Integration and excision by the large serine recombinase φRv1 integrase

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Abstract
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.