id: Q22436 gene_symbol: sqst-1 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:6239 label: Caenorhabditis elegans description: SQST-1 is the C. elegans ortholog of mammalian p62/SQSTM1 and functions as a selective autophagy receptor. It contains conserved functional domains including a C-terminal UBA (ubiquitin-associated) domain that binds ubiquitinated cargo, an LIR (LC3-interacting region) motif for binding LGG-1/LGG-2 (Atg8/LC3 family proteins), a PB1 domain for self-oligomerization required for cargo clustering, and a ZZ-type zinc finger domain. SQST-1 bridges ubiquitinated protein aggregates to autophagosomes for degradation via aggrephagy, playing critical roles in proteostasis maintenance. SQST-1 accumulation (as puncta or protein levels) serves as a widely used readout for autophagic flux - accumulation indicates reduced flux, while decreased SQST-1 indicates increased flux. existing_annotations: - term: id: GO:0035973 label: aggrephagy evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: Aggrephagy is a core function of SQST-1. The protein is required for degradation of ubiquitinated protein aggregates via selective autophagy. SQST-1 binds ubiquitinated cargo via its UBA domain and recruits autophagosomes via LGG-1 interaction. action: ACCEPT reason: This is the primary biological process function of SQST-1. The deep research clearly establishes that SQST-1 binds ubiquitinated protein aggregates and delivers them to autophagosomes via LGG-1 interactions. The IBA inference from mammalian p62 is fully supported by direct experimental evidence in C. elegans. supported_by: - reference_id: PMID:23530068 supporting_text: epg-7 functions as a scaffold protein mediating autophagic degradation of several protein aggregates, including aggregates of the p62 homologue SQST-1 - reference_id: file:worm/sqst-1/sqst-1-deep-research-falcon.md supporting_text: As a selective autophagy receptor, SQST-1 bridges ubiquitinated cargoes to the autophagy machinery by binding ubiquitin via UBA and recruiting isolation membranes through LGG-1/Atg8 interaction via its LIR. Oligomerization (PB1) promotes phase separation/condensates and cargo clustering, facilitating autophagosome formation and turnover of aggregates (aggrephagy) - term: id: GO:0000423 label: mitophagy evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: While mammalian p62/SQSTM1 has been implicated in mitophagy, direct experimental evidence for SQST-1 in C. elegans mitophagy is limited. The deep research notes that direct worm evidence for SQST-1's role in mitophagy remains less defined than aggrephagy. action: KEEP_AS_NON_CORE reason: The IBA inference is phylogenetically sound given p62's role in mammalian mitophagy, but the primary worm literature emphasizes aggrephagy rather than mitophagy for SQST-1. Reviews infer conserved roles in organelle quality control based on domain conservation, but worm-specific mitophagy by SQST-1 has not been directly demonstrated. This is a plausible secondary function inferred from orthology rather than a demonstrated core function in C. elegans. supported_by: - reference_id: file:worm/sqst-1/sqst-1-deep-research-falcon.md supporting_text: direct worm evidence for SQST-1's role in mitophagy or specific organelle-selective autophagy remains less defined than aggrephagy in the curated set - term: id: GO:0005080 label: protein kinase C binding evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: Mammalian p62 interacts with atypical PKC isoforms via its PB1 domain. While SQST-1 contains a conserved PB1 domain that mediates self-oligomerization, direct evidence for PKC binding in C. elegans has not been reported in the literature reviewed. action: UNDECIDED reason: The IBA inference is based on mammalian p62 PKC interactions. SQST-1 has a PB1 domain and presumably retains similar binding capabilities, but no C. elegans-specific experimental evidence was found. The PB1 domain in worm literature is discussed primarily in the context of self-oligomerization for cargo clustering rather than PKC signaling. Without worm-specific data, this remains uncertain. supported_by: - reference_id: PMID:23530068 supporting_text: p62 contains a self-polymerization PB1 domain, a conserved LC3-interacting region (LIR), and a ubiquitin-associating (UBA) domain - term: id: GO:0007032 label: endosome organization evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: Mammalian p62 has been implicated in endosomal trafficking, but this is not a well-documented function for C. elegans SQST-1. The primary literature on SQST-1 focuses on its role in autophagy and proteostasis rather than endosome organization. action: KEEP_AS_NON_CORE reason: The IBA inference is phylogenetically sound but not supported by direct C. elegans evidence in the literature reviewed. SQST-1 is primarily studied in the context of autophagy in worms. This may be a peripheral function inferred from mammalian ortholog studies. - term: id: GO:0044753 label: amphisome evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: Amphisomes are intermediate compartments formed by fusion of autophagosomes with endosomes before final lysosomal fusion. SQST-1 is documented to localize to autophagic structures that colocalize with LGG-1 puncta. action: ACCEPT reason: Given SQST-1's role as an autophagy cargo receptor that bridges cargo to LGG-1-labeled autophagic structures, localization to amphisomes (intermediate autophagy compartments) is consistent with its function. The IBA inference aligns with experimental observations of SQST-1 colocalization with LGG-1 puncta in C. elegans. supported_by: - reference_id: file:worm/sqst-1/sqst-1-deep-research-falcon.md supporting_text: it forms puncta that frequently colocalize with LGG-1-labeled autophagic structures in adults. Accumulation of SQST-1 puncta/protein is a classic indicator of reduced autophagic flux - term: id: GO:0070530 label: K63-linked polyubiquitin modification-dependent protein binding evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: SQST-1 contains a conserved UBA domain (residues 654-693) that binds ubiquitin. The protein functions by binding ubiquitinated cargo for delivery to autophagosomes. Mammalian p62 shows preference for K63-linked ubiquitin chains. action: ACCEPT reason: This molecular function is central to SQST-1's role as a selective autophagy receptor. The UBA domain is clearly documented in the UniProt record and functionally important for cargo recognition. While the specific K63-linkage preference has not been directly tested in C. elegans, the IBA inference from mammalian p62 is strongly supported by conservation of the UBA domain and the functional requirement for ubiquitin binding in aggrephagy. supported_by: - reference_id: PMID:23530068 supporting_text: p62 contains a self-polymerization PB1 domain, a conserved LC3-interacting region (LIR), and a ubiquitin-associating (UBA) domain - reference_id: file:worm/sqst-1/sqst-1-uniprot.txt supporting_text: DOMAIN 654..693 /note="UBA" /evidence="ECO:0000259|PROSITE:PS50030" - term: id: GO:0016235 label: aggresome evidence_type: IBA original_reference_id: GO_REF:0000033 review: summary: SQST-1 is observed to form puncta/aggregates, particularly in autophagy mutants or under proteotoxic stress. These SQST-1-positive structures accumulate when autophagic flux is impaired and represent sites of cargo accumulation. action: ACCEPT reason: SQST-1 puncta formation is extensively documented in C. elegans literature as a readout for autophagic flux. The protein accumulates into visible aggregates when autophagy is blocked, consistent with aggresome localization. This is experimentally validated in worm studies showing SQST-1::GFP puncta accumulation in autophagy mutants. supported_by: - reference_id: PMID:23530068 supporting_text: 'NA: SQST-1 aggregates are absent in wild-type embryos' - reference_id: file:worm/sqst-1/sqst-1-deep-research-falcon.md supporting_text: Accumulation of SQST-1 puncta/protein is a classic indicator of reduced autophagic flux - term: id: GO:0008270 label: zinc ion binding evidence_type: IEA original_reference_id: GO_REF:0000120 review: summary: SQST-1 contains a ZZ-type zinc finger domain (residues 179-229) as documented in UniProt. This domain coordinates zinc ions via conserved cysteine residues. action: ACCEPT reason: The ZZ-type zinc finger domain is clearly present in the protein sequence and annotated in InterPro (IPR000433). The IEA inference from domain composition is valid. supported_by: - reference_id: file:worm/sqst-1/sqst-1-uniprot.txt supporting_text: DOMAIN 179..229 /note="ZZ-type" /evidence="ECO:0000259|PROSITE:PS50135" - term: id: GO:0046872 label: metal ion binding evidence_type: IEA original_reference_id: GO_REF:0000043 review: summary: This is a parent term of zinc ion binding. SQST-1 binds zinc via its ZZ-type zinc finger domain. action: ACCEPT reason: This IEA is valid based on the zinc ion binding annotation. The broader metal ion binding term is subsumed by the more specific zinc ion binding annotation but is not incorrect. