TRIM16 (estrogen-responsive B box protein, EBBP) is a cytoplasmic member of the TRIM/RBCC family that is atypical in lacking a canonical N-terminal RING domain: its architecture comprises B-box zinc finger(s), a coiled-coil that mediates homodimerization (and heterodimerization with other TRIMs such as MID1, TRIM24 and PML), and a C-terminal B30.2/SPRY domain. Despite lacking a RING, TRIM16 has been reported to act as an atypical E3 ubiquitin ligase that autoubiquitinates via its B-boxes. Its principal modern function is in selective autophagy of damaged endomembranes: TRIM16 serves as a scaffold/receptor that, in a ULK1-dependent manner, interacts with galectin-3 (LGALS3) to sense and direct autophagy of damaged lysosomes and phagosomes (lysophagy), and it assembles core autophagy machinery (BECN1, ATG16L1, SQSTM1/p62 and LC3B/MAP1LC3B) to drive autophagic clearance of protein aggregates. Through these activities it regulates the p62-KEAP1-NRF2 axis (modulating NRF2 ubiquitination and stability) and protects cells against oxidative-stress-induced death following endomembrane damage; it is itself phosphorylated by ULK1. TRIM16 localizes mainly to the cytoplasm/cytosol (and has been observed in nuclear PML bodies). It was originally characterized as the estrogen-responsive B box protein with reported roles in keratinocyte differentiation, retinoid (retinoic acid receptor) signaling, interleukin-1beta production (binding IL-1 and the NALP1 NACHT domain), and tumor suppression (inhibiting cytoplasmic vimentin and nuclear E2F1 in neuroblastoma).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Combined-IEA assignment of cytoplasmic localization; the core compartment for TRIM16. Reason: Correct core localization; redundant with multiple experimental IDA/EXP cytoplasm annotations. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based electronic assignment of zinc ion binding by the B-box zinc finger. Reason: Correct (the B-box coordinates Zn2+) but generic; the informative MF relates to autophagy scaffolding/ubiquitination. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt Auto-ubiquitinates via its B-Boxes. |
| GO:0061630 ubiquitin protein ligase activity | IEA GO_REF:0000003 | KEEP AS NON CORE | Summary: EC 2.3.2.27-based electronic assignment of ubiquitin protein ligase activity; note EC mapping presumes a RING that TRIM16 lacks. Reason: TRIM16 lacks a canonical RING; the EC-based IEA is weak and redundant with the experimentally supported (EXP) ligase-activity annotation, which derives from atypical B-box-dependent autoubiquitination. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt Auto-ubiquitinates via its B-Boxes. |
| GO:0005515 protein binding | IPI PMID:20729920 TRIM16 acts as a tumour suppressor by inhibitory effects on ... | KEEP AS NON CORE | Summary: Interactions with vimentin (VIM) and E2F1 from the neuroblastoma tumor-suppressor study. Bare protein binding is uninformative. Reason: Records real interactions (VIM, E2F1) but bare protein binding is uninformative per curation guidelines. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt O95361; P08670: VIM; NbExp=3; IntAct=EBI-727384, EBI-353844; |
| GO:0005515 protein binding | IPI PMID:21044950 Genome-wide YFP fluorescence complementation screen identifi... | KEEP AS NON CORE | Summary: Interaction (TINF2) from a telomere-signaling YFP complementation screen. Bare protein binding is uninformative. Reason: High-throughput interaction; bare protein binding is uninformative. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt O95361; Q9BSI4: TINF2; NbExp=2; IntAct=EBI-727384, EBI-717399; |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | KEEP AS NON CORE | Summary: Interaction with TRIM16L (Q309B1) from an interactome study. Bare protein binding is uninformative. Reason: High-throughput interactome; bare protein binding is uninformative. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt O95361; Q309B1: TRIM16L; NbExp=4; IntAct=EBI-727384, EBI-21372540; |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | KEEP AS NON CORE | Summary: Interaction with TRIM16L (Q309B1) from a cell-specific interactome study. Bare protein binding is uninformative. Reason: High-throughput interactome; bare protein binding is uninformative. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt O95361; Q309B1: TRIM16L; NbExp=4; IntAct=EBI-727384, EBI-21372540; |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | KEEP AS NON CORE | Summary: Interaction with TRIM16L (Q309B1) from a multimodal cell-map study. Bare protein binding is uninformative. Reason: High-throughput interactome; bare protein binding is uninformative. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt O95361; Q309B1: TRIM16L; NbExp=4; IntAct=EBI-727384, EBI-21372540; |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence-based (HPA) cytosolic localization, consistent with the core cytoplasmic site of action. Reason: Correct cytosolic localization, consistent with the cytoplasmic autophagy-scaffold role. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0005737 cytoplasm | EXP PMID:27693506 TRIMs and Galectins Globally Cooperate and TRIM16 and Galect... | ACCEPT | Summary: Experimental evidence of cytoplasmic localization in the galectin-3/lysophagy study. Core localization. Reason: Core cellular component, experimentally demonstrated where TRIM16 directs autophagy of damaged endomembranes. