title: The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups.
abstract: The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. In an analysis of 18 such plasmids these elements fall into two organizational classes, Group I and Group II, based on the sites at which cargo DNA is located. Cladograms constructed from proteins of the transfer and quorum-sensing components indicated that those of the Group I plasmids, while coevolving, have diverged from those coevolving proteins of the Group II plasmids. Moreover, within these groups the phylogenies of the proteins usually occupy similar, if not identical, tree topologies. Remarkably, such relationships were not seen among proteins of the replication system; although RepA and RepB coevolve, RepC does not. Nor do the replication proteins coevolve with the proteins of the transfer and quorum-sensing systems. Functional analysis was mostly consistent with phylogenies. TraR activated promoters from plasmids within its group, but not between groups and dimerized with TraR proteins from within but not between groups. However, oriT sequences, which are highly conserved, were processed by the transfer system of plasmids regardless of group. We conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign.
authors.forename: Margaret E
authors.initials: ME
authors.lastname: Wetzel
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign.
authors.forename: Vandana
authors.initials: V
authors.lastname: Chakravartty
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign stephenf@life.illinois.edu.
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Farrand
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004265:DNA Helicases / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D010957:Plasmids / Q000235:genetics; D053038:Quorum Sensing / Q000235:genetics*; D012230:Rhizobiaceae / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; C048817:RepB protein, Bacteria; D015534:Trans-Activators; C045264:replication initiator protein; D004265:DNA Helicases
keywords: Alphaproteobacteria; RepABC; conjugative transfer genes; horizontal transfer; plasmid evolution; quorum-sensing