Tomato DET1 (Q9ZNU6; gene DET1, synonyms hp2/dg; also called tDET1, "Light-mediated development protein DET1", "High pigmentation protein 2", "Protein dark green") is the tomato ortholog of Arabidopsis DE-ETIOLATED1 and is genetically defined as the HIGH PIGMENT 2 (hp2) locus, with dark-green (dg) as a further allele. It is a conserved NEGATIVE regulator of photomorphogenesis - a repressor that holds back light-driven development. Mechanistically it is not an enzyme acting on a small-molecule substrate but a nuclear regulatory adaptor: it participates in the CDD complex (with DDB1 and the E2 variant COP10) and, in tomato, is a substrate-selection component of a CUL4-DDB1-DET1 (CRL4) E3 ubiquitin ligase that targets transcription factors for 26S-proteasome degradation. The best-defined tomato substrate is the GOLDEN2-LIKE 2 (SlGLK2) transcription factor; in Arabidopsis the repressive output is mediated by degradation of photomorphogenesis-promoting factors such as HY5. DET1 localizes to the nucleus (UniProt; tomato YFP assays show nucleus and cytoplasm). Loss-of-function alleles (hp-2, hp-2j, dg) are constitutively/exaggeratedly photomorphogenic ("high pigment"): plants are darker and shorter with elevated anthocyanins, and fruits over-accumulate chlorophyll, carotenoids (lycopene), tocopherols and flavonoids - the basis of DET1 down-regulation as a biofortification target. The tomato hp-2 phenotype is strictly dependent on active phytochrome, placing DET1 as a downstream nuclear repressor within (rather than a photoreceptor-level component of) the light/phytochrome signaling network.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009585 red, far-red light phototransduction | IEA GO_REF:0000043 | MODIFY | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Phytochrome signaling pathway"; snapshot-only, removed in the current GOA release. DET1 is a conserved NEGATIVE regulator of photomorphogenesis - a downstream nuclear repressor acting via a CUL4-DDB1-DET1 E3 ligase / the CDD complex - not a photoreceptor-level phototransduction component. Reason: GOA's removal of this keyword-derived annotation was JUSTIFIED, and the term is mis-placed. GO:0009585 is defined as "the sequence of reactions within a cell required to convert absorbed photons from red or far-red light into a molecular signal" - i.e. photoreceptor-level signal conversion (the job of phytochromes), which DET1 does not perform. DET1 acts far downstream: it is a nuclear repressor that, through the CUL4-DDB1-DET1 (CRL4) ubiquitin ligase and the CDD complex, promotes degradation of photomorphogenesis-promoting factors such as HY5/transcription factors, thereby repressing light-driven development [file:SOLLC/DET1/DET1-uniprot.txt; file:SOLLC/DET1/DET1-deep-research-falcon.md]. Genetically, tomato hp-2/DET1 was cloned precisely because HP genes were proposed to be negative regulators of phytochrome signal transduction, and loss of DET1 yields exaggerated/constitutive photomorphogenesis [PMID:9927635]. The accurate term for DET1's role is therefore "negative regulation of photomorphogenesis" (GO:0010100), not red/far-red phototransduction. Proposed replacements: negative regulation of photomorphogenesis Supporting Evidence: PMID:9927635 It has been proposed that HP genes encode negative regulators of phytochrome signal transduction. PMID:9927635 encodes the tomato homolog of the nuclear protein DEETIOLATED1 (DET1) from Arabidopsis. Mutations in DET1 are known to result in constitutive deetiolation in darkness. file:SOLLC/DET1/DET1-uniprot.txt Repression of photomorphogenesis is CC probably mediated by ubiquitination and subsequent degradation of CC photomorphogenesis-promoting factors such as HY5. |
| GO:0010017 red or far-red light signaling pathway | IEA GO_REF:0000043 | MODIFY | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Phytochrome signaling pathway"; snapshot-only, removed in the current GOA release. DET1 participates in light/phytochrome signaling, but as a broad NEGATIVE regulator of photomorphogenesis rather than a red/far-red-specific signaling component. Reason: GOA's removal of this keyword-derived annotation was reasonable. The term is not entirely wrong - the tomato hp-2/DET1 phenotype is strictly dependent on active phytochrome, so DET1 does act within the red/far-red (phytochrome) signaling network [PMID:9927635] - but GO:0010017 ("the series of molecular signals initiated upon sensing by photoreceptor molecules of red light or far red light") implies a wavelength-specific signaling role. DET1 is instead a convergent, downstream nuclear repressor of photomorphogenesis that is not red/far-red-specific: in the conserved CDD/CRL4 machinery it represses outputs of multiple photoreceptor pathways (its Arabidopsis context includes blue/UV cryptochrome inputs), acting by targeting photomorphogenesis-promoting factors (e.g. HY5) for ubiquitin-dependent degradation [file:SOLLC/DET1/DET1-uniprot.txt]. The dg allele links the DET1 locus to the photomorphogenic de-etiolation response generally [PMID:12589545]. The function is therefore more accurately captured by "negative regulation of photomorphogenesis" (GO:0010100). Proposed replacements: negative regulation of photomorphogenesis Supporting Evidence: PMID:9927635 whereas det1 mutations are epistatic to mutations in phytochrome genes, analysis of similar double mutants in tomato showed that manifestation of the phenotype of the hp-2 mutant is strictly dependent upon the presence of active phytochrome. PMID:12589545 the tomato homolog of the DEETIOLATED1 (DET1) gene, involved in the signal transduction cascade of light perception and morphogenesis. file:SOLLC/DET1/DET1-uniprot.txt FUNCTION: Component of light signal transduction machinery. |
| GO:0016567 protein ubiquitination | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation propagated across the DET1 phylogenetic group. DET1 is a substrate- selection component of a CUL4-DDB1-DET1 (CRL4) E3 ubiquitin ligase that drives ubiquitination and proteasomal degradation of regulatory transcription factors. Reason: Well supported and core to DET1's mechanism. In tomato, DET1 is part of a CUL4-DDB1-DET1 E3 ligase complex that mediates ubiquitin-conjugated degradation of the GOLDEN2-LIKE 2 (SlGLK2) transcription factor, with two ubiquitination-relevant lysines (K11, K253) and MG132-sensitive turnover [file:SOLLC/DET1/DET1-deep-research-falcon.md]. The UniProt FUNCTION statement likewise attributes DET1's repression of photomorphogenesis to ubiquitination and degradation of factors such as HY5 [file:SOLLC/DET1/DET1-uniprot.txt]. The IBA term is at an appropriate level of specificity for the process the complex carries out. Supporting Evidence: file:SOLLC/DET1/DET1-deep-research-falcon.md promotes **ubiquitin-mediated proteasomal degradation** of the transcription factor **GOLDEN2-LIKE 2 (SlGLK2)**. file:SOLLC/DET1/DET1-uniprot.txt Repression of photomorphogenesis is CC probably mediated by ubiquitination and subsequent degradation of CC photomorphogenesis-promoting factors such as HY5. |
| GO:0031461 cullin-RING ubiquitin ligase complex | IBA GO_REF:0000033 | MODIFY | Summary: IBA annotation: DET1 is part of a cullin-RING ubiquitin ligase complex. The tomato and Arabidopsis evidence specifies this as a CUL4-based (CRL4) complex, so a more precise term is available. Reason: The annotation is correct but can be made more informative. DET1 specifically assembles into a CUL4-DDB1-DET1 cullin4-RING (CRL4) ligase: in Arabidopsis, CUL4 assembles with DDB1, RBX1, DET1 and DDB2 in vitro and in planta [PMID:16792691], and in tomato DET1 is part of a CUL4-DDB1-DET1 E3 ligase complex [file:SOLLC/DET1/DET1-deep-research-falcon.md]. GO:0080008 "Cul4-RING E3 ubiquitin ligase complex" is defined as a complex "in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein", which precisely describes DET1's complex. MODIFY to the CUL4-specific child term. Proposed replacements: Cul4-RING E3 ubiquitin ligase complex Supporting Evidence: PMID:16792691 Arabidopsis cullin 4 is shown to assemble with DDB1, RBX1, DET1 and DDB2 in vitro and in planta. file:SOLLC/DET1/DET1-deep-research-falcon.md the tomato hp1/hp2 loci (DDB1/DET1) are described as core components of a **CUL4-type E3 ubiquitin ligase** controlling plastid levels and pigment accumulation in fruit. |
