Open Access Research article

Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

Takaaki Horinouchi1, Kuniyasu Tamaoka1, Chikara Furusawa1*, Naoaki Ono1, Shingo Suzuki1, Takashi Hirasawa1, Tetsuya Yomo123 and Hiroshi Shimizu1*

Author Affiliations

1 Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan

2 Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), 1-5 Yamadaoka, Suita, Osaka, Japan

3 Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan

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BMC Genomics 2010, 11:579  doi:10.1186/1471-2164-11-579

Published: 19 October 2010



Understanding ethanol tolerance in microorganisms is important for the improvement of bioethanol production. Hence, we performed parallel-evolution experiments using Escherichia coli cells under ethanol stress to determine the phenotypic changes necessary for ethanol tolerance.


After cultivation of 1,000 generations under 5% ethanol stress, we obtained 6 ethanol-tolerant strains that showed an approximately 2-fold increase in their specific growth rate in comparison with their ancestor. Expression analysis using microarrays revealed that common expression changes occurred during the adaptive evolution to the ethanol stress environment. Biosynthetic pathways of amino acids, including tryptophan, histidine, and branched-chain amino acids, were commonly up-regulated in the tolerant strains, suggesting that activating these pathways is involved in the development of ethanol tolerance. In support of this hypothesis, supplementation of isoleucine, tryptophan, and histidine to the culture medium increased the specific growth rate under ethanol stress. Furthermore, genes related to iron ion metabolism were commonly up-regulated in the tolerant strains, which suggests the change in intracellular redox state during adaptive evolution.


The common phenotypic changes in the ethanol-tolerant strains we identified could provide a fundamental basis for designing ethanol-tolerant strains for industrial purposes.