The Evolution of Sinorhizobium meliloti.

Abstract

The genome of the a-proteobacterium Sinorhizobium meliloti has been completely sequenced and annotated. providing a wealth of information about this endosymbiotic N2 fixing organism. Although the structure of the genome, consisting of a circular chromosome and two smaller pSymA and pSymB replicons, has long been known, only a small portion of ORFs have previously been characterized. Sequence analysis of pSymB has revealed that a large portion of the 1570 ORFs code for solute uptake systems and polysaccharide biosynthesis. The pSymB replicon been referred to as a "megaplasmid," implying that pSymB is non-essential for viability of the organism. However, coded on pSymB are several essential genes, including a tRNA ArgCCG gene and the minCDE genes, which are not found elsewhere in the genome. Replication of pSymB is controlled by repABC genes, a typical property of plasmids among Rhizobiaceae. Therefore, the genome signature, a compositional analysis that allows comparison of whole replicons rather than focusing on particular genes, was used to provide support for designation of pSymB as a second chromosome in S. mdiloti. It was found that among a-proteobacteria, plasmids and chromosomes have distinctive patterns of dinucleotide biases, and in this respect, pSymB is chromosome-like while pSymA is plasmid-like. This brings into question how the pSymB replicon came to acquire chromosome-like properties while appearing to be maintained as a plasmid in the genome. Whole-genome nearest neighbor analysis shows that the linear chromosome of Agrobacterium tumefaciens and pSymB may have a common origin. Despite conservation of gene order within small groups of genes, it is evident that rearrangements, duplications, and horizontal transfer of genes since the divergence of these species have contributed to the mosaic nature of pSymB. Since synteny between the S. meliloti chromosome and A. tumefaciens circular chromosome is highly conserved, it appears that the instability of pSy mB has played a key role in the adaptation and evolution of S. meliloti.