Abstract
BackgroundBacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. During adaptive evolution, phenotype and genotype dynamically changes; however, the relationship between these changes and associated constraints is yet to be fully elucidated.ResultsIn this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and were similar among independently evolved ethanol tolerant populations, which indicate the existence of evolutionary constraints in the dynamics of adaptive evolution. Furthermore, the contribution of identified mutations in one of the tolerant strains was evaluated using site-directed mutagenesis. The result demonstrated that the introduction of all identified mutations cannot fully explain the observed tolerance in the tolerant strain.ConclusionsThe results demonstrated that the convergence of adaptive phenotypic changes and diverse genotypic changes, which suggested that the phenotype–genotype mapping is complex. The integration of transcriptome and genome data provides a quantitative understanding of evolutionary constraints.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0454-6) contains supplementary material, which is available to authorized users.
Highlights
Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution
In the previous study of laboratory evolution under the ethanol stress condition [16], we found that the overall gene expression changes before and after long-term cultivation were similar among independently evolved tolerant strains
To elucidate the phenotypic changes that occurred during adaptive evolution, we first quantified the time-series of the expression changes by microarray analysis
Summary
Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. Biological systems possess the ability to adapt to environmental changes, which can generate a variety of phenotypes and genotypes. Such emergence of phenotypic and genotypic diversity is considered a result of stochastically fixed genomic mutations during the process of evolution. The pioneering studies by Waddington [2], which have been corroborated by several other studies, suggests the latter, i.e., constraints on evolutionary dynamics is ubiquitous. One example of such evolutionary constraint is that the earliest embryo of various organisms shows a conserved morphological pattern called the phylotypic period, which is a constrained distribution of phenotype [3]. The relationship between evolutionary constraints and phenotypic plasticity without genetic
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