Chib Savita, Ali Farhan, Seshasayee Aswin Sai Narain
National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India.
mSphere. 2017 May 24;2(3). doi: 10.1128/mSphere.00059-17. eCollection 2017 May-Jun.
Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.
延长的稳定期是对呈现一系列压力的自然环境的一种近似。在延长的稳定期中存活需要替代的代谢途径。本研究描述了在溶原肉汤中饥饿群体中积累的突变库。在稳定期的1个月过程中积累了广泛的突变。单核苷酸多态性（SNP）占所有突变的64%。这些突变中的大多数是非同义的，并且位于保守位点。随着时间的推移，进化群体中的遗传多样性增加。稳定期进化的计算机模拟表明，我们实验群体中观察到的突变的最大频率不能用中性漂变来解释。此外，群体间频繁出现遗传平行性，表明这些突变受到正选择。最后，突变的功能分析表明，调控突变是选择的常见靶点。与名称相反，细菌中的延长稳定期是高度动态的，极端的营养限制是主要压力。稳定期培养物通过快速选择在稳定期赋予生长优势的一个或多个突变（GASP）来适应。饥饿群体的表型多样性已得到详细研究；然而，在延长稳定期中积累的突变只有少数被描述。本研究记录了在28天延长饥饿期间出现的突变谱。群体的遗传多样性在稳定期随时间增加到一个无法用随机中性漂变解释的程度。这表明延长的稳定期为通过自然选择研究适应性进化提供了一个很好的模型系统。
