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Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli c...

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Autores principales: Cao, Huansheng, Wei, Du, Yang, Yuedong, Shang, Yu, Li, Gaoyang, Zhou, Yaoqi, Ma, Qin, Xu, Ying
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353561/
https://www.ncbi.nlm.nih.gov/pubmed/28300180
http://dx.doi.org/10.1038/srep44150
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author Cao, Huansheng
Wei, Du
Yang, Yuedong
Shang, Yu
Li, Gaoyang
Zhou, Yaoqi
Ma, Qin
Xu, Ying
author_facet Cao, Huansheng
Wei, Du
Yang, Yuedong
Shang, Yu
Li, Gaoyang
Zhou, Yaoqi
Ma, Qin
Xu, Ying
author_sort Cao, Huansheng
collection PubMed
description Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli cells with computationally predicated ethanol-binding proteins and experimentally identified ethanol tolerance genes. Our analysis suggests: (1) ethanol damages cell wall and membrane integrity, causing increased stresses, particularly reactive oxygen species, which damages DNA and reduces the O(2) level; (2) decreased cross-membrane proton gradient from membrane damage, coupled with hypoxia, leads to reduced ATP production by aerobic respiration, driving cells to rely more on fatty acid oxidation, anaerobic respiration and fermentation for ATP production; (3) the reduced ATP generation results in substantially decreased synthesis of macromolecules; (4) ethanol can directly bind 213 proteins including transcription factors, altering their functions; (5) all these changes together induce multiple stress responses, reduced biosynthesis, cell viability and growth; and (6) ethanol-adapted E. coli cells restore the majority of these reduced activities through selection of specific genomic mutations and alteration of stress responses, ultimately restoring normal ATP production, macromolecule biosynthesis, and growth. These new insights into the energy and mass balance will inform design of more ethanol-tolerant strains.
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spelling pubmed-53535612017-03-20 Systems-level understanding of ethanol-induced stresses and adaptation in E. coli Cao, Huansheng Wei, Du Yang, Yuedong Shang, Yu Li, Gaoyang Zhou, Yaoqi Ma, Qin Xu, Ying Sci Rep Article Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli cells with computationally predicated ethanol-binding proteins and experimentally identified ethanol tolerance genes. Our analysis suggests: (1) ethanol damages cell wall and membrane integrity, causing increased stresses, particularly reactive oxygen species, which damages DNA and reduces the O(2) level; (2) decreased cross-membrane proton gradient from membrane damage, coupled with hypoxia, leads to reduced ATP production by aerobic respiration, driving cells to rely more on fatty acid oxidation, anaerobic respiration and fermentation for ATP production; (3) the reduced ATP generation results in substantially decreased synthesis of macromolecules; (4) ethanol can directly bind 213 proteins including transcription factors, altering their functions; (5) all these changes together induce multiple stress responses, reduced biosynthesis, cell viability and growth; and (6) ethanol-adapted E. coli cells restore the majority of these reduced activities through selection of specific genomic mutations and alteration of stress responses, ultimately restoring normal ATP production, macromolecule biosynthesis, and growth. These new insights into the energy and mass balance will inform design of more ethanol-tolerant strains. Nature Publishing Group 2017-03-16 /pmc/articles/PMC5353561/ /pubmed/28300180 http://dx.doi.org/10.1038/srep44150 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Cao, Huansheng
Wei, Du
Yang, Yuedong
Shang, Yu
Li, Gaoyang
Zhou, Yaoqi
Ma, Qin
Xu, Ying
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title_full Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title_fullStr Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title_full_unstemmed Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title_short Systems-level understanding of ethanol-induced stresses and adaptation in E. coli
title_sort systems-level understanding of ethanol-induced stresses and adaptation in e. coli
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353561/
https://www.ncbi.nlm.nih.gov/pubmed/28300180
http://dx.doi.org/10.1038/srep44150
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