Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis
Abstract
Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13C metabolic flux analysis (13C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13C-MFA using the optimal tracers [1,2-13C]glucose, [1,6-13C]glucose, [1,2-13C]xylose and [5-13C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-13C]glucose and [U-13C]xylose tracers. We demonstrate that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO2 originates from biomass turnover. Using knockout strains, we also demonstrate that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factormore »
- Authors:
-
- Univ. of Delaware, Newark, DE (United States)
- Publication Date:
- Research Org.:
- Univ. of Delaware, Newark, DE (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E)
- OSTI Identifier:
- 1463265
- Alternate Identifier(s):
- OSTI ID: 1397057
- Grant/Contract Number:
- AR0000432
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Metabolic Engineering
- Additional Journal Information:
- Journal Volume: 39; Journal Issue: C; Journal ID: ISSN 1096-7176
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Gonzalez, Jacqueline E., Long, Christopher P., and Antoniewicz, Maciek R. Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. United States: N. p., 2016.
Web. doi:10.1016/j.ymben.2016.11.003.
Gonzalez, Jacqueline E., Long, Christopher P., & Antoniewicz, Maciek R. Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. United States. https://doi.org/10.1016/j.ymben.2016.11.003
Gonzalez, Jacqueline E., Long, Christopher P., and Antoniewicz, Maciek R. Fri .
"Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis". United States. https://doi.org/10.1016/j.ymben.2016.11.003. https://www.osti.gov/servlets/purl/1463265.
@article{osti_1463265,
title = {Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis},
author = {Gonzalez, Jacqueline E. and Long, Christopher P. and Antoniewicz, Maciek R.},
abstractNote = {Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13C metabolic flux analysis (13C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13C-MFA using the optimal tracers [1,2-13C]glucose, [1,6-13C]glucose, [1,2-13C]xylose and [5-13C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-13C]glucose and [U-13C]xylose tracers. We demonstrate that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO2 originates from biomass turnover. Using knockout strains, we also demonstrate that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH2, NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology.},
doi = {10.1016/j.ymben.2016.11.003},
journal = {Metabolic Engineering},
number = C,
volume = 39,
place = {United States},
year = {Fri Nov 11 00:00:00 EST 2016},
month = {Fri Nov 11 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
13C metabolic flux analysis: optimal design of isotopic labeling experiments
journal, December 2013
- Antoniewicz, Maciek R.
- Current Opinion in Biotechnology, Vol. 24, Issue 6
Methods and advances in metabolic flux analysis: a mini-review
journal, January 2015
- Antoniewicz, Maciek R.
- Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 3
Parallel labeling experiments for pathway elucidation and 13C metabolic flux analysis
journal, December 2015
- Antoniewicz, Maciek R.
- Current Opinion in Biotechnology, Vol. 36
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
journal, July 2006
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Metabolic Engineering, Vol. 8, Issue 4
Accurate Assessment of Amino Acid Mass Isotopomer Distributions for Metabolic Flux Analysis
journal, October 2007
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Analytical Chemistry, Vol. 79, Issue 19
Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
journal, January 2007
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Metabolic Engineering, Vol. 9, Issue 1
Measuring Deuterium Enrichment of Glucose Hydrogen Atoms by Gas Chromatography/Mass Spectrometry
journal, April 2011
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Analytical Chemistry, Vol. 83, Issue 8
Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
journal, May 2007
- Antoniewicz, M.; Kraynie, D.; Laffend, L.
- Metabolic Engineering, Vol. 9, Issue 3
Evaluation of regression models in metabolic physiology: predicting fluxes from isotopic data without knowledge of the pathway
journal, March 2006
- Antoniewicz, Maciek R.; Stephanopoulos, Gregory; Kelleher, Joanne K.
- Metabolomics, Vol. 2, Issue 1
Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for 13C metabolic flux analysis
journal, November 2014
- Au, Jennifer; Choi, Jungik; Jones, Shawn W.
- Metabolic Engineering, Vol. 26
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
journal, March 2007
- Becker, Scott A.; Feist, Adam M.; Mo, Monica L.
- Nature Protocols, Vol. 2, Issue 3
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003
- Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 84, Issue 6
A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β-oxidation pathway: Anaerobic fatty acid degradation
journal, January 2003
- Campbell, John W.; Morgan-Kiss, Rachael M.; E. Cronan, John
- Molecular Microbiology, Vol. 47, Issue 3
Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli
journal, January 2011
- Chen, Xuewen; Alonso, Ana P.; Allen, Doug K.
- Metabolic Engineering, Vol. 13, Issue 1
Biorefineries for the production of top building block chemicals and their derivatives
journal, March 2015
- Choi, Sol; Song, Chan Woo; Shin, Jae Ho
- Metabolic Engineering, Vol. 28
Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy
journal, June 2011
- Choudhary, Madhuresh K.; Yoon, Jong Moon; Gonzalez, Ramon
- Biotechnology and Bioprocess Engineering, Vol. 16, Issue 3
13C metabolic flux analysis of the extremely thermophilic, fast growing, xylose-utilizing Geobacillus strain LC300
journal, January 2016
- Cordova, Lauren T.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 33
Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by 13 C metabolic flux analysis and whole genome sequencing
journal, September 2016
- Cordova, Lauren T.; Lu, Jing; Cipolla, Robert M.
