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

Abstract

Members of the <i>Mesorhizobium</i> genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised <i>Mesorhizobium</i> 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 <i>Mesorhizobium</i> 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 ICE<i>M</i>spSym^AA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICE<i>Ml</i>Sym^R7A, with each carrying conserved genes for conjugative pilus formation (<i>trb</i>), excision (<i>rdfS</i>), DNA transfer (<i>rlxS</i>) and regulation (<i>fseA</i>). 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 <i>trbK</i>. 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 <i>Mesorhizobium</i> genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICE<i>Ml</i>Sym^R7A.