Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum
Abstract
Cellulolytic bacteria have the potential to perform lignocellulose hydrolysis and fermentation simultaneously. The metabolic pathways of these bacteria, therefore, require more comprehensive and quantitative understanding. Using isotope tracer, gas chromatography-mass spectrometry, and metabolic flux modeling, we decipher the metabolic network of Clostridium thermocellum, a model cellulolytic bacterium which represents as an attractive platform for conversion of lignocellulose to dedicated products. We uncover that the Embden-Meyerhof-Parnas (EMP) pathway is the predominant glycolytic route whereas the Entner-Doudoroff (ED) pathway and oxidative pentose phosphate pathway are inactive. We also observe that C. thermocellum's TCA cycle is initiated by both Si- and Re-citrate synthase, and it is disconnected between 2-oxoglutarate and oxaloacetate in the oxidative direction; C. thermocellum uses a citramalate shunt to synthesize isoleucine; and both the one-carbon pathway and the malate shunt are highly active in this bacterium. To gain a quantitative understanding, we further formulate a fluxome map to quantify the metabolic fluxes through central metabolic pathways. This work represents the first global in vivo investigation of the principal carbon metabolism of C. thermocellum. In conclusion, our results elucidate the unique structure of metabolic network in this cellulolytic bacterium and demonstrate the capability of isotope-assisted metabolite studies in understanding microbial metabolismmore »
- Publication Date:
- Research Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Hydrogen Fuel Cell Technologies Office; USDOE National Renewable Energy Laboratory (NREL), Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1471551
- Report Number(s):
- NREL/JA-2700-72400
Journal ID: ISSN 1664-302X
- Grant/Contract Number:
- AC36-08GO28308
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 9; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; 13C-isotope tracer; cellulolytic bacteria; citrate synthase; glycolytic pathways; isoleucine biosynthesis; metabolic flux analysis; tricarboxylic acid cycle
Citation Formats
Xiong, Wei, Lo, Jonathan, Chou, Katherine J., Wu, Chao, Magnusson, Lauren R., Dong, Tao, and Maness, PinChing. Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum. United States: N. p., 2018.
Web. doi:10.3389/fmicb.2018.01947.
Xiong, Wei, Lo, Jonathan, Chou, Katherine J., Wu, Chao, Magnusson, Lauren R., Dong, Tao, & Maness, PinChing. Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum. United States. https://doi.org/10.3389/fmicb.2018.01947
Xiong, Wei, Lo, Jonathan, Chou, Katherine J., Wu, Chao, Magnusson, Lauren R., Dong, Tao, and Maness, PinChing. Thu .
"Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum". United States. https://doi.org/10.3389/fmicb.2018.01947. https://www.osti.gov/servlets/purl/1471551.
@article{osti_1471551,
title = {Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum},
author = {Xiong, Wei and Lo, Jonathan and Chou, Katherine J. and Wu, Chao and Magnusson, Lauren R. and Dong, Tao and Maness, PinChing},
abstractNote = {Cellulolytic bacteria have the potential to perform lignocellulose hydrolysis and fermentation simultaneously. The metabolic pathways of these bacteria, therefore, require more comprehensive and quantitative understanding. Using isotope tracer, gas chromatography-mass spectrometry, and metabolic flux modeling, we decipher the metabolic network of Clostridium thermocellum, a model cellulolytic bacterium which represents as an attractive platform for conversion of lignocellulose to dedicated products. We uncover that the Embden-Meyerhof-Parnas (EMP) pathway is the predominant glycolytic route whereas the Entner-Doudoroff (ED) pathway and oxidative pentose phosphate pathway are inactive. We also observe that C. thermocellum's TCA cycle is initiated by both Si- and Re-citrate synthase, and it is disconnected between 2-oxoglutarate and oxaloacetate in the oxidative direction; C. thermocellum uses a citramalate shunt to synthesize isoleucine; and both the one-carbon pathway and the malate shunt are highly active in this bacterium. To gain a quantitative understanding, we further formulate a fluxome map to quantify the metabolic fluxes through central metabolic pathways. This work represents the first global in vivo investigation of the principal carbon metabolism of C. thermocellum. In conclusion, our results elucidate the unique structure of metabolic network in this cellulolytic bacterium and demonstrate the capability of isotope-assisted metabolite studies in understanding microbial metabolism of industrial interests.},
doi = {10.3389/fmicb.2018.01947},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {United States},
year = {Thu Aug 23 00:00:00 EDT 2018},
month = {Thu Aug 23 00:00:00 EDT 2018}
}
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- Xiong, Wei; Reyes, Luis H.; Michener, William E.
- Biotechnology and Bioengineering, Vol. 115, Issue 7
Consolidated bioprocessing of cellulosic biomass: an update
journal, October 2005
- Lynd, Lee R.; van Zyl, Willem H.; McBride, John E.
- Current Opinion in Biotechnology, Vol. 16, Issue 5, p. 577-583
Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum
journal, January 2013
- Deng, Yu; Olson, Daniel G.; Zhou, Jilai
- Metabolic Engineering, Vol. 15, p. 151-158
Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum
journal, September 2015
- Lin, Paul P.; Mi, Luo; Morioka, Amy H.
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Glycolysis without pyruvate kinase in Clostridium thermocellum
journal, January 2017
- Olson, Daniel G.; Hörl, Manuel; Fuhrer, Tobias
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How biotech can transform biofuels
journal, February 2008
- Lynd, Lee R.; Laser, Mark S.; Bransby, David
- Nature Biotechnology, Vol. 26, Issue 2, p. 169-172
Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism
journal, May 2005
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- Nature Genetics, Vol. 37, Issue 6
Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum
journal, October 2006
- Lu, Y.; Zhang, Y. -H. P.; Lynd, L. R.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 44
Deletion of the Cel48S cellulase from Clostridium thermocellum
journal, September 2010
- Olson, Daniel G.; Tripathi, Shital A.; Giannone, Richard J.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 41, p. 17727-17732
CO 2 -fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum
journal, October 2016
- Xiong, Wei; Lin, Paul P.; Magnusson, Lauren
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 46
INCA: a computational platform for isotopically non-stationary metabolic flux analysis
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- Young, J. D.
- Bioinformatics, Vol. 30, Issue 9
Purification and Properties of d-Gluconate Dehydratase from Clostridium pasteurianum
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- Bender, Rudolf; Gottschalk, Gerhard
- European Journal of Biochemistry, Vol. 40, Issue 1
Global View of the Clostridium thermocellum Cellulosome Revealed by Quantitative Proteomic Analysis
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The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading
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- Holwerda, Evert K.; Thorne, Philip G.; Olson, Daniel G.
- Biotechnology for Biofuels, Vol. 7, Issue 1
Discovery of a Ferredoxin:NAD+-Oxidoreductase (Rnf) in Acetobacterium woodii: A Novel Potential Coupling Site in Acetogens
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Works referencing / citing this record:
EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix
journal, April 2019
- Wu, Chao; Chen, Chia-hsin; Lo, Jonathan
- Frontiers in Microbiology, Vol. 10