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Title: Near-equilibrium glycolysis supports metabolic homeostasis and energy yield

Abstract

Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. In this work, we create a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. With this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [3];  [3];  [2]; ORCiD logo [2];  [2];  [4];  [3]; ORCiD logo [3]; ORCiD logo [2]
+ Show Author Affiliations
  1. Univ. of California, Los Angeles, CA (United States); Princeton Univ., NJ (United States)
  2. Princeton Univ., NJ (United States)
  3. Univ. of Wisconsin, Madison, WI (United States)
  4. Princeton Univ., NJ (United States); ExxonMobil Research and Engineering Company, Annandale, NJ (United States)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States); Princeton Univ., NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1570470
Grant/Contract Number:  
SC0018420; SC0012461; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Nature Chemical Biology
Additional Journal Information:
Journal Volume: 15; Journal Issue: 10; Journal ID: ISSN 1552-4450
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Park, Junyoung O., Tanner, Lukas B., Wei, Monica H., Khana, Daven B., Jacobson, Tyler B., Zhang, Zheyun, Rubin, Sara A., Li, Sophia Hsin-Jung, Higgins, Meytal B., Stevenson, David M., Amador-Noguez, Daniel, and Rabinowitz, Joshua D. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield. United States: N. p., 2019. Web. doi:10.1038/s41589-019-0364-9.
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Park, Junyoung O., Tanner, Lukas B., Wei, Monica H., Khana, Daven B., Jacobson, Tyler B., Zhang, Zheyun, Rubin, Sara A., Li, Sophia Hsin-Jung, Higgins, Meytal B., Stevenson, David M., Amador-Noguez, Daniel, & Rabinowitz, Joshua D. Near-equilibrium glycolysis supports metabolic homeostasis and energy yield. United States. doi:10.1038/s41589-019-0364-9.
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Park, Junyoung O., Tanner, Lukas B., Wei, Monica H., Khana, Daven B., Jacobson, Tyler B., Zhang, Zheyun, Rubin, Sara A., Li, Sophia Hsin-Jung, Higgins, Meytal B., Stevenson, David M., Amador-Noguez, Daniel, and Rabinowitz, Joshua D. Mon . "Near-equilibrium glycolysis supports metabolic homeostasis and energy yield". United States. doi:10.1038/s41589-019-0364-9. https://www.osti.gov/servlets/purl/1570470.
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@article{osti_1570470,
title = {Near-equilibrium glycolysis supports metabolic homeostasis and energy yield},
author = {Park, Junyoung O. and Tanner, Lukas B. and Wei, Monica H. and Khana, Daven B. and Jacobson, Tyler B. and Zhang, Zheyun and Rubin, Sara A. and Li, Sophia Hsin-Jung and Higgins, Meytal B. and Stevenson, David M. and Amador-Noguez, Daniel and Rabinowitz, Joshua D.},
abstractNote = {Glycolysis plays a central role in producing ATP and biomass. Its control principles, however, remain incompletely understood. In this work, we create a method that combines 2H and 13C tracers to determine glycolytic thermodynamics. With this method, we show that, in conditions and organisms with relatively slow fluxes, multiple steps in glycolysis are near to equilibrium, reflecting spare enzyme capacity. In Escherichia coli, nitrogen or phosphorus upshift rapidly increases the thermodynamic driving force, deploying the spare enzyme capacity to increase flux. Similarly, respiration inhibition in mammalian cells rapidly increases both glycolytic flux and the thermodynamic driving force. The thermodynamic shift allows flux to increase with only small metabolite concentration changes. Finally, we find that the cellulose-degrading anaerobe Clostridium cellulolyticum exhibits slow, near-equilibrium glycolysis due to the use of pyrophosphate rather than ATP for fructose-bisphosphate production, resulting in enhanced per-glucose ATP yield. Thus, near-equilibrium steps of glycolysis promote both rapid flux adaptation and energy efficiency.},
doi = {10.1038/s41589-019-0364-9},
journal = {Nature Chemical Biology},
number = 10,
volume = 15,
place = {United States},
year = {2019},
month = {9}
}
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DOI:  10.1038/s41589-019-0364-9
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Works referenced in this record:

