A Construction of Archaean Rest-Like Biology from Genomics

Dormancy and sequence-specific transcriptional repression are two pillars of microbial stress survival, yet their genetic basis across the archaeal domain has not been surveyed systematically. A unified comparative-genomic survey of 1,024 archaeal genomes (975 with a retrievable proteome, 318 genera) was conducted which quantifies two coupled layers of the archaeal regulatory economy from genome sequence alone. The effector layer mapped the coding potential for 30 stress-survival and dormancy protein families across nine functional modules using InterPro-validated profile hidden Markov models; the controller layer censused 19 curated Pfam families of small sequence-specific DNA-binding regulators—the archaeal structural analogue of eukaryotic REST/NRSF repressor logic, for which archaea encode no orthologue. The effector layer reveals a near-universal stress-and-storage toolkit (toxin–antitoxin, redox-poise, carbon storage, small heat-shock and chromatin proteins; ≥85%prevalence in every phylum) set against a complete absence of the bacterial endospore program, while a homology-versus-analogy verification layer, confirmed by structure, reassigns three families. The controller layer comprises 61,016 regulators (median ∼2%of the proteome); regulator investment is strongly lineage-dependent (Kruskal–Wallis p =7.7×10^−12), scales super-linearly with proteome size (log–log slope 1.58), and is built from lineage-specific dominant families. An exploratory group-level synthesis suggests the two layers may co-vary. Results must be considered as the coding potential across different groups of archaea, not as evidence of regulated dormancy behaviour, which only physiological and transcriptional experiments can establish.