Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics.

PLoS Computational Biology
Karen van EunenBarbara M Bakker

Abstract

A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was later applied to different experimental steady-state conditions, it often exhibited unrestrained metabolite accumulation.Here we resolve this issue by showing that the results of such ab initio modeling are improved substantially by (i) including appropriate allosteric regulation and (ii) measuring the enzyme kinetic parameters under conditions that resemble the intracellular environment. The following modifications proved crucial: (i) implementation of allosteric regulation of hexokinase and pyruvate kinase, (ii) implementation of V(max) values measured under conditions that resembled the yeast cytosol, and (iii) redetermination of the kinetic parameters of glyceraldehyde-3-phosphate dehydrogenase under physiological conditions.Model predictions and experiments were compared under five different conditions of yeast growth and starvation. When either the original model was used (which lacked important allosteric regulation), or the enz...Continue Reading

References

Oct 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·A BoiteuxB Hess
Jan 1, 1989·Bio Systems·A Boiteux, H G Busse
Nov 1, 1968·Hoppe-Seyler's Zeitschrift für physiologische Chemie·B Hess, A Boiteux
Jun 5, 1998·Trends in Biochemical Sciences·B TeusinkH V Westerhoff
Oct 31, 1998·Applied and Environmental Microbiology·P Van HoekJ T Pronk
Dec 18, 2001·Biophysical Chemistry·F HynneP G Sørensen
Dec 26, 2001·Nucleic Acids Research·Ida SchomburgDietmar Schomburg
Aug 31, 1970·FEBS Letters·A Boiteux, B Hess
Sep 2, 2003·Metabolic Engineering·Diana Visser, Joseph J Heijnen
Mar 1, 1965·Archives of Biochemistry and Biophysics·A BETZ, B CHANCE
Oct 20, 2004·Metabolic Engineering·Diana VisserJoseph J Heijnen
Mar 23, 2005·FEMS Yeast Research·Sergio RossellHans V Westerhoff
Jul 9, 2005·Biotechnology and Bioengineering·Joseph J Heijnen
Oct 26, 2005·Bio Systems·Jacky L SnoepHans V Westerhoff
Jul 20, 1997·Biotechnology and Bioengineering·U TheobaldM Reuss
Aug 20, 1997·Biotechnology and Bioengineering·M RizziM Reuss
Jan 14, 2010·The FEBS Journal·Karen van EunenBarbara M Bakker
Jan 21, 2010·Molecular Systems Biology·Thomas WaltherJean-Marie François

❮ Previous
Next ❯

Citations

Jun 3, 2014·BMC Systems Biology·Shodhan RaoBayu Jayawardhana
Jul 9, 2013·Molecular Neurobiology·Kazuhiro A FujitaRudi Balling
Jul 3, 2013·The Journal of Biological Chemistry·Alejandro E LerouxR Luise Krauth-Siegel
Jan 13, 2015·Current Opinion in Biotechnology·Edward J O'Brien, Bernhard O Palsson
Jan 3, 2016·Journal of Biotechnology·Rafael S CostaSusana Vinga
Sep 8, 2015·Current Opinion in Biotechnology·Ljubisa MiskovicVassily Hatzimanikatis
Sep 1, 2015·Current Opinion in Biotechnology·Anupam ChowdhuryCostas D Maranas
Nov 14, 2015·FEMS Yeast Research·Dan Fraenkel, Jens Nielsen
Jun 15, 2013·The FEBS Journal·Daniela Araiza-OliveraSalvador Uribe-Carvajal
Feb 19, 2014·Current Opinion in Biotechnology·Hannes LinkUwe Sauer
Jan 3, 2013·Environmental Microbiology·Gal Winter, Jens O Krömer
Jul 3, 2013·Biotechnology Journal·Joseph J Heijnen, Peter J T Verheijen
Jul 21, 2015·Integrative Biology : Quantitative Biosciences From Nano to Macro·Katja TummlerEdda Klipp
Mar 4, 2014·PLoS Computational Biology·Anupam ChowdhuryCostas D Maranas
Jan 5, 2017·Analytical Chemistry·Jan Christopher GuderHannes Link
Apr 21, 2017·International Journal of Molecular Sciences·Yanfei ZhangHans V Westerhoff
Jan 1, 2012·Metabolites·Jan BerkhoutBas Teusink
Jan 1, 2012·Metabolites·Robert A Dromms, Mark P Styczynski
Mar 3, 2018·The FEBS Journal·Neil SwainstonCarsten Kettner
Feb 10, 2018·Reports on Progress in Physics·Tyler M EarnestZaida Luthey-Schulten
Feb 17, 2018·Biotechnology for Biofuels·Mojdeh FarajiEberhard O Voit
Aug 27, 2014·FEMS Yeast Research·Eduard J KerkhovenJens Nielsen
Jul 14, 2020·Biotechnology and Bioengineering·Sebastian WenkArren Bar-Even
Oct 30, 2015·BMC Evolutionary Biology·Russell A HermansenRyan N Gutenkunst
Sep 18, 2018·Current Medicinal Chemistry·Emma SaavedraPaul A M Michels
Dec 24, 2018·Proceedings of the National Academy of Sciences of the United States of America·Thomas P Wytock, Adilson E Motter
Feb 17, 2017·Journal of the Royal Society, Interface·Herbert M Sauro
May 26, 2018·Bioinformatics and Biology Insights·Daisuke TominagaSachiyo Aburatani
Jul 29, 2018·BMC Systems Biology·Håvard G FrøysaNello Blaser
Sep 30, 2017·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Monica P McNerney, Mark P Styczynski
Dec 29, 2020·Current Opinion in Biotechnology·Charles J FosterCostas D Maranas
Dec 30, 2020·Proceedings of the National Academy of Sciences of the United States of America·Douglas L RothmanRobert G Shulman
Apr 20, 2021·Annual Review of Chemical and Biomolecular Engineering·Nick FacklerMichael Köpke
Jun 29, 2021·Molecular Systems Biology·Sanchari BhattacharyyaEugene I Shakhnovich

❮ Previous
Next ❯

Related Concepts

Related Feeds

Calcium & Bioenergetics

Bioenergetic processes, including cellular respiration and photosynthesis, concern the transformation of energy by cells. Here is the latest research on the role of calcium in bioenergetics.