Experimental Evolultion of Escherichia coli Under Various Chemical Compounds Using High-Throughput Automated Culture System

Biological systems can adapt to various environmental conditions by changing their phenotype and genotype. Experimental evolution is a powerful tool to trace phenotypic and genotypic changes in adaptive evolution. By integrating experimental evolution approach and recent omics technologies including high-throughput sequencing, we can obtain genome-wide information on the adaptation dynamics to environmental changes, which facilitate better understandings of the nature of adaptive evolution and provide possible strategies for bioengineering. However, to maintain a large number of long-term cultures is often hard at work for experimental biologists, which limits the number of cultures to be maintained simultaneously. To overcome the limitation of manual culture experiments, we developed a fully-automated culture system which can maintain massive parallel experimental evolutions by a rapid serial transfers [1]. Using this system, we performed experimental evolutions of Escherichia coli MDS42 strain under various stressors including acid, alkali, saline, and surfactant agent. First, we obtained stress tolerant strains which can grow faster than parent strain in each stress. Next, we performed transcriptome analysis and genome re-sequence analysis of these tolerant strains. We found that the overall gene expression changes during experimental evolution were similar among independently evolved tolerant strains for same stressors. We also found that several mutations were commonly fixed in same genes among independently evolved tolerant strains for same stressors. We evaluated the effects of commonly fixed mutations to introduce mutations in the genome of the parent strain. From these results, we can discuss about stress adaptation mechanism and breeding strategies for useful microorganisms.

[1] T. Horinouchi et al., J. Lab. Autom., 19(5), pp. 478-482, 2014.