Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Aug 25;19(16):4413–4419. doi: 10.1093/nar/19.16.4413

Molecular mechanism of negative autoregulation of Escherichia coli crp gene.

A Hanamura 1, H Aiba 1
PMCID: PMC328628  PMID: 1715982

Abstract

Transcription of the Escherichia coli crp gene encoding cAMP receptor protein (CRP) is negatively regulated by CRP-cAMP complex that binds to a specific site located downstream from the transcription start site. The binding of CRP-cAMP to this site activates transcription from a second divergent overlapping promoter. The mechanism of this negative autoregulation of the crp gene has been investigated by in vitro transcription, gel shift, DNase I footprinting, and exonuclease III protection assays. We demonstrated that the crp and divergent promoters are reciprocally and coordinately regulated by CRP-cAMP. The abortive initiation assay revealed that the divergent RNA itself is not required for the inhibition of crp transcription. Detailed binding studies revealed that CRP-cAMP stimulates the binding of RNA polymerase to the divergent promoter and thus blocks the occupation of the crp promoter by RNA polymerase.

Full text

PDF
4413

Images in this article

4415Image
on p.4415
4416Image
on p.4416
4416Image
on p.4416
4416Image
on p.4416
4417Image
on p.4417
4417Image
on p.4417
4417Image
on p.4417

