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. 1988 Nov;85(21):7947–7951. doi: 10.1073/pnas.85.21.7947

Recognition helices of lac and lambda repressor are oriented in opposite directions and recognize similar DNA sequences.

N Lehming 1, J Sartorius 1, S Oehler 1, B von Wilcken-Bergmann 1, B Müller-Hill 1
PMCID: PMC282330  PMID: 3186699

Abstract

Exchanges in positions 1 and 2 of the putative recognition helix allow lac repressor to bind to ideal lac operator variants in which base pair 4 has been replaced. We show here that an Arg-22----Asn exchange in position 6 of the putative recognition helix of lac repressor abolishes lac repressor binding to ideal lac operator. This lac repressor variant, however, binds to a variant of the ideal lac operator 5' TTTGAGCGCTCAAA 3' in which the original G.C of position 6 has been replaced by T.A. This result and our previous data confirm our suggestion that the N terminus of the recognition helix of lac repressor enters the major groove close to the center of symmetry of lac operator and that its C terminus leaves the major groove further away from the center of symmetry. The consequences of this model are discussed in regard to various phage and bacterial repressor operator systems.

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Selected References

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  1. Adler K., Beyreuther K., Fanning E., Geisler N., Gronenborn B., Klemm A., Müller-Hill B., Pfahl M., Schmitz A. How lac repressor binds to DNA. Nature. 1972 Jun 9;237(5354):322–327. doi: 10.1038/237322a0. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Anderson J. E., Ptashne M., Harrison S. C. Structure of the repressor-operator complex of bacteriophage 434. 1987 Apr 30-May 6Nature. 326(6116):846–852. doi: 10.1038/326846a0. [DOI] [PubMed] [Google Scholar]
  4. Beyreuther K., Adler K., Geisler N., Klemm A. The amino-acid sequence of lac repressor. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3576–3580. doi: 10.1073/pnas.70.12.3576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boelens R., Scheek R. M., van Boom J. H., Kaptein R. Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance. J Mol Biol. 1987 Jan 5;193(1):213–216. doi: 10.1016/0022-2836(87)90638-3. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7274–7278. doi: 10.1073/pnas.81.23.7274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature. 1984 Sep 20;311(5983):232–235. doi: 10.1038/311232a0. [DOI] [PubMed] [Google Scholar]
  9. Ebright R. H., Kolb A., Buc H., Kunkel T. A., Krakow J. S., Beckwith J. Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6083–6087. doi: 10.1073/pnas.84.17.6083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gicquel-Sanzey B., Cossart P. Homologies between different procaryotic DNA-binding regulatory proteins and between their sites of action. EMBO J. 1982;1(5):591–595. doi: 10.1002/j.1460-2075.1982.tb01213.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gilbert W., Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3581–3584. doi: 10.1073/pnas.70.12.3581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gilbert W., Müller-Hill B. Isolation of the lac repressor. Proc Natl Acad Sci U S A. 1966 Dec;56(6):1891–1898. doi: 10.1073/pnas.56.6.1891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gilbert W., Müller-Hill B. The lac operator is DNA. Proc Natl Acad Sci U S A. 1967 Dec;58(6):2415–2421. doi: 10.1073/pnas.58.6.2415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Grosschedl R., Schwarz E. Nucleotide sequence of the cro-cII-oop region of bacteriophage 434 DNA. Nucleic Acids Res. 1979 Mar;6(3):867–881. doi: 10.1093/nar/6.3.867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hogan M. E., Austin R. H. Importance of DNA stiffness in protein-DNA binding specificity. Nature. 1987 Sep 17;329(6136):263–266. doi: 10.1038/329263a0. [DOI] [PubMed] [Google Scholar]
  16. Hsiang M. W., Cole R. D., Takeda Y., Echols H. Amino acid sequence of Cro regulatory protein of bacteriophage lambda. Nature. 1977 Nov 17;270(5634):275–277. doi: 10.1038/270275a0. [DOI] [PubMed] [Google Scholar]
  17. Irani M. H., Orosz L., Adhya S. A control element within a structural gene: the gal operon of Escherichia coli. Cell. 1983 Mar;32(3):783–788. doi: 10.1016/0092-8674(83)90064-8. [DOI] [PubMed] [Google Scholar]
  18. Irwin N., Ptashne M. Mutants of the catabolite activator protein of Escherichia coli that are specifically deficient in the gene-activation function. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8315–8319. doi: 10.1073/pnas.84.23.8315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. JACOB F., MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318–356. doi: 10.1016/s0022-2836(61)80072-7. [DOI] [PubMed] [Google Scholar]
