Mosaic plasmids and mosaic replicons: evolutionary lessons from the analysis of genetic diversity in IncFII-related replicons

School of Biological Sciences, Life Science Building, The University of Liverpool, PO Box 147, Liverpool L69 7ZB, UK 1 Department of Medical Biochemistry 2 and Department of Medical Microbiology 3 , Medical School, University of Cape Town, Observatory 7925, Cape Town, South Africa Department of Biochemistry, University of Otago, Dunedin, New Zealand 4 Institute of Freshwater Ecology, Windermere Laboratories, The Ferry House, Ambleside, Cumbria LA22 0LP, UK 5 Author for correspondence: A. Mark Osborn. Tel: +44 1206 87 3763. Fax: +44 1206 87 2592. e-mail: osborn{at}essex.ac.uk The alpha replicons of the multi-replicon plasmids pGSH500 and pLV1402 have been characterized by DNA sequence analysis. Analysis of the DNA sequence of a 3672 bp Hin dIII fragment from pFDT100, which contains the pGSH500 alpha replicon, revealed similarity to a number of replicons belonging to, or related to, those of the IncFII family. The replicon region contains copA , tapA , repA and oriR , and replication initiation and termination sites are related to those from the IncFII replicon of R1. A copB gene was found to lie upstream of the Hin dIII site in the parental plasmid pGSH500. Downstream of oriR , a 707 bp region shows 72·6% identity to a region of the Escherichia coli chromosome at 43·3', suggesting this region of pGSH500 may have been incorporated into the plasmid during a past chromosomal recombination event. Oligonucleotide primers homologous to consensus regions in the copB and repA genes, and the oriR regions from a number of IncFII-related replicons were used to amplify replication regions from pLV1402. Analysis of the amplified regions has shown the presence of copB , copA , tapA and repA genes. Phylogenetic analysis of Rep protein sequences from the RepFIIA family of antisense-control-regulated replicons revealed the presence of three distinct subgroups of Rep proteins. Comparative analysis of DNA and protein sequences from members of the RepFIIA family provides evidence supporting the roles of both non-selective divergence in co-integrate (multi-replicon) plasmids and Chi-mediated-recombination in replicon evolution, and in particular, that such processes may have been widespread in the evolution of the RepFIIA family. Keywords: plasmid, incompatibility, evolution, replicon, pGSH500 The EMBL accession numbers for the sequences reported in this paper are AJ009980 (pGSH500 alpha replicon) and AJ009981 (pLV1402 alpha replicon). a Present address: Department of Biologica