title: Mapping the λ Integrase bridges in the nucleoprotein Holliday junction intermediates of viral integrative and excisive recombination.
abstract: The site-specific recombinase encoded by bacteriophage λ [λ Integrase (Int)] is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. In contrast to the other well-studied and highly exploited tyrosine recombinase family members, such as Cre and Flp, Int carries out a reaction that is highly directional, tightly regulated, and depends on an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein that binds via its small amino-terminal domain to high affinity arm-type DNA sites and via its large, compound carboxyl-terminal domain to core-type DNA sites, where DNA cleavage and ligation are executed. Each of the four Int protomers, within a multiprotein 400-kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. Despite a wealth of genetic, biochemical, and functional information generated by many laboratories over the last 50 y, it has not been possible to decipher the patterns of Int bridges, an essential step in understanding the architectures responsible for regulated directionality of recombination. We used site-directed chemical cross-linking of Int in trapped Holliday junction recombination intermediates and recombination reactions with chimeric recombinases, to identify the unique and monogamous patterns of Int bridges for integrative and excisive recombination.
authors.affiliation: Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912; and.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Tong
authors.affiliation: Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912; and.
authors.forename: David
authors.initials: D
authors.lastname: Warren
authors.affiliation: Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912; and.
authors.forename: Nicole E
authors.initials: NE
authors.lastname: Seah
authors.affiliation: Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912; and.
authors.forename: Gurunathan
authors.initials: G
authors.lastname: Laxmikanthan
authors.affiliation: Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 vanduyne@mail.med.upenn.edu Arthur_Landy@brown.edu.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Van Duyne
authors.affiliation: Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912; and vanduyne@mail.med.upenn.edu Arthur_Landy@brown.edu.
authors.forename: Arthur
authors.initials: A
authors.lastname: Landy
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics* / Q000502:physiology*; D001665:Binding Sites; D003432:Cross-Linking Reagents; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D045566:DNA, Cruciform / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism / Q000821:virology; D019426:Integrases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009698:Nucleoproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011995:Recombination, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D014775:Virus Activation / Q000235:genetics; D016662:Virus Integration / Q000235:genetics
chemical_list: D003432:Cross-Linking Reagents; D004269:DNA, Bacterial; D045566:DNA, Cruciform; D009698:Nucleoproteins; D014764:Viral Proteins; D019426:Integrases
keywords: molecular machines; recombinogenic architectures; regulation of directionality; site-specific recombination
references.citation: Nucleic Acids Res. 2010 Oct;38(18):e175
references.pmid: 20693535
references.citation: Mol Microbiol. 1999 Aug;33(3):449-56
references.pmid: 10577069
references.citation: Science. 1992 Apr 10;256(5054):198-203
references.pmid: 1533056
references.citation: Annu Rev Biochem. 2006;75:567-605
references.pmid: 16756503
references.citation: Cell. 1988 Jan 15;52(1):9-17
references.pmid: 2964274
references.citation: EMBO J. 2006 Oct 4;25(19):4586-95
references.pmid: 16977316
references.citation: Mol Cell. 2003 Jul;12(1):187-98
references.pmid: 12887904
references.citation: Annu Rev Biochem. 2003;72:337-66
references.pmid: 14527324
references.citation: Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12372-7
references.pmid: 25114241
references.citation: Mol Microbiol. 2003 Oct;50(1):89-99
references.pmid: 14507366
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2109-14
references.pmid: 17287355
references.citation: J Mol Biol. 2007 Mar 23;367(2):328-43
references.pmid: 17275024
references.citation: Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18278-83
references.pmid: 19011106
references.citation: Nature. 1974 Feb 22;247(5442):543-5
references.pmid: 4818553
references.citation: Chem Biol. 2000 May;7(5):355-64
references.pmid: 10801473
references.citation: Genes Cells. 1996 May;1(5):453-63
references.pmid: 9078377
references.citation: Cell. 1996 Dec 27;87(7):1295-306
references.pmid: 8980235
references.citation: Nature. 2005 Jun 23;435(7045):1059-66
references.pmid: 15973401
references.citation: J Biol Chem. 2007 Aug 17;282(33):24004-16
references.pmid: 17573343
references.citation: Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3434-9
references.pmid: 11904406
references.citation: Nucleic Acids Res. 2001 Jun 1;29(11):2205-16
references.pmid: 11376138
references.citation: Bioorg Med Chem. 2006 May 1;14(9):3081-9
references.pmid: 16412655
references.citation: Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8176-81
references.pmid: 12832614
references.citation: Cell. 1984 Dec;39(3 Pt 2):707-16
references.pmid: 6096022
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4185-90
references.pmid: 11904359
references.citation: EMBO J. 1998 Sep 15;17(18):5484-96
references.pmid: 9736626
references.citation: J Biol Chem. 2008 May 2;283(18):12402-14
references.pmid: 18319248