Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, H3C 3J7, Canada.
Département de microbiologie, infectiologie et immunologie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, P. Québec, H3C 3J7, Canada.
DNA Repair (Amst). 2019 Dec;84:102693. doi: 10.1016/j.dnarep.2019.102693. Epub 2019 Aug 21.
DNA replication, the faithful copying of genetic material, must be tightly regulated to produce daughter cells with intact copies of the chromosome(s). This regulated replication is initiated by binding of specific proteins at replication origins, such as DnaA to oriC in bacteria. However, unregulated replication can sometimes be initiated at other sites, which can threaten genomic stability. One of the first systems of unregulated replication to be described is the one activated in Escherichia coli mutants lacking RNase HI (rnhA). In fact, rnhA mutants can replicate their chromosomes in a DnaA- and oriC-independent process. Because this replication occurs in cells lacking RNase HI, it is proposed that RNA from R-loops is used as a DNA polymerase primer. Replication from R-loops has recently attracted increased attention due to the advent of DNA:RNA hybrid immunoprecipitation coupled with high-throughput DNA sequencing that revealed the high prevalence of R-loop formation in many organisms, and the demonstration that R-loops can severely threaten genomic stability. Although R-loops have been linked to genomic instability mostly via replication stress, evidence of their toxic effects via unregulated replication has also been presented. Replication from R-loops may also beneficially trigger stress-induced mutagenesis (SIM) that assists bacterial adaptation to stress. Here, we describe the cis- and trans-acting elements involved in R-loop-dependent replication in bacteria, with an emphasis on new data obtained with type 1A topoisomerase mutants and new available technologies. Furthermore, we discuss about the mechanism(s) by which R-loops can reshape the genome with both negative and positive outcomes.
DNA 复制是遗传物质的忠实复制，必须进行严格调控，以产生染色体完整拷贝的子细胞。这种受调控的复制是通过特定蛋白质在复制起点的结合启动的，例如细菌中的 DnaA 与 oriC 的结合。然而，有时不受调控的复制也可以在其他位点起始，这可能会威胁基因组的稳定性。首先被描述的不受调控的复制系统之一是在缺乏 RNase HI（rnhA）的大肠杆菌突变体中激活的系统。事实上，rnhA 突变体可以在不依赖 DnaA 和 oriC 的情况下复制它们的染色体。由于这种复制发生在缺乏 RNase HI 的细胞中，因此有人提出 RNA 来自 R 环可作为 DNA 聚合酶引物。由于 DNA:RNA 杂交免疫沉淀与高通量 DNA 测序的出现，揭示了 R 环在许多生物体中的高形成率，以及 R 环可以严重威胁基因组稳定性的证据，因此 R 环的复制最近引起了更多的关注。尽管 R 环主要通过复制应激与基因组不稳定性相关，但也有证据表明它们通过不受调控的复制具有毒性作用。R 环的复制也可能通过应激诱导的突变（SIM）有益地触发，这有助于细菌适应应激。在这里，我们描述了细菌中 R 环依赖性复制涉及的顺式和反式作用元件，重点介绍了使用 1A 拓扑异构酶突变体获得的新数据和新的可用技术。此外，我们还讨论了 R 环如何通过产生消极和积极的结果来重塑基因组的机制。
