DNA methylation patterns differ between free-living Rhizobium leguminosarum RCAM1026 and bacteroids formed in symbiosis with pea (Pisum sativum L.)

Abstract

Rhizobium leguminosarum (Rl) is a common name for several genospecies of rhizobia able to form nitrogen-fixing nodules on the roots of pea (Pisum sativum L.) and undergo terminal differentiation into a symbiotic form called bacteroids. In this work, we compared the genomes of the free-living and differentiated forms of the Rl strain RCAM1026 using Oxford Nanopore long reads. No significant genome rearrangements were observed, but the relative abundances of replicons were different between the cell states. GANTC, GGCGCC and GATC methylated motifs have been found in the genome, along with genes for methyltransferases with matching predicted targets. Methylation patterns for the GANTC and GATC motives differed significantly depending on the cell state, which indicates their possible connection to the regulation of symbiotic differentiation. The GGCGCC motif was completely methylated in both bacteria states, and, apparently, is a target for the modification-restriction system. Currently, the methylation patterns in symbiotic bacteria are not extensively studied, so a further investigation of the topic coupled with gene expression data is needed to elucidate the function of differential methylation in terminal differentiation of R. leguminosarum and other rhizobia.