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. 1993 Dec;175(24):7982–7989. doi: 10.1128/jb.175.24.7982-7989.1993

Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp.

D R Gentry 1, V J Hernandez 1, L H Nguyen 1, D B Jensen 1, M Cashel 1
PMCID: PMC206978  PMID: 8253685

Abstract

Strains of Escherichia coli which lack detectable guanosine 3',5'-bispyrophosphate (ppGpp) display a pleiotropic phenotype that in some respects resembles that of rpoS (katF) mutants. This led us to examine whether ppGpp is a positive regulator of sigma s synthesis. sigma s is a stationary-phase-specific sigma factor that is encoded by the rpoS gene. We found that a ppGpp-deficient strain is defective in sigma s synthesis as cells enter stationary phase in a rich medium, as judged by immunoblots. Under more-defined conditions we found that the stimulation of sigma s synthesis following glucose, phosphate, or amino acid starvation of wild-type strains is greatly reduced in a strain lacking ppGpp. The failure of ppGpp-deficient strains to synthesize sigma s in response to these starvation regimens could indicate a general defect in gene expression rather than a specific dependence of rpoS expression on ppGpp. We therefore tested the effect of artificially elevated ppGpp levels on sigma s synthesis either with mutations that impair ppGpp decay or by gratuitously inducing ppGpp synthesis with a Ptac::relA fusion. In both instances, we observed enhanced sigma s synthesis. Apparently, ppGpp can activate sigma s synthesis under conditions of nutrient sufficiency as well as during entry into stationary phase. This finding suggests that changes in ppGpp levels function both as a signal of imminent stationary phase and as a signal of perturbations in steady-state growth.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aldea M., Garrido T., Pla J., Vicente M. Division genes in Escherichia coli are expressed coordinately to cell septum requirements by gearbox promoters. EMBO J. 1990 Nov;9(11):3787–3794. doi: 10.1002/j.1460-2075.1990.tb07592.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bochner B. R., Ames B. N. Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography. J Biol Chem. 1982 Aug 25;257(16):9759–9769. [PubMed] [Google Scholar]
  3. Bohannon D. E., Connell N., Keener J., Tormo A., Espinosa-Urgel M., Zambrano M. M., Kolter R. Stationary-phase-inducible "gearbox" promoters: differential effects of katF mutations and role of sigma 70. J Bacteriol. 1991 Jul;173(14):4482–4492. doi: 10.1128/jb.173.14.4482-4492.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dassa E., Tetu C., Boquet P. L. Identification of the acid phosphatase (optimum pH 2.5) of Escherichia coli. FEBS Lett. 1980 May 5;113(2):275–278. doi: 10.1016/0014-5793(80)80608-9. [DOI] [PubMed] [Google Scholar]
  5. Gaal T., Gourse R. L. Guanosine 3'-diphosphate 5'-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5533–5537. doi: 10.1073/pnas.87.14.5533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hecker M., Schroeter A. Synthese der alkalischen Phosphatase in einem stringent und relaxed kontrollierten Stamm von Escherichia coli nach Aminosäuren- und Phosphatlimitation. J Basic Microbiol. 1985;25(5):341–347. doi: 10.1002/jobm.3620250511. [DOI] [PubMed] [Google Scholar]
  7. Hengge-Aronis R. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli. Cell. 1993 Jan 29;72(2):165–168. doi: 10.1016/0092-8674(93)90655-a. [DOI] [PubMed] [Google Scholar]
  8. Hernandez V. J., Bremer H. Characterization of RNA and DNA synthesis in Escherichia coli strains devoid of ppGpp. J Biol Chem. 1993 May 25;268(15):10851–10862. [PubMed] [Google Scholar]
  9. Irr J. D. Control of nucleotide metabolism and ribosomal ribonucleic acid synthesis during nitrogen starvation of Escherichia coli. J Bacteriol. 1972 May;110(2):554–561. doi: 10.1128/jb.110.2.554-561.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Jensen K. F., Pedersen S. Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol Rev. 1990 Jun;54(2):89–100. doi: 10.1128/mr.54.2.89-100.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jones P. G., Cashel M., Glaser G., Neidhardt F. C. Function of a relaxed-like state following temperature downshifts in Escherichia coli. J Bacteriol. 1992 Jun;174(12):3903–3914. doi: 10.1128/jb.174.12.3903-3914.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kaasen I., Falkenberg P., Styrvold O. B., Strøm A. R. 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. 1992 Feb;174(3):889–898. doi: 10.1128/jb.174.3.889-898.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lange R., Hengge-Aronis R. Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):49–59. doi: 10.1111/j.1365-2958.1991.tb01825.x. [DOI] [PubMed] [Google Scholar]
