Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut
Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut
复制标题
DOI：
10.1111/mec.13851
复制
发表时间：
2017-04-01
影响因子：
4.9
通讯作者：
Tenaillon, Olivier
中科院分区：
文献类型：
--
作者：
Lescat, Mathilde;Launay, Adrien;Tenaillon, Olivier
虽然肠道的微生物生态学现在是一个主要的关注焦点，但对肠道微生物适应的分子决定因素知之甚少。实验进化加上全基因组测序可以提供对适应过程的见解。体外实验揭示了一些保守的模式：中间收敛，和上位性的有益突变和突变的全球监管机构之间的相互作用。为了测试这些模式的相关性，并确定体内作用的选择性压力，我们在链霉素治疗小鼠的消化道中对大肠杆菌天然分离株（链霉素耐药菌株536）进行了长期适应。经过一年的进化，对来自15个重复的克隆进行测序。与体外观察一致，所鉴定的突变揭示了突变、基因、操纵子和功能水平上的强烈趋同模式。然而，分子进化的速率低于体外，并且没有恢复全局调节因子的突变。观察到更具体的靶点：dgo操纵子，参与半乳糖酸途径，改善D-半乳糖酸的生长，以及rluD和gidB，参与核糖体的成熟，其突变仅在链霉素存在下改善生长。在体外，相同途径内突变的非随机关联表明上位性在塑造适应性景观中的作用。总的来说，我们表明，进化和序列的方法加上收敛的分析，当应用到一个自然的隔离，可以用来研究适应invivo和揭示特定的选择压力的环境。
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting invivo, we have performed a long-term adaptation of an E.coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with invitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in invitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As invitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation invivo and uncover the specific selective pressures of that environment.