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.
Highlights
Archaea, the third kingdom of life, have many unique properties that distinguish its members from most Bacteria and Eukarya
In this research we investigated the pathway from glyceraldehyde 3-phosphate (GAP) to pyruvate of the hypothermophylic Archaea S. solfataricus
We formulated three hypotheses that might have explained why glyceraldehyde-3-phosphate dehydrogenase (GAPN) is essential in hyperthermophilic organisms
Summary
The third kingdom of life, have many unique properties that distinguish its members from most Bacteria and Eukarya. The thermophilic Archaea thrive on temperatures between 60 and 80 ◦C, while hyperthermophiles live in the temperature range from 80 to 113 ◦C [2]. Life at high temperature requires efficient adaption strategies. The high temperatures always come with significant stress in terms of increased denaturation of proteins and membranes. When compared with the proteins from organisms that grow at moderate temperatures, proteins of hyperthermophiles are more stable at high temperatures and are often more resistant to chemical denaturants. The comparison of structural features from enzymes adapted to different temperature ranges revealed different adaptation strategies in (hyper)thermophilic proteins such as decrease in loop lengths, increase in oligomerization state and more distinct secondary structures [3]. Archaea have unique membrane spanning lipids with less hydrolysable ether linkages of glycerol to isoprenoid chains [4]
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