Next Article in Journal
Circadian Clock, Cell Division, and Cancer: From Molecules to Organism
Previous Article in Journal
Hepatitis E Virus Genotypes and Evolution: Emergence of Camel Hepatitis E Variants
Previous Article in Special Issue
Influence of Temperature on Transdermal Penetration Enhancing Mechanism of Borneol: A Multi-Scale Study
Article Menu
Issue 4 (April) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2017, 18(4), 876; doi:10.3390/ijms18040876

The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico

1
Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
2
Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg—Essen, Universitätsstr. 5, 45141 Essen, Germany
3
Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa
4
The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK
5
Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
*
Author to whom correspondence should be addressed.
Academic Editor: Samuel De Visser
Received: 12 March 2017 / Revised: 7 April 2017 / Accepted: 13 April 2017 / Published: 20 April 2017
(This article belongs to the Special Issue Computational Modelling of Enzymatic Reaction Mechanisms)
View Full-Text   |   Download PDF [951 KB, uploaded 24 April 2017]   |  

Abstract

Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5′-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate. View Full-Text
Keywords: mathematical models; Archaea; flux; flux control coefficient; non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; GAPN mathematical models; Archaea; flux; flux control coefficient; non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; GAPN
Figures

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Zhang, Y.; Kouril, T.; Snoep, J.L.; Siebers, B.; Barberis, M.; Westerhoff, H.V. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. Int. J. Mol. Sci. 2017, 18, 876.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top