phagophore assembly site

GO:0000407 · Other · Subcellular region · Proposed

Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction. [GO:0000407]

Synonyms: PAS; pre-autophagosomal structure

Part of: GO:0005737 — cytoplasm (no local record)

Xrefs: uniprot.location:SL-0220 — Preautophagosomal structure

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
phagophore assembly site Atg machinery	Protein	part of	Reviewed label only (reviewed name; no accession asserted)			ESSENTIAL	Atg protein machinery that concentrates at the PAS and organizes phagophore expansion during autophagosome formation. `GO:0000407` GO:0000407 defines the phagophore assembly site as a punctate site where Atg machinery assembles upon autophagy induction. `DOI:10.1093/emboj/20.21.5971` Suzuki et al. 2001 localized multiple Apg proteins to the yeast pre-autophagosomal structure and showed APG gene function is required for its organization.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast forms a phagophore assembly site near the vacuole during autophagosome biogenesis. [DOI:10.1093/emboj/20.21.5971]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Saccharomyces cerevisiae is the genetic and fluorescence microscopy model in which the PAS was defined as a punctate Apg/Atg organizing site for autophagosome formation. [DOI:10.1093/emboj/20.21.5971]

Functions

autophagosome assembly platform — The phagophore assembly site concentrates Atg machinery at a punctate cytoplasmic site to organize phagophore expansion and autophagosome formation.
- GO:0000045 GO:0000045 defines autophagosome assembly as the formation of a double-membrane-bounded autophagosome.
- DOI:10.1093/emboj/20.21.5971 Suzuki et al. 2001 showed that PAS organization by concerted APG gene functions is essential for autophagosome formation in yeast.

Mechanism graphs

Yeast PAS organizes Atg machinery (ASSEMBLY)

Atg machinery concentrates at the phagophore assembly site to organize autophagosome assembly in budding yeast.

Subject	Predicate	Object	Evidence
phagophore assembly site Atg machinery	localizes to	phagophore assembly site	`GO:0000407` GO:0000407 defines the site by Atg machinery assembly during autophagy induction. `DOI:10.1093/emboj/20.21.5971` Suzuki et al. 2001 observed punctate pre-autophagosomal localization of Apg proteins in Saccharomyces cerevisiae.
phagophore assembly site	organizes	autophagosome assembly	`DOI:10.1093/emboj/20.21.5971` Suzuki et al. 2001 showed that the pre-autophagosomal structure is essential for autophagosome formation.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral identifiers for the Atg machinery assembled at the phagophore assembly site. The first PAS record preserves the exact GO site boundary and leaves individual Atg protein and complex identities out until family-level identifiers can be verified.
INTERPRETATION (RESOLVED): Do not model a phagophore assembly site membrane as an exact component. GO:0000407 defines the current PAS class as a cytoplasmic Atg assembly site rather than a membrane-bounded compartment. No current exact source-neutral identifier was verified for a PAS membrane component.

Evidence

GO:0000407 Gene Ontology cellular-component term for phagophore assembly site.
GO:0110165 Gene Ontology cellular-component term for cellular anatomical structure.
GO:0005737 — cytoplasm Gene Ontology cellular-component term for cytoplasm.
GO:0000045 Gene Ontology biological-process term for autophagosome assembly.
uniprot.location:SL-0220 — Preautophagosomal structure UniProt Subcellular Location entry that maps Preautophagosomal structure to GO:0000407.
DOI:10.1093/emboj/20.21.5971 Suzuki et al. 2001, The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation, The EMBO Journal.

Curation history

2026-09-12T15:13:54Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-12T15:14:33Z codex · EXPANDED_RECORD — Added GO parentage and cytoplasm parthood, PAS synonymy, the UniProt Subcellular Location xref, a reviewed-label Atg machinery component, Saccharomyces cerevisiae scope, an autophagosome-assembly function, DOI/GO/UniProt evidence, a nonmechanistic Atg-organization graph, and boundary discussions for exact Atg groundings and the obsolete PAS membrane.
2026-09-12T15:15:19Z codex · TIGHTENED_DISCUSSION — Tightened the PAS membrane interpretation to avoid depending on an obsolete GO membrane term.
2026-09-12T15:18:06Z codex · FIX_DISCUSSION_ANCHOR — Retargeted the PAS membrane interpretation to the record identifier.
2026-09-12T15:21:38Z codex · ADDRESS_REVIEW — Resolved #666 by typing the broad reviewed-label PAS Atg machinery graph node as STRUCTURE instead of GENE_OR_PROTEIN.

Source: data/structures/other/phagophore_assembly_site.yaml