrossRef]
95. Muffler A, Barth M, Marschall C, Hengge-Aronis R. 1997. Heat shock regulation of σS turnover: a role for DnaK and relationship between stress responses mediated by σS and σ32 in Escherichia coli. J Bacteriol 179:445–452.[PubMed]
96. Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST. 2009. A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS. Proc Natl Acad Sci USA 106:611–616. [PubMed][CrossRef]
97. Repoila F, Majdalani N, Gottesman S. 2003. Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol Microbiol 48:855–861. [PubMed][CrossRef]
98. Sledjeski DD, Gupta A, Gottesman S. 1996. The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in E. coli. EMBO J 15:3993–4000.[PubMed]
99. Loewen PC, Triggs BL. 1984. Genetic mapping of katF, a locus that with katE affects the synthesis of a second catalase species in Escherichia coli. J Bacteriol 160:668–675.[PubMed]
100. Touati E, Dassa E, Boquet PL. 1986. Pleiotropic mutations in appR reduce pH 2.5 acid phosphatase expression and restore succinate utilization in CRP-deficient strains of Escherichia coli. Mol Gen Genet 202:257–264. [PubMed][CrossRef]
101. Sak BD, Eisenstark A, Touati D. 1989. Exonuclease III and the catalase hydroperoxidase II in Escherichia coli are both regulated by the katF product. Proc Natl Acad Sci USA 86:3271–3275. [PubMed][CrossRef]
102. Tuveson RW, Jonas RB. 1979. Genetic control of near-UV (300–400 nm) sensitivity independent of the recA gene in strains of Escherichia coli K-12. Photochem Photobiol 30:667–676. [PubMed][CrossRef]
103. Mulvey MR, Loewen PC. 1989. Nucleotide sequence of katF of Escherichia coli suggest KatF protein is a novel σ transcription factor. Nucleic Acids Res 17:9979–9991. [PubMed][CrossRef]
104. Nguyen LH, Jensen DB, Thompson NE, Gentry DR, Burgess RR. 1993. In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product. Biochemistry 32:11112–11117. [PubMed][CrossRef]
105. Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H. 1993. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, σ38, is a second principal sigma factor of RNA polymerase in stationary phase Escherichia coli. Proc Natl Acad Sci USA 90:3511–3515. [PubMed][CrossRef]
106. Helmann JD. 2011. Regulation by alternative sigma factors, p 31–44. In Storz G and Hengge R (ed), Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
107. Bordes P, Conter A, Moales V, Bouvier J, Kolb A, Gutierrez C. 2003. DNA supercoiling contributes to disconnect σS accumulation from σS-dependent transcription in Escherichia coli. Mol Microbiol 48:561–571. [PubMed][CrossRef]
108. Colland F, Fujita N, Kotlarz D, Ishihama A, Kolb A. 1999. Positioning of σS, the stationary phase σ factor, in Escherichia coli RNA polymerase-promoter open complexes. EMBO J 18:4049–4059. [PubMed][CrossRef]
109. Kusano S, Ding QQ, Fujita N, Ishihama A. 1996. Promoter selectivity of Escherichia coli RNA polymerase Eσ70 and Eσ38 holoenzymes – effect of DNA supercoiling. J Biol Chem 271:1998–2004. [PubMed][CrossRef]
110. Kuznedelov K, Minakhin L, Niedziela-Majka A, Dove SL, Rogulja D, Nickels BE, Hochschild A, Heyduk T, Severinov K. 2002. A role for interaction of the RNA polymerase flap domain with the s subunit in promoter recognition. Science 295:855–857. [PubMed][CrossRef]
111. Ding Q, Kusano S, Villarejo M, Ishihama A. 1995. Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by EσD and EσS holoenzymes. Mol Microbiol 16:649–656. [PubMed][CrossRef]
112. Gralla JD, Vargas DR. 2006. Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation. EMBO J 25:1515–1521. [PubMed][CrossRef]
113. Kim EY, Shin MS, Rhee JH, Choy HE. 2004. Factors influencing preferential utilization of RNA polymerase containing sigma-38 in stationary-phase gene expression in Escherichia coli. J Microbiol 42:103–110.[PubMed]
114. Lee SJ, Gralla JD. 2004. Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol Cell 14:153–162. [PubMed][CrossRef]
115. Ohnuma M, Fujita N, Ishihama A, Tanaka K, Takahashi H. 2000. A carboxy-terminal 16-amino-acid region of σ38 of Escherichia coli is important for transcription under high-salt conditions and sigma activities in vivo. J Bacteriol 182:4628–4631. [PubMed][CrossRef]
116. Rosenthal AZ, Hu M, Gralla JD. 2006. Osmolyte-induced transcription: −35 region elements and recognition by σ38. Mol Microbiol 59:1052–1061. [PubMed][CrossRef]
117. Rosenthal AZ, Kim Y, Gralla JD. 2008. Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons. Mol Microbiol 68. [PubMed][CrossRef]
118. Typas A, Stella S, Johnson RC, Hengge R. 2007. The -35 sequence location and the Fis-sigma factor interface determine σS selectivity of the proP (p2) promoter in Escherichia coli. Mol Microbiol 63:780–796.[PubMed]
119. Vassylyev DG, Sekine S-I, Laptenko O, LJ, Vassylyeva MN, Borukhov S, Yokoyama S. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417:712–719. [PubMed][CrossRef]
120. Gralla JD, Huo YX. 2008. Remodeling and activation of Escherichia coli RNA polymerase by osmolytes. Biochemistry 47:13189–12196. [PubMed][CrossRef]
121. Huo YX, Rosenthal AZ, Gralla JD. 2008. General stress response signalling: unwrapping transcription complexes by DNA relaxation via the sigma38 C-terminal domain. Mol Microbiol 70:369–378. [PubMed][CrossRef]
122. Rosenthal AZ, Kim Y, Gralla JD. 2008. Poising of Escherichia coli RNA polymerase and its release from the sigma38 C-terminal tail for osmY transcription. J Mol Biol 376:938–949. [PubMed][CrossRef]
123. Loewen PC, Hengge-Aronis R. 1994. The role of the sigma factor σS (KatF) in bacterial global regulation. Annu Rev Microbiol 48:53–80. [PubMed][CrossRef]
124. Tanaka K, Kusano S, Fujita N, Ishihama A, Takahashi H. 1995. Promoter determinants for Escherichia coli RNA polymerase holoenzyme containing σ38 (the rpoS gene product). Nucleic Acids Res 23:827–834. [PubMed][CrossRef]
125. Gaal T, Ross W, Estrem ST, Nguyen LH, Burgess RR, Gourse RL. 2001. Promoter recognition and discrimination by EσS RNA polymerase. Mol Microbiol 42:939–954. [PubMed][CrossRef]
