γ-Butyrolactone-induced coelimycin synthesis inhibits AtrA-dependent actinorhodin overproduction in Streptomyces coelicolor A3(2)

Streptomyces coelicolor A3(2) is a highly potent model antibiotic producer, with a chromosome harboring at least 20 secondary metabolite biosynthetic gene clusters (BGCs). Precise control of these multiple pathways is provided by a complex network of regulatory proteins and small signaling molecules. In this work, we show that coelimycin (CPK) and actinorhodin (ACT) production are exclusive processes. Induction of CPK synthesis by γ-butyrolactones inhibited ACT production when we simultaneously overexpressed the ACT upper activator protein AtrA; yet, this effect was not observed under overexpression of ActII-orf4-the direct activator of the ACT BGC and the direct AtrA target. We conclude that CPK intermediates inhibit the cascade of ACT induction at the level of AtrA pleiotropic regulator activity. Our proteomic data reveal that, besides being an ACT inducer, AtrA is a high-level regulator that activates arsenopolyketide synthesis but inhibits the production of undecylprodigiosin and calcium-dependent antibiotic. AtrA also downregulates primary metabolism of carbohydrates, lipids, and amino acids, along with the tricarboxylic acid cycle.IMPORTANCEBacteria from the genus Streptomyces possess one of the most complex gene regulation machineries in the bacterial kingdom, allowing them to coordinate production of multiple compounds at discrete timing. Navigating through these regulatory networks to unlock the biosynthetic potential is challenging. Expression of silent biosynthetic gene clusters (BGCs) often occurs only under strict culture conditions and, as in the case of coelimycin, can be coordinated via quorum sensing. Here, we have investigated the interplay between coelimycin and actinorhodin production in the model organism Streptomyces coelicolor A3(2). We show that even the products of BGCs can have a regulatory function. The richness of potentially competing biosynthetic pathways may hinder high-yield biosynthesis of the desired product under fermentation conditions. Our results show the importance of designing host organisms with lowered background regulation by γ-butyrolactones for the desired biosynthetic pathway activation.