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J Bacteriol. Jul 1985; 163(1): 376–384.
PMCID: PMC219124

Nucleotide sequence binding specificity of the LexA repressor of Escherichia coli K-12.


The specificity of LexA protein binding was investigated by quantifying the repressibility of several mutant recA and lexA operator-promoter regions fused to the Escherichia coli galactokinase (galK) gene. The results of this analysis indicate that two sets of four nucleotides, one set at each end of the operator (terminal-nucleotide contacts), are most critical for repressor binding. In addition, our results suggest that the repressor-operator interaction is symmetric in nature, in that mutations at symmetrically equivalent positions in the recA operator have comparable effects on repressibility. The symmetry of this interaction justified reevaluation of the consensus sequence by half-site comparison, which yielded the half-site consensus (5')CTGTATAT. Although the first four positions of this sequence were most important, the last four were well conserved among binding sites and appeared to modulate repressor affinity. The role of the terminal-nucleotide contacts and the mechanism by which the internal sequences affected repressor binding are discussed.

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Selected References

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  • Anderson WF, Ohlendorf DH, Takeda Y, Matthews BW. Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature. 1981 Apr 30;290(5809):754–758. [PubMed]
  • Brent R, Ptashne M. Mechanism of action of the lexA gene product. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4204–4208. [PMC free article] [PubMed]
  • Champoux JJ. Proteins that affect DNA conformation. Annu Rev Biochem. 1978;47:449–479. [PubMed]
  • Clark AJ. recA operator mutations and their usefulness. Biochimie. 1982 Aug-Sep;64(8-9):669–675. [PubMed]
  • Dickerson RE, Drew HR. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. [PubMed]
  • Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179–2183. [PMC free article] [PubMed]
  • Ginsburg H, Edmiston SH, Harper J, Mount DW. Isolation and characterization of an operator-constitutive mutation in the recA gene of E. coli K-12. Mol Gen Genet. 1982;187(1):4–11. [PubMed]
  • Hogan M, LeGrange J, Austin B. Dependence of DNA helix flexibility on base composition. Nature. 1983 Aug 25;304(5928):752–754. [PubMed]
  • Hübscher U, Lutz H, Kornberg A. Novel histone H2A-like protein of escherichia coli. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5097–5101. [PMC free article] [PubMed]
  • Huisman O, D'Ari R, Casaregola S. How Escherichia coli sets different basal levels in SOS operons. Biochimie. 1982 Aug-Sep;64(8-9):709–712. [PubMed]
  • Kahn M, Kolter R, Thomas C, Figurski D, Meyer R, Remaut E, Helinski DR. Plasmid cloning vehicles derived from plasmids ColE1, F, R6K, and RK2. Methods Enzymol. 1979;68:268–280. [PubMed]
  • Little JW. Autodigestion of lexA and phage lambda repressors. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1375–1379. [PMC free article] [PubMed]
  • Little JW, Mount DW. The SOS regulatory system of Escherichia coli. Cell. 1982 May;29(1):11–22. [PubMed]
  • Little JW, Mount DW, Yanisch-Perron CR. Purified lexA protein is a repressor of the recA and lexA genes. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4199–4203. [PMC free article] [PubMed]
  • Lomonossoff GP, Butler PJ, Klug A. Sequence-dependent variation in the conformation of DNA. J Mol Biol. 1981 Jul 15;149(4):745–760. [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]
  • Markham BE, Harper JE, Mount DW. Physiology of the SOS response: kinetics of lexA and recA transcriptional activity following induction. Mol Gen Genet. 1985;198(2):207–212. [PubMed]
  • McKay DB, Steitz TA. Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA. Nature. 1981 Apr 30;290(5809):744–749. [PubMed]
  • McKenney K, Shimatake H, Court D, Schmeissner U, Brady C, Rosenberg M. A system to study promoter and terminator signals recognized by Escherichia coli RNA polymerase. Gene Amplif Anal. 1981;2:383–415. [PubMed]
  • McPartland A, Green L, Echols H. Control of recA gene RNA in E. coli: regulatory and signal genes. Cell. 1980 Jul;20(3):731–737. [PubMed]
  • Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. [PubMed]
  • Mizusawa S, Gottesman S. Protein degradation in Escherichia coli: the lon gene controls the stability of sulA protein. Proc Natl Acad Sci U S A. 1983 Jan;80(2):358–362. [PMC free article] [PubMed]
  • Mount DW. A mutant of Escherichia coli showing constitutive expression of the lysogenic induction and error-prone DNA repair pathways. Proc Natl Acad Sci U S A. 1977 Jan;74(1):300–304. [PMC free article] [PubMed]
  • Pabo CO, Krovatin W, Jeffrey A, Sauer RT. The N-terminal arms of lambda repressor wrap around the operator DNA. Nature. 1982 Jul 29;298(5873):441–443. [PubMed]
  • Pabo CO, Lewis M. The operator-binding domain of lambda repressor: structure and DNA recognition. Nature. 1982 Jul 29;298(5873):443–447. [PubMed]
  • Pabo CO, Sauer RT. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. [PubMed]
  • Record MT, Jr, Lohman ML, De Haseth P. Ion effects on ligand-nucleic acid interactions. J Mol Biol. 1976 Oct 25;107(2):145–158. [PubMed]
  • Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature. 1982 Jul 29;298(5873):447–451. [PubMed]
  • Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. [PMC free article] [PubMed]
  • Shortle D, Nathans D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proc Natl Acad Sci U S A. 1978 May;75(5):2170–2174. [PMC free article] [PubMed]
  • Steitz TA, Ohlendorf DH, McKay DB, Anderson WF, Matthews BW. Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins. Proc Natl Acad Sci U S A. 1982 May;79(10):3097–3100. [PMC free article] [PubMed]
  • van den Elzen PJ, Maat J, Walters HH, Veltkamp E, Nijkamp HJ. The nucleotide sequence of the bacteriocin promoters of plasmids Clo DF13 and Co1 E1: role of lexA repressor and cAMP in the regulation of promoter activity. Nucleic Acids Res. 1982 Mar 25;10(6):1913–1928. [PMC free article] [PubMed]
  • Walker GC. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev. 1984 Mar;48(1):60–93. [PMC free article] [PubMed]
  • Wertman KF, Little JW, Mount DW. Rapid mutational analysis of regulatory loci in Escherichia coli K-12 using bacteriophage M13. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3801–3805. [PMC free article] [PubMed]
  • Zoller MJ, Smith M. Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any fragment of DNA. Nucleic Acids Res. 1982 Oct 25;10(20):6487–6500. [PMC free article] [PubMed]

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