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Nucleic Acids Res. Jun 10, 1988; 16(11): 5089–5105.
PMCID: PMC336719

Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity.


The DNA sequences in the operator sites of the arginine regulon and of the SOS regulon have been subject to a statistical analysis. A quantitative correlation is found between the statistics of sequence choice and the activity at individual operator sites in both systems, as expected from theoretical considerations [Berg & von Hippel, J.Mol.Biol. (1987) 193, 723-750]. Based on these correlations it is possible to predict the effect of various sequence mutations. There is a significant difference in the slopes of the correlation lines between sequence and activity for the two systems. From this difference it can be expected that individual point mutations in the ARG boxes will have a much smaller effect on activity than similar changes in the SOS boxes. This difference may be related to a strong cooperative activity at tandem ARG boxes while the binding at SOS boxes appears to be mostly noncooperative.

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Selected References

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  • Berg OG, von Hippel PH. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol. 1987 Feb 20;193(4):723–750. [PubMed]
  • Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. [PubMed]
  • von Hippel PH, Berg OG. On the specificity of DNA-protein interactions. Proc Natl Acad Sci U S A. 1986 Mar;83(6):1608–1612. [PMC free article] [PubMed]
  • Little JW, Mount DW. The SOS regulatory system of Escherichia coli. Cell. 1982 May;29(1):11–22. [PubMed]
  • Peterson KR, Mount DW. Differential repression of SOS genes by unstable lexA41 (tsl-1) protein causes a "split-phenotype" in Escherichia coli K-12. J Mol Biol. 1987 Jan 5;193(1):27–40. [PubMed]
  • Kitagawa Y, Akaboshi E, Shinagawa H, Horii T, Ogawa H, Kato T. Structural analysis of the umu operon required for inducible mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4336–4340. [PMC free article] [PubMed]
  • Rostas K, Morton SJ, Picksley SM, Lloyd RG. Nucleotide sequence and LexA regulation of the Escherichia coli recN gene. Nucleic Acids Res. 1987 Jul 10;15(13):5041–5049. [PMC free article] [PubMed]
  • Lloubes R, Baty D, Lazdunski C. The promoters of the genes for colicin production, release and immunity in the ColA plasmid: effects of convergent transcription and Lex A protein. Nucleic Acids Res. 1986 Mar 25;14(6):2621–2636. [PMC free article] [PubMed]
  • Irino N, Nakayama K, Nakayama H. The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation. Mol Gen Genet. 1986 Nov;205(2):298–304. [PubMed]
  • Mankovich JA, Lai PH, Gokul N, Konisky J. Organization of the colicin Ib gene. Promoter structure and immunity domain. J Biol Chem. 1984 Jul 25;259(14):8764–8768. [PubMed]
  • Cole ST, Saint-Joanis B, Pugsley AP. Molecular characterisation of the colicin E2 operon and identification of its products. Mol Gen Genet. 1985;198(3):465–472. [PubMed]
  • Wertman KF, Mount DW. Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12. J Bacteriol. 1985 Jul;163(1):376–384. [PMC free article] [PubMed]
  • Brent R, Ptashne M. A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene. Nature. 1984 Dec 13;312(5995):612–615. [PubMed]
  • Cunin R, Glansdorff N, Piérard A, Stalon V. Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev. 1986 Sep;50(3):314–352. [PMC free article] [PubMed]
  • Lim DB, Oppenheim JD, Eckhardt T, Maas WK. Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6697–6701. [PMC free article] [PubMed]
  • Piette J, Cunin R, Boyen A, Charlier D, Crabeel M, Van Vliet F, Glansdorff N, Squires C, Squires CL. The regulatory region of the divergent argECBH operon in Escherichia coli K-12. Nucleic Acids Res. 1982 Dec 20;10(24):8031–8048. [PMC free article] [PubMed]
  • Cunin R, Eckhardt T, Piette J, Boyen A, Piérard A, Glansdorff N. Molecular basis for modulated regulation of gene expression in the arginine regulon of Escherichia coli K-12. Nucleic Acids Res. 1983 Aug 11;11(15):5007–5019. [PMC free article] [PubMed]
  • Lissens W, Cunin R, Kelker N, Glansdorff N, Piérard A. In vitro synthesis of Escherichia coli carbamoylphosphate synthase: evidence for participation of the arginine repressor in cumulative repression. J Bacteriol. 1980 Jan;141(1):58–66. [PMC free article] [PubMed]

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