126. Hengge-Aronis R. 2002. Stationary phase gene regulation: what makes an Escherichia coli promoter σS-dependent? Curr Opin Microbiol 5:591–595. [PubMed][CrossRef]
127. Typas A, Becker G, Hengge R. 2007. The molecular basis of selective promoter activation by the σS subunit of RNA polymerase. Mol Microbiol 63:1296–1306. [PubMed][CrossRef]
128. Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolívar F. 2009. Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of σ38 in their expression, as a response to carbon limitation. PLoS One 4:e7466. [PubMed][CrossRef]
129. Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ. 2005. Holoenzyme switching and stochastic release of sigma factor from RNA polymerase in vivo. Mol Cell 20:357–366. [PubMed][CrossRef]
130. Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E. 2006. Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol 13:806–814. [PubMed][CrossRef]
131. Bordes P, Repoila R, Kolb A, Gutierrez C. 2000. Involvement of differential efficiency of transcription by EσS and Eσ70 RNA polymerase holenzymes in growth phase regulation of the Escherichia coli osmE promoter. Mol Microbiol 35:845–853. [PubMed][CrossRef]
132. Lacour S, Kolb A, Landini P. 2003. Nucleotides from −16 to −12 determine specific promoter recognition by bacterial σS-RNA polymerase. J Biol Chem 278:37160–37168. [PubMed][CrossRef]
133. Lee SJ, Gralla JD. 2001. Sigma38 (rpoS) RNA polymerase promoter engagement via −10 region nucleotides. J Biol Chem 276:30064–30071. [PubMed][CrossRef]
134. Typas A, Hengge R. 2006. Role of the spacer between the -35 and -10 region in σS promoter selectivity in Escherichia coli. Mol Microbiol 59:1037–1051. [PubMed][CrossRef]
135. Wise A, Brems R, Ramakrishnan V, Villarejo M. 1996. Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E σS. J Bacteriol 178:2785–2793.[PubMed]
136. Solis R, Bertani I, Degrassi G, Devescovi G, Venturi V. 2006. Involvement of quorum sensing and RpoS in rice seedling blight caused by Burkholderia plantarii. FEMS Microbiol Lett 259:106–112. [PubMed][CrossRef]
137. Becker G, Hengge-Aronis R. 2001. What makes an Escherichia coli promoter σS-dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of σS. Mol Microbiol 39:1153–1165. [PubMed][CrossRef]
138. Nguyen LH, Burgess RR. 1997. Comparative analysis of the interactions of Escherichia coli σS and σ70 RNA polymerase holoenzyme with the stationary phase-specific bolAp1 promoter. Biochemistry 36:1748–1754. [PubMed][CrossRef]
139. Haugen SP, Berkmen MB, Ross W, Gourse RL. 2006. rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase. Cell 125:1069–1082. [PubMed][CrossRef]
140. Josaitis CA, Gaal T, Gourse RL. 1995. Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements. Proc Natl Acad Sci USA 92:1117–1121. [PubMed][CrossRef]
141. Ojangu E-L, Tover A, Teras R, Kivisaar M. 2000. Effects of combination of different −10 hexamers and downstream sequences on stationary phase-specific sigma factor σS-dependent transcription in Pseudomonas putida. J Bacteriol 182:6707–6713. [PubMed][CrossRef]
142. Pruteanu M, Hengge-Aronis R. 2002. The cellular level of the recognition factor RssB is rate-limiting for σS proteolysis: Implications for RssB regulation and signal transduction in σS turnover in Escherichia coli. Mol Microbiol 45:1701–1714. [PubMed][CrossRef]
143. Hiratsu K, Shinagawa H, Makino K. 1995. Mode of promoter recognition by the Escherichia coli RNA polymerase holoenzyme containing the σS subunit: identification of the recognition sequence of the fic promoter. Mol Microbiol 18:841–850. [PubMed][CrossRef]
144. Weber H, Pesavento C, Possling A, Tischendorf G, Hengge R. 2006. Cyclic-di-GMP-mediated signaling within the σS network of Escherichia coli. Mol Microbiol 62:1014–1034. [PubMed][CrossRef]
145. Typas A, Hengge R. 2005. Differential ability of σS and σ70 of Escherichia coli to utilize promoters containing half or full UP-element sites. Mol Microbiol 55:250–260. [PubMed][CrossRef]
146. Estrem ST, Ross W, Gaal T, Chen ZWS, Niu W, Ebright RH, Gourse RL. 1999. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase a subunit. Genes Dev 13:2134–2147. [PubMed][CrossRef]
147. Gourse RL, Ross W, Gaal T. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37:687–695. [PubMed][CrossRef]
148. Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL. 1993. A third recognition element in bacterial promoters—DNA binding by the alpha-subunit of RNA polymerase. Science 262:1407–1413. [PubMed][CrossRef]
149. Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H. 2004. The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat Struct Mol Biol 11:551–557. [PubMed][CrossRef]
150. Deighan P, Pukhrambam C, Nickels BE, Hochschild A. 2011. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex. Genes Dev 25:77–88. [PubMed][CrossRef]
151. Nickels BE, Hochschild A. 2004. Regulation of RNA polymerase through the secondary channel. Cell 118:281–284. [PubMed][CrossRef]
152. Ring BZ, Yarnell WS, Roberts JW. 1996. Function of E. coli RNA polymerase sigma factor σ70 in promoter-proximal pausing. Cell 86:485–493. [PubMed][CrossRef]
153. Lim B, Gross CA. 2011. Cellular response to heat shock and cold shock, p 93–114. In Storz G and Hengge R (ed), Bacterial Stress Responses, 2nd ed. ASM Press, Washington, DC.
154. Kolb A, Kotlarz D, Kusano S, Ishihama A. 1995. Selectivity of the E. coli RNA polymerase Eσ38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res 23:819–826. [PubMed][CrossRef]
155. Nickels BE, Dove SL, Murakami KS, Darst SA, Hochschild A. 2002. Protein-protein and protein-DNA interactions of σ70 region 4 involved in transcription activation by lambda cI. J Mol Biol 324:17–34. [PubMed][CrossRef]
156. Santander J, Roland KL, Curtiss R III. 2008. Regulation of Vi capsular polysaccharide synthesis in Salmonella enterica serotype Typhi. J Infect Dev Ctries 2:412–420.
