Skip to main content
Genetics logoLink to Genetics
. 1988 Jan;118(1):21–29. doi: 10.1093/genetics/118.1.21

DNA Sequence Determinants of λ Repressor Binding in Vivo

N Benson 1, P Sugiono 1, P Youderian 1
PMCID: PMC1203262  PMID: 8608928

Abstract

The critical operator determinants for λ repressor recognition have been defined by analyzing the binding of wild-type repressor to a set of mutant operators in vivo. Base pair substitutions at six positions within the λ operator half-site impair binding severely, and define these base pairs as critical for operator function. One mutant operator binds repressor better than the consensus operator, and is a superoperator. The model proposed by M. Lewis in 1983 for the binding of λ repressor to its operator accurately predicts the observed operator requirements for binding in vivo, with several minor exceptions. The order of affinities of the six natural λ operators has also been determined.

Full Text

The Full Text of this article is available as a PDF (945.0 KB).

Selected References

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

  1. 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]
  2. Benson N., Sugiono P., Bass S., Mendelman L. V., Youderian P. General selection for specific DNA-binding activities. Genetics. 1986 Sep;114(1):1–14. doi: 10.1093/genetics/114.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Graña D., Youderian P., Susskind M. M. Mutations that improve the ant promoter of Salmonella phage P22. Genetics. 1985 May;110(1):1–16. doi: 10.1093/genetics/110.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Gómez-Eichelmann M. C. Deoxyribonucleic acid adenine and cytosine methylation in Salmonella typhimurium and Salmonella typhi. J Bacteriol. 1979 Nov;140(2):574–579. doi: 10.1128/jb.140.2.574-579.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  6. Hecht M. H., Nelson H. C., Sauer R. T. Mutations in lambda repressor's amino-terminal domain: implications for protein stability and DNA binding. Proc Natl Acad Sci U S A. 1983 May;80(9):2676–2680. doi: 10.1073/pnas.80.9.2676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. JACOB F., PERRIN D., SANCHEZ C., MONOD J. [Operon: a group of genes with the expression coordinated by an operator]. C R Hebd Seances Acad Sci. 1960 Feb 29;250:1727–1729. [PubMed] [Google Scholar]
  8. Johnson A. D., Meyer B. J., Ptashne M. Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5061–5065. doi: 10.1073/pnas.76.10.5061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Johnson A. D., Pabo C. O., Sauer R. T. Bacteriophage lambda repressor and cro protein: interactions with operator DNA. Methods Enzymol. 1980;65(1):839–856. doi: 10.1016/s0076-6879(80)65078-2. [DOI] [PubMed] [Google Scholar]
  10. Koudelka G. B., Harrison S. C., Ptashne M. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. 1987 Apr 30-May 6Nature. 326(6116):886–888. doi: 10.1038/326886a0. [DOI] [PubMed] [Google Scholar]
  11. Lewis M., Jeffrey A., Wang J., Ladner R., Ptashne M., Pabo C. O. Structure of the operator-binding domain of bacteriophage lambda repressor: implications for DNA recognition and gene regulation. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):435–440. doi: 10.1101/sqb.1983.047.01.051. [DOI] [PubMed] [Google Scholar]
  12. Meselson M., Yuan R. DNA restriction enzyme from E. coli. Nature. 1968 Mar 23;217(5134):1110–1114. doi: 10.1038/2171110a0. [DOI] [PubMed] [Google Scholar]
  13. Nelson H. C., Hecht M. H., Sauer R. T. Mutations defining the operator-binding sites of bacteriophage lambda repressor. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):441–449. doi: 10.1101/sqb.1983.047.01.052. [DOI] [PubMed] [Google Scholar]
  14. Nelson H. C., Sauer R. T. Lambda repressor mutations that increase the affinity and specificity of operator binding. Cell. 1985 Sep;42(2):549–558. doi: 10.1016/0092-8674(85)90112-6. [DOI] [PubMed] [Google Scholar]
  15. Ohlendorf D. H., Anderson W. F., Fisher R. G., Takeda Y., Matthews B. W. The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature. 1982 Aug 19;298(5876):718–723. doi: 10.1038/298718a0. [DOI] [PubMed] [Google Scholar]
  16. Pabo C. O., Krovatin W., Jeffrey A., Sauer R. T. The N-terminal arms of lambda repressor wrap around the operator DNA. Nature. 1982 Jul 29;298(5873):441–443. doi: 10.1038/298441a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. Susskind M. M. A new gene of bacteriophage P22 which regulates synthesis of antirepressor. J Mol Biol. 1980 Apr 25;138(4):685–713. doi: 10.1016/0022-2836(80)90060-1. [DOI] [PubMed] [Google Scholar]
  23. Woodbury C. P., Jr, Hagenbüchle O., von Hippel P. H. DNA site recognition and reduced specificity of the Eco RI endonuclease. J Biol Chem. 1980 Dec 10;255(23):11534–11548. [PubMed] [Google Scholar]
  24. Youderian P., Bouvier S., Susskind M. M. Sequence determinants of promoter activity. Cell. 1982 Oct;30(3):843–853. doi: 10.1016/0092-8674(82)90289-6. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES