Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021

Abstract

Sinorhizobium meliloti is an alpha-proteobacterium that forms agronomically important N(2)-fixing root nodules in legumes. We report here the complete sequence of the largest constituent of its genome, a 62.7% GC-rich 3,654,135-bp circular chromosome. Annotation allowed assignment of a function to 59% of the 3,341 predicted protein-coding ORFs, the rest exhibiting partial, weak, or no similarity with any known sequence. Unexpectedly, the level of reiteration within this replicon is low, with only two genes duplicated with more than 90% nucleotide sequence identity, transposon elements accounting for 2.2% of the sequence, and a few hundred short repeated palindromic motifs (RIME1, RIME2, and C) widespread over the chromosome. Three regions with a significantly lower GC content are most likely of external origin. Detailed annotation revealed that this replicon contains all housekeeping genes except two essential genes that are located on pSymB. Amino acid/peptide transport and degradation and sugar metabolism appear as two major features of the S. meliloti chromosome. The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.

Figure 1

(a) Distribution of GC content variation (sliding windows of 10,000 bp and a step of 5,000 bp). Six regions with a lower GC percentage are discernible. (b) GC skew [(G − C)/(G + C)] calculated with a sliding window of 10,000 bp and a step of 5,000 bp.

Figure 2

Structure of the chromosomal nucleotide cyclases of S. meliloti. *, the CyaC catalytic domain is masked by ProDom PD117127 domain (52). CyaJ is an intermediate between types I and II.