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 themore »
- Authors:
-
- Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Microbiology
- Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Microbiology and Carl R. Woese Inst. for Genomic Biology
- Publication Date:
- Research Org.:
- Univ. of Illinois at Urbana-Champaign, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1288452
- Grant/Contract Number:
- SC0006642; AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Biology and Evolution
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 12; Journal ID: ISSN 1759-6653
- Publisher:
- Society for Molecular Biology and Evolution
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plasmid evolution; RepABC; horizontal transfer; quorum-sensing; Alphaproteobacteria; conjugative transfer genes; multiple sequence alignment; complete nucleotide-sequence; tumefaciens ti plasmid; etli symbiotic plasmid; tumor-inducing ti; trar-like protein; broad-host-range; sp strain ngr234; agrobacterium-tumefaciens; conjugal transfer
Citation Formats
Wetzel, Margaret E., Olsen, Gary J., Chakravartty, Vandana, and Farrand, Stephen K. The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups. United States: N. p., 2015.
Web. doi:10.1093/gbe/evv227.
Wetzel, Margaret E., Olsen, Gary J., Chakravartty, Vandana, & Farrand, Stephen K. The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups. United States. https://doi.org/10.1093/gbe/evv227
Wetzel, Margaret E., Olsen, Gary J., Chakravartty, Vandana, and Farrand, Stephen K. Thu .
"The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups". United States. https://doi.org/10.1093/gbe/evv227. https://www.osti.gov/servlets/purl/1288452.
@article{osti_1288452,
title = {The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups},
author = {Wetzel, Margaret E. and Olsen, Gary J. and Chakravartty, Vandana and Farrand, Stephen K.},
abstractNote = {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. Here, 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.},
doi = {10.1093/gbe/evv227},
journal = {Genome Biology and Evolution},
number = 12,
volume = 7,
place = {United States},
year = {Thu Nov 19 00:00:00 EST 2015},
month = {Thu Nov 19 00:00:00 EST 2015}
}
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Works referencing / citing this record:
Quorum-dependent transfer of the opine-catabolic plasmid pAoF64/95 is regulated by a novel mechanism involving inhibition of the TraR antiactivator TraM
journal, April 2018
- Wetzel, Margaret E.; Asenstorfer, Robert E.; Tate, Max E.
- MicrobiologyOpen, Vol. 8, Issue 1
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex
posted_content, November 2019
- Cavassim, Maria Izabel A.; Moeskjær, Sara; Moslemi, Camous
- bioRxiv
Evolutionary Relatedness and Classification of Tumor-Inducing and Opine-Catabolic Plasmids in Three Rhizobium rhizogenes Strains Isolated from the Same Crown Gall Tumor
journal, April 2019
- Kuzmanović, Nemanja; Puławska, Joanna
- Genome Biology and Evolution, Vol. 11, Issue 6
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex
posted_content, November 2019
- Cavassim, Maria Izabel A.; Moeskjær, Sara; Moslemi, Camous
- bioRxiv