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PMID: 1824874 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

A switch in the formation of alternative DNA loops modulates lambda site-specific recombination.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 88 ·No. 2 ·1991-01-15 ·Pages 588-92

Moitoso de Vargas L, Landy A

Abstract

The virally encoded Xis protein is one of the components in the site-specific recombination reactions of bacteriophage lambda. It is required for excisive recombination and inhibits integrative recombination. The mechanism of Xis inhibition of the integration reaction was investigated by methylation protection assays (footprinting analyses) in conjunction with recombination assays. Xis is shown to mediate the formation of a specific attP looped structure involving cooperative and competitive long-range interactions among integrase, integration host factor, and Xis proteins. This higher-order structure precludes supercoiled attP from engaging in the productive partner interactions that lead to execution of the first strand exchange in integrative recombination. In addition to its previously characterized role in excision, Xis-induced DNA bending is postulated to act as a regulatory switch (in an alternative loop mechanism) that converts the attP intasome from an integrative-competent complex to a nonreactive one.

MeSH Terms
Bacterial Proteins/metabolism Bacteriophage lambda/genetics Base Sequence Carrier Proteins/metabolism DNA Nucleotidyltransferases/metabolism DNA, Viral/genetics DNA-Binding Proteins/metabolism Escherichia coli/genetics Escherichia coli Proteins Integration Host Factors Kinetics Models, Genetic Molecular Sequence Data Nucleic Acid Conformation Plasmids Recombination, Genetic Viral Proteins
Chemicals
Bacterial Proteins Carrier Proteins DNA, Viral DNA-Binding Proteins Escherichia coli Proteins Integration Host Factors Viral Proteins integration host factor, E coli DNA Nucleotidyltransferases excisionase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Moitoso de Vargas L
Division of Biology and Medicine, Brown University, Providence, RI 02912.
Landy A
References (38)
38 references, click to expand
  1. How eukaryotic transcriptional activators work.
    Nature. 1988 Oct 20;335(6192):683-9 PMID: 3050531
  2. Mutational analysis of integrase arm-type binding sites of bacteriophage lambda. Integration and excision involve distinct interactions of integrase with arm-type sites.
    J Mol Biol. 1986 Dec 5;192(3):513-27 PMID: 2951525
  3. Half-att site substrates reveal the homology independence and minimal protein requirements for productive synapsis in lambda excisive recombination.
    Cell. 1989 Oct 6;59(1):197-206 PMID: 2529039
  4. Dynamic, structural, and regulatory aspects of lambda site-specific recombination.
    Annu Rev Biochem. 1989;58:913-49 PMID: 2528323
  5. The mechanism of phage lambda site-specific recombination: site-specific breakage of DNA by Int topoisomerase.
    Cell. 1983 Dec;35(3 Pt 2):795-803 PMID: 6317202
  6. The lambda phage att site: functional limits and interaction with Int protein.
    Nature. 1980 May 8;285(5760):85-91 PMID: 6246439
  7. Site-specific DNA condensation and pairing mediated by the int protein of bacteriophage lambda.
    Proc Natl Acad Sci U S A. 1982 Oct;79(19):5837-41 PMID: 6310548
  8. Role of the Xis protein of bacteriophage lambda in a specific reactive complex at the attR prophage attachment site.
    Cell. 1983 Jan;32(1):161-8 PMID: 6297783
  9. Knotting of DNA caused by a genetic rearrangement. Evidence for a nucleosome-like structure in site-specific recombination of bacteriophage lambda.
    J Mol Biol. 1983 Oct 15;170(1):1-18 PMID: 6226803
  10. Patterns of lambda Int recognition in the regions of strand exchange.
    Cell. 1983 May;33(1):261-72 PMID: 6235918
  11. Purification of the bacteriophage lambda xis gene product required for lambda excisive recombination.
    J Biol Chem. 1982 Aug 25;257(16):9658-62 PMID: 6213611
  12. 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):7724-8 PMID: 6218502
  13. 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 1:429-37 PMID: 6457725
  14. Nicking-closing activity associated with bacteriophage lambda int gene product.