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:23530068 review: summary: SQST-1 was shown to directly interact with EPG-7 (Q22342) and LGG-1 (O45995) by co-immunoprecipitation experiments. SQST-1 was specifically coimmunoprecipitated by anti-EPG-7 antibody from embryonic extracts. action: MODIFY reason: While the protein binding is experimentally demonstrated, this term is too general and uninformative. The specific interactions with EPG-7 (a scaffold protein) and LGG-1/Atg8 (via LIR motif) should be captured with more specific terms. The core molecular function of SQST-1 as an autophagy cargo adaptor is better represented by GO:0160247. proposed_replacement_terms: - id: GO:0160247 label: autophagy cargo adaptor activity supported_by: - reference_id: PMID:23530068 supporting_text: "SQST-1 was specifically coimmunoprecipitated by anti\u2013\ EPG-7, but not by control IgG" - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:23530068 review: summary: Cytoplasmic localization of SQST-1 was directly observed using SQST-1::GFP reporters. The protein forms cytoplasmic puncta that colocalize with autophagic structures. action: ACCEPT reason: Direct experimental evidence from microscopy of SQST-1::GFP reporters. The paper documents cytoplasmic localization and puncta formation. SQST-1 is diffusely cytoplasmic under normal conditions and forms puncta under stress or in autophagy mutants. supported_by: - reference_id: PMID:23530068 supporting_text: SQST-1 directly interacts with EPG-7 and colocalizes with EPG-7 aggregates in autophagy mutants - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:21802374 review: summary: This publication (Lu et al. 2011) established the hierarchical relationship of autophagy genes in aggregate degradation. Cytoplasmic localization is implied by the use of autophagy reporters. action: ACCEPT reason: Although PMID:21802374 focuses on EPG-6 and autophagosome formation, it uses autophagy reporters that display cytoplasmic localization. The duplicate annotation with the same GO term but different evidence sources is acceptable. supported_by: - reference_id: PMID:21802374 supporting_text: We also established the hierarchical relationship of autophagy genes in degradation of protein aggregates - term: id: GO:0160247 label: autophagy cargo adaptor activity evidence_type: IDA original_reference_id: PMID:23530068 review: summary: SQST-1 functions as a selective autophagy receptor that bridges ubiquitinated cargo to the autophagy machinery. It binds ubiquitinated proteins via its UBA domain and recruits autophagosomes via LIR-mediated interaction with LGG-1/Atg8. This is the core molecular function that enables aggrephagy. action: NEW reason: This term precisely describes the core molecular function of SQST-1 as a cargo adaptor in selective autophagy. The existing GO annotations lack this key molecular function term. The experimental evidence directly supports this function. supported_by: - reference_id: PMID:23530068 supporting_text: A family of Atg8/LC3 (mammalian Atg8 homologue)-interacting proteins act as receptors that mediate delivery of specific cargoes to the autophagic machinery via Atg8/LC3 binding - reference_id: file:worm/sqst-1/sqst-1-deep-research-falcon.md supporting_text: As a selective autophagy receptor, SQST-1 bridges ubiquitinated cargoes to the autophagy machinery by binding ubiquitin via UBA and recruiting isolation membranes through LGG-1/Atg8 interaction via its LIR - term: id: GO:0005776 label: autophagosome evidence_type: IDA original_reference_id: PMID:23530068 review: summary: SQST-1 colocalizes with LGG-1-labeled autophagosomes. SQST-1 aggregates associate with LGG-1 puncta during autophagic degradation. action: NEW reason: This cellular component annotation is directly supported