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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 584.
Published online Dec 7, 2009. doi:  10.1186/1471-2164-10-584
PMCID: PMC2935791
Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement
Andrew P Jackson,corresponding author1 Gavin H Thomas,2 Julian Parkhill,1 and Nicholas R Thomson1
1The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
2Department of Biology, University of York, PO Box 373, York, YO10 5YW, UK
corresponding authorCorresponding author.
Andrew P Jackson: aj4/at/sanger.ac.uk; Gavin H Thomas: ght2/at/york.ac.uk; Julian Parkhill: parkhill/at/sanger.ac.uk; Nicholas R Thomson: nrt/at/sanger.ac.uk
Received July 28, 2009; Accepted December 7, 2009.
Abstract
Background
Rhs genes are prominent features of bacterial genomes that have previously been implicated in genomic rearrangements in E. coli. By comparing rhs repertoires across the Enterobacteriaceae, this study provides a robust explanation of rhs diversification and evolution, and a mechanistic model of how rhs diversity is gained and lost.
Results
Rhs genes are ubiquitous and comprise six structurally distinct lineages within the Enterobacteriaceae. There is considerable intergenomic variation in rhs repertoire; for instance, in Salmonella enterica, rhs are restricted to mobile elements, while in Escherichia coli one rhs lineage has diversified through transposition as older lineages have been deleted. Overall, comparative genomics reveals frequent, independent gene gains and losses, as well as occasional lateral gene transfer, in different genera. Furthermore, we demonstrate that Rhs 'core' domains and variable C-termini are evolutionarily decoupled, and propose that rhs diversity is driven by homologous recombination with circular intermediates. Existing C-termini are displaced by laterally acquired alternatives, creating long arrays of dissociated 'tips' that characterize the appearance of rhs loci.
Conclusion
Rhs repertoires are highly dynamic among Enterobacterial genomes, due to repeated gene gains and losses. In contrast, the primary structures of Rhs genes are evolutionarily conserved, indicating that rhs sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations. Hence, we predict that a large pool of dissociated rhs C-terminal tips exists episomally and these are potentially transmitted across taxonomic boundaries.
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