A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria

Abstract

This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

“…Rhizobial plasmid replicons have less synteny than chromosomes [33], and it is possible that such mosaic plasmid structure results from frequent genetic rearrangements [34]. Moreover, some of them are selftransmissible or can be transferred to other bacterial cells in the presence of other plasmids [35,36].…”

“…The frequency of plasmid transfer between rhizobial strains and the role of this genetic exchange in rhizobial evolution remains controversial [37][38][39][40]. However, the pool of plasmid replicons present in rhizobial cells is regarded as a (mostly) accessory genetic component which is evolving more rapidly than the chromosome [33], due to frequent changes (such as gene duplication, mutation or deletion) within particular replicons [41] or rearrangements between different replicons [42,43]. This distinction between the rhizobial chromosome and plasmids in the context of `evolutionary plasticity' and the role of these replicons in bacterial diversification resulted in the emergence of genomical concepts, which are similar to the pan-genome idea.…”

Rhizobial plasmids — replication, structure and biological role

“…viciae (Rlv) and trifoli (Rlt) are closely related species differing in their host-specificity but displaying very similar genome organization: a single circular chromosome and several large plasmids. Each of them carries the majority of nod-nif-fix genes on the plasmid, named pSym [17,36,46,47,82], but the pSyms of Rhe, Rlv and Rlt belong to different incompatibility groups and have quite different genes content other than those related to symbiotic performance [14,30,83]. In contrast to Sme, several major cluster of genes engaged in the biosynthesis of various surface polysaccharides are chromosomal.…”

“…Other essential plasmid genes include major heat-shock chaperone genes cpn10/cpn60 (groES/groEL) on pRL12JI, and ribosomal protein S21 on pRL10JI (pSym); however, these genes have chromosomal paralogs so the different copies may be simply functionally redundant [17,85]. pRL12JI similarly to the pRetCFN42f of Rhe carries some genes for flagella biosynthesis and oxidative stress protection [83]. Elimination of pRL12JI from Rlv 1061 strain (derivative of the same parental strain as the sequenced Rlv 3841), resulted in an auxotrophic phenotype, which might severely compromise fitness in nature [86].…”

“…Moreover, pRetCNF42f of Rhe carries panC and panB genes, which are indispensable for pantothenate synthesis and required for growth in minimal medium [90]. Putative nitric oxide removal genes are also located on this plasmid [83]. Nearly 11% of the genes of the pRetCNF42e are involved in primary metabolism, both in biosynthetic functions (cobalamin, cardiolipin, NAD, thiamine) and degradation (asparagine and melibiose) [36].…”