157. Germer J, Becker G, Metzner M, Hengge-Aronis R. 2001. Role of activator site position and a distal UP-element half-site for sigma factor selectivity at a CRP/H -NS activated σS-dependent promoter in Escherichia coli. Mol Microbiol 41:705–716. [PubMed][CrossRef]
158. Brown PK, Dozois CM, Nickerson CA, Zuppardo A, Terlonge J, Curtiss R III. 2001. MlrA, a novel regulator of curli (Agf) and extracellular matrix synthesis by Escherichia coli and Salmonella enterica serovar typhimurium. Mol Microbiol 41:349–363. [PubMed][CrossRef]
159. Brown NL, Stoyanov JV, Kidd SP, Hobman JL. 2003. The MerR family of transcriptional regulators. FEMS Microbiol Rev 27:145–163. [PubMed][CrossRef]
160. Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG. 2002. Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Natl Acad Sci USA 99:13471–13476. [PubMed][CrossRef]
161. Mangan MW, Lucchini S, Danino V, Cróinín TO, Hinton JC, Dorman CJ. 2006. The integration host factor (IHF) integrates stationary-phase and virulence gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol 59:1831–1847. [PubMed][CrossRef]
162. Bouvier J, Gordia S, Kampmann G, Lange R, Hengge-Aronis R, Gutierrez C. 1998. Interplay between global regulators of Escherichia coli: effect of RpoS, H-NS and Lrp on transcription of the gene osmC. Mol Microbiol 28:971–980. [PubMed][CrossRef]
163. Colland F, Barth M, Hengge-Aronis R, Kolb A. 2000. Sigma factor selectivity of Escherichia coli RNA polymerase: a role for CRP, IHF and Lrp transcription factors. EMBO J 19:3028–3037. [PubMed][CrossRef]
164. Landini P, Hajec LI, Nguyen LH, Burgess RR, Volkert MR. 1996. The leucine-responsive regulatory protein (Lrp) acts as a specific repressor for σS-dependent transcription of the Escherichia coli aidB gene. Mol Microbiol 20:947–955. [PubMed][CrossRef]
165. Dorman CJ. 2004. H-NS: a universal regulator for a dynamic genome. Nature Rev Microbiol 2:391–400. [PubMed][CrossRef]
166. Fang FC, Rimsky S. 2008. New insights into transcriptional regulation by H-NS. Curr Opin Microbiol 11:113–120. [PubMed][CrossRef]
167. Arnquist A, Olsén A, Normark S. 1994. σS-dependent growth phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by σ70 in the absence of the nucleoid-associated protein H-NS. Mol Microbiol 13:1021–1032. [PubMed][CrossRef]
168. Barth M, Marschall C, Muffler A, Fischer D, Hengge-Aronis R. 1995. A role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of σS and many σS-dependent genes in Escherichia coli. J Bacteriol 177:3455–3464.[PubMed]
169. Robbe-Saule V, Schaeffer F, Kowarz L, Norel F. 1997. Relationships between H-NS, σS, SpvR and growth phase in the control of spvR, the regulatory gene of the Salmonella plasmid virulence operon. Mol Gen Genet 256:333–347. [PubMed][CrossRef]
170. Shin M, Song M, Rhee JH, Hong Y, Kim YJ, Seok Y-J, Ha KS, Jung SH, Choy HE. 2005. DNA looping-mediated repression by histone-like protein H-NS: specific requirement of E σ70 as a cofactor for looping. Genes Dev 19:2388–2398. [PubMed][CrossRef]
171. Waterman SR, Small PL. 2003. Transcriptional expression of Escherichia coli glutamate-dependent acid resistance genes gadA and gadBC in an hns rpoS mutant. J Bacteriol 185:4644–4647. [PubMed][CrossRef]
172. Grainger DC, Goldberg MD, Lee DJ, Busby SJ. 2008. Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol Microbiol 68:1366–1377. [PubMed][CrossRef]
173. Altuvia S, Almirón M, Huisman G, Kolter R, Storz G. 1994. The dps promoter is activated by OxyR during growth and by IHF and σS in stationary phase. Mol Microbiol 13:265–272. [PubMed][CrossRef]
174. Giangrossi M, Zattoni S, Tramonti A, De Biase D, Falconi M. 2005. Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli. J Biol Chem 280:21498–21505. [PubMed][CrossRef]
175. Metzner M, Germer J, Hengge R. 2004. Multiple stress signal integration in the regulation of the complex σS-dependent csiD-ygaF-gabDTP operon in Escherichia coli. Mol Microbiol 51:799–811. [PubMed][CrossRef]
176. Bougdour A, Cunning C, Baptiste PJ, Elliott T, Gottesman S. 2008. Multiple pathways for regulation of sigmaS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors. Mol Microbiol 68:298–313. [PubMed][CrossRef]
177. Hengge R. 2009. Proteolysis of σS (RpoS) and the general stress response in Escherichia coli. Res Microbiol 160:667–676. [PubMed][CrossRef]
178. Jenal U, Hengge-Aronis R. 2003. Regulation by proteolysis in bacterial cells. Curr Opin Microbiol 6:163–172. [PubMed][CrossRef]
179. Zgurskaya HI, Keyhan M, Matin A. 1997. The σS level in starving Escherichia coli cells increases solely as a result of its increased stability, despite decreased synthesis. Mol Microbiol 24:643–651. [PubMed][CrossRef]
180. Lange R, Hengge-Aronis R. 1994. 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 13:733–743. [PubMed][CrossRef]
181. Uehara T, Parzych KR, Dinh T, Bernhardt TG. 2010. Daughter cell separation is controlled by cytokinetic ring-activated cell wall hydrolysis. EMBO J 29:1412–1422. [PubMed][CrossRef]
182. Takayanagi Y, Tanaka K, Takahashi H. 1994. Structure of the 5′ upstream region and the regulation of the rpoS gene of Escherichia coli. Mol Gen Genet 243:525–531. [PubMed][CrossRef]
183. Ihssen J, Egli T. 2004. Specific growth rate and not cell density controls the general stress response in Escherichia coli. Microbiology 150:1637–1648. [PubMed][CrossRef]
184. Teich A, Meyer S, Lin HY, Andersson L, Enfors SO, Neubauer P. 1999. Growth rate related concentration changes of the starvation response regulators σS and ppGpp in glucose-limited fed-batch and continuous cultures of Escherichia coli. Biotechnol Progr 15:123–129. [PubMed][CrossRef]
185. Mika F, Hengge R. 2005. A two-component phosphotransfer network involving ArcB, ArcA and RssB coordinates synthesis and proteolysis of σS in E. coli. Genes Dev 19:2770–2781. [PubMed][CrossRef]
186. Georgellis D, Kwon O, Lin ECC. 2001. Quinones as the redox signal for the Arc Two-component system of bacteria. Science 292:2314–2315. [PubMed][CrossRef]
187. Malpica R, Franco B, Rodriguez C, Kwon O, Georgellis D. 2004. Identification of quinone-sensitive redox switch in the ArcB sensor kinase. Proc Natl Acad Sci USA 101:13318–13323. [PubMed][CrossRef]
188. Sevcik M, Sebková A, Volf J, Rychlík I. 2001. Transcription of arcA and rpoS during growth of Salmonella typhimurium under aerobic and microaerobic conditions. Microbiology 147:701–708.[PubMed]
189. McCann MP, Fraley CD, Matin A. 1993. The putative s factor KatF is regulated posttranscriptionally during carbon starvation. J Bacteriol 175:2143–2149.[PubMed]
190. Hengge R. 2008. The two-component network and the general stress sigma factor RpoS (σS) in Escherichia coli. Adv Exp Med Biol 631:40–53. [PubMed][CrossRef]
191. Mukhopadhyay S, Audia JP, Roy RN, Schellhorn HE. 2000. Transcriptional induction of the conserved alternative sigma factor RpoS in Escherichia coli is dependent on BarA, a probable two-component regulator. Mol Microbiol 37:371–381. [PubMed][CrossRef]
192. Basineni SR, Madhugiri R, Kolmsee T, Hengge R, Klug G. 2009. The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its target rpoS in E. coli is growth phase dependent. RNA Biol 6:584–594. [PubMed][CrossRef]
193. McCullen CA, Benhammou JN, Majdalani N, Gottesman S. 2010. Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation. J Bacteriol 192:5559–5571. [PubMed][CrossRef]
194. Kolmsee T, Hengge R. 2011. Rare codons play a positive role in the expression of the stationary phase sigma factor RpoS (σS) in Escherichia coli. RNA Biol 8:913–921.
