title: Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading.
abstract: Bacteriophage-encoded serine-integrases are members of the large family of serine-recombinases and catalyze site-specific integrative recombination between a phage attP site and a bacterial attB site to form an integrated prophage. Prophage excision involves a second site-specific recombination event, in which the sites generated by integration, attL and attR, are used as substrates to regenerate attP and attB. Excision is catalyzed by integrase but also requires a phage-encoded recombination directionality factor (RDF). The Bxb1 recombination sites, attP and attB, are small (<50 bp), different in sequence, and quasisymmetrical, and they give rise to attL- and attR-recombinant products that are asymmetric but similar to each other, each being composed of B- and P-type half-sites. We show here that the determination of correct excision products is a two-step process, with a presynaptic RDF-dependent step that aligns attL and attR in the correct orientation and a postsynaptic step in which the nonpalindromic central dinucleotide confers identity to attL and attR and prevents each from recombining with itself.
authors.affiliation: Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Ghosh
authors.forename: Lori A
authors.initials: LA
authors.lastname: Bibb
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D001287:Attachment Sites, Microbiological; D004247:DNA; D019426:Integrases / Q000737:chemistry / Q000378:metabolism*; D009160:Mycobacteriophages / Q000201:enzymology; D009711:Nucleotides; D011487:Protein Conformation; D011995:Recombination, Genetic
chemical_list: D009711:Nucleotides; D004247:DNA; D019426:Integrases