Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1980 May;77(5):2482–2486. doi: 10.1073/pnas.77.5.2482

Site-specific recombination functions of bacteriophage λ: DNA sequence of regulatory regions and overlapping structural genes for Int and Xis

Ronald H Hoess 1,*, Carl Foeller 1, Karen Bidwell 1,*, Arthur Landy 1,†
PMCID: PMC349424  PMID: 6446713

Abstract

Site-specific recombination in bacteriophage λ is mediated by two phage-encoded proteins, Int and Xis. The structural genes encoding these proteins are located immediately to the right of their site of action, the phage att site. The DNA sequence for both the structural and regulatory regions of these genes has been determined. The location and reading frame of the xis gene were ascertained by sequence comparisons with the b538 deletion (that ends within xis) and with the xis6 amber mutation. From the DNA sequence Xis has a molecular weight of 8630; it is rich in basic amino acids with lysine and arginine comprising 25% of the 72 amino acids. Identification of the int reading frame was also unambiguous. From the DNA sequence, Int has a molecular weight of 40,330; of the 356 amino acids, 69 are basic and 46 are acidic. In the NH2-terminal portion of Int, 35% of the first 20 amino acids are basic. The site-specific recombination functions form a very tight cluster (att-int-xis) on the λ chromosome. The combined protein-encoding sequences of xis and int start 1347 base pairs, and terminate 84 base pairs, from the center of the phage att site. The two genes overlap one another by 20 base pairs (xis is upstream of int) and a possible means of controlling the relative synthesis rates of Int and Xis at the level of translation is proposed. Control at the level of transcription is also considered. The mutation intc226 leads to constitutive production of Int, independent of cII/cIII activator proteins normally required for transcription from the pI promoter. It is shown that this mutation is the result of a single base change (in the fMet codon of the xis gene) that generates an improved promoter heptamer sequence. This result, in conjunction with comparisons with other promoter sequences and other sequences responding to cII/cIII action, leads to a tentative identification of the pI promoter and site of cII/cIII action.