Selected References

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

  1. Aiba H., Adhya S., de Crombrugghe B. Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem. 1981 Nov 25;256(22):11905–11910. [PubMed] [Google Scholar]
  2. Aiba H. Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene. Cell. 1983 Jan;32(1):141–149. doi: 10.1016/0092-8674(83)90504-4. [DOI] [PubMed] [Google Scholar]
  3. Aiba H., Fujimoto S., Ozaki N. Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucleic Acids Res. 1982 Feb 25;10(4):1345–1361. doi: 10.1093/nar/10.4.1345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Aiba H. Transcription of the Escherichia coli adenylate cyclase gene is negatively regulated by cAMP-cAMP receptor protein. J Biol Chem. 1985 Mar 10;260(5):3063–3070. [PubMed] [Google Scholar]
  5. Berg O. G., von Hippel P. H. Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol. 1988 Apr 20;200(4):709–723. doi: 10.1016/0022-2836(88)90482-2. [DOI] [PubMed] [Google Scholar]
  6. Christman M. F., Storz G., Ames B. N. OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. Proc Natl Acad Sci U S A. 1989 May;86(10):3484–3488. doi: 10.1073/pnas.86.10.3484. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cossart P., Gicquel-Sanzey B. Cloning and sequence of the crp gene of Escherichia coli K 12. Nucleic Acids Res. 1982 Feb 25;10(4):1363–1378. doi: 10.1093/nar/10.4.1363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cossart P., Gicquel-Sanzey B. Regulation of expression of the crp gene of Escherichia coli K-12: in vivo study. J Bacteriol. 1985 Jan;161(1):454–457. doi: 10.1128/jb.161.1.454-457.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ebright R. H., Ebright Y. W., Gunasekera A. Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. Nucleic Acids Res. 1989 Dec 25;17(24):10295–10305. doi: 10.1093/nar/17.24.10295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Eilen E., Pampeno C., Krakow J. S. Production and properties of the alpha core derived from the cyclic adenosine monophosphate receptor protein of Escherichia coli. Biochemistry. 1978 Jun 27;17(13):2469–2473. doi: 10.1021/bi00606a001. [DOI] [PubMed] [Google Scholar]
  11. Eilen E., Pampeno C., Krakow J. S. Production and properties of the alpha core derived from the cyclic adenosine monophosphate receptor protein of Escherichia coli. Biochemistry. 1978 Jun 27;17(13):2469–2473. doi: 10.1021/bi00606a001. [DOI] [PubMed] [Google Scholar]
  12. Fukuda R., Iwakura Y., Ishihama A. Heterogeneity of RNA polymerase in Escherichia coli. I. A new holoenzyme containing a new sigma factor. J Mol Biol. 1974 Mar;83(3):353–367. doi: 10.1016/0022-2836(74)90284-8. [DOI] [PubMed] [Google Scholar]
  13. Gaston K., Kolb A., Busby S. Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences. Biochem J. 1989 Jul 15;261(2):649–653. doi: 10.1042/bj2610649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Henikoff S., Haughn G. W., Calvo J. M., Wallace J. C. A large family of bacterial activator proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jovanovich S. B. Regulation of a cya-lac fusion by cyclic AMP in Salmonella typhimurium. J Bacteriol. 1985 Feb;161(2):641–649. doi: 10.1128/jb.161.2.641-649.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kawamukai M., Kishimoto J., Utsumi R., Himeno M., Komano T., Aiba H. Negative regulation of adenylate cyclase gene (cya) expression by cyclic AMP-cyclic AMP receptor protein in Escherichia coli: studies with cya-lac protein and operon fusion plasmids. J Bacteriol. 1985 Nov;164(2):872–877. doi: 10.1128/jb.164.2.872-877.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Krakow J. S., Pastan I. Cyclic adenosine monophosphate receptor: loss of cAMP-dependent DNA binding activity after proteolysis in the presence of cyclic adenosine monophosphate. Proc Natl Acad Sci U S A. 1973 Sep;70(9):2529–2533. doi: 10.1073/pnas.70.9.2529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Malan T. P., McClure W. R. Dual promoter control of the Escherichia coli lactose operon. Cell. 1984 Nov;39(1):173–180. doi: 10.1016/0092-8674(84)90203-4. [DOI] [PubMed] [Google Scholar]
  19. McClure W. R., Cech C. L., Johnston D. E. A steady state assay for the RNA polymerase initiation reaction. J Biol Chem. 1978 Dec 25;253(24):8941–8948. [PubMed] [Google Scholar]
  20. Meiklejohn A. L., Gralla J. D. Entry of RNA polymerase at the lac promoter. Cell. 1985 Dec;43(3 Pt 2):769–776. doi: 10.1016/0092-8674(85)90250-8. [DOI] [PubMed] [Google Scholar]
  21. Mori K., Aiba H. Evidence for negative control of cya transcription by cAMP and cAMP receptor protein in intact Escherichia coli cells. J Biol Chem. 1985 Nov 25;260(27):14838–14843. [PubMed] [Google Scholar]
  22. Morita T., Shigesada K., Kimizuka F., Aiba H. Regulatory effect of a synthetic CRP recognition sequence placed downstream of a promoter. Nucleic Acids Res. 1988 Aug 11;16(15):7315–7332. doi: 10.1093/nar/16.15.7315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Musso R. E., Di Lauro R., Adhya S., de Crombrugghe B. Dual control for transcription of the galactose operon by cyclic AMP and its receptor protein at two interspersed promoters. Cell. 1977 Nov;12(3):847–854. doi: 10.1016/0092-8674(77)90283-5. [DOI] [PubMed] [Google Scholar]
  24. O'Halloran T. V., Frantz B., Shin M. K., Ralston D. M., Wright J. G. The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell. 1989 Jan 13;56(1):119–129. doi: 10.1016/0092-8674(89)90990-2. [DOI] [PubMed] [Google Scholar]
  25. Okamoto K., Freundlich M. Mechanism for the autogenous control of the crp operon: transcriptional inhibition by a divergent RNA transcript. Proc Natl Acad Sci U S A. 1986 Jul;83(14):5000–5004. doi: 10.1073/pnas.83.14.5000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Okamoto K., Hara S., Bhasin R., Freundlich M. Evidence in vivo for autogenous control of the cyclic AMP receptor protein gene (crp) in Escherichia coli by divergent RNA. J Bacteriol. 1988 Nov;170(11):5076–5079. doi: 10.1128/jb.170.11.5076-5079.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Polayes D. A., Rice P. W., Garner M. M., Dahlberg J. E. Cyclic AMP-cyclic AMP receptor protein as a repressor of transcription of the spf gene of Escherichia coli. J Bacteriol. 1988 Jul;170(7):3110–3114. doi: 10.1128/jb.170.7.3110-3114.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Straney D. C., Straney S. B., Crothers D. M. Synergy between Escherichia coli CAP protein and RNA polymerase in the lac promoter open complex. J Mol Biol. 1989 Mar 5;206(1):41–57. doi: 10.1016/0022-2836(89)90522-6. [DOI] [PubMed] [Google Scholar]
  29. Wek R. C., Hatfield G. W. Transcriptional activation at adjacent operators in the divergent-overlapping ilvY and ilvC promoters of Escherichia coli. J Mol Biol. 1988 Oct 5;203(3):643–663. doi: 10.1016/0022-2836(88)90199-4. [DOI] [PubMed] [Google Scholar]
  30. de Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science. 1984 May 25;224(4651):831–838. doi: 10.1126/science.6372090. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES