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. 1996 Aug 1;15(15):3993–4000.

The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli.

D D Sledjeski 1, A Gupta 1, S Gottesman 1
PMCID: PMC452119  PMID: 8670904

Abstract

dsrA encodes a small, untranslated RNA. When over-expressed, DsrA antagonizes the H-NS-mediated silencing of numerous promoters. Cells devoid of DsrA grow normally and show little change in the expression of a number of H-NS-silenced genes. Expression of a transcriptional fusion of lacZ to dsrB, the gene next to dsrA, is significantly lower in cells carrying mutations in dsrA. All expression of beta-galactosidase from the dsrB::lacZ fusion is also dependent on the stationary phase sigma factor, RpoS. DsrA RNA was found to regulate dsrB::lacZ indirectly, by modulating RpoS synthesis. Levels of RpoS protein are substantially lower in a dsrA mutant, both in stationary and exponential phase cells. Mutations in dsrA decrease the expression of an RpoS::LacZ translational fusion, but not a transcriptional fusion, suggesting that DsrA is acting after transcription initiation. While RpoS expression is very low in exponential phase at temperatures of 30 degrees C and above, at 20 degrees C there is substantial synthesis of RpoS during exponential growth, all dependent on DsrA RNA. dsrA expression is also increased at low temperatures. These results suggest a new role for RpoS during exponential growth at low temperatures, mediated by DsrA.

