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J. Biol. Chem., Vol. 282, Issue 30, 21798-21809, July 27, 2007

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Control and Regulation of KplE1 Prophage Site-specific Recombination

A NEW RECOMBINATION MODULE ANALYZED^*

From the Laboratoire de Chimie Bactérienne, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier, Marseille 13402, Cedex 20, France

KplE1 is one of the 10 prophage regions of Escherichia coli K12, located at 2464 kb on the chromosome. KplE1 is defective for lysis, but it is fully competent for excisive recombination. In this study, we have mapped the binding sites of the recombination proteins, namely IntS, TorI, and IHF on attL and attR, and the organization of these sites suggests that the intasome is architecturally different from the canonical form. We also measured the relative contribution of these proteins to both excisive and integrative recombination by using a quantitative in vitro assay. These experiments show a requirement of the TorI excisionase for excisive recombination and of the IntS integrase for both integration and excision. Moreover, we observed a strong influence of the supercoiled state of the substrates. The KplE1 recombination module, composed of the integrase and excisionase genes together with the attL and attR DNA regions, is highly similar to that of several phages infecting various E. coli strains as well as Shigella flexneri and Shigella sonnei. The in vitro recombination data reveal that HK620 and KplE1 att sequences are exchangeable. This study thus defines a new site-specific recombination module, and implications for the mechanism and regulation of recombination are discussed.

Received for publication, March 2, 2007 , and in revised form, May 22, 2007.

^* This work was supported by CNRS and by the Agence Nationale pour la Recherche (Grant JC05_41524 to M. A.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ A fellowship recipient from the French Research Ministry.

² To whom correspondence should be addressed: Tel.: 33-4-91-16-45-85; Fax: 33-4-91-71-89-14; E-mail: ansaldi{at}ibsm.cnrs-mrs.fr.

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