Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti

Abstract

The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

“…Rhizobial genomes are subdivided into genome regions specific for their life stages, with chromosomal loci expressed during free-living phases in the soil and symbiosis loci expressed inside of host cells [13,14]. Symbiosis loci required for host nodulation and nitrogen fixation are clustered onto large plasmids or genomic islands [15][16][17][18][19], that can be transferred among lineages, presumably via conjugation [20][21][22]. Non-nodulating rhizobia are also common [23,24], and these strains often lack some or all of the characterized symbiosis loci [23][24][25][26][27][28].…”

Genes commonly involved in acid tolerance are not overexpressed in the plant microsymbiont Mesorhizobium loti MAFF303099 upon acidic shock

“…%GC data: above average (red) and below average (orange). The symbiosis island is marked in blue in the chromosome plot (coordinates 4644792 to 5255766) (Kaneko et al 2000). Some of the most relevant genes in the acid shock response are mapped in the chromosome plot (Color figure online) Table 3 List of genes with higher increased expression (M≥2) upon the acidic shock NCBI gene annotation was used, except for grey-shaded gene descriptions, which are the result of Blast2GO analysis Chr chromosome, pMLa plasmid, pMLb plasmid, − COG not determined a COG category letters according to NCBI functional categories (http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi) correlation between exopolysaccharide synthesis and acid tolerance (Chen et al 1993).…”

“…Since the full-genome annotation available for M. loti strain MAFF303099 was published in 2000 (Kaneko et al 2000), most of the genes found to be overexpressed encode unknown or hypothetical proteins. We used Blast2GO (Götz et al 2008) to annotate all differentially expressed genes encoding unknown or hypothetical proteins and STRING (http://stringdb.org) to assign Clusters of Orthologous Groups (COGs) (http://www.ncbi.nlm.nih.gov/COG/) to these newly annotated genes (Szklarczyk et al 2011).…”

“…Low M values were considered, as long as p≤0.01, since low level changes in gene transcription, commonly disregarded, may be an important part of cells response, as pointed out by Wren and Conway (2006). From the 7,231 genes annotated in the M. loti MAFF303099 genome, 6,702 are located in the chromosome, 320 in pMLa and 209 in pMLb (Kaneko et al 2000). Replicon distribution analysis of the 433 differentially expressed genes showed that 400 (92 %) are chromosomal, 13 (3 %) are in pMLa and 20 (5 %) are in pMLb.…”

“…The expression level of genes located in the symbiosis island remains essentially unaltered (Fig. 2a), with only eight genes (approximately 1 %) being differentially expressed, namely, three overexpressed and five underexpressed, among a total of 580 genes (Kaneko et al 2000).…”