title: Nucleoprotein architectures regulating the directionality of viral integration and excision.
abstract: The virally encoded site-specific recombinase Int collaborates with its accessory DNA bending proteins IHF, Xis, and Fis to assemble two distinct, very large, nucleoprotein complexes that carry out either integrative or excisive recombination along regulated and essentially unidirectional pathways. The core of each complex consists of a tetramer of Integrase protein (Int), which is a heterobivalent DNA binding protein that binds and bridges a core-type DNA site (where strand cleavage and ligation are executed), and a distal arm-type site, that is brought within range by one or more DNA bending proteins. The recent determination of the patterns of these Int bridges has made it possible to think realistically about the global architecture of the recombinogenic complexes. Here, we combined the previously determined Int bridging patterns with in-gel FRET experiments and in silico modeling to characterize and differentiate the two 400-kDa multiprotein Holiday junction recombination intermediates formed during λ integration and excision. The results lead to architectural models that explain how integration and excision are regulated in λ site-specific recombination. Our confidence in the basic features of these architectures is based on the redundancy and self-consistency of the underlying data from two very different experimental approaches to establish bridging interactions, a set of strategic intracomplex distances from FRET experiments, and the model's ability to explain key aspects of the integrative and excisive recombination pathways, such as topological changes, the mechanism of capturing attB, and the features of asymmetry and flexibility within the complexes.
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: 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: 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: 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; D003198:Computer Simulation; 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; D031541:Fluorescence Resonance Energy Transfer; D019426:Integrases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008242:Lysogeny / Q000235:genetics*; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; 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*
chemical_list: D004269:DNA, Bacterial; D045566:DNA, Cruciform; D046912:Multiprotein Complexes; D009698:Nucleoproteins; D014764:Viral Proteins; D019426:Integrases
keywords: molecular machines; recombinogenic architectures; regulation of directionality; topology
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