195. Brown L, Elliott T. 1997. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol 179:656–662.[PubMed]
196. Cunning C, Elliott T. 1999. RpoS synthesis is growth rate regulated in Salmonella typhimurium but its turnover is not dependent on acetyl phosphate synthesis or PTS function. J Bacteriol 181:4853–4862.[PubMed]
197. Lease RA, Belfort M. 2000. A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci USA 97:9919–9924. [PubMed][CrossRef]
198. Lease RA, Cusick ME, Belfort M. 1998. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interaction at multiple loci. Proc Natl Acad Sci USA 95:12456–12461. [PubMed][CrossRef]
199. Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S. 1998. DsrA RNA regulates translation of RpoS message by an anti-antisense mechanisms, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci USA 95:12462–12467. [PubMed][CrossRef]
200. Lange R, Barth M, Hengge-Aronis R. 1993. Complex transcriptional control of the σS-dependent stationary phase-induced and osmotically regulated osmY (csi-5) gene suggests novel roles for Lrp, cyclic AMP (cAMP) receptor protein-cAMP complex and integration host factor in the stationary phase response of Escherichia coli. J Bacteriol 175:7910–7917.[PubMed]
201. Brown L, Elliott T. 1996. Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene. J Bacteriol 178:3763–3770.[PubMed]
202. 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 the translational regulation of rpoS in Escherichia coli. Genes Dev 10:1143–1151. [PubMed][CrossRef]
203. Sledjeski DD, Whitman C, Zhang A. 2001. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183:1997–2005. [PubMed][CrossRef]
204. Franze de Fernandez MT, Eoyang L, August JT. 1968. Factor fraction required for the synthesis of bacteriophage Qb RNA. Nature (London) 219:588–590. [PubMed][CrossRef]
205. Tsui H-CT, Leung H-CL, Winkler ME. 1994. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol 13:35–49. [PubMed][CrossRef]
206. Muffler A, Traulsen DD, Fischer D, Lange R, Hengge-Aronis R. 1997. The RNA-binding protein HF-I plays a global regulatory role which is largely, but not exclusively, due to its role in expression of the σS subunit of RNA polymerase in Escherichia coli. J Bacteriol 179:297–300.[PubMed]
207. Vytvytska O, Jakobsen JS, Balcunatie G, Andersen JS, Baccarini M, von Gabain A. 1998. Host factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and regulates its stability. Proc Natl Acad Sci USA 95:14118–14123. [PubMed][CrossRef]
208. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S. 2003. Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:1111–1124. [PubMed][CrossRef]
209. Fender A, Elf J, Hampel K, Zimmermann B, Wagner EGH. 2010. RNAs actively cycle on the Sm-like protein Hfq. Genes Dev 24:2621–2626. [PubMed][CrossRef]
210. Møller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG, Valentin-Hansen P. 2002. Hfq, a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9:23–30. [PubMed][CrossRef]
211. Sauter C, Basquin J, Suck D. 2003. Sm-like protein in eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res 31:4091–4098. [PubMed][CrossRef]
212. Schumacher MA, Pearson RF, Møller T, Valentin-Hansen P, Brennan RG. 2002. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J 21:3546–3556. [PubMed][CrossRef]
213. Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, Feig AL. 2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 11:1206–1214. [PubMed][CrossRef]
214. Olsen AS, Møller-Jensen J, Brennan RG, Valentin-Hansen P. 2010. C-terminally truncated derivatives of Escherichia coli Hfq are proficient in riboregulation. J Mol Biol 404:173–182. [PubMed][CrossRef]
215. Rajkowitsch L, Schroeder R. 2007. Dissecting RNA chaperone activity. RNA 13:2053–2060. [PubMed][CrossRef]
216. Valentin-Hansen P, Eriksen M, Udesen C. 2004. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol 51:1525–1533. [PubMed][CrossRef]
217. Altuvia S, Wagner EGH. 2000. Switching on and off with RNA. Proc Natl Acad Sci USA 97:9824–9826. [PubMed][CrossRef]
218. Gottesman S. 2005. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21:399–404. [PubMed][CrossRef]
219. Gottesman S. 2011. Roles of mRNA stability, translational regulation, and small RNAs in stress response regulation, p 59–74. In Storz G and Hengge R (ed), Bacterial Stress Responses. ASM Press, Washington, DC.
220. Lease RA, Belfort M. 2000. Riboregulation by DsrA RNA: transactions for global economy. Mol Microbiol 38:667–672. [PubMed][CrossRef]
221. Storz G, Altuvia S, Wassarman KM. 2005. An abundance of RNA regulators. Annu Rev Biochem 74:199–217. [PubMed][CrossRef]
222. Storz G, Opdyke JA, Zhang A. 2004. Controlling mRNA stability and translation with small, non-coding RNAs. Curr Opin Microbiol 7:140–144. [PubMed][CrossRef]
223. Sledjeski D, Gottesman S. 1995. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci USA 92:2003–2007. [PubMed][CrossRef]
224. Majdalani N, Chen S, Murrow J, St K. John, Gottesman S. 2001. Regulation of RpoS by a novel small RNA: the characterization of RprA. Mol Microbiol 39:1382–1394. [PubMed][CrossRef]
225. Majdalani N, Hernandez D, Gottesman S. 2002. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol 46:813–826. [PubMed][CrossRef]
226. Mandin P, Gottesman S. 2010. Integrating anaerobic/aer obic sensing and the general stress response through the ArcZ small RNA. EMBO J 29:3094–3104. [PubMed][CrossRef]
227. Arluison V, Hohng S, Roy R, Pellegrini O, Régnier P, Ha T. 2007. Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by small non-conding RNA. Nucleic Acids Res 35:999–1006. [PubMed][CrossRef]
228. Updegrove T, Wilf N, Sun X, Wartell RM. 2008. Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5´rpoS mRNA leader region. Biochemistry 47:11184–11195. [PubMed][CrossRef]
229. Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA. 2010. Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci USA 107:9602–9607. [PubMed][CrossRef]
230. Vecerek B, Beich-Frandsen M, Resch A, Bläsi U. 2010. Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding. Nucleic Acids Res 38:1284–1293. [PubMed][CrossRef]
231. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R, Storz G. 1998. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 17:6061–6068. [PubMed][CrossRef]
232. Altuvia S, Weinstein-Fischer D, Zhang A, Postow L, Storz G. 1997. A small, stable RNA induced by oxidative stress: roles as a pleiotropic regulator and antimutator. Cell 90:43–53. [PubMed][CrossRef]
233. Resch A, Vecerek B, Palavra K, Bläsi U. 2010. Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA. RNA Biol 7:96–102. [CrossRef]
234. Cohen-Or I, Shenhar Y, Biran D, Ron EZ. 2010. CspC regulates rpoS transcript levels and complements hfq deletions. Res Microbiol 161:694–700. [PubMed][CrossRef]
