Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1995 Feb 14;92(4):1117–1121. doi: 10.1073/pnas.92.4.1117

Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements.

C A Josaitis 1, T Gaal 1, R L Gourse 1
PMCID: PMC42649  PMID: 7862645

Abstract

Escherichia coli uses at least two regulatory systems, stringent control and growth-rate-dependent control, to adjust rRNA output to amino acid availability and the steady-state growth rate, respectively. We examined transcription from rrnB P1 promoters containing or lacking the cis-acting UP element and FIS protein binding sites after amino acid starvation. The "core promoter" responds to amino acid starvation like the full-length wild-type promoter; thus, neither the UP element nor FIS plays a role in stringent control. To clarify the relationship between growth-rate-dependent regulation and stringent control, we measured transcription from growth-rate-independent promoters during amino acid starvation. Four rrnB P1 mutants defective for growth-rate control and two other growth-rate-independent promoters (rrnB P2 and pS10) still displayed stringent regulation. Thus, the two systems have different promoter determinants, consistent with the idea that they function by different mechanisms. Two mutations disrupted stringent control of rrnB P1: (i) a multiple base change in the "discriminator" region between the -10 hexamer and the transcription start site and (ii) a double substitution making the promoter resemble the E sigma 70 consensus promoter. These results have important implications for the mechanisms of both stringent control and growth-rate-dependent control of rRNA transcription.

Full text

PDF
1121

Images in this article

1118Fig. 2
on p.1118
1119Fig. 4
on p.1119
1119Fig. 5
on p.1119
1120Fig. 7
on p.1120

