title: The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis.
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.
authors.affiliation: Laboratory of Phytopathology, Wageningen University, 6708 PD, Wageningen, the Netherlands; Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, the Netherlands.
authors.forename: Chunxu
authors.initials: C
authors.lastname: Song
authors.forename: Menno
authors.initials: M
authors.lastname: van der Voort
authors.forename: Judith
authors.initials: J
authors.lastname: van de Mortel
authors.forename: Karl A
authors.initials: KA
authors.lastname: Hassan
authors.forename: Liam D H
authors.initials: LD
authors.lastname: Elbourne
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Joyce E
authors.initials: JE
authors.lastname: Loper
authors.forename: Jos M
authors.initials: JM
authors.lastname: Raaijmakers
mesh_terms: D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D055666:Lipopeptides / Q000096:biosynthesis*; D011551:Pseudomonas fluorescens / Q000235:genetics* / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000378:metabolism*; D018085:Regulon
chemical_list: D055666:Lipopeptides; D058727:RNA, Small Untranslated