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. 1993 Feb;175(3):693–700. doi: 10.1128/jb.175.3.693-700.1993

Xis and Fis proteins prevent site-specific DNA inversion in lysogens of phage HK022.

L Dorgai 1, J Oberto 1, R A Weisberg 1
PMCID: PMC196207  PMID: 8423145

Abstract

HK022, a temperate coliphage related to lambda, forms lysogens by inserting its DNA into the bacterial chromosome through site-specific recombination. The Escherichia coli Fis and phage Xis proteins promote excision of HK022 DNA from the bacterial chromosome. These two proteins also act during lysogenization to prevent a prophage rearrangement: lysogens formed in the absence of either Fis or Xis frequently carried a prophage that had suffered a site-specific internal DNA inversion. The inversion is a product of recombination between the phage attachment site and a secondary attachment site located within the HK022 left operon. In the absence of both Fis and Xis, the majority of lysogens carried a prophage with an inversion. Inversion occurs during lysogenization at about the same time as prophage insertion but is rare during lytic phage growth. Phages carrying the inverted segment are viable but have a defect in lysogenization, and we therefore suggest that prevention of this rearrangement is an important biological role of Xis and Fis for HK022. Although Fis and Xis are known to promote excision of lambda prophage, they had no detectable effect on lambda recombination at secondary attachment sites. HK022 cIts lysogens that were blocked in excisive recombination because of mutation in fis or xis typically produced high yields of phage after thermal induction, regardless of whether they carried an inverted prophage. The usual requirement for prophage excision was bypassed in these lysogens because they carried two or more prophages inserted in tandem at the bacterial attachment site; in such lysogens, viable phage particles can be formed by in situ packaging of unexcised chromosomes.

