Dynamics of Transcription-Coupled Repair of Cyclobutane Pyrimidine Dimers and (6-4) Photoproducts in E. coli

DNA repair processes modulate genotoxicity, mutagenesis and adaption. Nucleotide excision repair removes bulky DNA damage, and in E. coli, basal excision repair, carried out by UvrA, B, C, and D, with DNA PolI and DNA ligase, occurs genome-wide. In transcription-coupled repair (TCR), the Mfd protein targets template strand (TS) lesions that block RNA polymerase for accelerated repair by the basal repair enzymes. Accelerated repair is also seen with particular adducts. Notably, of the two major UV-photoproducts, basal repair of (6-4) photoproducts [(6-4)PPs] is about 10x faster than repair of cyclobutane pyrimidine dimers (CPDs). To better understand repair prioritization in E. coli, we used XR-seq to measure TCR of UV photoproducts genome-wide. With CPDs, we found that TCR was dependent upon Mfd, occurred at early time points, and increased with transcription level; later, with completion of TS repair, nontranscribed strand (NTS) repair predominated. With (6-4)PP, when analyzing all genes, TCR was not observed; in fact, among the most highly transcribed genes, slightly more repair of (6-4)PPs in the NTS was evident. Thus the very rapid basal repair of (6-4)PP in the NTS was faster than TCR of (6-4)PPs in the TS. Overall, TCR is of limited importance in (6-4)PP repair, and TCR of CPDs is limited to the TS of more highly transcribed genes. These results are consistent with the modest effect of mfd deletion on UV survival, and bear upon UV mutagenesis and adaptive responses in E. coli.