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

Lisa C Crossman,J Peter W Young,Georgina Meakin,Ismael Hernández-González,José L Acosta,Luis Lozano,Alan W Walker,Georgios S Vernikos,Víctor González,Zara F Ghazoui,Michael F Hynes,Craig Mcannula,Julian Parkhill,Guillermo Dávila,Santiago Castillo-Ramírez,Andrew W B Johnston,David Romero,J Allan Downie,Richard R Copley

doi:10.1371/journal.pone.0002567

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.

Highlights

Rhizobium etli and Rhizobium leguminosarum bv viciae are closely related species which are able to fix atmospheric nitrogen in symbiosis with specific leguminous plants
Main features of the compared species Both R. etli CFN42 and R. leguminosarum 3841 have large genomes composed of a circular chromosome and six large plasmids [1,2]
In R. leguminosarum, pRL7 and pRL8 are transmissible by conjugation, neither carries a full set of tra genes [2]

Summary

Introduction

Rhizobium etli and Rhizobium leguminosarum bv viciae ( called R. leguminosarum) are closely related species which are able to fix atmospheric nitrogen in symbiosis with specific leguminous plants. We reported the complete genome sequences of a strain of R. etli and a strain of R. leguminosarum [1,2], but no comprehensive genome comparison between these species had been carried out. Several other complete genome sequences of symbiotic nitrogen fixing bacteria have been published: Mesorhizobium loti, Bradyrhizobium japonicum, B. spp. Our comparisons of R. etli and R. leguminosarum show that: 1) Rhizobium genomes are composed of ‘‘core’’ and ‘‘accessory’’ components; 2) the chromosomes are markedly conserved in gene content (despite differences in size) and amongst the closest species gene order is conserved; 3) the plasmids are heterogeneous in size and gene content and in some cases no synteny can be seen even in comparison with phylogenetic neighbours

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Conclusion