- Metabolic Engineering, Vol. 37
Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells
journal, January 2012
- Crown, Scott B.; Ahn, Woo; Antoniewicz, Maciek R.
- BMC Systems Biology, Vol. 6, Issue 1
Selection of tracers for 13C-Metabolic Flux Analysis using Elementary Metabolite Units (EMU) basis vector methodology
journal, March 2012
- Crown, Scott B.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 14, Issue 2
Publishing 13C metabolic flux analysis studies: A review and future perspectives
journal, November 2013
- Crown, Scott B.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 20
Integrated 13 C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
journal, March 2015
- Crown, Scott B.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 28
Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system
journal, November 2016
- Crown, Scott B.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 38
Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes
journal, December 2015
- Crown, Scott B.; Marze, Nicholas; Antoniewicz, Maciek R.
- PLOS ONE, Vol. 10, Issue 12
Characterizing the metabolic phenotype: A phenotype phase plane analysis
journal, December 2001
- Edwards, Jeremy S.; Ramakrishna, Ramprasad; Palsson, Bernhard O.
- Biotechnology and Bioengineering, Vol. 77, Issue 1, p. 27-36
Investigating xylose metabolism in recombinant Saccharomyces cerevisiae via 13C metabolic flux analysis
journal, January 2013
- Feng, Xueyang; Zhao, Huimin
- Microbial Cell Factories, Vol. 12, Issue 1
Correction of13C Mass Isotopomer Distributions for Natural Stable Isotope Abundance
journal, March 1996
- Fernandez, Charles A.; Rosiers, Christine Des; Previs, Stephen F.
- Journal of Mass Spectrometry, Vol. 31, Issue 3
Hemicelluloses for fuel ethanol: A review
journal, July 2010
- Gírio, F. M.; Fonseca, C.; Carvalheiro, F.
- Bioresource Technology, Vol. 101, Issue 13
RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
journal, January 2012
- Kim, Joonhoon; Reed, Jennifer L.
- Genome Biology, Vol. 13, Issue 9
Next-generation genome-scale models for metabolic engineering
journal, December 2015
- King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.
- Current Opinion in Biotechnology, Vol. 35
Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis
journal, September 2012
- Leighty, Robert W.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 14, Issue 5
COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis
journal, November 2013
- Leighty, Robert W.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 20
Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook
journal, August 2014
- Long, Christopher P.; Antoniewicz, Maciek R.
- Current Opinion in Biotechnology, Vol. 28
Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry
journal, September 2014
- Long, Christopher P.; Antoniewicz, Maciek R.
- Analytical Chemistry, Vol. 86, Issue 19
13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling
journal, November 2016
- Long, Christopher P.; Au, Jennifer; Gonzalez, Jacqueline E.
- Metabolic Engineering, Vol. 38
Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism
journal, September 2016
- Long, Christopher P.; Gonzalez, Jacqueline E.; Sandoval, Nicholas R.
- Metabolic Engineering, Vol. 37
Measuring the Composition and Stable-Isotope Labeling of Algal Biomass Carbohydrates via Gas Chromatography/Mass Spectrometry
journal, April 2016
- McConnell, Brian O.; Antoniewicz, Maciek R.
- Analytical Chemistry, Vol. 88, Issue 9
The Energetic Conversion Competence of Escherichia coli during Aerobic Respiration Studied by 31P NMR Using a Circulating Fermentation System
journal, October 2004
- Noguchi, Y.
- Journal of Biochemistry, Vol. 136, Issue 4
Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology
journal, March 2016
- Sandberg, Troy E.; Long, Christopher P.; Gonzalez, Jacqueline E.
- PLOS ONE, Vol. 11, Issue 3
The quantitative and condition-dependent Escherichia coli proteome
journal, December 2015
- Schmidt, Alexander; Kochanowski, Karl; Vedelaar, Silke
- Nature Biotechnology, Vol. 34, Issue 1
Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002
- Segre, D.; Vitkup, D.; Church, G. M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
Regulatory on/off minimization of metabolic flux changes after genetic perturbations
journal, May 2005
- Shlomi, T.; Berkman, O.; Ruppin, E.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 21
Engineering a Homo-Ethanol Pathway in Escherichia coli: Increased Glycolytic Flux and Levels of Expression of Glycolytic Genes during Xylose Fermentation
journal, May 2001
- Tao, H.; Gonzalez, R.; Martinez, A.
- Journal of Bacteriology, Vol. 183, Issue 10
Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry
journal, May 2010
- Taymaz-Nikerel, Hilal; Borujeni, Amin Espah; Verheijen, Peter J. T.
