The peculiar glycolytic pathway in hyperthermophylic archaea : understanding its whims by experimentation in silico

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dc.contributor.authorZhang, Yanfeien_ZA
dc.contributor.authorKouril, Theresaen_ZA
dc.contributor.authorSnoep, Jacky L.en_ZA
dc.contributor.authorSiebers, Bettinaen_ZA
dc.contributor.authorBarberis, Matteoen_ZA
dc.contributor.authorWesterhoff, Hans V.en_ZA
dc.date.accessioned2018-01-23T08:54:47Z
dc.date.available2018-01-23T08:54:47Z
dc.date.issued2017
dc.descriptionCITATION: Zhang, Y., et al. 2017. The peculiar glycolytic pathway in hyperthermophylic archaea : understanding its whims by experimentation in silico. International Journal of Molecular Sciences, 18(4):876, doi:10.3390/ijms18040876.
dc.descriptionThe original publication is available at http://www.mdpi.com
dc.description.abstractMathematical 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.en_ZA
dc.description.urihttp://www.mdpi.com/1422-0067/18/4/876
dc.description.versionPublisher's versionen_ZA
dc.format.extent18 pages : illustrationsen_ZA
dc.identifier.citationZhang, Y., et al. 2017. The peculiar glycolytic pathway in hyperthermophylic archaea : understanding its whims by experimentation in silico. International Journal of Molecular Sciences, 18(4):876, doi:10.3390/ijms18040876
dc.identifier.issn1422-0067 (online)
dc.identifier.issn1661-6596 (online)
dc.identifier.otherdoi:10.3390/ijms18040876
dc.identifier.urihttp://hdl.handle.net/10019.1/103077
dc.language.isoen_ZAen_ZA
dc.publisherMDPIen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectMathematical modelsen_ZA
dc.subjectHyperthermophylic archaeaen_ZA
dc.subjectNon-phosphorylating glyceraldehyde-3-phosphate dehydrogenaseen_ZA
dc.titleThe peculiar glycolytic pathway in hyperthermophylic archaea : understanding its whims by experimentation in silicoen_ZA
dc.typeArticleen_ZA
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