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Schocke L, Bräsen C, Siebers B. Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms. Curr Opin Biotechnol 2019; 59:71-77. [PMID: 30875666 DOI: 10.1016/j.copbio.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/29/2019] [Accepted: 02/09/2019] [Indexed: 12/16/2022]
Abstract
Archaea dominate extreme habitats and possess unique cellular and metabolic properties with novel or modified metabolic pathways and unusual enzymes. Thermoacidophilic Sulfolobus species and their thermo(acido)philic enzymes gained special attention due to their adaptation toward two extremes, high temperature (75-80°C) and low pH (pH 2-5), that matches harsh process conditions in industrial applications. For different Sulfolobus species versatile genetic systems have been established and significant metabolic and physiological information from classical biochemistry and genetic as well as poly-omics and systems biology approaches is available. Their ease of growth under aerobic or microaerophilic conditions and established fermentation technologies gaining high cell yields promote Sulfolobus as source for extremozymes and as valuable novel platform organism for industrial biotechnology.
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Affiliation(s)
- Larissa Schocke
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany.
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Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. Int J Mol Sci 2017; 18:ijms18040876. [PMID: 28425930 PMCID: PMC5412457 DOI: 10.3390/ijms18040876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Yanfei Zhang
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
| | - Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
- 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.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
- 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.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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