An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis
An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis
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DOI：
10.1073/pnas.1416651112
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发表时间：
2015-03-10
影响因子：
11.1
通讯作者：
Merrikh, Houra
中科院分区：
文献类型：
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作者：
Million-Weaver, Samuel;Samadpour, Ariana N.;Merrikh, Houra
我们之前报道过，在枯草芽孢杆菌中，滞后链基因比前导链编码的基因积累突变的速度更快。尽管我们提出复制和转录之间的定向特异性相遇是这种现象的基础，但导致滞后链基因突变增加的机制仍然未知。在这里，我们报告基因突变率的转录依赖性和方向特异性差异需要枯草芽孢杆菌 Y 家族聚合酶 PolY1 (yqjH)。我们发现，如果没有 PolY1，复制解旋酶 DnaC 和重组蛋白 RecA 与滞后链基因的关联会以转录依赖性方式增加。这些数据表明，PolY1 通过滞后链基因促进有效的复制体进展，从而减少这些位点的潜在有害断裂和单链 DNA。 Y 家族聚合酶可以通过促进 DNA 损伤旁路、D 环延伸或切除修复来减轻复制体进展的潜在障碍。我们发现核苷酸切除修复（NER）蛋白 UvrA、UvrB 和 UvrC，而不是 RecA，是两个方向上基因突变率转录依赖性不对称所必需的。此外，我们发现转录偶联修复因子 Mfd 在与 PolY1 相同的途径中发挥作用，并且也是增加滞后链基因诱变所必需的。枯草芽孢杆菌基因组的实验和 SNP 分析显示突变足迹与这些发现一致。我们提出，复制和转录之间的相互作用增加了尤其是滞后链基因的损伤敏感性，激活了 Mfd 依赖性的易错 NER 机制。我们认为这个过程至少部分是滞后链基因加速进化的基础。
We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand in Bacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require the B. subtilis Y-family polymerase, PolY1 (yqjH). We find that without PolY1, association of the replicative helicase, DnaC, and the recombination protein, RecA, with lagging-strand genes increases in a transcription-dependent manner. These data suggest that PolY1 promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci. Y-family polymerases can alleviate potential obstacles to replisome progression by facilitating DNA lesion bypass, extension of D-loops, or excision repair. We find that the nucleotide excision repair (NER) proteins UvrA, UvrB, and UvrC, but not RecA, are required for transcription-dependent asymmetry in mutation rates of genes in the two orientations. Furthermore, we find that the transcription-coupling repair factor Mfd functions in the same pathway as PolY1 and is also required for increased mutagenesis of lagging-strand genes. Experimental and SNP analyses of B. subtilis genomes show mutational footprints consistent with these findings. We propose that the interplay between replication and transcription increases lesion susceptibility of, specifically, lagging-strand genes, activating an Mfd-dependent error-prone NER mechanism. We propose that this process, at least partially, underlies the accelerated evolution of lagging-strand genes.