Keywords: att, pI, intc226, cII/cIII

Full text

PDF
2483

Selected References

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

  1. Abraham J., Mascarenhas D., Fischer R., Benedik M., Campbell A., Echols H. DNA sequence of regulatory region for integration gene of bacteriophage lambda. Proc Natl Acad Sci U S A. 1980 May;77(5):2477–2481. doi: 10.1073/pnas.77.5.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Belin D., Hedgpeth J., Selzer G. B., Epstein R. H. Temperature-sensitive mutation in the initiation codon of the rIIB gene of bacteriophage T4. Proc Natl Acad Sci U S A. 1979 Feb;76(2):700–704. doi: 10.1073/pnas.76.2.700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chung S., Echols H. Positive regulation of integrative recombination by the cII and cIII genes of bacteriophase lambda. Virology. 1977 Jun 15;79(2):312–319. doi: 10.1016/0042-6822(77)90358-0. [DOI] [PubMed] [Google Scholar]
  4. Davis R. W., Parkinson J. S. Deletion mutants of bacteriophage lambda. 3. Physical structure of att-phi. J Mol Biol. 1971 Mar 14;56(2):403–423. doi: 10.1016/0022-2836(71)90473-6. [DOI] [PubMed] [Google Scholar]
  5. Egan J., Landy A. Structural analysis of the tRNA1Tyr gene of Escherichia coli. A 178 base pair sequence that is repeated 3.14 times. J Biol Chem. 1978 May 25;253(10):3607–3622. [PubMed] [Google Scholar]
  6. Enquist L. W., Kikuchi A., Weisberg R. A. The role of lambda integrase in integration and excision. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 2):1115–1120. doi: 10.1101/sqb.1979.043.01.124. [DOI] [PubMed] [Google Scholar]
  7. Enquist L. W., Weisberg R. A. A genetic analysis of the att-int-xis region of coliphage lambda. J Mol Biol. 1977 Apr;111(2):97–120. doi: 10.1016/s0022-2836(77)80117-4. [DOI] [PubMed] [Google Scholar]
  8. Enquist L., Honigman A., Hu S. L., Szybalski W. Expression of lambda int gene function in ColE1 hybrid plasmids carrying the C fragment of bacteriophage lambda. Virology. 1979 Jan 30;92(2):557–560. doi: 10.1016/0042-6822(79)90157-0. [DOI] [PubMed] [Google Scholar]
  9. Fischer R., Takeda Y., Echols H. Transcription of the int gene of bacteriophage lambda. New RNA polymerase binding site and RNA start generated by int-constitutive mutations. J Mol Biol. 1979 Apr 15;129(3):509–514. doi: 10.1016/0022-2836(79)90510-2. [DOI] [PubMed] [Google Scholar]
  10. Gingery R., Echols H. Mutants of bacteriophage lambda unable to integrate into the host chromosome. Proc Natl Acad Sci U S A. 1967 Oct;58(4):1507–1514. doi: 10.1073/pnas.58.4.1507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gottesman M. E., Yarmolinsky M. B. Integration-negative mutants of bacteriophage lambda. J Mol Biol. 1968 Feb 14;31(3):487–505. doi: 10.1016/0022-2836(68)90423-3. [DOI] [PubMed] [Google Scholar]
  12. Guarneros G., Echols H. New mutants of bacteriophage lambda with a specific defect in excision from the host chromosome. J Mol Biol. 1970 Feb 14;47(3):565–574. doi: 10.1016/0022-2836(70)90323-2. [DOI] [PubMed] [Google Scholar]
  13. Heffernan L., Benedik M., Campbell A. Regulatory structure of the insertion region of bacteriophage lambda. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 2):1127–1134. doi: 10.1101/sqb.1979.043.01.126. [DOI] [PubMed] [Google Scholar]
  14. Honigman A., Hu S. L., Szybalski W. Regulation of integration by coliphage lambda: activation of int transcription by the cII and cIII proteins. Virology. 1979 Jan 30;92(2):542–556. doi: 10.1016/0042-6822(79)90156-9. [DOI] [PubMed] [Google Scholar]
  15. Kaiser A. D., Masuda T. Evidence for a prophage excision gene in lambda. J Mol Biol. 1970 Feb 14;47(3):557–564. doi: 10.1016/0022-2836(70)90322-0. [DOI] [PubMed] [Google Scholar]
  16. Katzir N., Oppenheim A., Belfort M., Oppenheim A. B. Activation of the lambda int gene by the cii and ciii gene products. Virology. 1976 Oct 15;74(2):324–331. doi: 10.1016/0042-6822(76)90339-1. [DOI] [PubMed] [Google Scholar]
  17. Kikuchi Y., Nash H. A. The bacteriophage lambda int gene product. A filter assay for genetic recombination, purification of int, and specific binding to DNA. J Biol Chem. 1978 Oct 25;253(20):7149–7157. [PubMed] [Google Scholar]
  18. Landy A., Ross W. Viral integration and excision: structure of the lambda att sites. Science. 1977 Sep 16;197(4309):1147–1160. doi: 10.1126/science.331474. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Nash H. A. Integration and excision of bacteriophage lambda. Curr Top Microbiol Immunol. 1977;78:171–199. doi: 10.1007/978-3-642-66800-5_6. [DOI] [PubMed] [Google Scholar]
  21. Ogata R. T., Gilbert W. An amino-terminal fragment of lac repressor binds specifically to lac operator. Proc Natl Acad Sci U S A. 1978 Dec;75(12):5851–5854. doi: 10.1073/pnas.75.12.5851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pabo C. O., Sauer R. T., Sturtevant J. M., Ptashne M. The lambda repressor contains two domains. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1608–1612. doi: 10.1073/pnas.76.4.1608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pilacinski W., Mosharrafa E., Edmundson R., Zissler J., Fiandt M., Szybalski W. Insertion sequence IS2 associated with int-constitutive mutants of bacteriophage lambda. Gene. 1977;2(2):61–74. doi: 10.1016/0378-1119(77)90073-7. [DOI] [PubMed] [Google Scholar]
  24. Robinson L. H., Landy A. HindII, HindIII, and HpaI restriction fragment maps of bacteriophage lambda DNA. Gene. 1977 Sep;2(1):1–31. doi: 10.1016/0378-1119(77)90019-1. [DOI] [PubMed] [Google Scholar]
  25. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  26. Shimada K., Campbell A. Int-constitutive mutants of bacteriophage lambda. Proc Natl Acad Sci U S A. 1974 Jan;71(1):237–241. doi: 10.1073/pnas.71.1.237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Shimada K., Campbell A. Lysogenization and curing by int-constitutive mutants of phage lambda. Virology. 1974 Jul;60(1):157–165. doi: 10.1016/0042-6822(74)90373-0. [DOI] [PubMed] [Google Scholar]
  28. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shulman M. J., Mizuuchi K., Gottesman M. M. New att mutants of phage lambda. Virology. 1976 Jul 1;72(1):13–22. doi: 10.1016/0042-6822(76)90307-x. [DOI] [PubMed] [Google Scholar]
  30. Yates J. L., Gette W. R., Furth M. E., Nomura M. Effects of ribosomal mutations on the read-through of a chain termination signal: studies on the synthesis of bacteriophage lambda O gene protein in vitro. Proc Natl Acad Sci U S A. 1977 Feb;74(2):689–693. doi: 10.1073/pnas.74.2.689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Zissler J. Integration-negative (int) mutants of phage lambda. Virology. 1967 Jan;31(1):189–189. doi: 10.1016/0042-6822(67)90030-x. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES