LUMINIDEPENDENS (LD) is a largely disordered nuclear regulatory protein that promotes flowering by repressing FLOWERING LOCUS C (FLC). It associates with FLD and SDG26 in an autonomous-pathway chromatin complex and with APRF1 and TOPP4 in a transcription-termination-associated phosphatase module. Structural and interaction evidence links LD to the Ref2/PNUTS family of phosphatase regulatory scaffolds. LD thereby connects RNA processing with FLD-dependent histone H3K4me1 regulation and a repressive FLC chromatin state. LD also binds the FLC activator SUF4, with genetic evidence for antagonistic regulation. The available studies support a scaffold/regulatory role rather than an established sequence-specific DNA-binding transcription-factor activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: DNA binding inferred from a homeobox-like InterPro signature. Reason: Early domain or author-statement inference suggested DNA binding or a transcription-factor role. Modern target interaction and structural work supports a largely disordered Ref2/PNUTS-like regulator linking the FLD complex and termination machinery; it does not demonstrate sequence-specific DNA recognition by LD. The specific binding/TF claim is over-annotated relative to this evidence, without asserting that every possible DNA interaction has been experimentally excluded. In PMID:35766439 Fig3C, purified LD did not bind the tested FLC DNA probe, whereas SDG26-C did; this is a target assay on one probe, not an assertion that all DNA interactions have been excluded. Supporting Evidence: PMID:38851185 Nevertheless, all of them share similar features—a TFIIS domain in the N terminus in an overall highly unstructured protein (Figures 2B and S4B−S4D). PMID:35766439 Moreover, we found that the AuPC component SDG26 associates with FLC chromatin via a previously uncharacterized DNA-binding domain and regulates FLC expression and flowering time independently of its histone methyltransferase activity. |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:10363371 The Arabidopsis flowering-time gene LUMINIDEPENDENS is expre... | MARK AS OVER ANNOTATED | Summary: DNA-binding transcription factor activity asserted (TAS) on the basis of a putative homeodomain and nuclear localization. Reason: Early domain or author-statement inference suggested DNA binding or a transcription-factor role. Modern target interaction and structural work supports a largely disordered Ref2/PNUTS-like regulator linking the FLD complex and termination machinery; it does not demonstrate sequence-specific DNA recognition by LD. The specific binding/TF claim is over-annotated relative to this evidence, without asserting that every possible DNA interaction has been experimentally excluded. In PMID:35766439 Fig3C, purified LD did not bind the tested FLC DNA probe, whereas SDG26-C did; this is a target assay on one probe, not an assertion that all DNA interactions have been excluded. Supporting Evidence: PMID:10363371 Subcellular localization studies indicate that LD is a nuclear protein, consistent with its previously proposed transcriptional regulatory role. PMID:38851185 14–16 Close examination revealed that LD is structurally related to Ref2 in yeast and PNUTS in mammals. |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:7907507 Isolation of LUMINIDEPENDENS: a gene involved in the control... | MARK AS OVER ANNOTATED | Summary: DNA-binding transcription factor activity asserted (TAS) at cloning of LD. Reason: Early domain or author-statement inference suggested DNA binding or a transcription-factor role. Modern target interaction and structural work supports a largely disordered Ref2/PNUTS-like regulator linking the FLD complex and termination machinery; it does not demonstrate sequence-specific DNA recognition by LD. The specific binding/TF claim is over-annotated relative to this evidence, without asserting that every possible DNA interaction has been experimentally excluded. In PMID:35766439 Fig3C, purified LD did not bind the tested FLC DNA probe, whereas SDG26-C did; this is a target assay on one probe, not an assertion that all DNA interactions have been excluded. Supporting Evidence: PMID:7907507 The predicted amino acid sequence of the LD protein contains 953 residues and includes two putative bipartite nuclear localization signals and a glutamine-rich region. |
| GO:0005515 protein binding | IPI PMID:17138694 SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger pro... | MODIFY | Summary: LD interacts directly with the C2H2 zinc-finger protein SUF4. Reason: SUF4 is a DNA-binding transcription factor that activates FLC; LD binds SUF4 and is proposed to suppress its activity. DNA-binding transcription factor binding (GO:0140297) is more informative than protein binding. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:17138694 In addition, suf4 suppresses luminidependens ( ld ), a late-flowering mutation that causes an increase of FLC , and SUF4 protein directly interacts with LD. PMID:17138694 Thus, we propose that LD binds to SUF4 to suppress its activity in the absence of FRI . |
| GO:0005515 protein binding | IPI PMID:19452453 Proteomic profiling of tandem affinity purified 14-3-3 prote... | REMOVE | Summary: Co-purification with TAP-tagged 14-3-3 (GRF2) in a large-scale screen. Reason: Uninformative 'protein binding' from a high-throughput screen; removal does not dispute the interaction. Supporting Evidence: PMID:19452453 After purifying TAP-tagged 14-3-3 complexes, in parallel with a control TAP-tagged green fluorescence protein (GFP), the co-purifying proteins were subjected to in-solution protease digestion followed by matrix assisted laser desorption ionization time of flight (MALDI)-based multiple dimensional protein identification technology (MudPIT) analysis. |
