Abstract
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 ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, 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 ICEMlSymR7A.
Highlights
Horizontal gene transfer (HGT) is a major force shaping bacterial evolution [1,2,3,4,5]
Most genomes analysed here are from strains isolated from root nodules of legume hosts Cicer, Lotus or Biserrula and included are single strains isolated from Astragalus sinicus and Robinia pseudoacacia
Of the pangenome genes present on an identifiable mobile genetic elements (MGE) (12 %), more than 70 % were present across 56 integrative and conjugative elements (ICEs) related to ICEMlSymR7A, including the largest mobile ICE characterised to date, ICEMsp.SymAA22
Summary
Horizontal gene transfer (HGT) is a major force shaping bacterial evolution [1,2,3,4,5]. Transfer of suites of genes encoding metabolic pathways refined by selection in a donor organism can endow recipients of HGT with the ability to colonise. The conjugative machinery of ICEs and conjugative plasmids can facilitate horizontal transfer of co-resident non-conjugative elements such as mobilizable plasmids and integrative mobilizable elements (IMEs) [24]
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