Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses.
<h4>Background</h4>Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. Howev...
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oai:doaj.org-article:c5895a602b4e48c1bb728e69658c23602021-11-18T07:37:31ZSystems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses.1932-620310.1371/journal.pone.0068886https://doaj.org/article/c5895a602b4e48c1bb728e69658c23602013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874800/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and 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 its ethanol stress response have not been elucidated fully.<h4>Methodology/principal findings</h4>In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% 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 that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher.<h4>Conclusions</h4>Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated "omics" approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.Shihui YangChongle PanTimothy J TschaplinskiGregory B HurstNancy L EngleWen ZhouPhuongan DamYing XuMiguel RodriguezLezlee DiceCourtney M JohnsonBrian H DavisonSteven D BrownPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68886 (2013) |
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Medicine R Science Q Shihui Yang Chongle Pan Timothy J Tschaplinski Gregory B Hurst Nancy L Engle Wen Zhou Phuongan Dam Ying Xu Miguel Rodriguez Lezlee Dice Courtney M Johnson Brian H Davison Steven D Brown Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| description |
<h4>Background</h4>Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and 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 its ethanol stress response have not been elucidated fully.<h4>Methodology/principal findings</h4>In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% 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 that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher.<h4>Conclusions</h4>Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated "omics" approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress. |
| format |
article |
| author |
Shihui Yang Chongle Pan Timothy J Tschaplinski Gregory B Hurst Nancy L Engle Wen Zhou Phuongan Dam Ying Xu Miguel Rodriguez Lezlee Dice Courtney M Johnson Brian H Davison Steven D Brown |
| author_facet |
Shihui Yang Chongle Pan Timothy J Tschaplinski Gregory B Hurst Nancy L Engle Wen Zhou Phuongan Dam Ying Xu Miguel Rodriguez Lezlee Dice Courtney M Johnson Brian H Davison Steven D Brown |
| author_sort |
Shihui Yang |
| title |
Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| title_short |
Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| title_full |
Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| title_fullStr |
Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| title_full_unstemmed |
Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. |
| title_sort |
systems biology analysis of zymomonas mobilis zm4 ethanol stress responses. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/c5895a602b4e48c1bb728e69658c2360 |
| work_keys_str_mv |
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| _version_ |
1718423188648493056 |