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 16 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.
Highlights
Computational searches of intergenic regions, promoters and rho-independent transcription terminators (Livny et al, 2005; 2006; Sridhar and Gunasekaran, 2013; Wright et al, 2013) combined with experimental approaches (Sharma and Vogel, 2009) have revealed the presence of several small RNAs in bacterial genomes
Bacterial Ribonuclease P (PflSS101_0956) was found in the SS101 genome and represents a ribonucleoprotein complex comprised of a single RNA (∼ 400 nt) and a single small protein subunit (∼ 14 kDa) with the RNA as the catalytic subunit of the enzyme involved in the maturation of tRNA transcripts (Ellis and Brown, 2009)
Subsequent experiments revealed, for the first time, that the Rsm signal transduction pathway plays a critical role in the regulation of massetolide biosynthesis, a cyclic lipopeptide important for biofilm formation, swarming motility, antimicrobial activity and induction of systemic resistance in plants
Summary
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 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. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/RsmZ are Received 15 July, 2014; revised 29 September, 2014; accepted 2 October, 2014. 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
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