The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis

摘要

Interpretive Summary: Biological control provides a promising strategy for managing plant diseases, but has not yet been utilized widely in agriculture due, in part, to unexplained variation in its success in managing disease. Our research goals are to identify sources of variation in biological control, and devise ways to make it more reliable. We focus on Pseudomonas fluorescens, which is a species of bacteria that occurs naturally on plant surfaces such as leaves and roots. In this study, we evaluated the roles of two small RNAs (called rsmY and rsmZ) of gene expression in the plant-associated bacterium P. fluorescens SBW25. We show that these small RNAs influenced the transcription of many genes that have diverse functions in this bacterium. We conclude that the rsmY and rsmZ of P. fluorescens SS101 plays critical role in the regulation of lipopeptide biosynthesis and control the expression of other genes involved in motility, competition and survival in the plant rhizosphere. Technical Abstract: The rhizobacterium Pseudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome-wide search for sRNAs and performed transcriptomic analyses to identify genes associated with the Rsm (repressor of secondary metabolites) regulon. In silico analysis led to the identification of sixteen putative sRNAs in the SS101 genome. In frame deletion of the sRNAs rsmY and rsmZ showed that the Rsm system regulates the biosynthesis of the lipopeptide massetolide A and involves the two repressor proteins RsmA and RsmE, with the LuxR-type transcriptional regulator MassAR as their most likely target. Transcriptome analyses of the rsmYZ mutant further revealed that genes associated with iron acquisition, motility and chemotaxis were significantly upregulated, whereas genes of the type VI secretion system were downregulated. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/RsmZ are also controlled by the GacS/GacA two-component system. We conclude that the Rsm regulon of P. fluorescens SS101 plays a critical role in the regulation of lipopeptide biosynthesis and controls the expression of other genes involved in motility, competition and survival in the plant rhizosphere.