| GO:0031625 ubiquitin protein ligase binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: DET1 binds the cullin-RING ubiquitin ligase machinery (DDB1/CUL4), anchoring it within the CRL4/CDD complex. Reason: Supported. DET1 physically associates with DDB1 and CUL4: Arabidopsis CUL4 assembles with DDB1, RBX1 and DET1 [PMID:16792691], and the IntAct interaction underlying the IPI annotation in this gene is with DDB1 (UniProtKB:Q8LGH4). In tomato, SlDET1 co-occurs in the CUL4-DDB1-DET1 complex [file:SOLLC/DET1/DET1-deep-research-falcon.md]. Binding to the ligase scaffold is consistent with DET1's role as the CRL4 substrate-recognition adaptor; the IBA term is appropriate. Supporting Evidence: PMID:16792691 CUL4 associates with DDB1 and DET1 file:SOLLC/DET1/DET1-deep-research-falcon.md SlGLK2 physically associates with SlDET1 (and SlDDB1/SlCUL4) in plant cells |
| GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: DET1 promotes proteasomal degradation of its substrate transcription factors. Directly supported by tomato data showing DET1-dependent turnover of SlGLK2. Reason: Supported and consistent with DET1's repressor mechanism. As the substrate-selection adaptor of the CRL4 ligase, DET1 promotes ubiquitin-26S-proteasome degradation of target proteins: SlGLK2 turnover is retarded when CUL4/DDB1/DET1 are impaired and is stabilized by the proteasome inhibitor MG132 [file:SOLLC/DET1/DET1-deep-research-falcon.md]; in Arabidopsis the repressive output is degradation of photomorphogenesis-promoting factors such as HY5 [file:SOLLC/DET1/DET1-uniprot.txt]. The IBA term accurately captures DET1's positive role in driving substrate proteolysis. Supporting Evidence: file:SOLLC/DET1/DET1-deep-research-falcon.md its turnover is retarded when CUL4/DDB1/DET1 are genetically impaired; proteasome inhibition (MG132) stabilizes SlGLK2. file:SOLLC/DET1/DET1-uniprot.txt Repression of photomorphogenesis is CC probably mediated by ubiquitination and subsequent degradation of CC photomorphogenesis-promoting factors such as HY5. |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: DET1 functions as the substrate-recognition adaptor of the CRL4 E3 ligase, bridging target transcription factors to the ubiquitination machinery. This is DET1's core molecular function. Reason: This is the most informative molecular-function annotation for DET1 and is well supported. DET1 is not a catalytic enzyme but a regulatory scaffold/adaptor that helps the CUL4-DDB1 E3 ligase recognize and destabilize specific protein substrates such as SlGLK2 [file:SOLLC/DET1/DET1-deep-research-falcon.md]. The GO:0080008 definition of the DET1 complex explicitly notes that "substrate specificity is conferred by an adaptor protein", matching the substrate-adaptor MF. ACCEPT as a core function. Supporting Evidence: file:SOLLC/DET1/DET1-deep-research-falcon.md it is not an enzyme that catalyzes a small-molecule reaction, but a **regulatory scaffold/adaptor** that helps the E3 ligase recognize and destabilize specific protein substrates. PMID:16792691 Cullins are central scaffolding subunits in eukaryotic E3 ligases that facilitate the ubiquitination of target proteins. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation (UniProt subcellular-location keyword mapping) for nuclear localization. Strongly supported: DET1 is a nuclear protein, consistent with its role as a nuclear transcriptional/proteostatic repressor. Reason: Correct and well supported. UniProt annotates DET1 subcellular location as Nucleus, and it carries two predicted nuclear localization signals [file:SOLLC/DET1/DET1-uniprot.txt]. Arabidopsis DET1 is a nuclear-localized protein that associates with histones, and in tomato YFP-tagged SlDET1 localizes to the nucleus (and cytoplasm), with strong nuclear BiFC signal for the SlDET1-SlGLK2 interaction [file:SOLLC/DET1/DET1-deep-research-falcon.md]. Nuclear localization is a core location for DET1's repressor function. Supporting Evidence: file:SOLLC/DET1/DET1-uniprot.txt SUBCELLULAR LOCATION: Nucleus PMID:9927635 encodes the tomato homolog of the nuclear protein DEETIOLATED1 (DET1) from Arabidopsis. |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | REMOVE | Summary: IEA annotation from InterPro (IPR008928, six-hairpin glycosidase superfamily fold). This is a spurious structural-fold-based mapping; DET1 has no role in carbohydrate metabolism. Reason: This annotation is a false-positive driven by remote structural similarity, not function. The InterPro signature IPR008928 is the "six-hairpin glycosidase-like" superfamily FOLD (SSF48208), which DET1 shares only at the level of overall fold architecture (the De-etiolated_protein_1_Det1 family, IPR019138/PF09737, is the function-relevant signature) [file:SOLLC/DET1/DET1-uniprot.txt]. DET1 is a nuclear ubiquitin-ligase adaptor and photomorphogenesis repressor with no glycoside-hydrolase or carbohydrate-metabolic activity in any of the experimental literature [file:SOLLC/DET1/DET1-deep-research-falcon.md]. Mapping a structural superfamily to "carbohydrate metabolic process" is an over-annotation and should be removed. Supporting Evidence: file:SOLLC/DET1/DET1-uniprot.txt InterPro; IPR008928; 6-hairpin_glycosidase_sf. file:SOLLC/DET1/DET1-deep-research-falcon.md it is not an enzyme that catalyzes a small-molecule reaction, but a **regulatory scaffold/adaptor** that helps the E3 ligase recognize and destabilize specific protein substrates. |
| GO:0005515 protein binding | IPI PMID:16792691 CUL4 associates with DDB1 and DET1 and its downregulation af... | MODIFY | Summary: IPI annotation (IntAct) recording a binary interaction between tomato DET1 and UniProtKB:Q8LGH4 (DDB1), from the Arabidopsis CUL4-DDB1-DET1 study. "Protein binding" is uninformative; the interactor is the CRL4 ligase scaffold DDB1. Reason: Per curation guidelines, bare "protein binding" (GO:0005515) should be replaced with a more informative molecular-function term. The IntAct partner Q8LGH4 is DDB1, the adaptor/scaffold of the CUL4-based E3 ligase, and the cited paper demonstrates that CUL4 associates with DDB1 and DET1 [PMID:16792691]. This specific interaction with the ubiquitin-ligase machinery is captured by "ubiquitin protein ligase binding" (GO:0031625), which is also independently supported by the IBA annotation above. MODIFY to the more informative term. Proposed replacements: ubiquitin protein ligase binding Supporting Evidence: PMID:16792691 CUL4 associates with DDB1 and DET1 PMID:16792691 Arabidopsis cullin 4 is shown to assemble with DDB1, RBX1, DET1 and DDB2 in vitro and in planta. |
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Download this section (compressed HTML)Q: Which transcription-factor substrates does tomato DET1 select in vegetative versus fruit tissue, and are HY5 and PIFs direct CRL4-DET1 substrates in tomato as they are in Arabidopsis?
Suggested experts: Yongsheng Liu, Chris Bowler
Q: Does DET1 confer substrate specificity directly (as a DCAF-like adaptor binding substrate) or indirectly via partner adaptors within the CDD/CRL4 complex?
Suggested experts: Xing Wang Deng
Experiment: Reconstitute the tomato CUL4-DDB1-DET1 ligase from purified subunits and assay in vitro polyubiquitination of candidate substrates (SlGLK2, SlBBX20, HY5) with and without DET1, to establish DET1 as the substrate-selection adaptor.
Hypothesis: DET1 is required for ligase-mediated ubiquitination of specific transcription factors and acts as the substrate-recognition module of the CRL4 complex.
Type: in vitro reconstituted ubiquitination assay
Experiment: Generate tomato det1 lines crossed into phytochrome-deficient and cryptochrome-deficient backgrounds and quantify de-etiolation/pigmentation, to test whether DET1 represses outputs of multiple photoreceptor pathways rather than red/far-red signaling specifically.
Hypothesis: DET1 is a convergent repressor of photomorphogenesis acting downstream of multiple photoreceptors, not a red/far-red-specific signaling component.
Type: genetic epistasis analysis
Experiment: Perform quantitative proteomics of det1/hp-2 versus wild-type seedlings and fruit to identify the set of proteins stabilized upon DET1 loss (candidate CRL4-DET1 substrates).
Hypothesis: DET1 loss stabilizes a defined set of photomorphogenesis-promoting and pigment biosynthesis transcription factors.
Type: comparative quantitative proteomics
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