Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea

Abstract

The emergence of eukaryotes from Asgard archaeal ancestors likely required a specialized cell envelope that enabled sustained physical and metabolic interactions with proto-mitochondrial symbionts. While the protrusion-rich cell architecture of Asgard archaea may enable such interactions, the molecular composition of their cell surface and its role in establishing cell-cell contacts remains unknown. Here, we developed a "visual surfaceomics" approach, integrating subtomogram averaging, predictive structural modeling, transcriptomics, proteomics, and expansion microscopy to identify surface proteins in situ. We show that Asgard cell bodies and protrusions lack an archaea-typical paracrystalline S-layer and are instead decorated by two main classes of surface proteins: subtilisin-like serine proteases (SubSs) and oligopeptide-binding proteins (OppAs). SubSs were detected as membrane-anchored dimers and were sparsely distributed across the surface. OppAs showed near-total membrane coverage but lacked any rigid, higher order assembly. Thermal shift assays and single particle cryo-EM showed that OppA binds oligopeptides in vitro. Comparative genomics, transcriptomics, and proteomics suggest that this peptidophilic surface architecture is conserved across Asgard archaeal phyla. Finally, we discovered that the cell surface was remodeled at cell-cell contact sites. Altogether, our integrative approach revealed a metabolically specialized and structurally flexible cell surface that couples extracellular protein degradation with peptide capture and uptake, while potentially contributing to establishing and maintaining the symbiotic interactions of Asgard archaea.