Song Chunxu, van der Voort Menno, van de Mortel Judith, Hassan Karl A, Elbourne Liam D H, Paulsen Ian T, Loper Joyce E, Raaijmakers Jos M
Laboratory of Phytopathology, Wageningen University, 6708 PD, Wageningen, the Netherlands; Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB, Wageningen, the Netherlands.
Microb Biotechnol. 2015 Mar;8(2):296-310. doi: 10.1111/1751-7915.12190. Epub 2014 Dec 9.
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.
荧光假单胞菌SS101可抑制卵菌和真菌病原体的生长，并诱导植物对病原体和昆虫产生抗性。为了阐明SS101中次级代谢产物产生的调控途径，我们对sRNA进行了全基因组搜索，并进行了转录组分析，以鉴定与Rsm（次级代谢产物阻遏物）调控子相关的基因。通过计算机分析，在SS101基因组中鉴定出16个假定的sRNA。对sRNA rsmY和rsmZ进行框内缺失分析表明，Rsm系统调控脂肽马西菌素A的生物合成，涉及两个阻遏蛋白RsmA和RsmE，最有可能的靶标是LuxR型转录调节因子MassAR。对rsmYZ突变体的转录组分析进一步表明，与铁摄取、运动性和趋化性相关的基因显著上调，而VI型分泌系统的基因则下调。比较转录组分析表明，RsmY/RsmZ控制的大多数（但不是全部）基因也受GacS/GacA双组分系统的控制。我们得出结论，荧光假单胞菌SS101的Rsm调控子在脂肽生物合成调控中起关键作用，并控制参与植物根际运动、竞争和存活的其他基因的表达。
