Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution.

Minjeong Kang,Byung-Kwan Cho,Suhyung Cho,Bernhard Palsson,Donghui Choe,Sun Chang Kim,Kangsan Kim

doi:10.3389/fmicb.2019.01845

Abstract

Adaptive laboratory evolution (ALE) is used to find causal mutations that underlie improved strain performance under the applied selection pressure. ALE studies have revealed that mutator populations tend to outcompete their non-mutator counterparts following the evolutionary trajectory. Among them, mutS-inactivated mutator cells, characterize d by a dysfunctional methyl-mismatch repair system, are frequently found in ALE experiments. Here, we examined mutS inactivation as an approach to facilitate ALE of Escherichia coli. The wild-type E. coli MG1655 and mutS knock-out derivative (ΔmutS) were evolved in parallel for 800 generations on lactate or glycerol minimal media in a serial-transfer experiment. Whole-genome re-sequencing of each lineage at 100-generation intervals revealed that (1) mutations emerge rapidly in the ΔmutS compared to in the wild-type strain; (2) mutations were more than fourfold higher in the ΔmutS strain at the end-point populations compared to the wild-type strain; and (3) a significant number of random mutations accumulated in the ΔmutS strains. We then measured the fitness of the end-point populations on an array of non-adaptive carbon sources. Interestingly, collateral fitness increases on non-adaptive carbon sources were more pronounced in the ΔmutS strains than the parental strain. Fitness measurement of single mutants revealed that the collateral fitness increase seen in the mutator lineages can be attributed to a pool of random mutations. Together, this study demonstrates that short-term mutator ALE extensively expands possible genotype space, resulting in versatile bacteria with elevated fitness levels across various carbon sources.

Highlights

Bacterial cells are under constant selection pressure to adapt to ever changing environmental conditions
Two biological replicates from each of E. coli K-12 MG1655 wild-type and mutS knock-out derivate strains were propagated in M9 minimal medium containing either lactate or glycerol
Several studies have shown that in microbial cells, elevated mutation rates can be exploited to facilitate Adaptive laboratory evolution (ALE) toward better fitness compared with non-mutator cells (Sniegowski et al, 1997; Giraud et al, 2001a; Notley-McRobb et al, 2002; Barrick et al, 2009; LaCroix et al, 2015)

Summary

Introduction

Bacterial cells are under constant selection pressure to adapt to ever changing environmental conditions. While adaptive evolution results in the rewiring of cellular regulatory and metabolic networks, mutation rate itself may be subject to adaptation through a selection pressure on the genes associated with DNA repair (Rosche and Foster, 1999; Giraud et al, 2001b; Sprouffske et al, 2018). It has been well documented that the emergence of mutator lineages during adaptive evolution results in a more rapid adaptation compared to wild-type strains (Sniegowski et al, 1997; Giraud et al, 2001a; Notley-McRobb et al, 2002; Barrick et al, 2009; LaCroix et al, 2015; Shibai et al, 2017). Mounting evidence suggests the role of non-adaptive mutations in shaping novel adaptive phenotypes in the process of adaptation (Wagner, 2008; Szappanos et al, 2016)

Methods

Results

Conclusion