  20. Kania J., Brown D. T. The functional repressor parts of a tetrameric lac repressor-beta-galactosidase chimaera are organized as dimers. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3529–3533. doi: 10.1073/pnas.73.10.3529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lehming N., Sartorius J., Niemöller M., Genenger G., v Wilcken-Bergmann B., Müller-Hill B. The interaction of the recognition helix of lac repressor with lac operator. EMBO J. 1987 Oct;6(10):3145–3153. doi: 10.1002/j.1460-2075.1987.tb02625.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Maizels N. M. The nucleotide sequence of the lactose messenger ribonucleic acid transcribed from the UV5 promoter mutant of Escherichia coli. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3585–3589. doi: 10.1073/pnas.70.12.3585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Martin K., Huo L., Schleif R. F. The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3654–3658. doi: 10.1073/pnas.83.11.3654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Müller-Hill B., Crapo L., Gilbert W. Mutants that make more lac repressor. Proc Natl Acad Sci U S A. 1968 Apr;59(4):1259–1264. doi: 10.1073/pnas.59.4.1259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Müller-Hill B., Kania J. Lac repressor can be fused to beta-galactosidase. Nature. 1974 Jun 7;249(457):561–563. doi: 10.1038/249561a0. [DOI] [PubMed] [Google Scholar]
  27. Pabo C. O., Lewis M. The operator-binding domain of lambda repressor: structure and DNA recognition. Nature. 1982 Jul 29;298(5873):443–447. doi: 10.1038/298443a0. [DOI] [PubMed] [Google Scholar]
  28. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  29. Peticolas W. L., Wang Y., Thomas G. A. Some rules for predicting the base-sequence dependence of DNA conformation. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2579–2583. doi: 10.1073/pnas.85.8.2579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pfahl M. Genetic map of the lactose repressor gene (i) of Escherichia coli. Genetics. 1972 Nov;72(3):393–410. doi: 10.1093/genetics/72.3.393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Poteete A. R., Ptashne M., Ballivet M., Eisen H. Operator sequences of bacteriophages P22 and 21. J Mol Biol. 1980 Feb 15;137(1):81–91. doi: 10.1016/0022-2836(80)90158-8. [DOI] [PubMed] [Google Scholar]
  32. Ptashne M. ISOLATION OF THE lambda PHAGE REPRESSOR. Proc Natl Acad Sci U S A. 1967 Feb;57(2):306–313. doi: 10.1073/pnas.57.2.306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Ptashne M. Specific binding of the lambda phage repressor to lambda DNA. Nature. 1967 Apr 15;214(5085):232–234. doi: 10.1038/214232a0. [DOI] [PubMed] [Google Scholar]
  34. Riggs A. D., Bourgeois S., Cohn M. The lac repressor-operator interaction. 3. Kinetic studies. J Mol Biol. 1970 Nov 14;53(3):401–417. doi: 10.1016/0022-2836(70)90074-4. [DOI] [PubMed] [Google Scholar]
  35. Roberts T. M., Shimatake H., Brady C., Rosenberg M. Sequence of Cro gene of bacteriophage lambda. Nature. 1977 Nov 17;270(5634):274–275. doi: 10.1038/270274a0. [DOI] [PubMed] [Google Scholar]
  36. Sadler J. R., Sasmor H., Betz J. L. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc Natl Acad Sci U S A. 1983 Nov;80(22):6785–6789. doi: 10.1073/pnas.80.22.6785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sauer R. T., Anderegg R. Primary structure of the lambda repressor. Biochemistry. 1978 Mar 21;17(6):1092–1100. doi: 10.1021/bi00599a024. [DOI] [PubMed] [Google Scholar]
  38. Sauer R. T., Pan J., Hopper P., Hehir K., Brown J., Poteete A. R. Primary structure of the phage P22 repressor and its gene c2. Biochemistry. 1981 Jun 9;20(12):3591–3598. doi: 10.1021/bi00515a044. [DOI] [PubMed] [Google Scholar]
  39. Sauer R. T., Yocum R. R., Doolittle R. F., Lewis M., Pabo C. O. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature. 1982 Jul 29;298(5873):447–451. doi: 10.1038/298447a0. [DOI] [PubMed] [Google Scholar]
  40. Schevitz R. W., Otwinowski Z., Joachimiak A., Lawson C. L., Sigler P. B. The three-dimensional structure of trp repressor. 1985 Oct 31-Nov 6Nature. 317(6040):782–786. doi: 10.1038/317782a0. [DOI] [PubMed] [Google Scholar]
  41. Simons A., Tils D., von Wilcken-Bergmann B., Müller-Hill B. Possible ideal lac operator: Escherichia coli lac operator-like sequences from eukaryotic genomes lack the central G X C pair. Proc Natl Acad Sci U S A. 1984 Mar;81(6):1624–1628. doi: 10.1073/pnas.81.6.1624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Stokes H. W., Hall B. G. Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor. Mol Biol Evol. 1985 Nov;2(6):478–483. doi: 10.1093/oxfordjournals.molbev.a040373. [DOI] [PubMed] [Google Scholar]
  43. Valentin-Hansen P., Højrup P., Short S. The primary structure of the DeoR repressor from Escherichia coli K-12. Nucleic Acids Res. 1985 Aug 26;13(16):5927–5936. doi: 10.1093/nar/13.16.5927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Weber I. T., Steitz T. A. Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3973–3977. doi: 10.1073/pnas.81.13.3973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Youderian P., Vershon A., Bouvier S., Sauer R. T., Susskind M. M. Changing the DNA-binding specificity of a repressor. Cell. 1983 Dec;35(3 Pt 2):777–783. doi: 10.1016/0092-8674(83)90110-1. [DOI] [PubMed] [Google Scholar]
  46. von Wilcken-Bergmann B., Müller-Hill B. Sequence of galR gene indicates a common evolutionary origin of lac and gal repressor in Escherichia coli. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2427–2431. doi: 10.1073/pnas.79.8.2427. [DOI] [PMC free article] [PubMed] [Google Scholar]

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