The structural history of Eukarya.

Authors

Diandra Daumiller, Qiuzhen Li, Patrick Bryant

Published in

Science advances. Volume 12. Issue 44. Pages eaeh2524. Oct 30, 2026. Epub Oct 28, 2026.

Abstract

Comparative genomics has traditionally relied on sequence-based markers, yet the global evolutionary landscape of protein architecture remains largely unexplored. We present the Structural History of Eukarya (SHE), a structural similarity-derived phylogeny from all-vs-all structural comparisons on the proteome level of 1542 eukaryotic species, encompassing nearly 300 trillion pairwise protein alignments. This proteome-scale analysis reveals a bipartite model of eukaryotic evolution: a rigid Strict Core dominated by cytoskeletal architecture, supporting a more plastic Operational Engine centered on translational machinery. We identify lineage-specific accelerations of structural evolution in species such as birds and ants that are decoupled from proteome expansion. Finally, we demonstrate that proteome-wide structural fidelity enables the functional annotation of uncharacterized proteins and a data-driven framework for model organism selection, replacing heuristic choices with quantitative matching to human biological processes. SHE is freely accessible as an interactive portal.

PMID:
42950045
Bibliographic data and abstract were imported from PubMed on 29 Oct 2026.

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