235. Phadtare S, Inouye M. 2001. Role CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli. J Bacteriol 183:1205–1214. [PubMed][CrossRef]
236. Balandina A, Claret L, Hengge-Aronis R, Rouvière-Yaniv J. 2001. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol Microbiol 39:1069–1079. [PubMed][CrossRef]
237. Yamashino T, Ueguchi C, Mizuno T. 1995. Quantitative control of the stationary phase-specific sigma factor, σS, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J 14:594–602.[PubMed]
238. Bonnefoy E, Rouviere-Yaniv J. 1991. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J 10:687–696.[PubMed]
239. Claret L, Rouvière-Yaniv J. 1997. Variation in HU composition during growth of E. coli: the heterodimer is required for long term survival. J Mol Biol 273:93–104. [PubMed][CrossRef]
240. Zhou Y, Gottesman S. 2006. Modes of regulation of RpoS by H-NS. J Bacteriol 188:7022–7025. [PubMed][CrossRef]
241. Klauck E, Böhringer J, Hengge-Aronis R. 1997. The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA. Mol Microbiol 25:559–569. [PubMed][CrossRef]
242. Ranquet C, Gottesman S. 2007. Translational regulation of the Escherichia coli stress factor RpoS: a role for SsrA and Lon. J Bacteriol 189:4872–4879. [PubMed][CrossRef]
243. Rockabrand D, Arthur T, Korinek G, Livers K, Blum P. 1995. An essential role for the Escherichia coli DnaK protein in starvation-induced thermotolerance, H2O2 resistance, and reductive division. J Bacteriol 177:3695–3703.[PubMed]
244. Rockabrand D, Livers K, Austin T, Kaiser R, Jensen D, Burgess R, Blum P. 1998. Roles of DnaK and RpoS in starvation-induced thermotolerance of Escherichia coli. J Bacteriol 180:846–854.[PubMed]
245. Ueguchi C, Misonou N, Mizuno T. 2001. Negative control of rpoS expression by phosphoenolpyruvate: carbohydrate phosphotransferase system in Escherichia coli. J Bacteriol 183:520–527. [PubMed][CrossRef]
246. Böhringer J, Fischer D, Mosler G, Hengge-Aronis R. 1995. UDP-glucose is a potential intracellular signal molecule in the control of expression of σS and σS-dependent genes in Escherichia coli. J Bacteriol 177:413–422.[PubMed]
247. Peterson CN, Mandel MJ, Silhavy TJ. 2005. Escherichia coli starvation diets: essential nutrients weigh in distinctly. J Bacteriol 187:7549–7553. [PubMed][CrossRef]
248. Schweder T, Lee K-H, Lomovskaya O, Matin A. 1996. Regulation of Escherichia coli starvation sigma factor (σ38) by ClpXP protease. J Bacteriol 178:470–476.[PubMed]
249. Muffler A, Fischer D, Altuvia S, Storz G, Hengge-Aronis R. 1996. The response regulator RssB controls stability of the σS subunit of RNA polymerase in Escherichia coli. EMBO J 15:1333–1339.[PubMed]
250. Pratt LA, Silhavy TJ. 1996. The response regulator, SprE, controls the stability of RpoS. Proc Natl Acad Sci USA 93:2488–2492. [PubMed][CrossRef]
251. Zhou AN, Gottesman S. 1998. Regulation of proteolysis of the stationary-phase sigma factor RpoS. J Bacteriol 180:1154–1158.[PubMed]
252. 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 96:6439–6444. [PubMed][CrossRef]
253. Becker G, Klauck E, Hengge-Aronis R. 2000. The response regulator RssB, a recognition factor for σS proteolysis in Escherichia coli, can act like an anti-σS factor. Mol Microbiol 35:657–666. [PubMed][CrossRef]
254. Klauck E, Lingnau M, Hengge-Aronis R. 2001. Role of the response regulator RssB in σS recognition and initiation of σS proteolysis in Escherichia coli. Mol Microbiol 40:1381–1390. [PubMed][CrossRef]
255. Moreno M, Audia JP, Bearson SMD, Webb C, Foster JW. 2000. Regulation of sigma-S degradation in Salmonella enterica serovar typhimurium: in vivo interactions between sigma-S, the response regulator MviA (RssB) and ClpX. J Mol Microbiol Biotechnol 2:245–254.[PubMed]
256. Zhou Y, Gottesman S, Hoskins JR, Maurizi MR, Wickner S. 2001. The RssB response regulator directly targets σS for degradation by ClpXP. Genes Dev 15:627–637. [PubMed][CrossRef]
257. Stüdemann A, Noirclerc-Savoye M, Klauck E, Becker G, Schneider D, Hengge R. 2003. Sequential recognition of two distinct sites in σS by the proteolytic targeting factor RssB and ClpX. EMBO J 22:4111–4120. [PubMed][CrossRef]
258. Peterson CN, Ruiz N, Silhavy TJ. 2004. RpoS proteolysis is regulated by a mechanism that does not require the SprE (RssB) response regulator phosphorylation site. J Bacteriol 186:7403–7410. [PubMed][CrossRef]
259. Bouché, S, Klauck E, Fischer D, Lucassen M, Jung K, Hengge-Aronis R. 1998. Regulation of RssB-dependent proteolysis in Escherichia coli: a role for acetyl phosphate in a response regulator-controlled process. Mol Microbiol 27:787–795. [PubMed][CrossRef]
260. Hengge R, Turgay K. 2009. Proteolysis in prokaryotes—from molecular machines to a systems perspective. Res Microbiol 160:615–617. [PubMed][CrossRef]
261. Baker TA, Sauer RT. 2006. ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci 31:647–653. [PubMed][CrossRef]
262. Kress W, Maglica Z, Weber-Ban E. 2009. Clp chaperone-proteases: structure and function. Res Microbiol 160:618–628. [PubMed][CrossRef]
263. Klein AH, Shulla A, Reimann SA, Keating DH, Wolfe AJ. 2007. The intracellular concentration of acetyl phosphate in Escherichia coli is sufficient for direct phosphorylation of two-component response regulators. J Bacteriol 189:5574–5581. [PubMed][CrossRef]
264. McCleary WR, Stock JB. 1994. Acetyl phosphate and the activation of two-component response regulators. J Biol Chem 269:31567–31572.[PubMed]
265. Malpica R, Sandoval GR, Rodriguez C, Franco B, Georgellis D. 2006. Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression. Antioxid Redox Signal 8:781–795. [PubMed][CrossRef]
266. Ruiz N, Peterson CN, Silhavy TJ. 2001. RpoS-dependent transcriptional control of sprE : regulatory feedback loop. J Bacteriol 183:5974–5981. [PubMed][CrossRef]
267. Badger JL, Miller VL. 1995. Role of RpoS in survival of Yersinia enterocolitica to a variety of environmental stresses. J Bacteriol 177:5370–5373.[PubMed]
268. Bougdour A, Wickner S, Gottesman S. 2006. Modulating RssB activity: IraP, a novel regulator of σS stability in Escherichia coli. Genes Dev 20:884–897. [PubMed][CrossRef]
269. Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA. 2006. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proc Natl Acad Sci USA 103:13503–13508. [PubMed][CrossRef]
270. Eguchi Y, Ishii E, Hata K, Utsumi R. 2010. Regulation of acid resistance by connectors of two-component signal transduction systems in Escherichia coli. J Bacteriol 193:1222–1228. [PubMed][CrossRef]
271. Mitrophanov AY, Groisman EA. 2008. Signal integration in bacterial two-component regulatory systems. Genes Dev 22:2601–2611. [PubMed][CrossRef]
