Journal article
Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations
University of California at San Diego1
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark2
Bacterial Cell Factories, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3
Research Groups, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4
iLoop, Translational Management, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark5
Big Data 2 Knowledge, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark6
Network Reconstruction in Silico Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark7
Department of Systems Biology, Technical University of Denmark8
Drug Resistance and Community Dynamics, Department of Systems Biology, Technical University of Denmark9
Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths.
Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across two or more strains. This mutational recurrence pointed to the key genetic targets underlying the evolved fitness increase. Genome engineering was used to introduce the novel ALE-acquired alleles in random combinations into the ancestral strain, and competition between these engineered strains reaffirmed the impact of the key mutations on the growth rate at 42 °C.
Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype. Additionally, transcriptomic analysis of the ancestral and evolved strains revealed a general trend for restoration of the global expression state back toward preheat stressed levels.
This restorative effect was previously documented following evolution to metabolic perturbations, and thus may represent a general feature of ALE experiments. The widespread evolved expression shifts were enabled by a comparatively scant number of regulatory mutations, providing a net fitness benefit but causing suboptimal expression levels for certain genes, such as those governing flagellar formation, which then became targets for additional ameliorating mutations.
Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future implementation of ALE as a tool for scientific research and engineering.
Language: | English |
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Publisher: | Oxford University Press |
Year: | 2014 |
Pages: | 2647-2662 |
ISSN: | 15371719 and 07374038 |
Types: | Journal article |
DOI: | 10.1093/molbev/msu209 |
ORCIDs: | Herrgard, Markus , Palsson, Bernhard , Sommer, Morten and Feist, Adam |
Adaptation, Biological Escherichia coli Escherichia coli K12 Evolution, Molecular Gene Expression Profiling Gene Expression Regulation, Bacterial Genetic Engineering Genetic Fitness Genome, Bacterial MAGE Mutation Temperature adaptive laboratory evolution temperature stress transcriptomics