Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

Abstract

BackgroundSinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains.ResultsWith sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.ConclusionsIn conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

Rhizobial peptidase HrrP cleaves host-encoded signaling peptides and mediates symbiotic compatibility

“…The genetic landscape adjacent to hrrP has been determined for only two plasmids: the pHR from strain B800 and an accessory plasmid (pSINME01) from S. meliloti strain AK83, which is noted for its ineffective nitrogen fixation (16). Despite 97.4% nucleotide sequence identity between these hrrP homologs, there is no synteny surrounding the hrrP coding region; even the promoter regions are highly divergent (Fig.…”

Effect of the plant flavonoid luteolin on Ensifer meliloti 3001 phenotypic responses

“…Notably, the NodD regulon, comprising luteolin-inducible and NodDdependent genes (Barnett et al 2004;Capela et al 2005), showed that the biosynthesis of NFs is one of the major pathways induced by the luteolin, but not the only one. Indeed, other additional genes are induced by the perception of plant flavonoid signals or show in their promoter region putative binding sites for NodD besides those related to NF biosynthesis (Batista and Hungria 2012;Galardini et al 2011;Lang et al 2008;Guerreiro et al 1997;Tolin et al 2013). Similarly to other plant flavonoids, luteolin was found to induce in E. meliloti, in addition to nod genes, the expression of genes encoding the EmrAB efflux pump, the GroES and GroEL chaperonins, as well as the SyrM transcriptional regulator and three hypothetical proteins (Capela et al 2005).…”

Development of promiscous rhizobia for diverse rabi legumes (Chickpea, Pea and Lentil)

“…The previous studies indicate that plasmid transfer or plasmid loss may increase nodulation or nitrogen fixation in Rhizobia strains (DeJonj et al, 1982, Pankhurst et al, 1986. Previous studies show that plasmid can be transferred from different genomic backgrounds that can extend nodulation hostrange (Galardini et al, 2011, Gonzalo et al, 2011. These observations taken together indicate that these isolates behave like parasitic organisms rather than bona-fide legume symbionts (Kundu and Dudeja, 2008, Oldroyd et al, 2011and Nadwani and Dudeja, 2013.…”