Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea
- 1Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenossische Technische Hochschule Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
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.
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BibTeX
@misc{malit2026visual,
title = {{Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea}},
author = {J. J. L. Malit and D. Amendola and J. Xu and L. Dufresne and A. Kokhanovska and A. Gonet and C. P. Wiegand and J. Clavien and F. Wollweber and M. Pilhofer},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.05.763656},
url = {https://www.biorxiv.org/content/10.64898/2026.11.05.763656v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea
AU - J. J. L. Malit
AU - D. Amendola
AU - J. Xu
AU - L. Dufresne
AU - A. Kokhanovska
AU - A. Gonet
AU - C. P. Wiegand
AU - J. Clavien
AU - F. Wollweber
AU - M. Pilhofer
PY - 2026
DA - 2026/11/05
PB - bioRxiv
DO - 10.64898/2026.11.05.763656
UR - https://www.biorxiv.org/content/10.64898/2026.11.05.763656v1
AB - 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.
ER -