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0061630 ubiquitin protein ligase activity | EXP PMID:22629402 TRIM16 acts as an E3 ubiquitin ligase and can heterodimerize... | ACCEPT | Summary: Experimental evidence that TRIM16 acts as an E3 ubiquitin ligase (autoubiquitination via its B-boxes), despite lacking a canonical RING. Reason: Experimentally supported by UniProt (EC ECO:0000269|PubMed:22629402); TRIM16 is an atypical B-box-dependent E3 ligase. Retained per guideline not to overrule experimental annotations, though the activity is unusual and the EC/IEA derivation is weaker. Supporting Evidence: PMID:22629402 TRIM16 acts as an E3 ubiquitin ligase and can heterodimerize with other TRIM family members. |
| GO:0005515 protein binding | IPI PMID:25127057 TRIM proteins regulate autophagy and can target autophagic s... | KEEP AS NON CORE | Summary: Interaction with LC3B/MAP1LC3B (O95166) from the TRIM-autophagy study. Bare protein binding is uninformative. Reason: Records a real, functionally relevant autophagy interaction (LC3B) but bare protein binding is uninformative. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt Interacts with p62/SQSTM and LC3B/MAP1LC3B. |
| GO:0003677 DNA binding | IDA PMID:16636064 The estrogen-responsive B box protein is a novel regulator o... | KEEP AS NON CORE | Summary: Direct evidence of DNA binding from the EBBP/retinoid-signaling study. Reason: Experimentally reported (older EBBP-era work) but TRIM16 lacks a classical DNA-binding domain and the modern core function is cytoplasmic autophagy scaffolding; defer to curator who read the full text. Supporting Evidence: PMID:16636064 The estrogen-responsive B box protein is a novel regulator of the retinoid signal. |
| GO:0005515 protein binding | IPI PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of i... | KEEP AS NON CORE | Summary: Interactions (IL-1, NALP1) from the IL-1beta-secretion study. Bare protein binding is uninformative. Reason: Records real interactions but bare protein binding is uninformative; captured more specifically by the IL-1 binding and NACHT domain binding annotations. Supporting Evidence: PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of interleukin-1beta secretion. |
| GO:0005737 cytoplasm | IDA PMID:11919186 The estrogen-responsive B box protein: a novel regulator of ... | ACCEPT | Summary: Direct evidence of cytoplasmic localization in the keratinocyte-differentiation study. Core localization. Reason: Correct core localization, experimentally demonstrated. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0005737 cytoplasm | IDA PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of i... | ACCEPT | Summary: Direct evidence of cytoplasmic localization in the IL-1beta study. Core localization. Reason: Correct core localization, experimentally demonstrated. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0005737 cytoplasm | IDA PMID:9817599 The novel estrogen-responsive B-box protein (EBBP) gene is t... | ACCEPT | Summary: Direct evidence of cytoplasmic localization in the EBBP-discovery study. Core localization. Reason: Correct core localization, experimentally demonstrated. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:27693506}. |
| GO:0016605 PML body | IDA PMID:16636064 The estrogen-responsive B box protein is a novel regulator o... | KEEP AS NON CORE | Summary: Direct evidence of localization to nuclear PML bodies (EBBP heterodimerizes with PML). Reason: Experimentally supported but a secondary nuclear-body localization (older EBBP work); the dominant pool is cytoplasmic. Defer to curator. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt Heterodimerizes with |
| GO:0019966 interleukin-1 binding | IPI PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of i... | KEEP AS NON CORE | Summary: Direct interaction evidence that TRIM16/EBBP binds interleukin-1 (IL-1). Reason: Experimentally supported specific MF from EBBP-era work; a secondary activity relative to the core autophagy-scaffold function. Supporting Evidence: PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of interleukin-1beta secretion. |
| GO:0032089 NACHT domain binding | IPI PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of i... | KEEP AS NON CORE | Summary: Direct interaction evidence that TRIM16/EBBP binds the NACHT domain of NALP1. Reason: Experimentally supported specific MF from EBBP-era work; secondary to the core autophagy-scaffold function. Supporting Evidence: PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of interleukin-1beta secretion. |
| GO:0032526 response to retinoic acid | IEP PMID:16636064 The estrogen-responsive B box protein is a novel regulator o... | KEEP AS NON CORE | Summary: Expression-pattern evidence that TRIM16/EBBP responds to retinoic acid. Reason: Supported response/context term from EBBP-era retinoid work; not the core autophagy function. Supporting Evidence: PMID:16636064 The estrogen-responsive B box protein is a novel regulator of the retinoid signal. |
