Biosignatures & Paleobiology

Nitrogenase Structural Evolution Across Earth’s History

By Keith Cowing

Status Report

biorxiv.org

December 27, 2024

Filed under biochemistry, biogeochemistry, biophysics, biorxiv.org, evolution, extremophile, genomics, Nitrogenase

Nitrogenase Structural Evolution Across Earth’s History — A schematic illustrating habitability of physical spaces as a function of physical and chemical conditions. The diagram is a simplified depiction of niche space (here three dimensions are shown – in reality, the space is an n-dimensional hypervolume) and the extent to which these niche conditions are occupied in physical spaces. The habitable space for life is enclosed within a much larger (red) space that is uninhabitable (also see Figure 4). The blue object represents habitable space that is inhabited. At the edge of this habitable and inhabited set of physical and chemical conditions is a putative yellow ‘rind’ of habitat space at the edges of life which could be inhabited by life with appropriate evolutionary innovations. Within the habitable and inhabited space there are grey shapes depicting localized physical spaces that are habitable, but uninhabited (uninhabited habitats). The purpose of the schematic is to illustrate that uninhabited, but habitable spaces exist both within physical spaces that are known to be permissive for microbial growth and potentially at the limits of life at extremes. Life, especially using technology, can establish itself in conditions away from the blue spheroid with appropriate expenditure of energy (e.g., a self1317 sustaining space settlement), shown as isolated blue objects in the red space. — FEMS Microbiology Reviews

Life on Earth is more than 3.5 billion years old—nearly as old as the age of the planet. Over this vast expanse of time, life and its biomolecules adapted to and triggered profound changes to the Earth’s environment

Certain critical enzymes evolved early in the history of life and have persisted through planetary extremes. While sequence data is widely used to trace evolutionary trajectories, enzyme structure remains an underexplored resource for understanding how proteins evolve over long timescales.

Here, we implement an integrated approach to study nitrogenase, an ancient, globally critical enzyme essential for nitrogen fixation. Despite the ecological diversity of its host microbes, nitrogenase has strict functional limitations, including extreme oxygen sensitivity, energy requirements and substrate availability.

By combining phylogenetics, ancestral sequence reconstruction, protein crystallography and deep-learning based structural prediction, we resurrected three billion years of nitrogenase structural history.

We present the first effort to predict all extant and ancestral structures along the evolutionary tree of an enzyme and present a total of ∼5000 structures. Our approach lays the foundation for reconstructing key structural constraints that influence protein evolution and studying ancient enzyme evolution in the light of phylogenetic and environmental change.

Nitrogenase structural evolution across Earth’s history, biorxiv.org (open access)
Astrobiology,

Keith Cowing

Explorers Club Fellow, ex-NASA Space Station Payload manager/space biologist, Away Teams, Journalist, Lapsed climber, Synaesthete, Na’Vi-Jedi-Freman-Buddhist-mix, ASL, Devon Island and Everest Base Camp veteran, (he/him) 🖖🏻

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