The σ(54) system directly regulates bacterial natural product genes

Bacterial-derived polyketide and non-ribosomal peptide natural products are crucial sources of therapeutics and yet little is known about the conditions that favor activation of natural product genes or the regulatory machinery controlling their transcription. Recent findings suggest that the σ(54) system, which includes σ(54)-loaded RNA polymerase and transcriptional activators called enhancer binding proteins (EBPs), might be a common regulator of natural product genes. Here, we explored this idea by analyzing a selected group of putative σ(54) promoters identified in Myxococcus xanthus natural product gene clusters. We show that mutations in putative σ(54)-RNA polymerase binding regions and in putative Nla28 EBP binding sites dramatically reduce in vivo promoter activities in growing and developing cells. We also show in vivo promoter activities are reduced in a nla28 mutant, that Nla28 binds to wild-type fragments of these promoters in vitro, and that in vitro binding is lost when the Nla28 binding sites are mutated. Together, our results indicate that M. xanthus uses σ(54) promoters for transcription of at least some of its natural product genes. Interestingly, the vast majority of experimentally confirmed and putative σ(54) promoters in M. xanthus natural product loci are located within genes and not in intergenic sequences.