Extended Data Fig. 3: Identification of previously undetected vesicular trafficking ESPs in Asgard archaea.

Schematic representation of a eukaryotic cell in which ESPs involved in membrane trafficking and endosomal sorting that have been identified in Asgard archaea are highlighted. Colored subunits have been detected in some Asgard archaea while grey ones seem to be absent from all current representatives. Only major protein complexes are depicted. Additional components can be found in Fig. 2. From left to right, top to bottom: RC, Retromer complex. Retromer is a coat-like complex associated with endosome-to-Golgi retrograde traffic³⁵. It is formed by Vacuolar protein sorting-associated protein 35, Vps5, Vps17, Vps26 and Vps29¹¹⁸. During cargo recycling, retromer is recruited to the endosomal membrane via the Vps5-Vps17 dimer. Cargo recognition is thought to be mediated primarily through Vps26 and possibly by Vps35. Finally, the BAR domains of Vps5-Vps17 deform the endosomal membrane to form cargo-containing recycling vesicles. Their distribution is sparse, but we have detected Asgard archaeal homologs of all subunits except for Vps17. Interestingly, the Thorarchaeia Vps5-BAR ___domain is often fused to Vps28, a subunit of the ESCRT machinery complex I, suggesting a functional link between BAR ___domain proteins and the thorarchaeial ESCRT complex. The best-characterized retromer cargo is Vps10. This transmembrane protein receptor is known in yeast and mammal cells to be involved in the sorting and transport of lipoproteins between the Golgi and the endosome. The Vps10 receptor releases its cargo to the endosome and is recycled back to the Golgi via the retromer complex¹¹⁹. CORVET: Class C core vacuole/endosome tethering complex; HOPS: Homotypic fusion and protein sorting complex. Endosomal fusion and autophagy depend on the CORVET and HOPS hexameric complexes³⁷; they share the core subunits Vps11, Vps16, Vps18, and Vps33¹²⁰. In addition, HOPS is composed of Vps41 and Vps39¹²¹. Vps39, found associated to late endosomes and lysosomes, promotes endosomes/lysosomes clustering and their fusion with autophagosomes¹²². AP, Adaptor Proteins. Asgard archaea genomes from diverse phyla encode key functional domains of the AP complexes. The eukaryotic AP tetraheteromeric structure is depicted, each color corresponding to a PFAM functional ___domain (Medium green: Adaptin, N terminal region; Dark green: Alpha adaptin, C-terminal ___domain; Light green: Beta2-adaptin appendage, C-terminal sub-___domain; Dark pink/clear outline: Clathrin adaptor complex small chain; Light pink/dark outline: C-ter ___domain of the mu subunit); all five domains were detected in Asgard archaea, although not fused to each other. GARP: Golgi-associated retrograde protein complex. The GARP complex is a multisubunit tethering complex located at the trans-Golgi network where it functions to tether retrograde transport vesicles derived from endosomes^36,123. GARP comprises four subunits, VPS51, VPS52, VPS53, and VPS54. ESCRT: Endosomal Sorting Complex Required for Transport system. This complex machinery performs a topologically unique membrane bending and scission reaction away from the cytoplasm. While numerous components of the ESCRT-I, II and III systems have been previously detected in Asgard archaea^2,3,38, we here report Asgard homologs for several ESCRT-III regulators Vfa1, Vta1, Ist1, and Bro1. The bottom panel shows where these complexes mainly act in eukaryotic cells. Ub: Ubiquitin; Vps: vacuolar protein sorting. Subunit names in grey indicate that no homologs were detected in Asgard archaea. Domains newly identified as part of this study are indicated with an asterisk. Figure created using BioRender (https://www.biorender.com).