- Biotechnology and Bioengineering, Vol. 107, Issue 2
Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data
journal, January 2012
- Toya, Yoshihiro; Nakahigashi, Kenji; Tomita, Masaru
- Molecular BioSystems, Vol. 8, Issue 10, p. 2593-2604
Metabolomic and 13 C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase: Xylose Metabolic Flux Analysis
journal, November 2014
- Wasylenko, Thomas M.; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 112, Issue 3
Metabolic Engineering: Past and Future
journal, June 2013
- Woolston, Benjamin M.; Edgar, Steven; Stephanopoulos, Gregory
- Annual Review of Chemical and Biomolecular Engineering, Vol. 4, Issue 1
Quantifying carbon sources for de novo lipogenesis in wild-type and IRS-1 knockout brown adipocytes
journal, July 2004
- Yoo, Hyuntae; Stephanopoulos, Gregory; Kelleher, Joanne K.
- Journal of Lipid Research, Vol. 45, Issue 7
Works referencing / citing this record:
Metabolic engineering of l -leucine production in Escherichia coli and Corynebacterium glutamicum : a review
journal, May 2019
- Wang, Ying-Yu; Xu, Jian-Zhong; Zhang, Wei-Guo
- Critical Reviews in Biotechnology, Vol. 39, Issue 5
The impact of CO 2 /HCO 3 - availability on anaplerotic flux in PDHC-deficient Corynebacterium glutamicum strains
journal, June 2019
- Krüger, Aileen; Wiechert, Johanna; Gätgens, Cornelia
- Journal of Bacteriology
Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations
journal, July 2017
- Matsuoka, Yu; Kurata, Hiroyuki
- Biotechnology for Biofuels, Vol. 10, Issue 1
A guide to 13C metabolic flux analysis for the cancer biologist
journal, April 2018
- Antoniewicz, Maciek R.
- Experimental & Molecular Medicine, Vol. 50, Issue 4
High Gravity Fermentation of Sugarcane Bagasse Hydrolysate by Saccharomyces pastorianus to Produce Economically Distillable Ethanol Concentrations: Necessity of Medium Components Examined
journal, January 2020
- Harcum, Sarah W.; Caldwell, Thomas P.
- Fermentation, Vol. 6, Issue 1
Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search
journal, October 2019
- Kurgan, Gavin; Kurgan, Logan; Schneider, Aidan
- Applied Microbiology and Biotechnology, Vol. 103, Issue 21-22
Metabolism of sucrose in a non-fermentative Escherichia coli under oxygen limitation
journal, May 2019
- Olavarria, Karel; Fina, Albert; Velasco, Mariana I.
- Applied Microbiology and Biotechnology, Vol. 103, Issue 15
Impact of CO 2 /HCO 3 – Availability on Anaplerotic Flux in Pyruvate Dehydrogenase Complex-Deficient Corynebacterium glutamicum Strains
journal, July 2019
- Krüger, Aileen; Wiechert, Johanna; Gätgens, Cornelia
- Journal of Bacteriology, Vol. 201, Issue 20
Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose–xylose co-substrate
journal, January 2020
- Fujiwara, Ryosuke; Noda, Shuhei; Tanaka, Tsutomu
- Nature Communications, Vol. 11, Issue 1
Parallel experimental evolution reveals a novel repressive control of GalP on xylose fermentation in Escherichia coli
journal, May 2019
- Kurgan, Gavin; Sievert, Christian; Flores, Andrew
- Biotechnology and Bioengineering, Vol. 116, Issue 8
Characterization of Hydrogen Production by Escherichia coli Wild-type and Mutants of Hydrogenases Utilizing Xylose as Fermentation Substrate
journal, August 2019
- Poladyan, Anna; Trchounian, Armen
- BioEnergy Research, Vol. 12, Issue 4
Intracellular Fate of Universally Labelled 13C Isotopic Tracers of Glucose and Xylose in Central Metabolic Pathways of Xanthomonas oryzae
journal, October 2018
- Shree, Manu; K. Masakapalli, Shyam
- Metabolites, Vol. 8, Issue 4
Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
journal, April 2019
- Maeda, Kazuhiro; Westerhoff, Hans V.; Kurata, Hiroyuki
- npj Systems Biology and Applications, Vol. 5, Issue 1
Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
journal, December 2017
- Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 1
An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling
journal, November 2017
- Upton, Daniel J.; McQueen-Mason, Simon J.; Wood, A. Jamie
- Biotechnology for Biofuels, Vol. 10, Issue 1
FluxPyt: a Python-based free and open-source software for 13 C-metabolic flux analyses
journal, January 2018
- Desai, Trunil S.; Srivastava, Shireesh
- PeerJ, Vol. 6
High-resolution 13C metabolic flux analysis
journal, August 2019
- Long, Christopher P.; Antoniewicz, Maciek R.
- Nature Protocols, Vol. 14, Issue 10
Engineering E. coli for simultaneous glucose–xylose utilization during methyl ketone production
journal, January 2018
- Wang, Xi; Goh, Ee-Been; Beller, Harry R.
- Microbial Cell Factories, Vol. 17, Issue 1
Charting the Metabolic Landscape of the Facultative Methylotroph Bacillus methanolicus
journal, October 2020
- Delépine, Baudoin; López, Marina Gil; Carnicer, Marc
- mSystems, Vol. 5, Issue 5