Selected References

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

  1. Bartlett M. S., Gourse R. L. Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli. J Bacteriol. 1994 Sep;176(17):5560–5564. doi: 10.1128/jb.176.17.5560-5564.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Borukhov S., Sagitov V., Josaitis C. A., Gourse R. L., Goldfarb A. Two modes of transcription initiation in vitro at the rrnB P1 promoter of Escherichia coli. J Biol Chem. 1993 Nov 5;268(31):23477–23482. [PubMed] [Google Scholar]
  3. Cole J. R., Olsson C. L., Hershey J. W., Grunberg-Manago M., Nomura M. Feedback regulation of rRNA synthesis in Escherichia coli. Requirement for initiation factor IF2. J Mol Biol. 1987 Dec 5;198(3):383–392. doi: 10.1016/0022-2836(87)90288-9. [DOI] [PubMed] [Google Scholar]
  4. Condon C., French S., Squires C., Squires C. L. Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. EMBO J. 1993 Nov;12(11):4305–4315. doi: 10.1002/j.1460-2075.1993.tb06115.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dickson R. R., Gaal T., deBoer H. A., deHaseth P. L., Gourse R. L. Identification of promoter mutants defective in growth-rate-dependent regulation of rRNA transcription in Escherichia coli. J Bacteriol. 1989 Sep;171(9):4862–4870. doi: 10.1128/jb.171.9.4862-4870.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Freedman L. P., Zengel J. M., Lindahl L. Genetic dissection of stringent control and nutritional shift-up response of the Escherichia coli S10 ribosomal protein operon. J Mol Biol. 1985 Oct 20;185(4):701–712. doi: 10.1016/0022-2836(85)90055-5. [DOI] [PubMed] [Google Scholar]
  7. Gaal T., Barkei J., Dickson R. R., deBoer H. A., deHaseth P. L., Alavi H., Gourse R. L. Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J Bacteriol. 1989 Sep;171(9):4852–4861. doi: 10.1128/jb.171.9.4852-4861.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Gafny R., Cohen S., Nachaliel N., Glaser G. Isolated P2 rRNA promoters of Escherichia coli are strong promoters that are subject to stringent control. J Mol Biol. 1994 Oct 21;243(2):152–156. doi: 10.1006/jmbi.1994.1641. [DOI] [PubMed] [Google Scholar]
  10. Gilbert S. F., de Boer H. A., Nomura M. Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):211–224. doi: 10.1016/0092-8674(79)90309-x. [DOI] [PubMed] [Google Scholar]
  11. Gourse R. L., Takebe Y., Sharrock R. A., Nomura M. Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1069–1073. doi: 10.1073/pnas.82.4.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gourse R. L., de Boer H. A., Nomura M. DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell. 1986 Jan 17;44(1):197–205. doi: 10.1016/0092-8674(86)90498-8. [DOI] [PubMed] [Google Scholar]
  13. Hernandez V. J., Bremer H. Guanosine tetraphosphate (ppGpp) dependence of the growth rate control of rrnB P1 promoter activity in Escherichia coli. J Biol Chem. 1990 Jul 15;265(20):11605–11614. [PubMed] [Google Scholar]
  14. Jensen K. F. The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol. 1993 Jun;175(11):3401–3407. doi: 10.1128/jb.175.11.3401-3407.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lamond A. I., Travers A. A. Genetically separable functional elements mediate the optimal expression and stringent regulation of a bacterial tRNA gene. Cell. 1985 Feb;40(2):319–326. doi: 10.1016/0092-8674(85)90146-1. [DOI] [PubMed] [Google Scholar]
  16. Metzger S., Schreiber G., Aizenman E., Cashel M., Glaser G. Characterization of the relA1 mutation and a comparison of relA1 with new relA null alleles in Escherichia coli. J Biol Chem. 1989 Dec 15;264(35):21146–21152. [PubMed] [Google Scholar]
  17. 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]
  18. Newlands J. T., Ross W., Gosink K. K., Gourse R. L. Factor-independent activation of Escherichia coli rRNA transcription. II. characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. J Mol Biol. 1991 Aug 5;220(3):569–583. doi: 10.1016/0022-2836(91)90101-b. [DOI] [PubMed] [Google Scholar]
  19. Nomura M., Gourse R., Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem. 1984;53:75–117. doi: 10.1146/annurev.bi.53.070184.000451. [DOI] [PubMed] [Google Scholar]
  20. Olins P. O., Nomura M. Regulation of the S10 ribosomal protein operon in E. coli: nucleotide sequence at the start of the operon. Cell. 1981 Oct;26(2 Pt 2):205–211. doi: 10.1016/0092-8674(81)90303-2. [DOI] [PubMed] [Google Scholar]
  21. Rao L., Ross W., Appleman J. A., Gaal T., Leirmo S., Schlax P. J., Record M. T., Jr, Gourse R. L. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol. 1994 Feb 4;235(5):1421–1435. doi: 10.1006/jmbi.1994.1098. [DOI] [PubMed] [Google Scholar]
  22. Ross W., Gosink K. K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R. L. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 1993 Nov 26;262(5138):1407–1413. doi: 10.1126/science.8248780. [DOI] [PubMed] [Google Scholar]
  23. Ross W., Thompson J. F., Newlands J. T., Gourse R. L. E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 1990 Nov;9(11):3733–3742. doi: 10.1002/j.1460-2075.1990.tb07586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ryals J., Little R., Bremer H. Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate. J Bacteriol. 1982 Sep;151(3):1261–1268. doi: 10.1128/jb.151.3.1261-1268.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sarmientos P., Sylvester J. E., Contente S., Cashel M. Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids. Cell. 1983 Apr;32(4):1337–1346. doi: 10.1016/0092-8674(83)90314-8. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Spadaro A., Spena A., Santonastaso V., Conini P. Stringency without ppGpp accumulation. Nature. 1981 May 21;291(5812):256–258. doi: 10.1038/291256a0. [DOI] [PubMed] [Google Scholar]
  28. Sørensen M. A., Jensen K. F., Pedersen S. High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli. J Mol Biol. 1994 Feb 18;236(2):441–454. doi: 10.1006/jmbi.1994.1156. [DOI] [PubMed] [Google Scholar]
  29. Travers A. A. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol. 1980 Feb;141(2):973–976. doi: 10.1128/jb.141.2.973-976.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Travers A. RNA polymerase specificity and the control of growth. Nature. 1976 Oct 21;263(5579):641–646. doi: 10.1038/263641a0. [DOI] [PubMed] [Google Scholar]
  31. Vogel U., Pedersen S., Jensen K. F. An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli. J Bacteriol. 1991 Feb;173(3):1168–1174. doi: 10.1128/jb.173.3.1168-1174.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Zacharias M., Göringer H. U., Wagner R. Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity. EMBO J. 1989 Nov;8(11):3357–3363. doi: 10.1002/j.1460-2075.1989.tb08498.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. de Boer H. A. A versatile plasmid system for the study of prokaryotic transcription signals in Escherichia coli. Gene. 1984 Oct;30(1-3):251–255. doi: 10.1016/0378-1119(84)90129-x. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES