Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Türkiye.
Department of Computational Science-Biological Sciences, Scientific and Technological Research Council of Türkiye (TUBITAK) Research Institute for Fundamental Sciences, Gebze 41470, Türkiye.
Proc Natl Acad Sci U S A. 2024 Oct 29;121(44):e2416877121. doi: 10.1073/pnas.2416877121. Epub 2024 Oct 23.
DNA repair processes modulate genotoxicity, mutagenesis, and adaption. Nucleotide excision repair removes bulky DNA damage, and in , 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 10× faster than repair of cyclobutane pyrimidine dimers (CPDs). To better understand repair prioritization in , we used XR-seq to measure TCR of UV photoproducts genome-wide. With CPDs, we found that TCR occurred at early time points, increased with transcription level, and was Mfd dependent; 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 significant role of Mfd in mutagenesis and the modest effect of deletion on UV survival and bear upon the response of to bulky DNA damage.
DNA 修复过程调节遗传毒性、突变和适应。核苷酸切除修复去除大块 DNA 损伤，而在基底切除修复中，由 UvrA、B、C 和 D 与 DNA PolI 和 DNA 连接酶一起，在全基因组范围内发生。在转录偶联修复 (TCR) 中，Mfd 蛋白靶向模板链 (TS) 上的损伤，这些损伤会阻止 RNA 聚合酶的转录，从而通过基底修复酶加速修复。对于特定的加合物也会看到加速修复。值得注意的是，在两种主要的 UV 光产物中，基底修复 (6-4) 光产物 [(6-4)PPs] 的速度比修复环丁烷嘧啶二聚体 (CPDs) 快约 10 倍。为了更好地理解修复优先级，我们使用 XR-seq 测量全基因组范围内的 TCR 对 UV 光产物的修复。对于 CPDs，我们发现 TCR 发生在早期，随着转录水平的增加而增加，并且依赖于 Mfd；后来，随着 TS 修复的完成，非转录链 (NTS) 修复占主导地位。对于 (6-4)PP，当分析所有基因时，未观察到 TCR；实际上，在转录水平最高的基因中，NTS 中 (6-4)PP 的修复略多。因此，NTS 中 (6-4)PP 的快速基底修复速度比 TS 中 (6-4)PP 的 TCR 更快。总体而言，TCR 在 (6-4)PP 修复中意义不大，而 CPDs 的 TCR 仅限于转录水平较高的基因的 TS。这些结果与 Mfd 在突变中的重要作用以及 缺失对 UV 存活的适度影响一致，并影响到对大块 DNA 损伤的反应。
