Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

Many bacterial lineages lack seemingly essential metabolic genes. Previous work suggested selective benefits could drive the loss of biosynthetic functions from bacterial genomes when the corresponding metabolites are sufficiently available in the environment. However, the factors that govern this ‘genome streamlining’ remain poorly understood. Here we determine the effect of plasticity and epistasis on the fitness of Escherichia coli genotypes from whose genome biosynthetic genes for one, two, or three different amino acids have been deleted. Competitive fitness experiments between auxotrophic mutants and prototrophic wild type cells in one of two carbon environments revealed that plasticity and epistasis strongly affected the mutants’ fitness individually and interactively. Positive and negative epistatic interactions were prevalent, yet on average cancelled each other out. Moreover, epistasis correlated negatively with the expected effects of combined auxotrophy-causing mutations, th...诸多细菌支系缺失看似必需的代谢基因。既往研究显示，当环境中相应代谢物供给充足时，选择优势可驱动细菌基因组丢失生物合成功能。然而，调控这一‘基因组精简（genome streamlining）’过程的核心因素仍未得到充分解析。本研究旨在探究可塑性（plasticity）与上位性（epistasis）对大肠杆菌（Escherichia coli）基因型适合度的影响，实验所用大肠杆菌的基因组中分别缺失了编码1种、2种或3种不同氨基酸的生物合成基因。研究人员在两种碳源环境中的一种内，开展了营养缺陷型突变体（auxotrophic mutants）与原养型野生型（prototrophic wild type）细胞的竞争适合度实验，结果显示可塑性与上位性可分别以及交互地对突变体的适合度产生显著影响。正、负上位性交互作用均广泛存在，但二者的平均效应相互抵消。此外，上位性与联合致营养缺陷突变的预期效应呈负相关，……