Exploring the genome-wide expression level of the bacterial strain belonging to Bacillus safensis (MM19) against Phomopsis viticola

Abstract

IntroductionRhizobacteria has the suppression ability to compete with pathogenic microorganisms and help for plant immunity and defense mechanism. Their growth and survival in rhizosphere ensure biological balance in favor of the host plant. MethodsIn our study, with agar diffusion assays, we found a rhizobacterium species belonging to Bacillus safensis, which can significantly suppress Phomopsis viticola. To elucidate the antagonistic mechanism, genome-wide gene expression profiling of B. safensis (strain MM19) was performed in the presence and absence of P. viticola. We used RNA-seq analysis to obtain a comprehensive overview of the responsive B. safensis whole gene expression classified according to biological and metabolic process to P. viticola concomitant growth in liquid culture. ResultsThe differential gene expression profiles of B. safensis (MM19) revealed significantly increased expression of prominent genes related to thiamine biosynthesis involving various metabolites and enzymes that play role in the suppression of mycelium growth and pathogen inhibition. Correspondingly, the expression of three major genes (HOG1, FUS3, SGI) involving in the virulence of P. viticola was followed using qPCR analysis. HOG1 was the highest expressed gene in the pathogen when it co-cultivated with MM19. Based on these findings, we performed molecular docking and dynamics analysis to explore the interaction between HOG1 and thiamine, besides expression of network analysis constructed using Cytoscape. DiscussionThe results proved that the functional genomic data related to thiamine biosynthesis and corresponding pathways ensure a priming role in the antagonistic behavior of B. safensis (MM19) against P. viticola as a supporter for plant immunity.