Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
Genome Biol Evol. 2021 Dec 1;13(12). doi: 10.1093/gbe/evab257.
How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments.
微生物如何适应新环境是进化生物学的一个核心问题。尽管适应性进化必须由有益突变来驱动，但更高的突变率是否能促进适应性进化的速度尚不清楚。为了解决这个问题，我们培养了大肠杆菌超突变种群，其中一种有缺陷的甲基定向错配修复途径导致单核苷酸突变率增加 140 倍。与野生型大肠杆菌平行培养的是含有 LB 肉汤的试管，LB 肉汤是一种复杂的培养基，已知能促进亚种群结构的进化。经过 900 天的进化，在三种具有不同种群大小瓶颈的转移方案中，超突变体的适应性总是与对照组相似。波动试验表明，超突变体的突变率在进化上与野生型种群趋同，这可能是导致适应性差异缺失的原因。进一步的基因组序列分析显示，尽管超突变体种群的基因组进化速度较高，但这主要反映了强烈的遗传连锁。尽管存在这些连锁效应，但进化后的种群在固定突变中表现出平行性，包括那些可能与生物膜形成、转录调控和突变率进化相关的突变。总的来说，这些结果与突变率与进化适应性速度之间存在正相关关系的假设不一致，并为了解在新环境中克隆适应性是如何发生的提供了线索。
