Aromatic metabolites regulate prodigiosin production in Serratia marcescens through SlyA

Some Serratia marcescens (Sm) strains produce the red pigment prodigiosin, which exhibits immunosuppressive, antimicrobial, and antitumoral properties. Prodigiosin biosynthesis is controlled by a complex regulatory network that includes SlyA, a MarR-family transcriptional regulator. However, the molecular mechanism by which SlyA regulates prodigiosin production remains largely unknown. Here, we showed that methyl benzoate, paeonol, salicylic acid, and p-coumaric acid reduce pigment production in Sm. Given previous evidence that small aromatic molecules can allosterically regulate MarR-family proteins, we generated a homodimeric structural model of Sm SlyA. Molecular docking analyses suggested that these aromatic metabolites bind within the two cavities of the SlyA homodimer, and molecular dynamics simulations identified methyl benzoate as the most stable ligand. Consistently, in vitro assays showed that the binding of recombinant SlyA to the prodigiosin promoter was altered in the presence of methyl benzoate and phenolic metabolites. Finally, exogenous methyl benzoate, paeonol, and salicylic acid significantly reduced pigA–gfp transcription in Sm, and this effect became more pronounced upon expression of slyA from a multicopy plasmid. Together, these findings support a model in which SlyA functions as an allosterically regulated sensor, coupling the perception of aromatic carbonyl compounds to the control of prodigiosin biosynthesis in Sm.