FLOWERING LOCUS D (FLD) is a nuclear, chromatin-associated LSD1-family protein with SWIRM and flavin amine-oxidase domains. Conserved architecture and target-specific chromatin experiments support histone H3K4 demethylase activity, particularly removal of H3K4me1, although the cited studies do not establish a purified FLD catalytic reaction. FLD associates with LD and SDG26 and participates in repression of FLOWERING LOCUS C (FLC), promoting the floral transition. RNA processing and termination are linked to this chromatin regulation through FY-associated machinery and an APRF1/LD/TOPP4 module. FLD also regulates genes with convergent overlapping transcription and interacts with histone deacetylases. Additional genetic roles include systemic acquired resistance and dehydroabietinal-responsive flowering.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:21398257 HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and re... | MODIFY | Summary: FLD interacts with HDA6 (BiFC, pull-down, co-IP) via its N-terminal SWIRM domain. Reason: The interaction partner is a histone deacetylase; histone deacetylase binding (GO:0042826) is the more informative term. Proposed replacements: histone deacetylase binding Supporting Evidence: PMID:21398257 Bimolecular fluorescence complementation, in vitro pull-down, and coimmunoprecipitation assays revealed the protein-protein interaction between HDA6 and the histone demethylase FLD. |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | UNDECIDED | Summary: Predicted mitochondrion localization remains unresolved. Reason: The original ISM assertion is a localization prediction. Nuclear/chromatin experiments establish a major FLD pool but do not test or exclude an additional mitochondrion pool. No source-specific targeting or fractionation result resolving this prediction was recovered. The previous REMOVE relied on absence of organellar evidence, which does not establish absence of the location. Supporting Evidence: PMID:33649596 FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. |
| GO:0006338 chromatin remodeling | IEA GO_REF:0000108 | ACCEPT | Summary: Chromatin remodeling inferred from the histone demethylase activity annotation. Reason: FLD-dependent H3K4 demethylation changes chromatin state at FLC and convergently transcribed genes. This broad chromatin process remains informative across loci and is supported by target chromatin profiling; it does not imply ATP-dependent nucleosome sliding. Supporting Evidence: PMID:17996704 These data support a close association of FCA and FLD in mediating H3K4 demethylation and thus transcriptional silencing of FLC and reveal roles for antisense RNA processing and DCL3 function in this regulation. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | UNDECIDED | Summary: Predicted chloroplast localization remains unresolved. Reason: The original ISM assertion is a localization prediction. Nuclear/chromatin experiments establish a major FLD pool but do not test or exclude an additional chloroplast pool. No source-specific targeting or fractionation result resolving this prediction was recovered. The previous REMOVE relied on absence of organellar evidence, which does not establish absence of the location. Supporting Evidence: PMID:33649596 FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. |
| GO:0009627 systemic acquired resistance | IMP PMID:32392578 Dehydroabietinal promotes flowering time and plant defense i... | KEEP AS NON CORE | Summary: fld mutants are defective in systemic acquired resistance, including dehydroabietinal-induced SAR. Reason: Genetic requirement in SAR is reported, but the mechanism is unclear and bifurcates from the FLC-dependent flowering function; non-core. Supporting Evidence: PMID:32392578 We suggest that SAR and flowering time signaling pathways bifurcate at a step downstream of FLD, REF6, and FVE, with an FLC-dependent arm controlling flowering time, and an FLC-independent pathway controlling SAR. |
| 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 fld) are delayed in the floral transition. Reason: FLD promotes the vegetative-to-reproductive transition by repressing FLC. Supporting Evidence: PMID:19755537 We find reduced levels of both H3K27me3 and CLF at FLC chromatin in several autonomous pathway mutants. PMID:17921315 The vernalization pathway represses FLC in response to a prolonged cold exposure, whereas the autonomous pathway, which includes FLOWERING LOCUS D ( FLD ) and FVE , constitutively represses FLC. |
| GO:0016491 oxidoreductase activity | IBA GO_REF:0000033 | MODIFY | Summary: The conserved oxidoreductase function can be refined to LSD1-like H3K4 demethylation. Reason: The PAINT ancestral assertion of oxidoreductase activity is biologically sound. FLD SWIRM/amine-oxidase architecture and target-specific H3K4me1 phenotypes support the more informative H3K4-demethylase assignment. This is a refinement, not a rejected ancestral function or a claim of a purified FLD assay. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000743742 SUPPORTS TRANSFER The ancestral oxidoreductase assertion is retained in meaning; target LSD1-like architecture and chromatin evidence warrant a narrower activity. Extant donor count is not used to challenge PAINT. Proposed replacements: histone H3K4 demethylase activity Supporting Evidence: PMID:17996704 Here, we show that FCA requires FLOWERING LOCUS D (FLD), a homolog of the human lysine-specific demethylase 1 (LSD1) for FLC downregulation. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: Oxidoreductase activity from amine oxidase InterPro signature. Reason: Too general; replace with histone H3K4 demethylase activity. Proposed replacements: histone H3K4 demethylase activity Supporting Evidence: PMID:17996704 Here, we show that FCA requires FLOWERING LOCUS D (FLD), a homolog of the human lysine-specific demethylase 1 (LSD1) for FLC downregulation. |
