Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions
Zymomonas mobilis 8b is an ethanologenic bacterium engineered to utilize both glucose and xylose. The impacts of lignocellulosic hydrolyzate inhibitors on the growth of Zymomonas mobilis 8b have been investigated. However, the molecular responses of these inhibitors have not been completely elucidat...
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doaj-9144c57f0af04e83af9ee0bfaa5b71532020-11-25T02:25:49ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-01-011110.3389/fmicb.2020.00013496034Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose ConditionsShihui Yang0Shihui Yang1Mary Ann Franden2Xia Wang3Yat-Chen Chou4Yun Hu5Steven D. Brown6Steven D. Brown7Philip T. Pienkos8Min Zhang9State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, ChinaNational Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United StatesNational Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United StatesState Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, ChinaNational Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United StatesState Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, ChinaBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United StatesBioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United StatesNational Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United StatesNational Bioenergy and Biosciences Centers, National Renewable Energy Laboratory, Golden, CO, United StatesZymomonas mobilis 8b is an ethanologenic bacterium engineered to utilize both glucose and xylose. The impacts of lignocellulosic hydrolyzate inhibitors on the growth of Zymomonas mobilis 8b have been investigated. However, the molecular responses of these inhibitors have not been completely elucidated yet. In this study, molecular responses to furfural were investigated using transcriptomic approaches of both chip-based microarray and a directional mRNA-Seq. Furfural acute shock time-course experiment with 3 g/L furfural supplemented when cells reached exponential phase and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the physiological and transcriptional profiles of short-term and long-term effects of furfural on 8b. Furfural negatively affected 8b growth in terms of final biomass and the fermentation time. Transcriptomic studies indicated that the response of 8b to furfural was dynamic and complex, and differences existed between short-term shock and long-term stress responses. However, the gene function categories were similar with most down-regulated genes related to translation and biosynthesis, while the furfural up-regulated genes were mostly related to general stress responses. Several gene candidates have been identified and genetic studies indicated that expression of ZMO0465 and cysteine synthase operon ZMO0003-0006 driven by its native promoter in a shuttle vector enhanced the furfural tolerance of 8b. In addition, the relationship between microarray and mRNA-Seq was compared with good correlations. The directional mRNA-Seq data not only provided the gene expression profiling, but also can be applied for transcriptional architecture improvement to identify and confirm operons, novel transcripts, hypothetical gene functions, transcriptional start sites, and promoters with different strength.https://www.frontiersin.org/article/10.3389/fmicb.2020.00013/fullZymomonas mobilis 8bfurfuralxylosetranscriptomicsmicroarraydirectional mRNA-Seq |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shihui Yang Shihui Yang Mary Ann Franden Xia Wang Yat-Chen Chou Yun Hu Steven D. Brown Steven D. Brown Philip T. Pienkos Min Zhang |
spellingShingle |
Shihui Yang Shihui Yang Mary Ann Franden Xia Wang Yat-Chen Chou Yun Hu Steven D. Brown Steven D. Brown Philip T. Pienkos Min Zhang Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions Frontiers in Microbiology Zymomonas mobilis 8b furfural xylose transcriptomics microarray directional mRNA-Seq |
author_facet |
Shihui Yang Shihui Yang Mary Ann Franden Xia Wang Yat-Chen Chou Yun Hu Steven D. Brown Steven D. Brown Philip T. Pienkos Min Zhang |
author_sort |
Shihui Yang |
title |
Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions |
title_short |
Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions |
title_full |
Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions |
title_fullStr |
Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions |
title_full_unstemmed |
Transcriptomic Profiles of Zymomonas mobilis 8b to Furfural Acute and Long-Term Stress in Both Glucose and Xylose Conditions |
title_sort |
transcriptomic profiles of zymomonas mobilis 8b to furfural acute and long-term stress in both glucose and xylose conditions |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2020-01-01 |
description |
Zymomonas mobilis 8b is an ethanologenic bacterium engineered to utilize both glucose and xylose. The impacts of lignocellulosic hydrolyzate inhibitors on the growth of Zymomonas mobilis 8b have been investigated. However, the molecular responses of these inhibitors have not been completely elucidated yet. In this study, molecular responses to furfural were investigated using transcriptomic approaches of both chip-based microarray and a directional mRNA-Seq. Furfural acute shock time-course experiment with 3 g/L furfural supplemented when cells reached exponential phase and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the physiological and transcriptional profiles of short-term and long-term effects of furfural on 8b. Furfural negatively affected 8b growth in terms of final biomass and the fermentation time. Transcriptomic studies indicated that the response of 8b to furfural was dynamic and complex, and differences existed between short-term shock and long-term stress responses. However, the gene function categories were similar with most down-regulated genes related to translation and biosynthesis, while the furfural up-regulated genes were mostly related to general stress responses. Several gene candidates have been identified and genetic studies indicated that expression of ZMO0465 and cysteine synthase operon ZMO0003-0006 driven by its native promoter in a shuttle vector enhanced the furfural tolerance of 8b. In addition, the relationship between microarray and mRNA-Seq was compared with good correlations. The directional mRNA-Seq data not only provided the gene expression profiling, but also can be applied for transcriptional architecture improvement to identify and confirm operons, novel transcripts, hypothetical gene functions, transcriptional start sites, and promoters with different strength. |
topic |
Zymomonas mobilis 8b furfural xylose transcriptomics microarray directional mRNA-Seq |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2020.00013/full |
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