Integration and excision by the large serine recombinase φRv1 integrase

Authors

  • Lori A. Bibb,

    1. Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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  • Maria I. Hancox,

    1. Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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  • Graham F. Hatfull

    Corresponding author
    1. Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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E-mail gfh@pitt.edu; Tel. (+1) 412 624 4350; Fax (+1) 412 624 4870.

Summary

The Mycobacterium tuberculosis prophage-like element φRv1 encodes a site-specific recombination system utilizing an integrase of the serine recombinase family. Recombination occurs between a putative attP site and the host chromosome, but is unusual in that the attB site lies within a redundant repetitive element (REP13E12)  of  which  there  are  seven  copies  in  the M. tuberculosis genome; four of these elements contain attB sites suitable for φRv1 integration in vivo. Although the mechanism of directional control of large serine integrases is poorly understood, a recombination directionality factor (RDF) has been identified that is required for φRv1 integrase-mediated excisive recombination in vivo. Here we describe defined in vitro recombination reactions for both φRv1 integrase-mediated integration and excision and show that the φRv1 RDF is not only required for excision but inhibits integrative recombination; neither reaction requires DNA supercoiling, host factors, or high-energy cofactors. Integration, excision and excise-mediated inhibition of integration require simple substrates sites, indicating that the control of directionality does not involve the manipulation of higher-order protein–DNA architectures as described for the tyrosine integrases.

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