Prediction of Stress Resistance By Gene Expression Profiles

Advances of technologies now make it possible to reveal the phenotypic and genetic changes responsible for adaptive evolution. Such detailed information of evolutionary traits provides a basis for understanding the nature of adaptive evolution, for example, what phenotypic changes are due to genetic mutation and which are not. In this study, we performed parallel evolution experiments of Escherichia coli under various stress environments, and as the results, we obtained several independently evolved stress resistant strains. Then, for these resistant strains, we performed gene expression analysis by microarrays and resequencing analysis by next-gen sequencer. Furthermore, cross-resistance/sensitivity to other stresses were quantified for these resistance strains. The results revealed that, although the patterns of cross-resistance/sensitivity and expression profiles were similar among the resistant strains for same stress. Based on these large-scale data, we demonstrated that the resistances could be quantitatively predicted by the expression changes of a small number of genes. Several candidate mutations contributing to the resistances were identified, while phenotype-genotype mapping was suggested to be complex and included various mutations that caused similar phenotypic changes. The integration of transcriptome and genome data enables us to extract essential phenotypic changes for stress resistances, and based on these results, we will discuss possible applications of these phenotype-genotype analyses of evolutionary dynamics on bioengineering.