    Proc Natl Acad Sci U S A. 1979 Aug;76(8):3760-4 PMID: 226979
  15. Involement of supertwisted DNA in integrative recombination of bacteriophage lambda.
    J Mol Biol. 1978 May 25;121(3):375-92 PMID: 353288
  16. A new method for sequencing DNA.
    Proc Natl Acad Sci U S A. 1977 Feb;74(2):560-4 PMID: 265521
  17. Integrative recombination of bacteriophage lambda DNA in vitro.
    Proc Natl Acad Sci U S A. 1975 Mar;72(3):1072-6 PMID: 1055366
  18. Interactions between lambda Int molecules bound to sites in the region of strand exchange are required for efficient Holliday junction resolution.
    J Mol Biol. 1990 Oct 20;215(4):523-35 PMID: 2146396
  19. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in lambda attL.
    Cell. 1990 Nov 16;63(4):773-81 PMID: 2146029
  20. DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase.
    Science. 1989 Jun 23;244(4911):1457-61 PMID: 2544029
  21. Bending of the bacteriophage lambda attachment site by Escherichia coli integration host factor.
    J Biol Chem. 1988 Mar 15;263(8):3554-7 PMID: 2831189
  22. Directional control of site-specific recombination by bacteriophage lambda. Evidence that a binding site for Int protein far from the crossover point is required for integrative but not excisive recombination.
    J Mol Biol. 1986 Dec 5;192(3):677-80 PMID: 3031315
  23. Suicide recombination substrates yield covalent lambda integrase-DNA complexes and lead to identification of the active site tyrosine.
    J Biol Chem. 1988 Jun 5;263(16):7678-85 PMID: 2836392
  24. Synapsis of attachment sites during lambda integrative recombination involves capture of a naked DNA by a protein-DNA complex.
    Cell. 1988 Jan 15;52(1):9-17 PMID: 2964274
  25. Autonomous DNA binding domains of lambda integrase recognize two different sequence families.
    Cell. 1988 Sep 23;54(7):923-9 PMID: 2843292
  26. The interaction of recombination proteins with supercoiled DNA: defining the role of supercoiling in lambda integrative recombination.
    Cell. 1986 Sep 26;46(7):1011-21 PMID: 3019560
  27. Helical-repeat dependence of integrative recombination of bacteriophage lambda: role of the P1 and H1 protein binding sites.
    Proc Natl Acad Sci U S A. 1988 Sep;85(17):6323-7 PMID: 2842765
  28. Gene regulation by proteins acting nearby and at a distance.
    Nature. 1986 Aug 21-27;322(6081):697-701 PMID: 3018583
  29. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes.
    Nucleic Acids Res. 1988 Oct 25;16(20):9687-705 PMID: 2972993
  30. Bacteriophage lambda site-specific recombination proceeds with a defined order of strand exchanges.
    J Mol Biol. 1988 Nov 5;204(1):95-107 PMID: 2975338
  31. Control of directionality in lambda site specific recombination.
    Science. 1985 Nov 22;230(4728):906-11 PMID: 2932798
  32. Mutations in an integration host factor-binding site: effect on lambda site-specific recombination and regulatory implications.
    J Bacteriol. 1986 Dec;168(3):1343-51 PMID: 2946666
  33. Genetic rearrangement of DNA induces knots with a unique topology: implications for the mechanism of synapsis and crossing-over.
    Proc Natl Acad Sci U S A. 1985 May;82(10):3124-8 PMID: 3159013
  34. 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):901-8 PMID: 2957063
  35. Protein-protein interactions in a higher-order structure direct lambda site-specific recombination.
    J Mol Biol. 1987 Jun 5;195(3):481-93 PMID: 2958633
  36. Functional replacement of a protein-induced bend in a DNA recombination site.
    Nature. 1989 Sep 21;341(6239):251-4 PMID: 2528697
  37. Site-specific recombination intermediates trapped with suicide substrates.
    Cell. 1987 Aug 28;50(5):779-88 PMID: 3040260
  38. Heteroduplex substrates for bacteriophage lambda site-specific recombination: cleavage and strand transfer products.
    EMBO J. 1989 Nov;8(11):3523-33 PMID: 2555168
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.88.2.588
Published
1991-01-15
Pages
588-92
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC50857
Subset
IM
Grants
NIAID NIH HHS · AI13544 · United States
NIGMS NIH HHS · GM33928 · United States
External Links
PubMed source DOI: 10.1073/pnas.88.2.588 PMC Full Text View journal details
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