| GO:0032731 positive regulation of interleukin-1 beta production | IMP PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of i... | KEEP AS NON CORE | Summary: Mutant-phenotype evidence that TRIM16/EBBP enhances IL-1beta secretion/production. Reason: Experimentally supported (EBBP-era) but a secondary process relative to the core autophagy-scaffold function. Supporting Evidence: PMID:16575408 The estrogen-responsive B box protein: a novel enhancer of interleukin-1beta secretion. |
| GO:0045618 positive regulation of keratinocyte differentiation | IDA PMID:11919186 The estrogen-responsive B box protein: a novel regulator of ... | KEEP AS NON CORE | Summary: Direct evidence that TRIM16/EBBP positively regulates keratinocyte differentiation. Reason: Experimentally supported (original EBBP characterization) but a tissue-specific role secondary to the core autophagy function. Supporting Evidence: PMID:11919186 The estrogen-responsive B box protein: a novel regulator of keratinocyte differentiation. |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:16636064 The estrogen-responsive B box protein is a novel regulator o... | KEEP AS NON CORE | Summary: Direct evidence that TRIM16/EBBP positively regulates transcription in the retinoid-signaling context. Reason: Experimentally reported (EBBP-era) but secondary; TRIM16 acts largely as a cytoplasmic autophagy scaffold rather than a core transcriptional regulator. Defer to curator. Supporting Evidence: PMID:16636064 The estrogen-responsive B box protein is a novel regulator of the retinoid signal. |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:19147277 The estrogen-responsive B box protein (EBBP) restores retino... | KEEP AS NON CORE | Summary: Direct evidence (via histone acetylation effects restoring retinoid sensitivity) that TRIM16/EBBP positively regulates transcription. Reason: Experimentally reported (EBBP-era retinoid work) but secondary to the core autophagy function. Defer to curator. Supporting Evidence: PMID:19147277 restores retinoid sensitivity in retinoid-resistant cancer cells via effects on histone acetylation |
| GO:0048386 positive regulation of retinoic acid receptor signaling pathway | IDA PMID:16636064 The estrogen-responsive B box protein is a novel regulator o... | KEEP AS NON CORE | Summary: Direct evidence that TRIM16/EBBP positively regulates retinoic acid receptor signaling. Reason: Experimentally supported (EBBP-era) but a secondary process relative to the core autophagy function. Supporting Evidence: PMID:16636064 The estrogen-responsive B box protein is a novel regulator of the retinoid signal. |
| GO:0060416 response to growth hormone | IDA PMID:11919186 The estrogen-responsive B box protein: a novel regulator of ... | KEEP AS NON CORE | Summary: Direct evidence that TRIM16/EBBP responds to growth hormone. Reason: Supported response/context term from EBBP-era work; not the core autophagy function. Supporting Evidence: PMID:11919186 The estrogen-responsive B box protein: a novel regulator of keratinocyte differentiation. |
| GO:0006914 autophagy | IDA PMID:27693506 TRIMs and Galectins Globally Cooperate and TRIM16 and Galect... | NEW | Summary: Proposed new annotation. TRIM16 directs selective autophagy of damaged endomembranes (lysophagy) and protein aggregates; this core modern function is documented in UniProt and PMID:27693506 but absent from the current GOA. Reason: The galectin-3/ULK1-dependent lysophagy and aggrephagy role is the core modern function of TRIM16 and should be annotated; it is currently missing from the GOA. Supporting Evidence: PMID:27693506 TRIMs and Galectins Globally Cooperate and TRIM16 and Galectin-3 Co-direct Autophagy in Endomembrane Damage Homeostasis. |
| GO:0030674 protein-macromolecule adaptor activity | IPI PMID:27693506 TRIMs and Galectins Globally Cooperate and TRIM16 and Galect... | NEW | Summary: Proposed new annotation. TRIM16 acts as a scaffold/adaptor bridging galectin-3-decorated damaged membranes and autophagy receptors/machinery (SQSTM1/p62, ATG16L1, LC3B, BECN1). Reason: Captures TRIM16's core autophagy-receptor/scaffold molecular function (adaptor linking damaged endomembranes to the autophagy apparatus); currently missing from the GOA. Supporting Evidence: file:human/TRIM16/TRIM16-uniprot.txt Acts as a scaffold protein and facilitates |
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Download this section (compressed HTML)Q: Given that TRIM16 lacks a canonical RING domain, what is the structural and mechanistic basis for its reported B-box-dependent E3 ubiquitin ligase activity, and is the activity intrinsic or dependent on heterodimerization with RING-bearing TRIMs?
Q: The current GOA annotations for TRIM16 do not include an autophagy biological-process term despite the well-established galectin-3/lysophagy role - should an autophagy/selective-autophagy-receptor annotation be added based on PMID:27693506?
Experiment: Reconstitute TRIM16 E3 ligase activity in vitro with purified TRIM16 (wild-type vs B-box mutants) and candidate E2s to determine whether autoubiquitination/substrate ubiquitination is intrinsic to the B-boxes or requires a heterodimeric RING-bearing TRIM partner.
Experiment: Use galectin-3- and ULK1-phosphosite TRIM16 mutants in lysosomal-damage assays (e.g. LLOMe treatment) to dissect how galectin-3 binding and ULK1 phosphorylation control TRIM16-directed lysophagy and aggregate clearance.
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