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

Area of Science:

• Microbiology
• Evolutionary Biology
• Genetics

Background:

• Adaptive laboratory evolution (ALE) is a powerful tool for identifying genetic mutations that enhance microbial performance under specific selective pressures.
• Mutator strains, particularly those with inactivated mutS genes affecting DNA mismatch repair, often dominate ALE experiments.
• Understanding the role of mutS inactivation in ALE can optimize strain development for industrial and research applications.

Purpose of the Study:

• To investigate the utility of mutS inactivation in facilitating ALE of Escherichia coli.
• To compare the mutation dynamics and fitness outcomes between wild-type and ΔmutS E. coli strains during ALE.
• To determine the impact of mutS inactivation on collateral fitness gains in E. coli.

Main Methods:

• Parallel ALE of wild-type E. coli MG1655 and a ΔmutS derivative for 800 generations using serial-transfer in minimal media with lactate or glycerol.
• Whole-genome re-sequencing of lineages at 100-generation intervals to track mutation accumulation.
• Fitness assays of endpoint populations and single mutants across various non-adaptive carbon sources.

Main Results:

• The ΔmutS strain exhibited significantly faster mutation emergence and accumulated over fourfold more mutations than the wild-type strain.
• A substantial number of random mutations were observed in the ΔmutS lineages.
• ΔmutS strains showed more pronounced collateral fitness increases on non-adaptive carbon sources, attributed to accumulated random mutations.

Conclusions:

• Short-term mutator ALE using ΔmutS E. coli extensively expands the accessible genotype space.
• This approach yields versatile bacterial strains with broadly elevated fitness levels across different metabolic conditions.
• MutS inactivation is a viable strategy to accelerate ALE and enhance microbial strain development.