Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

Dae-Hee Lee,Christian L Barrett,Adam M Feist,Bernhard Ø Palsson,Katy C Kao

doi:10.1371/journal.pone.0026172

Dae-Hee Lee, Christian L Barrett + Show 3 more

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https://doi.org/10.1371/journal.pone.0026172

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Journal: PloS one	Publication Date: Oct 18, 2011
Citations: 60	License type: CC BY 4.0

Affiliation: University of California, San Diego

Abstract

Adaptive laboratory evolution (ALE) under controlled conditions has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a given selection pressure. Conventionally, the timescale in ALE experiments has been set in terms of number of generations. As mutations are believed to occur primarily during cell division in growing cultures, the cumulative number of cell divisions (CCD) would be an alternative way to set the timescale for ALE. Here we show that in short-term ALE (up to 40–50 days), Escherichia coli, under growth rate selection pressure, was found to undergo approximately 1011.2 total cumulative cell divisions in the population to produce a new stable growth phenotype that results from 2 to 8 mutations. Continuous exposure to a low level of the mutagen N-methyl-N′-nitro-N-nitrosoguanidine was found to accelerate this timescale and led to a superior growth rate phenotype with a much larger number of mutations as determined with whole-genome sequencing. These results would be useful for the fundamental kinetics of the ALE process in designing ALE experiments and provide a basis for its quantitative description.

Highlights

Adaptive laboratory evolution (ALE) has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a strict selection pressure [1,2]
One can use the cumulative number of cell divisions (CCD) in the history of the population being carried at a given time as a more meaningful measure of timescale in ALE experiments
We found: 1) that the CCD needed for the generation of reproducible growth phenotypes during short-term ALE is about 1011.2, 2) that this rate can be accelerated using a continuous exposure to a nontoxic low level of a mutagen, and 3) that in the presence of the mutagen, the number of mutations that are explored by whole-genome sequencing increases significantly, leading to improved growth phenotypes as compared to the endpoint strains generated without the mutagen

Summary

Introduction

Adaptive laboratory evolution (ALE) has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a strict selection pressure [1,2]. ALE experiments, as presented in this study, are carried out for a sufficient time period to generate an apparently stable phenotype or when non-detectable changes are observed in the selected phenotypic trait (Fig. 1A). One can use the cumulative number of cell divisions (CCD) in the history of the population being carried at a given time as a more meaningful measure of timescale in ALE experiments. This timescale can be accelerated by a constant presence of a non-toxic level of a mutagen, as it increases the probability of a mutation occurring during a cell division. The CCD parameter can improve our understanding of ALE processes by incorporating the actual number of cells responsible for a phenotypic outcome and allow for a more precise analysis of phenotypic outcomes on a per cell basis (Fig. 1B)

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