Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs

RNA polymerase (RNAP) encounters various roadblocks during transcription. These obstacles can impede RNAP movement, influence transcription, ultimately necessitating the activity of RNAP associated factors. One such factor is the bacterial protein Mfd; a highly conserved DNA translocase and evolvability factor that interacts with RNAP. Although Mfd is thought to function primarily in the repair of DNA lesions that stall RNAP, increasing evidence suggests that it may also be important for transcription regulation. However, this is yet to be fully characterized. To shed light on Mfds in vivo functions, we identified the chromosomal regions where it associates. We analyzed Mfds impact on RNAP association and transcription regulation genome-wide. We found that Mfd represses RNAP association at many chromosomal regions. We found that these regions show increased RNAP pausing, suggesting that they are hard-to-transcribe. Interestingly, we noticed that the majority of the regions where Mfd regulates transcription contain highly structured regulatory RNAs. The RNAs identified regulate a myriad of biological processes, ranging from metabolism, to tRNA regulation, to toxin-antitoxin (TA) functions. We found that transcription regulation by Mfd, at least at some TA loci, is critical for cell survival. Lastly, we found that Mfd promotes mutagenesis in at least one toxin gene, suggesting that its function in regulating transcription may promote evolution of certain TA systems, and other regions containing strong RNA secondary structures. We conclude that Mfd is an RNAP co-factor that is important, and at times critical, for transcription regulation at hard-to-transcribe regions, especially those that express structured regulatory RNAs. SignificanceThe bacterial DNA translocase Mfd binds to stalled RNAPs and is generally thought to facilitate transcription-coupled DNA repair. Most of our knowledge about Mfd is based on data from biochemical studies. However, little is known about Mfds function in living cells, especially in the absence of exogenous DNA damage. Here, we show that Mfd modulates RNAP association and alters transcription at a variety of chromosomal loci, especially those containing highly structured, regulatory RNAs. As such, this work improves our understanding of Mfds function in living cells, and assigns it a new function as a transcription regulator.