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. 1989 Jan;121(1):5–12. doi: 10.1093/genetics/121.1.5

Phage λ Cro Protein and Ci Repressor Use Two Different Patterns of Specific Protein-DNA Interactions to Achieve Sequence Specificity in Vivo

N Benson 1, P Youderian 1
PMCID: PMC1203605  PMID: 2521838

Abstract

By assaying the binding of wild-type Cro to a set of 40 mutant λ operators in vivo, we have determined that the 14 outermost base pairs of the 17 base pair, consensus λ operator are critical for Cro binding. Cro protein recognizes 4 base pairs in a λ operator half-site in different ways than cI repressor. The sequence determinants of Cro binding at these critical positions in vivo are nearly perfectly consistent with the model proposed by W. F. ANDERSON, D. H. OHLENDORF, Y. TAKEDA and B. W. MATTHEWS and modified by Y. TAKEDA, A. SARAI and V. M. RIVERA for the specific interactions between Cro and its operator, and explain the relative order of affinities of the six natural λ operators for Cro. Our data call into question the idea that λ repressor and Cro protein recognize the consensus λ operator by nearly identical patterns of specific interactions.

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Selected References

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

  1. Bass S., Sugiono P., Arvidson D. N., Gunsalus R. P., Youderian P. DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes Dev. 1987 Aug;1(6):565–572. doi: 10.1101/gad.1.6.565. [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. Benson N., Sugiono P., Youderian P. DNA sequence determinants of lambda repressor binding in vivo. Genetics. 1988 Jan;118(1):21–29. doi: 10.1093/genetics/118.1.21. [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. Hochschild A., Douhan J., 3rd, Ptashne M. How lambda repressor and lambda Cro distinguish between OR1 and OR3. Cell. 1986 Dec 5;47(5):807–816. doi: 10.1016/0092-8674(86)90523-4. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Hughes K. T., Youderian P., Simon M. I. Phase variation in Salmonella: analysis of Hin recombinase and hix recombination site interaction in vivo. Genes Dev. 1988 Aug;2(8):937–948. doi: 10.1101/gad.2.8.937. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Johnson A., Meyer B. J., Ptashne M. Mechanism of action of the cro protein of bacteriophage lambda. Proc Natl Acad Sci U S A. 1978 Apr;75(4):1783–1787. doi: 10.1073/pnas.75.4.1783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kim J. G., Takeda Y., Matthews B. W., Anderson W. F. Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol. 1987 Jul 5;196(1):149–158. doi: 10.1016/0022-2836(87)90517-1. [DOI] [PubMed] [Google Scholar]
  11. Lebreton B., Prasad P. V., Jayaram M., Youderian P. Mutations that improve the binding of yeast FLP recombinase to its substrate. Genetics. 1988 Mar;118(3):393–400. doi: 10.1093/genetics/118.3.393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. Ohlendorf D. H., Anderson W. F., Lewis M., Pabo C. O., Matthews B. W. Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol. 1983 Sep 25;169(3):757–769. doi: 10.1016/s0022-2836(83)80169-7. [DOI] [PubMed] [Google Scholar]
  16. Ptashne M., Jeffrey A., Johnson A. D., Maurer R., Meyer B. J., Pabo C. O., Roberts T. M., Sauer R. T. How the lambda repressor and cro work. Cell. 1980 Jan;19(1):1–11. doi: 10.1016/0092-8674(80)90383-9. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Takeda Y., Folkmanis A., Echols H. Cro regulatory protein specified by bacteriophage lambda. Structure, DNA-binding, and repression of RNA synthesis. J Biol Chem. 1977 Sep 10;252(17):6177–6183. [PubMed] [Google Scholar]

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