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Nucleic Acids Research Advance Access published online on November 13, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp990
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity

Clara Frumerie1, Magaly Ducos-Galand1, Deshmukh N. Gopaul2 and Didier Mazel1,*

1Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS URA 2171 and 2Unité d'I;mmunologie Structurale, CNRS URA 2185, 25 rue du Dr Roux, 75724, Paris, France

*To whom correspondence should be addressed. Tel: +33 1 40 61 32 84; Fax: +33 1 45 68 88 34; Email: mazel{at}pasteur.fr

Received August 10, 2009. Revised October 14, 2009. Accepted October 15, 2009.

Integrons are able to incorporate exogenous genes embedded in mobile cassettes, by a site-specific recombination mechanism. Gene cassettes are collected at the attI site, via an integrase mediated recombination between the cassette recombination site, attC, and the attI site. Interestingly, only three nucleotides are conserved between attC and attI. Here, we have determined the requirements of these in recombination, using the recombination machinery from the paradigmatic class 1 integron. We found that, strikingly, the only requirement is to have identical first nucleotide in the two partner sites, but not the nature of this nucleotide. Furthermore, we showed that the reaction is close to wild-type efficiency when one of the nucleotides in the second or third position is mutated in either the attC or the attI1 site, while identical mutations can have drastic effects when both sites are mutated, resulting in a dramatic decrease of recombination frequency compared to that of the wild-type sites. Finally, we tested the functional role of the amino acids predicted from structural data to interact with the cleavage site. We found that, if the recombination site triplets are tolerant to mutation, the amino acids interacting with them are extremely constrained.

Present address: Clara Frumerie. Department of Molecular Biology and Functional Genomics, Stockholm University, Svante Ahrenius väg 18F, 106 91 Stockholm, Sweden.


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