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments
journal, January 2016

  • Dona, Anthony C.; Kyriakides, Michael; Scott, Flora
  • Computational and Structural Biotechnology Journal, Vol. 14
  • DOI: 10.1016/j.csbj.2016.02.005

Covalent modification of bacterial glutamine synthetase: physiological significance
journal, January 1984

  • Kustu, Sydney; Hirschman, Jodi; Burton, Doris
  • MGG Molecular & General Genetics, Vol. 197, Issue 2
  • DOI: 10.1007/BF00330979

Pyrophosphate-dependent phosphofructokinase, an anaerobic glycolytic enzyme?
journal, July 1991

Quantitative assessment of regulation in metabolic systems
journal, August 1991

α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition
journal, October 2011

  • Doucette, Christopher D.; Schwab, David J.; Wingreen, Ned S.
  • Nature Chemical Biology, Vol. 7, Issue 12
  • DOI: 10.1038/nchembio.685

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
  • DOI: 10.1016/j.ymben.2006.01.004

Metabolomics‐driven quantitative analysis of ammonia assimilation in E. coli
journal, January 2009

  • Yuan, Jie; Doucette, Christopher D.; Fowler, William U.
  • Molecular Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1038/msb.2009.60

Optimality and evolutionary tuning of the expression level of a protein
journal, July 2005

Glutamine‐driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia
journal, January 2013

  • Fan, Jing; Kamphorst, Jurre J.; Mathew, Robin
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.65

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol
journal, November 2017

  • Tian, Liang; Perot, Skyler J.; Stevenson, David
  • Biotechnology for Biofuels, Vol. 10, Issue 1
  • DOI: 10.1186/s13068-017-0961-3

Metabolite Measurement: Pitfalls to Avoid and Practices to Follow
journal, June 2017

Water Suppression That Works. Excitation Sculpting Using Arbitrary Wave-Forms and Pulsed-Field Gradients
journal, February 1995

  • Hwang, T. L.; Shaka, A. J.
  • Journal of Magnetic Resonance, Series A, Vol. 112, Issue 2
  • DOI: 10.1006/jmra.1995.1047

Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase
journal, April 2012

  • Xu, Yi-Fan; Amador-Noguez, Daniel; Reaves, Marshall Louis
  • Nature Chemical Biology, Vol. 8, Issue 6
  • DOI: 10.1038/nchembio.941

Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis
journal, June 2015

  • Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.
  • Applied and Environmental Microbiology, Vol. 81, Issue 17
  • DOI: 10.1128/AEM.01324-15

Systems-level analysis of mechanisms regulating yeast metabolic flux
journal, October 2016

Pyrophosphatase is essential for growth of Escherichia coli.
journal, October 1990

Overflow metabolism in Escherichia coli results from efficient proteome allocation
journal, December 2015

  • Basan, Markus; Hui, Sheng; Okano, Hiroyuki
  • Nature, Vol. 528, Issue 7580
  • DOI: 10.1038/nature15765

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
journal, July 2007

  • Beg, Q. K.; Vazquez, A.; Ernst, J.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 31
  • DOI: 10.1073/pnas.0609845104

Toward Identification of Acid/Base Catalysts in the Active Site of Enolase:  Comparison of the Properties of K345A, E168Q, and E211Q Variants †
journal, January 1996

  • Poyner, Russell R.; Laughlin, L. Timothy; Sowa, Gwendolyn A.
  • Biochemistry, Vol. 35, Issue 5
  • DOI: 10.1021/bi952186y