272. Frederiksson A, Ballesteros M, Peterson CN, Persson O, Silhavy TJ, Nyström T. 2007. Decline in ribosomal fidelity contributes to the accumulation and stabilization of master stress response regulator sigmaS upon carbon starvation. Genes Dev 21:862–874. [PubMed][CrossRef]
273. Martin A, Baker TA, Sauer RT. 2008. Protein unfolding by a AAA+ protease is dependent on ATP hydrolysis rates and substrate energy landscapes. Nat Struct Mol Biol 15:139–145. [PubMed][CrossRef]
274. Holland A-M, Rather PN. 2008. Evidence for extracellular control of RpoS proteolysis in Escherichia coli. FEMS Microbiol Lett 286:50–59. [PubMed][CrossRef]
275. Jasieki J, Wegrzyn G. 2003. Growth-rate dependent RNA polyadenylation in Escherichia coli. EMBO Rep 4:172–177. [PubMed][CrossRef]
276. Santos JM, Freire P, Mika F, Hengge R, Arraiano CM. 2006. Bacterial polyadenylation links transcription with mRNA degradation via σS proteolysis. Mol Microbiol 60:177–188. [PubMed][CrossRef]
277. Carabetta VJ, Mohanty BK, Kushner SR, Silhavy TJ. 2009. The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J Bacteriol 191:6812–6821. [PubMed][CrossRef]
278. Carabetta VJ, Silhavy TJ, Cristea IM. 2010. Teh response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. J Bacteriol 192:3713–3721. [PubMed][CrossRef]
279. Ishihama A. 2000. Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54:499–518. [PubMed][CrossRef]
280. 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 178:5447–5451.[PubMed]
281. Ilag LL, Westblade LF, Deshayes C, Kolb A, Busby SJ, Robinson CV. 2004. Mass spectrometry of Escherichia coli RNA polymerase: interactions of the core enzyme with sigma70 and Rsd protein. Structure (Camb.) 12:269–275.[PubMed]
282. Wassarman KM, Storz G. 2000. 6S RNA regulates E. coli RNA polymerase activity. Cell 101:613–623. [PubMed][CrossRef]
283. Arnquist A, Olsén A, Pfeifer J, Russell DG, Normark S. 1992. The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101. Mol Microbiol 6:2443–2452. [PubMed][CrossRef]
284. Robbe-Saule V, Lopes MD, Kolb A, Norel F. 2007. Physiological effects of Crl in Salmonella are modulated by σS level and promoter specificity. J Bacteriol 189:2976–2987. [PubMed][CrossRef]
285. Robbe-Saule V, Jaumouille V, Prevost MC, Guadagnini S, Talhouarne C, Mathout H, Kolb A, Norel F. 2006. Crl activates transcription initiation of RpoS-regulated genes involved in the multicellular behavior of Salmonella enterica serovar typhimurium. J Bacteriol 188:3983–3994. [PubMed][CrossRef]
286. Gaal T, Mandel MJ, Silhavy TJ, Gourse RL. 2006. Crl facilitates RNA polymerase holoenzyme formation. J Bacteriol 188:7966–7970. [PubMed][CrossRef]
287. Lee CR, Cho SH, Kim HJ, Peterkofsky A, Seok Y-J. 2010. Potassium mediates Escherichia coli enzyme IIA(Ntr)-dependent regulation of sigma factor selectivity. Mol Microbiol 78:1468–1483. [PubMed][CrossRef]
288. Dong T, Schellhorn HE. 2009. Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933. BMC Genomics 3:349. [CrossRef]
289. Lacour S, Landini P. 2004. σS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of σS-dependent genes and identification of their promoter sequences. J Bacteriol 186:7186–7195. [PubMed][CrossRef]
290. Brombacher E, Baratto A, Dorel C, Landini P. 2006. Gene expression regulation by the curli activator CsgD protein: modulation of cellulose biosynthesis and control of negative determinants for microbial adhesion. J Bacteriol 188:2027–2037. [PubMed][CrossRef]
291. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. 2002. Network motifs: simple building blocks of complex networks. Science 298:824–827. [PubMed][CrossRef]
292. Shen-Orr SS, Milo R, Mangan S, Alon U. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64–68. [PubMed][CrossRef]
293. Brombacher E, Dorel C, Zehnder AJB, Landini P. 2003. The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli. Microbiology 149:2847–2857. [PubMed][CrossRef]
294. Prigent-Combaret C, Brombacher E, Vidal O, Ambert A, Lejeune P, Landini P, Dorel C. 2001. Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene. J Bacteriol 2001:7213–7223. [CrossRef]
295. Römling U, Rohde M, Olsén A, Normark S, Reinköster J. 2000. AgfD, the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways. Mol Microbiol 36:10–23. [PubMed][CrossRef]
296. Römling U, Sierralta WD, Eriksson K, Normark S. 1998. Multicellular and aggregative behaviour of Salmonella typhimurium strains is controlled by mutations in the agfD promoter. Mol Microbiol 28:249–264. [PubMed][CrossRef]
297. Römling U. 2005. Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae. Cell Mol Life Sci 62:1234–1246. [PubMed][CrossRef]
298. Sommerfeldt N, Possling A, Becker G, Pesavento C, Tschowri N, Hengge R. 2009. Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli. Microbiology 155:1318–1331. [PubMed][CrossRef]
299. Hengge R. 2009. Principles of cyclic-di-GMP signaling. Nat Rev Microbiol 7:263–273. [PubMed][CrossRef]
300. Jenal U, Malone J. 2006. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet 40:385–407. [PubMed][CrossRef]
301. Jenal U. 2004. Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria? Curr Opin Microbiol 7:185–191. [PubMed][CrossRef]
302. Römling U, Amikam D. 2006. Cyclic di-GMP as a second messenger. Curr Opin Microbiol 9:218–228. [PubMed][CrossRef]
303. Römling U, Gomelsky M, Galperin MY. 2005. C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 57:629–639. [PubMed][CrossRef]
304. Ko M, Park C. 2000. Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. J Mol Biol 303:371–382. [PubMed][CrossRef]
305. Rychlik I, Martin G, Methner U, Lovell M, Cardova L, Sebkova A, Sevcik M, Damborsky J, Barrow PA. 2002. Identification of Salmonella enterica serovar Typhimurium genes associated with growth suppression in stationary-phase nutrient broth cultures and in the chicken intestine. Arch Microbiol 178:411–420. [PubMed][CrossRef]
306. Jubelin G, Vianney A, Beloin C, Ghigo JM, Lazzaroni JC, Lejeune P, Dorel C. 2005. CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli. J Bacteriol 187:2038–2049. [PubMed][CrossRef]
307. Vidal O, Longin R, Prigent-Combaret C, Dorel C, Heooreman M, Lejeune P. 1998. Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression. J Bacteriol 180:2442–2449.[PubMed]
308. Tschowri N, Busse S, Hengge R. 2009. The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue light response of E. coli. Genes Dev 23:522–534. [PubMed][CrossRef]
309. Foster JW. 2004. Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2:898–907. [PubMed][CrossRef]
310. Opdyke JA, Kang J-G, Storz G. 2004. GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 186:6698–6705. [PubMed][CrossRef]
311. Tramonti A, De Canio M, De Biase D. 2008. GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Mol Microbiol 70:965–982.[PubMed]
