Comparative genomics of the PGPR isolate Methylobacterium sp. 2A

Abstract

Methylobacterium sp. 2A is a plant growth-promoting rhizobacteria (PGPR) that was isolated from roots of potato plants and enhanced growth in potato and Arabidopsis plants under high salt conditions. Whole genome sequencing revealed metabolic pathways associated with its plant growth promoter capacity. A comparative genomic analysis was performed through the pangenomic approach between Methylobacterium sp. 2A and four closest relatives of the genus: M. phyllostachyos BL47, M. organophilum DSM 760, M. radiotolerans JCM 2831, and M. pseudosasicola BL36. A core-genome of 3,584 genes was identified, while 724 genes were exclusive of this isolate. The genomic island (GI) prediction of Methylobacterium sp. 2A and related species was performed by IslandViewer using integrated methods. Although weak, a correlation between GC content and percentage of exclusive genes in GIs was inferred in all species. In the Methylobacterium sp. 2A assembly, 26 genomic islands were predicted with a total of 473 protein-coding genes, representing 8.6 % of the entire genome. The prediction showed that the largest GI has a length of 68.6 Kbp and the smallest 4.3 kbp. Also, a comparison of these organisms was carried out by the functional annotation of COGs and the assignment of them to one of the 26 functional categories. COG analysis showed that COG0784 and COG0840 containing CheY chemotaxis proteins and methyl-accepting chemotaxis proteins (MCPs) are the most abundant ones in the analyzed pangenome. MCPs are chemoreceptors that sense a vast set of environmental signals enabling soil bacteria to establish plant-microbe interactions. Both, MCPs and CheY are involved in signal transduction mechanisms that modulate cell motility. The MCP signaling domain is highly conserved because it maintains multiple protein-protein interactions within the chemoreceptor-kinase complex, while MCP sensory domains are quite variable in sequence. Preliminary phylogenetic analysis of the 55 Methylobacterium sp. 2A MCPs suggests that these proteins are grouped in at least four big clusters. ScanProsite analysis revealed the presence of one or two transducing domains, HAMP, PAS and/or PAC domains in the different analyzed protein sequences. The comparative genomic analysis presented in this work revealed the relationship between Methylobacterium sp. 2A with related members of the genus, providing valuable information on its genetic and evolutionary diversity.