  14. Lazzarini R. A., Cashel M., Gallant J. On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains of Escherichia coli. J Biol Chem. 1971 Jul 25;246(14):4381–4385. [PubMed] [Google Scholar]
  15. Loewen P. C., von Ossowski I., Switala J., Mulvey M. R. KatF (sigma S) synthesis in Escherichia coli is subject to posttranscriptional regulation. J Bacteriol. 1993 Apr;175(7):2150–2153. doi: 10.1128/jb.175.7.2150-2153.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. McCann M. P., Fraley C. D., Matin A. The putative sigma factor KatF is regulated posttranscriptionally during carbon starvation. J Bacteriol. 1993 Apr;175(7):2143–2149. doi: 10.1128/jb.175.7.2143-2149.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. McCann M. P., Kidwell J. P., Matin A. The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J Bacteriol. 1991 Jul;173(13):4188–4194. doi: 10.1128/jb.173.13.4188-4194.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Mulvey M. R., Loewen P. C. Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor. Nucleic Acids Res. 1989 Dec 11;17(23):9979–9991. doi: 10.1093/nar/17.23.9979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mulvey M. R., Switala J., Borys A., Loewen P. C. Regulation of transcription of katE and katF in Escherichia coli. J Bacteriol. 1990 Dec;172(12):6713–6720. doi: 10.1128/jb.172.12.6713-6720.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nguyen L. H., Jensen D. B., Thompson N. E., Gentry D. R., Burgess R. R. In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product. Biochemistry. 1993 Oct 19;32(41):11112–11117. doi: 10.1021/bi00092a021. [DOI] [PubMed] [Google Scholar]
  22. Rao N. N., Wang E., Yashphe J., Torriani A. Nucleotide pool in pho regulon mutants and alkaline phosphatase synthesis in Escherichia coli. J Bacteriol. 1986 Apr;166(1):205–211. doi: 10.1128/jb.166.1.205-211.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Romeo T., Preiss J. Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts. J Bacteriol. 1989 May;171(5):2773–2782. doi: 10.1128/jb.171.5.2773-2782.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Sarubbi E., Rudd K. E., Cashel M. Basal ppGpp level adjustment shown by new spoT mutants affect steady state growth rates and rrnA ribosomal promoter regulation in Escherichia coli. Mol Gen Genet. 1988 Aug;213(2-3):214–222. doi: 10.1007/BF00339584. [DOI] [PubMed] [Google Scholar]
  25. Sarubbi E., Rudd K. E., Xiao H., Ikehara K., Kalman M., Cashel M. Characterization of the spoT gene of Escherichia coli. J Biol Chem. 1989 Sep 5;264(25):15074–15082. [PubMed] [Google Scholar]
  26. Schellhorn H. E., Stones V. L. Regulation of katF and katE in Escherichia coli K-12 by weak acids. J Bacteriol. 1992 Jul;174(14):4769–4776. doi: 10.1128/jb.174.14.4769-4776.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Schreiber G., Metzger S., Aizenman E., Roza S., Cashel M., Glaser G. Overexpression of the relA gene in Escherichia coli. J Biol Chem. 1991 Feb 25;266(6):3760–3767. [PubMed] [Google Scholar]
  28. Spector M. P., Cubitt C. L. Starvation-inducible loci of Salmonella typhimurium: regulation and roles in starvation-survival. Mol Microbiol. 1992 Jun;6(11):1467–1476. doi: 10.1111/j.1365-2958.1992.tb00867.x. [DOI] [PubMed] [Google Scholar]
  29. Svitil A. L., Cashel M., Zyskind J. W. Guanosine tetraphosphate inhibits protein synthesis in vivo. A possible protective mechanism for starvation stress in Escherichia coli. J Biol Chem. 1993 Feb 5;268(4):2307–2311. [PubMed] [Google Scholar]
  30. Tanaka K., Takayanagi Y., Fujita N., Ishihama A., Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3511–3515. doi: 10.1073/pnas.90.8.3511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Towbin H., Staehelin T., Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4350–4354. doi: 10.1073/pnas.76.9.4350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. VanBogelen R. A., Neidhardt F. C. Ribosomes as sensors of heat and cold shock in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5589–5593. doi: 10.1073/pnas.87.15.5589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Xiao H., Kalman M., Ikehara K., Zemel S., Glaser G., Cashel M. Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem. 1991 Mar 25;266(9):5980–5990. [PubMed] [Google Scholar]
  34. Yamagishi M., Matsushima H., Wada A., Sakagami M., Fujita N., Ishihama A. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993 Feb;12(2):625–630. doi: 10.1002/j.1460-2075.1993.tb05695.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zambrano M. M., Siegele D. A., Almirón M., Tormo A., Kolter R. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science. 1993 Mar 19;259(5102):1757–1760. doi: 10.1126/science.7681219. [DOI] [PubMed] [Google Scholar]

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