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach
journal, July 2008

  • Bennett, Bryson D.; Yuan, Jie; Kimball, Elizabeth H.
  • Nature Protocols, Vol. 3, Issue 8
  • DOI: 10.1038/nprot.2008.107

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
  • DOI: 10.1016/j.ymben.2006.09.001

Four Key Steps Control Glycolytic Flux in Mammalian Cells
journal, July 2018

Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes
journal, January 2007

Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP
journal, April 2016

  • Bren, Anat; Park, Junyoung O.; Towbin, Benjamin D.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep24834

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
journal, May 2016

  • Park, Junyoung O.; Rubin, Sara A.; Xu, Yi-Fan
  • Nature Chemical Biology, Vol. 12, Issue 7
  • DOI: 10.1038/nchembio.2077

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method
journal, June 2018

Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics
journal, January 2015

  • Xu, Yi-Fan; Lu, Wenyun; Rabinowitz, Joshua D.
  • Analytical Chemistry, Vol. 87, Issue 4
  • DOI: 10.1021/ac504118y

Clostridium cellulolyticum : model organism of mesophilic cellulolytic clostridia
journal, September 2005

Glycolytic strategy as a tradeoff between energy yield and protein cost
journal, April 2013

  • Flamholz, A.; Noor, E.; Bar-Even, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 24
  • DOI: 10.1073/pnas.1215283110

Identification and quantification of water-soluble metabolites by cryoprobe-assisted nuclear magnetic resonance spectroscopy applied to microbial fermentation
journal, May 2009

  • Carrieri, Damian; McNeely, Kelsey; De Roo, Ana C.
  • Magnetic Resonance in Chemistry, Vol. 47, Issue S1
  • DOI: 10.1002/mrc.2420

Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer
journal, April 2010

  • Lu, Wenyun; Clasquin, Michelle F.; Melamud, Eugene
  • Analytical Chemistry, Vol. 82, Issue 8
  • DOI: 10.1021/ac902837x

Metabolite Spectral Accuracy on Orbitraps
journal, May 2017

Consistent Estimation of Gibbs Energy Using Component Contributions
journal, July 2013

Multidimensional Optimality of Microbial Metabolism
journal, May 2012

Salmonella typhimuriumApparently Perceives External Nitrogen Limitation as Internal Glutamine Limitation
journal, June 1996

  • Ikeda, Timothy P.; Shauger, Andrea E.; Kustu, Sydney
  • Journal of Molecular Biology, Vol. 259, Issue 4
  • DOI: 10.1006/jmbi.1996.0342

Thermodynamics-Based Metabolic Flux Analysis
journal, March 2007

  • Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily
  • Biophysical Journal, Vol. 92, Issue 5
  • DOI: 10.1529/biophysj.106.093138

Interdependence of Cell Growth and Gene Expression: Origins and Consequences
journal, November 2010

Rapid Analysis of Glycolytic and Oxidative Substrate Flux of Cancer Cells in a Microplate
journal, October 2014

Atypical Glycolysis in Clostridium thermocellum
journal, February 2013

  • Zhou, Jilai; Olson, Daniel G.; Argyros, D. Aaron
  • Applied and Environmental Microbiology, Vol. 79, Issue 9, p. 3000-3008
  • DOI: 10.1128/AEM.04037-12

NMR Studies of the Role of Hydrogen Bonding in the Mechanism of Triosephosphate Isomerase †
journal, December 1997

  • Harris, Thomas K.; Abeygunawardana, Chitrananda; Mildvan, Albert S.
  • Biochemistry, Vol. 36, Issue 48
  • DOI: 10.1021/bi972039v

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
journal, June 2009

  • Bennett, Bryson D.; Kimball, Elizabeth H.; Gao, Melissa
  • Nature Chemical Biology, Vol. 5, Issue 8
  • DOI: 10.1038/nchembio.186

Compounds Which Serve as the Sole Source of Carbon or Nitrogen for Salmonella typhimurium LT-2
journal, January 1969

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