Integration and excision by the large serine recombinase φRv1 integrase

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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