The small RNA ArcZ coordinates contact-dependent antibacterial killing and diffusible antifungal inhibition via the transcription factor SlyA in Dickeya solani

How the production of these distinct weapons is coordinated remains incompletely understood. Here, we identify a two-tier regulatory cascade through which the Hfq-dependent small RNA (sRNA) ArcZ controls both antibacterial and antifungal antagonism in the phytopathogen Dickeya solani.

High-throughput RNA interactome analysis (RIL-seq) shows that ArcZ interacts broadly across the transcriptome and directly base-pairs with the 5′ untranslated region of the mRNA encoding the MarR-family transcription factor SlyA, activating its translation. SlyA subsequently binds directly to selected promoter regions within the solanimycin biosynthetic cluster (sol) and the type VI secretion system (T6SS) loci and activates their transcription.