Beyond presence and absence: a survey of TOR and AMPK across 210 eukaryotes reveals unusually long coccidian AMPKγ

Abstract

Energy and nutrient regulation in eukaryotes depends on AMP-activated protein kinase (AMPK) and target of rapamycin (TOR), yet their evolution is usually described by which components are present or absent. We surveyed 10 TOR- and AMPK-related targets across 210 eukaryotic species and paired that inventory with sequence- and structure-level measurements of the proteins that remain. Across 2100 species-by-target cells, 1255 were coded present, 683 absent and 162 not assessable, with repertoires differing among lineages. Phylogenetically corrected analyses recovered associations among a subset of component absences, especially within canonical complexes, although correlated non-detection in incomplete proteomes remains an alternative explanation. Sequence features varied substantially. In TOR, N-terminal HEAT-region divergence was associated with absence of several TOR-complex partners in discrete-state analyses. In AMPK, the activation-loop threonine was retained in every species with a readable site, while other features varied strongly: {beta} carbohydrate-binding-module conservation covaried with C-terminal length under the primary phylogenetic model, and AMPK{gamma} showed pronounced lineage-associated length variation. In the focal coccidian-group cohort, {gamma} sequences had a median length of 909 residues versus 396 in other sampled copies; the median was 924 among the nine sequences with a tree-based orthology determination, while two Eimeria sequences remain provisional candidates. Low primary nucleotide-contact-site identity was shared more broadly across sampled Apicomplexa. Together, these analyses reveal lineage-structured variation in TOR and AMPK at three levels: component repertoires, sequence features of retained proteins, and associations among components. Signaling architecture cannot be inferred from presence and absence alone.