Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Microsoft Research, Microsoft, Redmond, WA 98052, USA.
Mol Biol Evol. 2024 Nov 1;41(11). doi: 10.1093/molbev/msae224.
Although synonymous mutations are commonly assumed neutral or nearly so, recent years have seen reports of fitness effects of synonymous mutations detected under laboratory conditions. In a previous study, we used genome editing to construct thousands of yeast mutants each carrying a synonymous or nonsynonymous mutation in one of 21 genes, and discovered that most synonymous and most nonsynonymous mutations are deleterious. A concern was raised that this observation could be caused by the fitness effects of potential CRISPR/Cas9 off-target edits and/or secondary mutations, and an experiment that would be refractory to such effects was proposed. Using genome sequencing, we here show that no CRISPR/Cas9 off-target editing occurred, although some mutants did carry secondary mutations. Analysis of mutants with negligible effects from secondary mutations and new data collected from the proposed experiment confirms the original conclusion. These findings, along with other reports of fitness effects of synonymous mutations from both case and systematic studies, necessitate a paradigm shift from assuming (near) neutrality of synonymous mutations.
虽然同义突变通常被认为是中性或近中性的，但近年来已有报道称，在实验室条件下检测到的同义突变具有适应度效应。在之前的一项研究中，我们使用基因组编辑构建了数千个酵母突变体，每个突变体在 21 个基因中的一个基因中携带同义或非同义突变，发现大多数同义突变和大多数非同义突变都是有害的。有人担心这种观察结果可能是由潜在的 CRISPR/Cas9 脱靶编辑和/或次级突变的适应度效应引起的，并提出了一个对此类效应具有抗性的实验。使用基因组测序，我们在这里表明没有发生 CRISPR/Cas9 脱靶编辑，尽管一些突变体确实携带了次级突变。对次级突变影响可忽略不计的突变体的分析以及从拟议实验中收集的新数据证实了最初的结论。这些发现，以及来自案例和系统研究的同义突变适应度效应的其他报道，需要从假设同义突变（近）中性转变。
