Genome-wide Transcription-coupled Repair in E.coli is Mediated by the Mfd Protein

Transcription-coupled DNA repair is widespread in nature having been found in organisms from E. coli to yeast to humans. In E. coli, the transcription-repair coupling factor (TRCF) encoded by the mfd gene recognizes RNA polymerase (RNAP) stalled at a damage site and recruits the excision repair proteins to the stalled RNAP and promotes damage recognition while displacing RNAP and the truncated transcript from the damage site and in doing so, enhances the rate of repair of the transcribed strand (TS). Recently, it has been reported that there are other E. coli proteins that mediate transcription-coupled repair (TCR) independently of the Mfd protein. To understand the relative contributions of various proteins to and mechanisms of TCR we used the recently developed nucleotide excision repair sequencing (XR-seq) method for genome-wide analysis of excision repair to generate excision repair maps of entire genomes of various E. coli strains with deletions of genes implicated in TCR. Our data show that the Mfd protein catalyzes TCR throughout the genome. Overall design: Examination of excision products in E.coli: WT and mutants of phr, mfd, uvrD.