Azospirillum: effective plasmid management

Abstract

Azospirillum is a genus of nitrogen-fixing alpha-proteobacteria whose genomes consist of a chromosome and several large secondary replicons. The organization and evolution of these replicons remain poorly understood. We analyzed 22 complete Azospirillum genomes, containing six to ten replicons, and characterized their gene composition, replication, segregation, and dimer resolution systems. The largest replicon contains most of the essential genes and is the chromosome. Other replicons can be classified based on genecomposition, similarity of the plasmid replication protein RepA, and similarity of the ParAB segregation proteins. Overall, groups obtained using different approaches agree with each other. Analysis of gene composition also identified fusions or splits of secondary replicons. None of the large secondary replicons of Azospirillum strains contain the repABC replication system, and all of them are iteron plasmids. For all groups of replicons, the RepA box motifs and the structure of the plasmid replication origin oriV were predicted. Most replicons use the ParABS system for segregation. In rare cases, the replicon contains repA from one group and parAB from another. The position of the parAB operon relative to the replication origin is determined by the parAB group, and not by repA. Most secondary replicons apparently use an FtsK-dependent pathway for dimer resolution, relying instead on the chromosomally encoded XerCD proteins. In most cases, the identified dif motifs do not distinguish groups of replicons.