Baehr Stephan, Ho Wei-Chin, Perez Samuel, Cenzano Alyssa, Hancock Katelyn, Patrick Lea, Brown Adalyn, Miller Samuel, Lynch Michael
Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Genome Biol Evol. 2025 Apr 3;17(4). doi: 10.1093/gbe/evaf049.
The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though its execution is laborious. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of actual environmental living conditions. We propose that a fully liquid-phase MA experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling, and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR-E. coli in liquid LB culture vs. plate Lysogeny Broth culture. We detect a modified mutation spectrum with a transition skew of 4.7:1 of A:T→G:C vs. G:C→A:T mutations, highlighting the potential role of tautomerization as a mechanism of DNA mutation.
突变积累（MA）实验是进化生物学中的一项固定实验，尽管其实施过程很费力。MA实验通常需要数月到数年时间才能获得足够的突变来测量DNA突变率和突变谱。许多生物体的MA实验依赖于在琼脂平板上形成菌落和重复划线，乍一看，这种环境有点人为设计，是对实际环境生活条件的拙劣模仿。我们提出，全液相MA实验有时可能更准确地反映生物体的环境。我们还注意到，虽然平板划线的自动化是一个令人生畏的前景，但液体处理和连续稀释的自动化已经很常见。原则上，这种类型的MA实验可以实现自动化，以降低测量突变率所需的人力资本。我们证明，液体MA实验重现了在液体LB培养基与平板溶原肉汤培养基中对错配修复缺陷型大肠杆菌估计的突变率。我们检测到一个改变的突变谱，其中A:T→G:C与G:C→A:T突变的转换偏斜为4.7:1，突出了互变异构化作为DNA突变机制的潜在作用。