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  1. Barth M., Marschall C., Muffler A., Fischer D., Hengge-Aronis R. Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli. J Bacteriol. 1995 Jun;177(12):3455–3464. doi: 10.1128/jb.177.12.3455-3464.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bertin P., Terao E., Lee E. H., Lejeune P., Colson C., Danchin A., Collatz E. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. J Bacteriol. 1994 Sep;176(17):5537–5540. doi: 10.1128/jb.176.17.5537-5540.1994. [DOI] [PMC free article] [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. Brill J. A., Quinlan-Walshe C., Gottesman S. Fine-structure mapping and identification of two regulators of capsule synthesis in Escherichia coli K-12. J Bacteriol. 1988 Jun;170(6):2599–2611. doi: 10.1128/jb.170.6.2599-2611.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen C. Y., Buchmeier N. A., Libby S., Fang F. C., Krause M., Guiney D. G. Central regulatory role for the RpoS sigma factor in expression of Salmonella dublin plasmid virulence genes. J Bacteriol. 1995 Sep;177(18):5303–5309. doi: 10.1128/jb.177.18.5303-5309.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chung C. T., Niemela S. L., Miller R. H. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172–2175. doi: 10.1073/pnas.86.7.2172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cukier-Kahn R., Jacquet M., Gros F. Two heat-resistant, low molecular weight proteins from Escherichia coli that stimulate DNA-directed RNA synthesis. Proc Natl Acad Sci U S A. 1972 Dec;69(12):3643–3647. doi: 10.1073/pnas.69.12.3643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dower W. J., Miller J. F., Ragsdale C. W. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 1988 Jul 11;16(13):6127–6145. doi: 10.1093/nar/16.13.6127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Falconi M., McGovern V., Gualerzi C., Hillyard D., Higgins N. P. Mutations altering chromosomal protein H-NS induce mini-Mu transposition. New Biol. 1991 Jun;3(6):615–625. [PubMed] [Google Scholar]
  10. Gottesman S., Clark W. P., de Crecy-Lagard V., Maurizi M. R. ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. J Biol Chem. 1993 Oct 25;268(30):22618–22626. [PubMed] [Google Scholar]
  11. Göransson M., Sondén B., Nilsson P., Dagberg B., Forsman K., Emanuelsson K., Uhlin B. E. Transcriptional silencing and thermoregulation of gene expression in Escherichia coli. Nature. 1990 Apr 12;344(6267):682–685. doi: 10.1038/344682a0. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Jacquet M., Cukier-Kahn R., Pla J., Gros F. A thermostable protein factor acting on in vitro DNA transcription. Biochem Biophys Res Commun. 1971 Dec 17;45(6):1597–1607. doi: 10.1016/0006-291x(71)90204-x. [DOI] [PubMed] [Google Scholar]
  14. Jishage M., Ishihama A. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38. J Bacteriol. 1995 Dec;177(23):6832–6835. doi: 10.1128/jb.177.23.6832-6835.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kawula T. H., Orndorff P. E. Rapid site-specific DNA inversion in Escherichia coli mutants lacking the histonelike protein H-NS. J Bacteriol. 1991 Jul;173(13):4116–4123. doi: 10.1128/jb.173.13.4116-4123.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Lange R., Hengge-Aronis R. 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. 1994 Jul 1;8(13):1600–1612. doi: 10.1101/gad.8.13.1600. [DOI] [PubMed] [Google Scholar]
  19. Lee I. S., Lin J., Hall H. K., Bearson B., Foster J. W. The stationary-phase sigma factor sigma S (RpoS) is required for a sustained acid tolerance response in virulent Salmonella typhimurium. Mol Microbiol. 1995 Jul;17(1):155–167. doi: 10.1111/j.1365-2958.1995.mmi_17010155.x. [DOI] [PubMed] [Google Scholar]
  20. Levinthal M., Lejeune P., Danchin A. The H-NS protein modulates the activation of the ilvIH operon of Escherichia coli K12 by Lrp, the leucine regulatory protein. Mol Gen Genet. 1994 Mar;242(6):736–743. doi: 10.1007/BF00283429. [DOI] [PubMed] [Google Scholar]
  21. Loewen P. C., Hengge-Aronis R. The role of the sigma factor sigma S (KatF) in bacterial global regulation. Annu Rev Microbiol. 1994;48:53–80. doi: 10.1146/annurev.mi.48.100194.000413. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Maurizi M. R., Trisler P., Gottesman S. Insertional mutagenesis of the lon gene in Escherichia coli: lon is dispensable. J Bacteriol. 1985 Dec;164(3):1124–1135. doi: 10.1128/jb.164.3.1124-1135.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. May G., Dersch P., Haardt M., Middendorf A., Bremer E. The osmZ (bglY) gene encodes the DNA-binding protein H-NS (H1a), a component of the Escherichia coli K12 nucleoid. Mol Gen Genet. 1990 Oct;224(1):81–90. doi: 10.1007/BF00259454. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Muffler A., Fischer D., Altuvia S., Storz G., Hengge-Aronis R. The response regulator RssB controls stability of the sigma(S) subunit of RNA polymerase in Escherichia coli. EMBO J. 1996 Mar 15;15(6):1333–1339. [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Schweder T., Lee K. H., Lomovskaya O., Matin A. Regulation of Escherichia coli starvation sigma factor (sigma s) by ClpXP protease. J Bacteriol. 1996 Jan;178(2):470–476. doi: 10.1128/jb.178.2.470-476.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shi X., Waasdorp B. C., Bennett G. N. Modulation of acid-induced amino acid decarboxylase gene expression by hns in Escherichia coli. J Bacteriol. 1993 Feb;175(4):1182–1186. doi: 10.1128/jb.175.4.1182-1186.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Simons R. W., Houman F., Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53(1):85–96. doi: 10.1016/0378-1119(87)90095-3. [DOI] [PubMed] [Google Scholar]
  31. Singer M., Baker T. A., Schnitzler G., Deischel S. M., Goel M., Dove W., Jaacks K. J., Grossman A. D., Erickson J. W., Gross C. A. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol Rev. 1989 Mar;53(1):1–24. doi: 10.1128/mr.53.1.1-24.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Sledjeski D., Gottesman S. A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2003–2007. doi: 10.1073/pnas.92.6.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Spassky A., Rimsky S., Garreau H., Buc H. H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro. Nucleic Acids Res. 1984 Jul 11;12(13):5321–5340. doi: 10.1093/nar/12.13.5321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Takayanagi Y., Tanaka K., Takahashi H. Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli. Mol Gen Genet. 1994 Jun 3;243(5):525–531. doi: 10.1007/BF00284200. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. 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]
  37. Volkert M. R., Hajec L. I., Matijasevic Z., Fang F. C., Prince R. Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene. J Bacteriol. 1994 Dec;176(24):7638–7645. doi: 10.1128/jb.176.24.7638-7645.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Yamashino T., Kakeda M., Ueguchi C., Mizuno T. An analogue of the DnaJ molecular chaperone whose expression is controlled by sigma s during the stationary phase and phosphate starvation in Escherichia coli. Mol Microbiol. 1994 Aug;13(3):475–483. doi: 10.1111/j.1365-2958.1994.tb00442.x. [DOI] [PubMed] [Google Scholar]
  39. Yamashino T., Ueguchi C., Mizuno T. Quantitative control of the stationary phase-specific sigma factor, sigma S, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J. 1995 Feb 1;14(3):594–602. doi: 10.1002/j.1460-2075.1995.tb07035.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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