by colocalization studies showing SQST-1 on autophagic structures. This is more informative than the existing cytoplasm annotation and complements the amphisome localization. supported_by: - reference_id: PMID:23530068 supporting_text: Mutations in epg-7 impair association of SQST-1 aggregates with LGG-1/Atg8 puncta references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000043 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:21802374 title: The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes. findings: - statement: Established hierarchical relationship of autophagy genes in aggregate degradation supporting_text: We also established the hierarchical relationship of autophagy genes in degradation of protein aggregates - statement: EPG-6 and ATG-2 regulate autophagosome progression supporting_text: epg-6 and atg-2 regulate progression of omegasomes to autophagosomes - id: PMID:23530068 title: The scaffold protein EPG-7 links cargo-receptor complexes with the autophagic assembly machinery. findings: - statement: EPG-7 functions as scaffold mediating autophagic degradation of SQST-1 aggregates supporting_text: epg-7 functions as a scaffold protein mediating autophagic degradation of several protein aggregates, including aggregates of the p62 homologue SQST-1 - statement: SQST-1 directly interacts with EPG-7 by co-immunoprecipitation supporting_text: "SQST-1 was specifically coimmunoprecipitated by anti\u2013EPG-7,\ \ but not by control IgG" - statement: SQST-1 colocalizes with EPG-7 aggregates in autophagy mutants supporting_text: SQST-1 directly interacts with EPG-7 and colocalizes with EPG-7 aggregates in autophagy mutants - statement: Mutations in epg-7 impair association of SQST-1 aggregates with LGG-1 puncta supporting_text: Mutations in epg-7 impair association of SQST-1 aggregates with LGG-1/Atg8 puncta - statement: SQST-1 is the C. elegans p62 homologue supporting_text: aggregates of the p62 homologue SQST-1 core_functions: - description: SQST-1 bridges ubiquitinated cargo to autophagosomes by binding ubiquitin via UBA domain and recruiting LGG-1/Atg8-decorated membranes via LIR motif molecular_function: id: GO:0160247 label: autophagy cargo adaptor activity directly_involved_in: - id: GO:0035973 label: aggrephagy locations: - id: GO:0005776 label: autophagosome - id: GO:0005737 label: cytoplasm supported_by: - reference_id: PMID:23530068 supporting_text: A family of Atg8/LC3 (mammalian Atg8 homologue)-interacting proteins act as receptors that mediate delivery of specific cargoes to the autophagic machinery via Atg8/LC3 binding - description: SQST-1 recognizes and binds K63-linked polyubiquitinated cargo for selective degradation molecular_function: id: GO:0070530 label: K63-linked polyubiquitin modification-dependent protein binding directly_involved_in: - id: GO:0035973 label: aggrephagy locations: - id: GO:0016235 label: aggresome - id: GO:0005737 label: cytoplasm supported_by: - reference_id: PMID:23530068 supporting_text: p62 contains a self-polymerization PB1 domain, a conserved LC3-interacting region (LIR), and a ubiquitin-associating (UBA) domain suggested_questions: - question: Does SQST-1 participate in C. elegans mitophagy, or are there other selective autophagy receptors (e.g., DCT-1/BNIP3) that fulfill this role? - question: What is the functional significance of the ZZ-type zinc finger domain in C. elegans SQST-1? Does it participate in signaling pathways similar to mammalian p62? - question: Does SQST-1 interact with atypical PKC orthologs in C. elegans similar to mammalian p62-PKC interactions? suggested_experiments: - description: Direct test of SQST-1 role in mitophagy using mitochondrial stress conditions and co-localization with mitophagy markers hypothesis: SQST-1 may participate in mitophagy in C. elegans similar to mammalian p62 - description: Biochemical characterization of ubiquitin chain-type specificity for SQST-1 UBA domain (K48 vs K63 vs linear chains) hypothesis: SQST-1 UBA domain preferentially binds K63-linked ubiquitin chains - description: Structure-function analysis of SQST-1 ZZ domain to determine if it has signaling functions beyond autophagy in C. elegans hypothesis: The ZZ domain may have additional signaling roles beyond autophagy tags: - caeel-mitophagy