RUI - dragon-phire: Deep-time Redox Analysis of the Geobiology Ontology Network - Protein Hardware Integrates Redox Evolution

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Researchers have hypothesized that elements like iron and nickel helped ancient forms of life on Earth eat, breathe, and perform other life functions. In fact, these metals are so important, that all life on Earth continue to use them today. The same metals are also preserved in ancient rocks that represent a snapshot into conditions how the Earth surface has been changing over 4.5 billion years. A new software package called dragon was previously developed to study how changes in Earth’s surface over billions of years have impacted the kinds of rocks or minerals that iron and nickel, and similar metals, can be a part of. The dragon-phire project extends this analysis to living systems and uses state-of-the-art network analysis to discover links between how metals behave in minerals compared to biological systems. This research will enhance the understanding of how the Earth itself has influenced 3.5 billion years of evolving life. Rowan University is a Predominantly Undergraduate Institution and the project will provide unique opportunities for minority and/or first- generation college students to participate in computational geoscience research.Life is electric, and all life on Earth obtains energy from electron transfer reactions. Electron transfer processes, and the availability of critical metal cofactors used to catalyze biological electron transfer, are regulated by planetary surface reduction-oxidation (redox) conditions in deep-time. This project will reconstruct planetary redox conditions preserved in the mineral record, and link planetary redox history to the origin and evolution of protein cofactor utilization. However, due to limited geochemical evidence preserved time, reconstructing the specific environmental redox conditions and catalytic cofactors from which electron transfer pathways evolved is a daunting challenge. The project team previously developed a new user-friendly interactive browser-based platform and R software package called: “Deep-time Redox Analysis of the Geobiology Ontology Network” or “dragon”, which constructs bipartite networks of minerals and their constituent elements. In this new project dragon’s functionality will be extended to build “Protein Hardware Integrates Redox Evolution” or “phire” networks that directly link structural and/or redox analogs in the mineral record with known protein folds that incorporate corresponding metal cofactors. The new phire functionality added to dragon will allow the dragon-phire project team to characterize the connections between mineral redox chemistry of crucial metal cofactors, such as Fe and Ni, and the core redox drivers behind the evolution of biological electron transfer processes. Rowan University is a Predominantly Undergraduate Institution and the project will provide opportunities for 10-15 undergraduates, including minority and/or first- generation college students, to participate in computational geoscience research and be involved in making the project results available to the wider public.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.