312. Richard H, Foster JW. 2007. Sodium regulates Escherichia coli acid resistance, and influences GadX- and GadW-dependent activation of gadE. Microbiology 153:3154–3161. [PubMed][CrossRef]
313. Shin S, Castanie-Cornet M-P, Foster JW, Crawford JA, Brinkley C, Kaper JB. 2001. An activator glutamate decarboxylate genes regulates the expression of enteropathogenic Escherichia coli virulence genes through control of the plasmid-encoded regulator, Per. Mol Microbiol 41:1133–1150. [PubMed][CrossRef]
314. Tramonti A, De Canio M, Delany I, Scarlato V, De Biase D. 2006. Mechanisms of transcription activation exerted by GadX and GadW at the gadA and gadBC gene promoters of the glutamate-based acid resistance system in Escherichia coli. J Bacteriol 188:8118–8127. [PubMed][CrossRef]
315. Tramonti A, Visca P, De Canio M, Falconi M, De Biase D. 2002. Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol 184:2603–2613. [PubMed][CrossRef]
316. Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T. 2003. Genes of the GadX-GadW regulon in Escherichia coli. J Bacteriol 185:3190–3201. [PubMed][CrossRef]
317. 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 184:7001–7012. [PubMed][CrossRef]
318. Ma Z, Gong S, Richard H, Tucker DL, Conway T, Foster JW. 2003. GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Mol Microbiol 49:1309–1320. [PubMed][CrossRef]
319. Vanaja SK, Bergholz TM, Whittam TS. 2009. Characterization of the Escherichia coli O157:H7 Sakai GadE regulon. J Bacteriol 191:1868–1877. [PubMed][CrossRef]
320. Castanié-Cornet M-P, Treffandier H, Francez-Charlot A, Gutierrez C, Cam K. 2007. The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF. Microbiology 153:238–246. [PubMed][CrossRef]
321. Castanié-Cornet M-P, Cam K, Bastiat B, Cros A, Bordes P, Gutierrez C. 2010. Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE. Nucleic Acids Res 38:3546–3554. [PubMed][CrossRef]
322. Krin E, Danchin A, Soutourina O. 2010. Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli. BMC Microbiol 10:273. [PubMed][CrossRef]
323. Krin E, Danchin A, Soutourina O. 2010. RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli. Res Microbiol 161:363–371. [PubMed][CrossRef]
324. Lee J, Page R, García-Contreras R, Palermino J-M, Zhang X-S, Doshi O, Wood TK, Peti W. 2007. Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid resistance. J Mol Biol 373:11–26. [PubMed][CrossRef]
325. Ma Z, Masuda N, Foster JW. 2004. Characterization of the EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli. J Bacteriol 186:7378–7389. [PubMed][CrossRef]
326. Masuda N, Church GM. 2002. Escherichia coli gene expression responsive to levels of the response regulator EvgA. J Bacteriol 184:6225–6234. [PubMed][CrossRef]
327. Masuda N, Church GM. 2003. Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol 48:699–712. [PubMed][CrossRef]
328. Nyström T, Larsson C, Gustafsson L. 1996. Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis. EMBO J 15:3219–3228.[PubMed]
329. Gualdi L, Tagliabue L, Landini P. 2007. Biofilm formation-gene expression relay system in Escherichia coli: modulation of σS-dependent gene expression by the CsgD regulatory protein via σS protein stabilization. J Bacteriol 189:8034–8043. [PubMed][CrossRef]
330. Gérard F, Dri AM, Moreau PL. 1999. Role of Escherichia coli RpoS, LexA, and H-NS global regulators in metabolism and survival under aerobic, phosphate-starvation conditions. Microbiology 145:1547–1562. [PubMed][CrossRef]
331. Hengge-Aronis R, Klein W, Lange R, Rimmele M, Boos W. 1991. Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary phase thermotolerance in Escherichia coli. J Bacteriol 173:7918–7924.[PubMed]
332. Kabir MS, Sagara T, Oshima T, Kawagoe Y, Mori H, Tsunedomi R, Yamada M. 2004. Effects of mutations in the rpoS gene on cell viability and global gene expression under nitrogen starvation in Escherichia coli. Microbiology 150:2543–2553.[PubMed]
333. Small P, Blankenhorn D, Welty D, Zinser E, Slonczewski JL. 1994. Acid and base resistance in Escherichia coli and Shigella flexneri: role of rpoS and growth pH. J Bacteriol 176:1729–1737.[PubMed]
334. Cheville AM, Arnold KW, Buchrieser C, Cheng CM, Kaspar CW. 1996. rpoS regulation of acid, heat, and salt tolerance in Escherichia coli O157:H7. Appl Environ Microbiol 62:1822–1824.[PubMed]
335. Dodd CE, Aldsworth TG. 2002. The importance of RpoS in the survival of bacteria through food processing. Int J Food Microbiol 74:189–194. [PubMed][CrossRef]
336. Gong L, Takayama K, Kjelleberg S. 2002. Role of spoT-dependent ppGpp accumulation in the survival of light-exposed starved bacteria. Microbiology 148:559–570.[PubMed]
337. Price SB, Cheng C-M, Kaspar CW, Wright JC, DeGraves FJ, Penfound TA, Castanié-Cornet M-P, Foster JW. 2000. Role of rpoS in acid resistance and fecal shedding of Escherichia coli O157:H7. Appl Environ Microbiol 66:632–637. [PubMed][CrossRef]
338. Rychlik I, Barrow PA. 2005. Salmonella stress management and its relevance to behaviour during intestinal colonisation and infection. FEMS Microbiol Rev 29:1021–1040. [PubMed][CrossRef]
339. Dong T, Schellhorn HE. 2009. Control of RpoS in global gene expression of Escherichia coli in minimal medium. Mol Genet Genomics 281:19–31. [PubMed][CrossRef]
340. Farewell A, Kvint K, Nyström T. 1998. Negative regulation by RpoS: a case of sigma factor competition. Mol Microbiol 29:1039–1051. [PubMed][CrossRef]
341. Germer J, Muffler A, Hengge-Aronis R. 1998. Trehalose is not relevant for in vivo activity of σS-containing RNA polymerase in Escherichia coli. J Bacteriol 180:1603–1606.[PubMed]
342. Kaasen I, Falkenberg P, Styrvold OB, Strøm AR. 1992. Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by KatF (AppR). J Bacteriol 174:889–898.[PubMed]
343. Stokes NR, Murray HD, Subramaniam C, Gourse RL, Louis P, Bartlett W, Miller S, Booth IR. 2003. A role for mechanosensitive channels in survival of stationary phase: regulation of channel expression by RpoS. Proc Natl Acad Sci USA 100:15959–15964. [PubMed][CrossRef]
344. Weber A, Kögl SA, Jung K. 2006. Time-dependent proteome alterations under osmotic stress during aerobic and anaerobic growth in Escherichia coli. J Bacteriol 188:7165–7175. [PubMed][CrossRef]
345. Boos W, Ehmann U, Forkl H, Klein W, Rimmele M, Postma P. 1990. Trehalose transport and metabolism in Escherichia coli. J Bacteriol 172:3450–3461.[PubMed]
346. Kaasen I, McDougall J, Strøm AR. 1994. Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phosphate synthase/phosphatase complex. Gene 145:9–15. [PubMed][CrossRef]
347. Strøm, AR, Kaasen I. 1993. Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression. Mol Microbiol 8:205–210. [PubMed][CrossRef]
