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Front Microbiol. 2019 Aug 16;10:1845. doi: 10.3389/fmicb.2019.01845. eCollection 2019.

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

Kang M1,2, Kim K1,2, Choe D1,2, Cho S1,2, Kim SC1,2,3, Palsson B4,5, Cho BK1,2,3.

Author information

1
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
2
KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
3
Intelligent Synthetic Biology Center, Daejeon, South Korea.
4
Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.
5
Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.

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.

KEYWORDS:

Escherichia coli; adaptive laboratory evolution; genotype space; mismatch repair; phenotype microarray

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