Expression of the Pseudomonas chlororaphis strain PA23 Rsm system is under control of GacA, RpoS, PsrA, quorum sensing and the stringent response

•The Pseudomonas chororaphis PA23 Rsm system consists of RsmZ, RsmA and RsmE.•RsmZ is controlled by GacA, RpoS, PsrA, the stringent response and quorum sensing.•RsmA is positively controlled by GacA and negatively controlled by the stringent response.•RsmE is activated by GacA, RpoS, PsrA, the stringent response and quorum sensing.

Pseudomonas chlororaphis strain PA23 is a plant-beneficial bacterium able to suppress disease caused by the pathogenic fungus Sclerotinia sclerotiorum. A number of compounds are believed to contribute to fungal antagonism including the antibiotics pyrrolnitrin and phenazine together with degradative enzymes. Overseeing production of these metabolites is a complex regulatory network that includes the GacS–GacA two-component system. In other bacteria, a second network, called Rsm, works in concert with Gac. The aim of the current study was to identify components of the Rsm system in PA23 and elucidate factors controlling their expression. Towards this end, genes encoding repressor proteins (RsmA and RsmE) and a regulatory RNA (RsmZ) were isolated. Through transcriptional fusion analysis, we discovered that rsmZ is positively regulated by GacA, PsrA, RpoS, the stringent response (SR) and the PhzI/PhzR quorum-sensing (QS) system. An upstream activating sequence (UAS) corresponding to the GacA recognition sequence was identified in the rsmZ promoter. Moreover, a PtrA box and a Phz box were present, suggesting that all three regulators activate rsmZ directly. rsmE was positively regulated by GacA, PsrA, RpoS, the SR and QS in PA23, but with the exception of RpoS, regulation was indirectly mediated. rsmA was negatively regulated by the SR and positively regulated by GacA. A UAS was not found in the promoter region of either rsmA or rsmE, suggesting indirect control by GacA. Identification of RsmZ, RsmA and RsmE and the discovery that these regulators are tightly controlled add to the increasingly complex network overseeing biocontrol in P. chlororaphis PA23.

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