348. Gutierrez C, Barondess J, Manoil C, Beckwith J. 1987. The use of transposon TnphoA to detect genes for cell envelope proteins subject to a common regulatory stimulus. J Mol Biol 195:289–297. [PubMed][CrossRef]
349. Barron A, May G, Bremer E, Villarejo M. 1986. Regulation of envelope protein composition during adaptation to osmotic stress in Escherichia coli. J Bacteriol 167:433–438.[PubMed]
350. Weichart D, Lange R, Henneberg N, Hengge-Aronis R. 1993. Identification and characterization of stationary phase-inducible genes in Escherichia coli. Mol Microbiol 10:407–420. [PubMed][CrossRef]
351. Yim HH, Villarejo M. 1992. osmY, a new hyperosmotically inducible gene, encodes a periplasmic protein in Escherichia coli. J Bacteriol 174:3637–3644.[PubMed]
352. Yim HH, Brems RL, Villarejo M. 1994. Molecular characterization of the promoter of osmY, an rpoS dependent gene. J Bacteriol 176:100–107.[PubMed]
353. Checroun C, Gutierrez C. 2004. σS-dependent regulation of yehZYXW, which encodes a putative osmoprotectant ABC transporter of Escherichia coli. FEMS Microbiol Lett 236:221–226.[PubMed]
354. Conter A, Gangneux C, Suzanne M, Gutierrez C. 2001. Survival of Escherichia coli during long-term starvation: effects of aeration, NaCl, and the rpoS and osmC gene products. Res Microbiol 152:17–26. [PubMed][CrossRef]
355. Gordia S, Gutierrez C. 1996. Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12. Mol Microbiol 19:729–736. [PubMed][CrossRef]
356. Gutierrez C, Devedjian JC. 1991. Osmotic induction of gene osmC expression in Escherichia coli. J Mol Biol 220:959–973. [PubMed][CrossRef]
357. Lesniak J, Barton WA, Nikolov DB. 2003. Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC. Protein Sci 12:2838–2843. [PubMed][CrossRef]
358. Berney M, Weilenmann HU, Ihssen J, Bassin C, Egli T. 2006. Specific growth rate determines the sensitivity of Escherichia coli to thermal, UVA, and solar disinfection. Appl Environ Microbiol 72:2586–2593. [PubMed][CrossRef]
359. Bucheli-Witschel M, Bassin C, Egli T. 2010. UV-C inactivation in Escherichia coli is affected by growth conditions preceding irradiation, in particular by the specific growth rate. J Appl Microbiol 109:1733–1744.[PubMed]
360. Dukan S, Nyström T. 1998. Bacterial senescence: stasis results in increased and differential oxidation of cytoplasmic proteins leading to developmental induction of the heat shock regulon. Genes Dev 12:3431–3441. [PubMed][CrossRef]
361. Eisenstark A, Calcutt MJ, Becker-Hapak M, Ivanova A. 1999. Role of Escherichia coli rpoS and associated genes in defense against oxidative damage. Free Rad Biol Med 21:975–993. [CrossRef]
362. Ivanova AB, Glinsky GV, Eisenstark A. 1997. Role of RpoS regulon in resistance to oxidative stress and near-UV radiation in Delta-oxyR suppressor mutants of Escherichia coli. Free Radical Biol Med 23:627–636. [PubMed][CrossRef]
363. Oppezzo OJ, Costa CS, Pizarro RA. 2011. Influence of rpoS mutations on the response of Salmonella enterica serovar Typhimurium to solar radiation. J Photochem Photobiol B 102:20–25. [PubMed][CrossRef]
364. Almirón M, Link A, Furlong D, Kolter R. 1992. A novel DNA binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev 6:2646–2654. [PubMed][CrossRef]
365. Dukan S, Touati D. 1996. Hypochlorous acid stress in Escherichia coli: resistance, DNA damage, and comparison with hydrogen peroxide stress. J Bacteriol 178:6145–6150.[PubMed]
366. Grant RA, Gilman DH, Finkel SE, Kolter R, Hogle JM. 1998. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5:294–303. [PubMed][CrossRef]
367. Martinez A, Kolter R. 1997. Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J Bacteriol 179:5188–5194.[PubMed]
368. Nair S, Finkel SE. 2004. Dps protects cells against multiple stresses during stationary phase. J Bacteriol 186:4192–4198. [PubMed][CrossRef]
369. Stephani K, Weichart D, Hengge R. 2003. Dynamic control of Dps protein levels by ClpXP and ClpAP proteases in Escherichia coli. Mol Microbiol 49:1605–1614. [PubMed][CrossRef]
370. Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A. 1999. DNA protection by stress-induced biocrystallization. Nature 400:83–85. [PubMed][CrossRef]
371. Zhao G, Ceci P, Ilari A, Giangiacomo L, Laue TM, Chiancone E, Chasteen ND. 2002. Iron and hydrogen peroxide detoxification properties of DNA-binding protein form starved cells: a ferritin-like DNA-binding protein of Escherichia coli. J Biol Chem 277:27689–27696. [PubMed][CrossRef]
372. Demple B, Halbrook J, Linn S. 1983. Escherichia coli xth mutants are hypersensitive to hydrogen peroxide. J Bacteriol 153:1079–1082.[PubMed]
373. Eisenstark A. 1989. Bacterial genes involved in response to near-ultraviolet radiation. Adv Genet 26:99–147. [PubMed][CrossRef]
374. Persson O, Nyström T, Farewell A. 2010. UspB, a member of the sigma-S regulon, facilitates RuvC resolvase function. DNA Repair (Amst.) 9:1162–1169. [PubMed][CrossRef]
375. Ivanova A, Miller C, Glinsky G, Eisenstark A. 1994. Role of rpoS(katF) in oxyR-independent regulation of hydroperoxidase I in Escherichia coli. Mol Microbiol 12:571–578. [PubMed][CrossRef]
376. Loewen PC. 1992. Regulation of bacterial catalase synthesis, p 97–115. In J Scandalios (ed), Molecular Biology of Free Radical Scavenging Systems. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
377. Mulvey MR, Switala J, Borys A, Loewen PC. 1990. Regulation of transcription of katE and katF in Escherichia coli. J Bacteriol 172:6713–6720.[PubMed]
378. Schellhorn HE. 1995. Regulation of hydroperoxidase (catalase) expression in Escherichia coli. FEMS Microbiol Lett 131:113–119. [PubMed][CrossRef]
379. Becker-Hapak M, Eisenstark A. 1995. Role of rpoS in the regulation of glutathione oxidoreductase (gor) in Escherichia coli. FEMS Microbiol Lett 134:39–44.[PubMed]
380. Strohmeier-Gort A, Ferber DM, Imlay JA. 1999. The regulation and role of the periplasmic copper, zinc superoxide dismutase of Escherichia coli. Mol Microbiol 32:179–191. [PubMed][CrossRef]
381. Bou-Abdallah F, Lewin AC, Le Brun NE, Moore GR, Chasteen ND. 2002. Iron detoxification properties of Escherichia coli bacterioferritin: attenuation of oxyradical chemistry. J Biol Chem 277:37064–37069. [PubMed][CrossRef]
382. Dailey TA, Dailay HA. 2002. Identification of [2Fe-2S] clusters in microbial ferrochelatases. J Bacteriol 194:2460–2464. [CrossRef]
383. Lee JH, Yeo WS, Roe JH. 2004. Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor. Mol Microbiol 51:1745–1755. [PubMed][CrossRef]
384. Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G. 2001. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183:4562–4570. [PubMed][CrossRef]
385. Landini P, Volkert MR. 2000. Regulatory responses of the adaptive response to alkylation damage: a simple regulon with complex regulatory features. J Bacteriol 182:6543–6549. [PubMed][CrossRef]