Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

生物 遗传学 选择(遗传算法) 人类遗传学 大肠杆菌 基因组 适应性进化 计算生物学 基因 进化生物学 计算机科学 人工智能
作者
Tom M Conrad,Andrew R. Joyce,M. Kenyon Applebee,Christian Barrett,Bin Xie,Yuan Gao,Bernhard Ø. Palsson
出处
期刊:Genome Biology [BioMed Central]
卷期号:10 (10) 被引量:192
标识
DOI:10.1186/gb-2009-10-10-r118
摘要

Abstract Background Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. Results In the present study, we describe the genome sequencing of 11 endpoints of Escherichia coli that underwent 60-day laboratory adaptive evolution under growth rate selection pressure in lactate minimal media. Two to eight mutations were identified per endpoint. Generally, each endpoint acquired mutations to different genes. The most notable exception was an 82 base-pair deletion in the rph - pyrE operon that appeared in 7 of the 11 adapted strains. This mutation conferred an approximately 15% increase to the growth rate when experimentally introduced to the wild-type background and resulted in an approximately 30% increase to growth rate when introduced to a background already harboring two adaptive mutations. Additionally, most endpoints had a mutation in a regulatory gene ( crp or relA , for example) or the RNA polymerase. Conclusions The 82 base-pair deletion found in the rph - pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation.
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