A conserved archaeal protein with evolutionary links to bacterial ribosome hibernation and eukaryotic energy sensing

Abstract Ribosome hibernation helps cells survive stress by reversibly silencing translation and preserving ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation remains poorly understood. Using cryoEM of archaeal lysates, we identified AHA ( A MPKγ- H PF from A rchaea), a broadly conserved ribosome-associated factor composed of two modules. AHA bound across ribosomal subunits, occluding the mRNA channel and tRNA binding sites, supporting its role in ribosome hibernation. ΔAHA cells displayed reduced viability, loss of ribosomal proteins in the stationary phase, and impaired growth reentry in rich media. Phylogenetic analyses revealed that AHA’s C-terminal domain is homologous to the bacterial Hibernation Promoting Factor (HPF), consistent with inheritance from the last universal common ancestor and thereby identifying HPF as a universal hibernation module in prokaryotes. Strikingly, we observed two AMP molecules bound to AHA’s N-terminal CBS-tetrad, which showed both sequence and structural similarity to the eukaryotic energy sensor AMPKγ, supporting a shared evolutionary origin of the archaeal CBS-tetrad and the AMPKγ family. Together, these findings uncover a widespread archaeal ribosome hibernation factor and reveal an evolutionary connection between prokaryotic ribosomal hibernation and eukaryotic energy sensing.