Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter

Biotechnology for Biofuels

Lu Lin²  Yuetong Ji²  Qichao Tu¹  Ranran Huang²  Lin Teng²  Xiaowei Zeng²  Houhui Song²  Kun Wang²  Qian Zhou²  Yifei Li²  Qiu Cui²  Zhili He¹  Jizhong Zhou¹  Jian Xu² 

[1] Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA

[2] BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China

关键词: Thermophile;    Microevolution;    Ethanol;    Adaptation;    Shock;   

Others  :  797976
DOI  :  10.1186/1754-6834-6-103

 received in 2013-05-29, accepted in 2013-07-17,  发布年份 2013

【 摘 要 】

Introduction

The molecular links between shock-response and adaptation remain poorly understood, particularly for extremophiles. This has hindered rational engineering of solvent tolerance and correlated traits (e.g., productivity) in extremophiles. To untangle such molecular links, here we established a model that tracked the microevolution from shock to adaptation in thermophilic bacteria.

Method

Temporal dynamics of genomes and transcriptomes was tracked for Thermoanaerobacter sp. X514 which under increasing exogenous ethanol evolved from ethanol-sensitive wild-type (Strain X) to tolerance of 2%- (X_I) and eventually 6%-ethanol (X_II). Based on the reconstructed transcriptional network underlying stress tolerance, genetic engineering was employed to improve ethanol tolerance and production in Thermoanaerobacter.

Results

The spontaneous genome mutation rate (μ_g) of Thermoanaerobacter sp. X514, calculated at 0.045, suggested a higher mutation rate in thermophile than previously thought. Transcriptomic comparison revealed that shock-response and adaptation were distinct in nature, whereas the transcriptomes of X_II resembled those of the extendedly shocked X. To respond to ethanol shock, X employed fructose-specific phosphotransferase system (PTS), Arginine Deiminase (ADI) pathway, alcohol dehydrogenase (Adh) and a distinct mechanism of V-type ATPase. As an adaptation to exogenous ethanol, X_I mobilized resistance-nodulation-cell division (RND) efflux system and Adh, whereas X_II, which produced higher ethanol than X_I, employed ECF-type ϭ²⁴, an alcohol catabolism operon and phase-specific heat-shock proteins (Hsps), modulated hexose/pentose-transport operon structure and reinforced membrane rigidity. Exploiting these findings, we further showed that ethanol productivity and tolerance can be improved simultaneously by overexpressing adh or ϭ²⁴ in X.

Conclusion

Our work revealed thermophilic-bacteria specific features of adaptive evolution and demonstrated a rational strategy to engineer co-evolving industrial traits. As improvements of shock-response, stress tolerance and productivity have been crucial aims in industrial applications employing thermophiles, our findings should be valuable not just to the production of ethanol but also to a wide variety of biofuels and biochemicals.

【 授权许可】

   
2013 Lin et al.; licensee BioMed Central Ltd.

【 图 表 】

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