GlnR Dominates Rifamycin Biosynthesis by Activating the Cluster Genes Transcription Both Directly and Indirectly in

Because of the remarkable efficacy in treating infections, rifamycin and its derivatives are still first-line antimycobacterial drugs. It has been intensely studied to increase rifamycin yield from , and nitrate is found to provide a stable and remarkable stimulating effect on the rifamycin production, a phenomenon known as "nitrate-stimulating effect (NSE)". Although the NSE has been widely used for the industrial production of rifamycin, its detailed molecular mechanism remains ill-defined. And our previous study has established that the global nitrogen regulator GlnR may participate in the NSE, but the underlying mechanism is still enigmatic. Here, we demonstrate that GlnR directly controls rifamycin biosynthesis in and thus plays an essential role in the NSE. Firstly, GlnR specifically binds to the upstream region of , which leads us to uncover that has its own promoter. As RifZ is a pathway-specific activator for the whole cluster, GlnR indirectly upregulates the whole cluster transcription by directly activating the expression. Secondly, GlnR specifically binds to the upstream region of , which is also characterized to have its own promoter. It is well-known that RifK is a 3-amino-5-hydroxybenzoic acid (AHBA, the starter unit of rifamycin) synthase, thus GlnR can promote the supply of the rifamycin precursor by directly activating the transcription. Notably, GlnR and RifZ independently activate the transcription through binding to different sites in promoter region, which suggests that the cells have a sophisticated regulatory mechanism to control the AHBA biosynthesis. Collectively, this study reveals that GlnR activates the cluster transcription in both direct (for and ) and indirect (for the whole cluster) manners, which well interprets the phenomenon that the NSE doesn't occur in the null mutant. Furthermore, this study deepens our understanding about the molecular mechanism of the NSE.