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Title: Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses

Abstract

Zymomonas mobilis ZM4 is a capable ethanogenic bacterium with high ethanol productivity and high level of ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of ethanol stress response have not been elucidated fully. In this study, ethanol stress responses were investigated using systems biology tools. Medium supplementation with an initial 47.3 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. Metabolomic profiling showed that ethanol-treated ZM4 cells accumulated greater amounts of glycerol during the entire fermentation process, which may indicate an important role for this metabolite. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 56% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. There were fewer genes significantly differentially expressed in the exponential phase compared to that of stationary phase and early stationarymore » phase. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Correlations among the transcriptomics, proteomics and metabolism were examined and among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. This systems biology study elucidates key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [2];  [1];  [1];  [1]
  1. ORNL
  2. University of Georgia, Athens, GA
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC)
OSTI Identifier:
1092167
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 8; Journal Issue: 7; Journal ID: ISSN 1932--6203
Country of Publication:
United States
Language:
English
Subject:
BESC LDRD

Citation Formats

Yang, Shihui, Pan, Chongle, Tschaplinski, Timothy J, Hurst, Gregory, Engle, Nancy L, Zhou, Wen, Dam, Phuongan, Xu, Ying, Dice, Lezlee T, Davison, Brian H, and Brown, Steven D. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. United States: N. p., 2013. Web. doi:10.1371/journal.pone.0068886.
Yang, Shihui, Pan, Chongle, Tschaplinski, Timothy J, Hurst, Gregory, Engle, Nancy L, Zhou, Wen, Dam, Phuongan, Xu, Ying, Dice, Lezlee T, Davison, Brian H, & Brown, Steven D. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. United States. doi:10.1371/journal.pone.0068886.
Yang, Shihui, Pan, Chongle, Tschaplinski, Timothy J, Hurst, Gregory, Engle, Nancy L, Zhou, Wen, Dam, Phuongan, Xu, Ying, Dice, Lezlee T, Davison, Brian H, and Brown, Steven D. Tue . "Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses". United States. doi:10.1371/journal.pone.0068886.
@article{osti_1092167,
title = {Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses},
author = {Yang, Shihui and Pan, Chongle and Tschaplinski, Timothy J and Hurst, Gregory and Engle, Nancy L and Zhou, Wen and Dam, Phuongan and Xu, Ying and Dice, Lezlee T and Davison, Brian H and Brown, Steven D},
abstractNote = {Zymomonas mobilis ZM4 is a capable ethanogenic bacterium with high ethanol productivity and high level of ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of ethanol stress response have not been elucidated fully. In this study, ethanol stress responses were investigated using systems biology tools. Medium supplementation with an initial 47.3 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. Metabolomic profiling showed that ethanol-treated ZM4 cells accumulated greater amounts of glycerol during the entire fermentation process, which may indicate an important role for this metabolite. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 56% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. There were fewer genes significantly differentially expressed in the exponential phase compared to that of stationary phase and early stationary phase. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Correlations among the transcriptomics, proteomics and metabolism were examined and among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. This systems biology study elucidates key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.},
doi = {10.1371/journal.pone.0068886},
journal = {PLoS ONE},
issn = {1932--6203},
number = 7,
volume = 8,
place = {United States},
year = {2013},
month = {1}
}