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Journal of Bacteriology, June 2002, p. 3017-3026, Vol. 184, No. 11
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.11.3017-3026.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Characterization of the Class 3 Integron and the Site-Specific Recombination System It Determines

Christina M. Collis,1 Mi-Jurng Kim,2 Sally R. Partridge,1,2 H. W. Stokes,2 and Ruth M. Hall1*

Sydney Laboratory, CSIRO Molecular Science, North Ryde, New South Wales 1670,1 Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia2

Received 13 November 2001/ Accepted 6 March 2002

Integrons capture gene cassettes by using a site-specific recombination mechanism. As only one class of integron and integron-determined site-specific recombination system has been studied in detail, the properties of a second class, the only known class 3 integron, were examined. The configuration of the three potentially definitive features of integrons, the intI3 gene, the adjacent attI3 recombination site, and the Pc promoter that directs transcription of the cassettes, was similar to that found in the corresponding region (5' conserved segment) of class 1 integrons. The integron features are flanked by a copy of the terminal inverted repeat, IRi, from class 1 integrons on one side and a resolvase-encoding tniR gene on the other, suggesting that they are part of a transposable element related to Tn402 but with the integron module in the opposite orientation. The IntI3 integrase was active and able to recognize and recombine both known types of IntI-specific recombination sites, the attI3 site in the integron, and different cassette-associated 59-be (59-base element) sites. Both integration of circularized cassettes into the attI3 site and excision of integrated cassettes were also catalyzed by IntI3. The attI3 site was localized to a short region adjacent to the intI3 gene. Recombination between a 59-be and secondary sites was also catalyzed by IntI3, but at frequencies significantly lower than observed with IntI1, the class 1 integron integrase.

* Corresponding author. Mailing address: CSIRO Molecular Science, Sydney Laboratory, P.O. Box 184, NSW 1670, Australia. Phone: 61-2-94905162. Fax: 61-2-94905005. E-mail: Ruth.Hall{at}csiro.au.

Journal of Bacteriology, June 2002, p. 3017-3026, Vol. 184, No. 11
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.11.3017-3026.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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