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 the in vivo functions of Mfd, we identified the chromosomal regions where it associates. We analyzed the impact of Mfd 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.

中文翻译：

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Mfd调节体内RNA聚合酶与难以转录的区域的结合，尤其是那些具有结构化RNA的区域

RNA聚合酶（RNAP）在转录过程中遇到各种障碍。这些障碍会阻碍RNAP的移动，影响转录，最终需要RNAP相关因子的活性。一种这样的因子是细菌蛋白Mfd。与RNAP相互作用的高度保守的DNA转移酶和进化因子。尽管人们认为Mfd主要起使RNAP失速的DNA损伤修复的作用，但越来越多的证据表明Mfd对于转录调控也可能很重要。但是，这尚未完全表征。为了阐明Mfd的体内功能，我们鉴定了与Mfd结合的染色体区域。我们分析了Mfd对全基因组RNAP关联和转录调控的影响。我们发现Mfd在许多染色体区域抑制RNA缔合。我们发现这些区域显示出增加的RNAP暂停，表明它们很难转录。有趣的是，我们注意到Mfd调节转录的大多数区域都包含高度结构化的调节RNA。鉴定出的RNA调节无数的生物过程，从代谢到tRNA调节，再到毒素-抗毒素（TA）功能。我们发现，Mfd的转录调控，至少在某些TA位点，对细胞存活至关重要。最后，我们发现Mfd促进至少一种毒素基因的诱变，表明其在调节转录中的功能可能促进某些TA系统以及其他包含强RNA二级结构的区域的进化。我们得出结论，Mfd是一个重要且有时很关键的RNAP辅助因子，