| GO:0005515 protein binding | IPI PMID:35766439 Characterization of an autonomous pathway complex that promo... | REMOVE | Summary: LD co-purifies with FLD, SDG26, APRF1 and EFL proteins in the autonomous pathway complex (AuPC). Reason: Uninformative 'protein binding'; the biologically meaningful information is membership in the FLD/LD/SDG26 autonomous pathway complex, for which no specific GO complex term exists. Supporting Evidence: PMID:35766439 We demonstrate that these components form a multi-subunit autonomous pathway complex (AuPC). |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nucleus propagated by PAINT. Reason: LD is experimentally nuclear. Supporting Evidence: PMID:10363371 Subcellular localization studies indicate that LD is a nuclear protein, consistent with its previously proposed transcriptional regulatory role. |
| GO:0005634 nucleus | IDA PMID:10363371 The Arabidopsis flowering-time gene LUMINIDEPENDENS is expre... | ACCEPT | Summary: LD is a nuclear protein (IDA). Reason: Direct experimental evidence. Supporting Evidence: PMID:10363371 Subcellular localization studies indicate that LD is a nuclear protein, consistent with its previously proposed transcriptional regulatory role. |
| GO:0005634 nucleus | IDA PMID:17138694 SUPPRESSOR OF FRIGIDA4, encoding a C2H2-Type zinc finger pro... | ACCEPT | Summary: Nuclear localization (IDA) in the SUF4 study. Reason: Consistent experimental evidence. Supporting Evidence: PMID:17138694 The last component of the autonomous pathway, LUMINIDEPENDENS ( LD ), encodes a homeodomain protein that is localized to the nucleus ( Lee et al. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nucleus from UniProt subcellular location mapping. Reason: Consistent with experimental evidence. Supporting Evidence: PMID:10363371 Subcellular localization studies indicate that LD is a nuclear protein, consistent with its previously proposed transcriptional regulatory role. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nucleus predicted by AtSubP. Reason: Consistent with experimental evidence. Supporting Evidence: PMID:10363371 Subcellular localization studies indicate that LD is a nuclear protein, consistent with its previously proposed transcriptional regulatory role. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000108 | ACCEPT | Summary: Regulation of transcription inferred from the DNA-binding transcription factor activity annotation. Reason: Although the inference chain rests on an over-annotated MF, LD does regulate transcription of FLC (and convergently transcribed genes) as part of the FLD complex, so the general process term is correct. Note that this row needs re-grounding if the source MF (GO:0003700) is retired from GOA - the independent basis is LD's FLD-complex chromatin evidence (GO:0045814, PMID:32541063, PMID:33649596), not its homeobox-derived TF annotation. Supporting Evidence: PMID:33649596 Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS9, downregulates histone H3K4me1 in regions with convergent overlapping transcription. |
| GO:0010228 vegetative to reproductive phase transition of meristem | IBA GO_REF:0000033 | ACCEPT | Summary: Vegetative to reproductive phase transition propagated by PAINT (LD-specific node). Reason: Consistent with the late-flowering ld phenotype. Supporting Evidence: PMID:7907507 Mutations in this gene render Arabidopsis late flowering and appear to affect light perception. |
| GO:0010228 vegetative to reproductive phase transition of meristem | IMP PMID:19755537 A single amino acid change in the enhancer of zeste ortholog... | ACCEPT | Summary: Autonomous pathway mutants including ld are delayed in the floral transition. Reason: Well-established genetic role. Supporting Evidence: PMID:19755537 We find reduced levels of both H3K27me3 and CLF at FLC chromatin in several autonomous pathway mutants. PMID:7907507 Mutations in this gene render Arabidopsis late flowering and appear to affect light perception. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:32541063 The 3' processing of antisense RNAs physically links to chro... | NEW | Summary: NEW. LD is a core subunit of the FLD/LD/SDG26 complex that prevents H3K4me1 accumulation over FLC and promotes chromatin-based FLC silencing. Reason: LD contributes structurally to the chromatin-modifying complex that performs the H3K4 demethylation step (scaffold participation), and ld mutants share the fld chromatin phenotype. Supporting Evidence: PMID:32541063 Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body. |
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Download this section (compressed HTML)Q: Which direct substrate is dephosphorylated by the APRF1/LD/TOPP4 module, and how does LD determine substrate recruitment?
Q: How does the LD prion-like region influence assembly and persistence of transcriptional repression in native developmental contexts?
Experiment: Mutate a putative PP1-docking (RVxF-type) motif in LD, test TOPP4 binding and complementation of ld, and measure FLC proximal termination, H3K4me1 and flowering time.
Hypothesis: LD recruits PP1/TOPP4 via a PNUTS-like docking motif, and this is required for FLC repression.
Type: Mutagenesis + co-IP + genetic complementation
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