Microbiology Department, University of Washington, Seattle, USA.
Genome Biol Evol. 2016 Dec 1;8(12):3696-3702. doi: 10.1093/gbe/evw274.
We previously discovered that lagging strand genes evolve faster in Bacillus subtilis (and potentially other bacteria). Lagging strand genes are transcribed in the head-on orientation with respect to DNA replication, leading to collisions between the two machineries that stall replication and can destabilize genomes. Our previous work indicated that the increased mutagenesis of head-on genes depends on transcription-coupled repair and the activity of an error prone polymerase which is likely activated in response to these collisions. Recently, it was proposed that sequence context is a major contributor to the increased mutagenesis and evolution of head-on genes. These models are based on laboratory-based evolution experiments performed in B. subtilis. However, critical evolutionary analyses of naturally occurring single nucleotide polymorphisms (SNPs) in wild strains were not performed. Using the genomic sequences from nine closely related wild B. subtilis strains, we analyzed over 200,000 naturally occurring SNPs as a proxy for natural mutation patterns for all genes and in particular, head-on genes. Our analysis suggests that (frame-independent) triplet sequence context can impact mutation rates: certain triplet sequences (TAG, CCC, CTA, and ACC) accumulate SNPs at a higher rate and are depleted from the genome. However, the triplet sequences previously identified as mutagenic in laboratory experiments (CCG, GCG, and CAC) do not have an elevated rate of SNP accumulation and are not depleted from the genome. Importantly, dN/dS analyses indicate that the accelerated evolution of head-on genes is not dependent on any particular triplet sequence. Thus, in agreement with our previous results, mutagenic transcription-coupled repair, rather than sequence context, is sufficient to explain the accelerated evolution of head-on genes.
我们之前发现滞后链基因在枯草芽孢杆菌（以及其他潜在的细菌）中进化得更快。滞后链基因以与 DNA 复制头对头的方向转录，导致两种机制发生碰撞，从而导致复制停滞，并使基因组不稳定。我们之前的工作表明，头对头基因的突变增加取决于转录偶联修复和易错聚合酶的活性，这种聚合酶可能是对这些碰撞的反应而被激活的。最近，有人提出序列背景是导致头对头基因突变增加和进化的主要因素。这些模型是基于在枯草芽孢杆菌中进行的基于实验室的进化实验提出的。然而，并没有对野生菌株中自然发生的单核苷酸多态性（SNP）进行关键的进化分析。利用来自 9 个密切相关的野生枯草芽孢杆菌菌株的基因组序列，我们分析了超过 20 万个自然发生的 SNP，作为所有基因（特别是头对头基因）自然突变模式的替代物。我们的分析表明（框架独立）三核苷酸序列背景可以影响突变率：某些三核苷酸序列（TAG、CCC、CTA 和 ACC）以更高的速率积累 SNP，并从基因组中耗尽。然而，在实验室实验中被确定为诱变的三核苷酸序列（CCG、GCG 和 CAC）并没有增加 SNP 积累的速率，也没有从基因组中耗尽。重要的是，dN/dS 分析表明，头对头基因的加速进化并不依赖于任何特定的三核苷酸序列。因此，与我们之前的结果一致，诱变转录偶联修复，而不是序列背景，足以解释头对头基因的加速进化。
