Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae

Abstract

Burkholderia glumae is the primary causal agent of bacterial panicle blight of rice, which is becoming a major threat to global rice production. The genome of a highly virulent B. glumae strain, 336gr-1 that was isolated from rice in Louisiana, was sequenced to better understand the genome-scale characteristics, particularly that of its pathogenicity. Comparative genomic analyses with another strain, BGR1 that was isolated from Korea, revealed several unique regions present in the genomes of these two geographically separated phytopathogenic bacteria. Genome plasticity, primarily caused by a horizontal gene transfer, was observed in these closely related strains of Burkholderia that are capable of infecting the same host plant. The highly conserved nature of chromosome 2, along with the presence of important virulence determinant gene coding regions in it, such as those involved in type III secretion and toxoflavin production, indicates its importance in pathogenesis. The presence of multiple genomic islands, detectable pseudo genes, insertions, deletions, and paralogous genes indicates recent adaptation to diverse ecological niches and reduced selection pressures in specific regions of the B. glumae genome. These findings would help explain the genotype and host range diversity of B. glumae and augment characterization of its ecology and pathogenesis. Characterization of ECF σ70 gene and σ54 dependent response regulator gene in B. glumae has revealed that they are not directly involved in pathogenicity in this phytopathogenic bacterium. Global transcriptome analysis of B. glumae strain 336gr-1 has revealed that the expression of 87 genes is influenced by the quorum sensing genes tofI/tofR and their intergenic region, orf1. Especially, the genes for the type II secretion system and diguanylatecyclase activity, which play important roles in the pathogenesis of B. glumae, were found to be regulated by quorum sensing mechanism.