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Selected References

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

  1. Abremski K., Gottesman S. Purification of the bacteriophage lambda xis gene product required for lambda excisive recombination. J Biol Chem. 1982 Aug 25;257(16):9658–9662. [PubMed] [Google Scholar]
  2. Abremski K., Hoess R. Escherichia coli plasmid vectors for high-level regulated expression of the bacteriophage lambda xis gene product. Gene. 1983 Nov;25(1):49–58. doi: 10.1016/0378-1119(83)90166-x. [DOI] [PubMed] [Google Scholar]
  3. Ball C. A., Johnson R. C. Efficient excision of phage lambda from the Escherichia coli chromosome requires the Fis protein. J Bacteriol. 1991 Jul;173(13):4027–4031. doi: 10.1128/jb.173.13.4027-4031.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bauer C. E., Gardner J. F., Gumport R. I. Extent of sequence homology required for bacteriophage lambda site-specific recombination. J Mol Biol. 1985 Jan 20;181(2):187–197. doi: 10.1016/0022-2836(85)90084-1. [DOI] [PubMed] [Google Scholar]
  5. Bauer C. E., Gardner J. F., Gumport R. I., Weisberg R. A. The effect of attachment site mutations on strand exchange in bacteriophage lambda site-specific recombination. Genetics. 1989 Aug;122(4):727–736. doi: 10.1093/genetics/122.4.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cam K. M., Oberto J., Weisberg R. A. The early promoters of bacteriophage HK022: contrasts and similarities to other lambdoid phages. J Bacteriol. 1991 Jan;173(2):734–740. doi: 10.1128/jb.173.2.734-740.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
  8. Dhillon T. S., Dhillon E. K., Lai A. N. Genetic recombination between phage HK022, lambda, and phi 80. Virology. 1981 Feb;109(1):198–200. doi: 10.1016/0042-6822(81)90487-6. [DOI] [PubMed] [Google Scholar]
  9. Dhillon T. S., Dhillon E. K. Temperate coliphage HK022. Clear plaque mutants and preliminary vegetative map. Jpn J Microbiol. 1976 Oct;20(5):385–396. doi: 10.1111/j.1348-0421.1976.tb01004.x. [DOI] [PubMed] [Google Scholar]
  10. Dhillon T. S. Temperate coliphage HK022: virions, DNA, one-step growth, attachment site, and the prophage genetic map. J Gen Virol. 1981 Aug;55(Pt 2):487–492. doi: 10.1099/0022-1317-55-2-487. [DOI] [PubMed] [Google Scholar]
  11. Gottesman M. E., Yarmolinsky M. B. The integration and excision of the bacteriophage lambda genome. Cold Spring Harb Symp Quant Biol. 1968;33:735–747. doi: 10.1101/sqb.1968.033.01.084. [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. Hübner P., Arber W. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 1989 Feb;8(2):577–585. doi: 10.1002/j.1460-2075.1989.tb03412.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Johnson R. C., Ball C. A., Pfeffer D., Simon M. I. Isolation of the gene encoding the Hin recombinational enhancer binding protein. Proc Natl Acad Sci U S A. 1988 May;85(10):3484–3488. doi: 10.1073/pnas.85.10.3484. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kitts P. A., Nash H. A. An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA. Nucleic Acids Res. 1988 Jul 25;16(14B):6839–6856. doi: 10.1093/nar/16.14.6839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kornitzer D., Altuvia S., Oppenheim A. B. Genetic analysis of the cIII gene of bacteriophage HK022. J Bacteriol. 1991 Jan;173(2):810–815. doi: 10.1128/jb.173.2.810-815.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Leong J. M., Nunes-Düby S. E., Landy A. Generation of single base-pair deletions, insertions, and substitutions by a site-specific recombination system. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6990–6994. doi: 10.1073/pnas.82.20.6990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ljungquist E., Bukhari A. I. State of prophage Mu DNA upon induction. Proc Natl Acad Sci U S A. 1977 Aug;74(8):3143–3147. doi: 10.1073/pnas.74.8.3143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mizuuchi K., Weisberg R., Enquist L., Mizuuchi M., Buraczynska M., Foeller C., Hsu P. L., Ross W., Landy A. Structure and function of the phage lambda att site: size, int-binding sites, and location of the crossover point. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 1):429–437. doi: 10.1101/sqb.1981.045.01.057. [DOI] [PubMed] [Google Scholar]
  20. Moitoso de Vargas L., Landy A. A switch in the formation of alternative DNA loops modulates lambda site-specific recombination. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):588–592. doi: 10.1073/pnas.88.2.588. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mousset S., Thomas R. Ter, a function which generates the ends of the mature lambda chromosome. Nature. 1969 Jan 18;221(5177):242–244. doi: 10.1038/221242a0. [DOI] [PubMed] [Google Scholar]
  22. Nagaraja R., Weisberg R. A. Specificity determinants in the attachment sites of bacteriophages HK022 and lambda. J Bacteriol. 1990 Nov;172(11):6540–6550. doi: 10.1128/jb.172.11.6540-6550.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Numrych T. E., Gumport R. I., Gardner J. F. A genetic analysis of Xis and FIS interactions with their binding sites in bacteriophage lambda. J Bacteriol. 1991 Oct;173(19):5954–5963. doi: 10.1128/jb.173.19.5954-5963.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nunes-Düby S. E., Matsumoto L., Landy A. Site-specific recombination intermediates trapped with suicide substrates. Cell. 1987 Aug 28;50(5):779–788. doi: 10.1016/0092-8674(87)90336-9. [DOI] [PubMed] [Google Scholar]
  25. Oberto J., Weisberg R. A., Gottesman M. E. Structure and function of the nun gene and the immunity region of the lambdoid phage HK022. J Mol Biol. 1989 Jun 20;207(4):675–693. doi: 10.1016/0022-2836(89)90237-4. [DOI] [PubMed] [Google Scholar]
  26. Ross W., Landy A. Bacteriophage lambda int protein recognizes two classes of sequence in the phage att site: characterization of arm-type sites. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7724–7728. doi: 10.1073/pnas.79.24.7724. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Shimada K., Weisberg R. A., Gottesman M. E. Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogens. J Mol Biol. 1972 Feb 14;63(3):483–503. doi: 10.1016/0022-2836(72)90443-3. [DOI] [PubMed] [Google Scholar]
  28. Shimada K., Weisberg R. A., Gottesman M. E. Prophage lambda at unusual chromosomal locations. II. Mutations induced by bacteriophage lambda in Escherichia coli K12. J Mol Biol. 1973 Oct 25;80(2):297–314. doi: 10.1016/0022-2836(73)90174-5. [DOI] [PubMed] [Google Scholar]
  29. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  30. Sternberg N., Weisberg R. Packaging of coliphage lambda DNA. I. The role of the cohesive end site and the gene A protein. J Mol Biol. 1977 Dec 15;117(3):717–731. doi: 10.1016/0022-2836(77)90066-3. [DOI] [PubMed] [Google Scholar]
  31. Sternberg N., Weisberg R. Packaging of prophage and host DNA by coliphage lambda. Nature. 1975 Jul 10;256(5513):97–103. doi: 10.1038/256097a0. [DOI] [PubMed] [Google Scholar]
  32. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. doi: 10.1093/nar/16.20.9687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Thompson J. F., Moitoso de Vargas L., Koch C., Kahmann R., Landy A. Cellular factors couple recombination with growth phase: characterization of a new component in the lambda site-specific recombination pathway. Cell. 1987 Sep 11;50(6):901–908. doi: 10.1016/0092-8674(87)90516-2. [DOI] [PubMed] [Google Scholar]
  34. Yagil E., Dolev S., Oberto J., Kislev N., Ramaiah N., Weisberg R. A. Determinants of site-specific recombination in the lambdoid coliphage HK022. An evolutionary change in specificity. J Mol Biol. 1989 Jun 20;207(4):695–717. doi: 10.1016/0022-2836(89)90238-6. [DOI] [PubMed] [Google Scholar]
  35. Yin S., Bushman W., Landy A. Interaction of the lambda site-specific recombination protein Xis with attachment site DNA. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1040–1044. doi: 10.1073/pnas.82.4.1040. [DOI] [PMC free article] [PubMed] [Google Scholar]

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