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Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium

Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbio...

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Autores principales: Colombi, Elena, Perry, Benjamin J., Sullivan, John T., Bekuma, Amanuel A., Terpolilli, Jason J., Ronson, Clive W., Ramsay, Joshua P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627217/
https://www.ncbi.nlm.nih.gov/pubmed/34605762
http://dx.doi.org/10.1099/mgen.0.000657
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author Colombi, Elena
Perry, Benjamin J.
Sullivan, John T.
Bekuma, Amanuel A.
Terpolilli, Jason J.
Ronson, Clive W.
Ramsay, Joshua P.
author_facet Colombi, Elena
Perry, Benjamin J.
Sullivan, John T.
Bekuma, Amanuel A.
Terpolilli, Jason J.
Ronson, Clive W.
Ramsay, Joshua P.
author_sort Colombi, Elena
collection PubMed
description Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSym(AA22). The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSym(R7A), with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSym(R7A).
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spelling pubmed-86272172021-11-29 Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium Colombi, Elena Perry, Benjamin J. Sullivan, John T. Bekuma, Amanuel A. Terpolilli, Jason J. Ronson, Clive W. Ramsay, Joshua P. Microb Genom Research Articles Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSym(AA22). The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSym(R7A), with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSym(R7A). Microbiology Society 2021-10-04 /pmc/articles/PMC8627217/ /pubmed/34605762 http://dx.doi.org/10.1099/mgen.0.000657 Text en © 2021 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License.
spellingShingle Research Articles
Colombi, Elena
Perry, Benjamin J.
Sullivan, John T.
Bekuma, Amanuel A.
Terpolilli, Jason J.
Ronson, Clive W.
Ramsay, Joshua P.
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title_full Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title_fullStr Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title_full_unstemmed Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title_short Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
title_sort comparative analysis of integrative and conjugative mobile genetic elements in the genus mesorhizobium
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627217/
https://www.ncbi.nlm.nih.gov/pubmed/34605762
http://dx.doi.org/10.1099/mgen.0.000657
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