| GO:0032452 histone demethylase activity | IMP PMID:14593187 Regulation of flowering time by histone acetylation in Arabi... | MODIFY | Summary: Histone demethylase activity (IMP). fld mutants show increased H3K4 methylation at FLC; later genome-wide profiling showed FLD-dependent removal of H3K4me1. Reason: The evidence specifically concerns H3K4 (H3K4me1/me2) methylation, so the child term histone H3K4 demethylase activity (GO:0032453) is more precise. Note that FLD demethylase activity is inferred from mutant chromatin phenotypes and homology to LSD1; robust in vitro activity of FLD itself has not, to our knowledge, been reported. Proposed replacements: histone H3K4 demethylase activity Supporting Evidence: PMID:17996704 fca mutations increased levels of unspliced sense FLC transcript, altered processing of antisense FLC transcripts, and increased H3K4 dimethylation in the central region of FLC. 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:0048510 regulation of timing of transition from vegetative to reproductive phase | IMP PMID:25922987 Regulation of flowering time by the histone deacetylase HDA5... | ACCEPT | Summary: FLD promotes flowering via repression of FLC (interacts with HDA5 in a flowering-time complex). Reason: Well-supported genetic role in timing of the floral transition. Supporting Evidence: PMID:25922987 Bimolecular fluorescence complementation assays and co-immunoprecipitation assays showed that HDA5 interacts with FVE, FLD and HDA6, indicating that these proteins are present in a protein complex involved in the regulation of flowering time. |
| GO:1904629 response to diterpene | IEP PMID:32392578 Dehydroabietinal promotes flowering time and plant defense i... | KEEP AS NON CORE | Summary: FLD expression is induced by dehydroabietinal (IEP). Reason: Expression response; not a core function. Supporting Evidence: PMID:32392578 DA's promotion of flowering time was mediated through up-regulation of the autonomous pathway genes FLOWERING LOCUS D (FLD), RELATIVE OF EARLY FLOWERING 6 (REF6), and FVE, which repress expression of FLOWERING LOCUS C (FLC), a negative regulator of the key floral integrator FLOWERING LOCUS T (FT). |
| GO:1904629 response to diterpene | IMP PMID:32392578 Dehydroabietinal promotes flowering time and plant defense i... | KEEP AS NON CORE | Summary: fld mutants are impaired in dehydroabietinal responses (IMP). Reason: Pleiotropic, downstream physiological response; non-core. Supporting Evidence: PMID:32392578 DA's promotion of flowering time was mediated through up-regulation of the autonomous pathway genes FLOWERING LOCUS D (FLD), RELATIVE OF EARLY FLOWERING 6 (REF6), and FVE, which repress expression of FLOWERING LOCUS C (FLC), a negative regulator of the key floral integrator FLOWERING LOCUS T (FT). |
| GO:2000028 regulation of photoperiodism, flowering | IMP PMID:32392578 Dehydroabietinal promotes flowering time and plant defense i... | UNDECIDED | Summary: The photoperiod-specific interpretation of the diterpene flowering experiment is unresolved. Reason: PMID:32392578 explicitly supports DA-responsive flowering through FLD and FLC, but its accessible abstract does not resolve whether the experiment establishes regulation of the photoperiod response itself. The label autonomous does not by itself exclude participation in light-dependent flowering. Retain uncertainty pending the relevant full experimental design rather than replacing the term solely from pathway nomenclature. Supporting Evidence: PMID:14593187 The Arabidopsis autonomous floral-promotion pathway promotes flowering independently of the photoperiod and vernalization pathways by repressing FLOWERING LOCUS C (FLC), a MADS-box transcription factor that blocks the transition from vegetative to reproductive development. |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:17996704 The Arabidopsis RNA-binding protein FCA requires a lysine-sp... | NEW | Summary: NEW. FLD-mediated H3K4 demethylation is required for chromatin-based transcriptional silencing of FLC (and other loci with antisense transcription). Reason: FLD performs the chromatin-modifying step (H3K4 demethylation) of this silencing, so it participates rather than being merely required. Supported by mutant chromatin phenotypes and genome-wide profiling. Supporting Evidence: PMID:17996704 These data support a close association of FCA and FLD in mediating H3K4 demethylation and thus transcriptional silencing of FLC and reveal roles for antisense RNA processing and DCL3 function in this regulation. 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. |
| GO:0000785 chromatin | IDA PMID:33649596 Chromatin-based mechanisms to coordinate convergent overlapp... | NEW | Summary: NEW. FLD ChIP localizes to actively transcribed genes, colocalizing with elongating Pol II. Reason: No nuclear/chromatin localization is currently annotated for FLD despite direct genome-wide ChIP evidence. Supporting Evidence: PMID:33649596 FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. |
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Download this section (compressed HTML)Q: What purified FLD complex and substrate conditions reproduce the H3K4me1/me2 demethylation inferred from native chromatin experiments?
Q: How do FY-associated processing and APRF1/LD-associated termination cooperate in recruiting and regulating FLD across different genomic loci?
Experiment: Reconstitute recombinant FLD (with or without LD/SDG26) and test FAD-dependent demethylation of H3K4me1/me2 nucleosomes; complement fld with catalytic-dead FLD (FAD-binding or active-site lysine mutants) and measure FLC H3K4me1 and flowering time.
Hypothesis: FLD catalytic activity is required for FLC repression and directly demethylates H3K4me1.
Type: In vitro enzymology + genetic complementation
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