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

Abstract

Sinorhizobium meliloti is an ␣-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 acid͞peptide 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.

Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade

“…The other flagellin gene, flaE, is located on plasmid pRL11JI. The flagellin genes of R. leguminosarum encode proteins of around 300 amino acids, which are considerably shorter than the flagellins (321-401 amino acids) of S. meliloti (Capela et al, 2001). Five of the flagellin genes (flaABCEG) encode highly similar proteins, while flaD and flaH are quite divergent.…”

A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote–host interaction

“…It is common for members of the ␣-proteobacteria to have complex genome architectures (9). S. meliloti has three circular replicons: a chromosome (3.65 Mb) that encodes most of the housekeeping and essential genes (10) and two megaplasmids, pSymA (1.4 Mb) and pSymB (1.7 Mb) (11). pSymA is not essential for viability but contains many of the genes required for symbiosis [nod, nif, and most fix genes (12,13)].…”

The complete sequence of the 1,683-kb pSymB megaplasmid from the N 2 -fixing endosymbiont Sinorhizobium meliloti

“…Many (but not all) of the bacteria that form N 2 -fixing root nodules on leguminous plants are characterized by the presence of multiple plasmids greater than 400 kb in size. In the case of the N 2 -fixing symbiont Sinorhizobium meliloti, there are three replicons, a 3,654-kb circular chromosome (3,4) and two megaplasmids 1,354 and 1,683 kb in size (5)(6)(7). The smaller of the megaplasmids, variously called pSymA, pNod-Nif, or pRmeSU47a, is known to carry many of the genes involved in root nodule formation (nod) and nitrogen fixation (nif ) (8,9).…”