Using chemical thermodynamics on networks to understand the universality of biological sugar-phosphate metabolism
| Project/Area Number |
22K03792
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Review Section |
Basic Section 17050:Biogeosciences-related
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| Research Institution | Tokyo Institute of Technology |
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Principal Investigator |
スミス エリック 東京工業大学, 地球生命研究所, 特任教授 (50770468)
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| Co-Investigator(Kenkyū-buntansha) |
Smith Harrison 東京工業大学, 地球生命研究所, 特任准教授 (50843934)
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| Project Period (FY) |
2022-04-01 – 2025-03-31
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| Project Status |
Granted (Fiscal Year 2023)
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| Budget Amount *help |
¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2024: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2023: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2022: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
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| Keywords | Reaction networks / Rule-based modeling / Chemical graph grammars / Information geometry / Systems chemistry / Thermochemical databases / Sugar metabolism / Natural selection cost / Chemical networks / Rule-based systems / Evolution optimization / computational chemistry |
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| Outline of Research at the Start |
The most basic features of life are conserved across all living systems. Many are pathways of core metabolism, which all other living processes require. We will use computational chemistry to understand how uncontrolled chemical networks arise in nature and the way pathways are selected from them.
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| Outline of Annual Research Achievements |
We derived new mathematical results from information geometry relating reaction specificity to physiological cost of pathways. A publication was submitted to PLoS Computational Biology in November 2023. A preprint is available at https://www.biorxiv.org/content/10.1101/2023.12.11.571120v1
Parts of this work were presented by external collaborators N. Lauber and C. Flamm at the 12th annual ELSI symposium, in a talk "Generating Possibility Spaces for different Chemistries with Rule Based Modeling".
We have begun a graph-grammar model of a primordial autocatalytic carbon fixation network demonstrated by R. Krishnamurthy of Scripps Institute. A former student of the PI is applying our analyses to the the degradation of ecologically important pesticides, a spin-off benefit of this research.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
One manuscript was submitted with mathematical and technical results. The Co-I will present results at the conference Molecular Origins of Life in Munich in July 2024, titled "Chance and Necessity in Biological Sugar-Phosphate Chemistry". A second manuscript for a biological audience is in preparation and will be submitted in 2024.
We continue bimonthly conference calls with collaborators at University of Vienna and the University of Southern Denmark, to complete the full graphical and thermochemical analysis pipeline. A third publication is planned to present the computational high-throughput platform. We have also extended the model to include new reactions relevant to primordial carbon fixation, which we proposed as an extra accomplishment of the research in case of good progress.
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| Strategy for Future Research Activity |
Our work has benefitted from interest by research groups in Europe, who involve their students and post-docs in our program at no cost to the grant. It also benefitted from the graduation of a former Ph.D. student of the PI in the U.S. who independently carried out work on autocatalytic feedbacks in our networks, and is analyzing the thermodynamic and evolutionary costs which the PI began in the submission to PLoS. The postdoc will begin work in a Physics and Complex Systems group at U. Tokyo in 2024.
Some of the work on autocatalysis in networks is planned to be applied to a model system on early-Earth Nitrogen redox chemistry, with collaborators at RIKEN and Nara Women's University, through the JSPS-funded project CO Worlds, PI Yuichiro Ueno, on which the PI Smith is also a member.
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Report
(2 results)
Research Products
(10 results)
