EARLY FLOWERING 3 (ELF3; also PYK20) is a large (695 aa) nuclear protein with no recognisable enzymatic or DNA-binding domain. It is the central scaffold of the evening complex (EC), a dusk-phased transcriptional repressor complex of the Arabidopsis circadian clock made up of ELF3, ELF4 and the MYB-family DNA-binding protein LUX ARRHYTHMO. ELF3 is necessary and sufficient to bridge ELF4 and LUX. LUX targets the complex to promoters, and the EC then represses evening and midday clock genes (PRR9, PRR7, GI, LUX) and growth regulators such as PIF4 and PIF5, gating hypocotyl elongation to the end of the night. At PIF4, PIF5 and GI, repression has been shown to involve chromatin modification: ELF3 recruits the H3K4me3 demethylases JMJ17 and JMJ18 to the PIF4 and PIF5 loci, acts with PRR5, TOC1 and the SWR1 complex to deposit H2A.Z at PIF4, and modulates H2A.Z at GI. ELF3 is required for sustained rhythms in continuous light and under temperature cycles. It acts as a zeitnehmer that antagonises light input to the clock during the night, and it also delivers temperature input to the clock, a role that appears not to require the rest of the EC. A C-terminal polyglutamine-containing prion-like domain lets ELF3 sense ambient temperature: warmth drives reversible phase separation into nuclear speckles and reduces EC binding to its targets, which links the clock to thermomorphogenesis. ELF3 also binds phytochrome B and acts as a substrate adaptor that lets COP1 ubiquitinate GIGANTEA. With ELF4 and LUX it attenuates abscisic acid signalling in seeds by repressing the function and accumulation of ABI3 and ABI5. A shorter ELF3Ξ² product, from an alternative promoter in intron 2, binds full-length ELF3 and disrupts EC formation. Loss of ELF3 causes photoperiod-insensitive early flowering, long hypocotyls and arrhythmia in the light.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000122 negative regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: ELF3 is the scaffold of the evening complex, which represses transcription of clock genes (PRR9, LUX) and growth regulators (PIF4/PIF5). Reason: Consistent with experimental IDA (ComplexPortal) and EC ChIP/expression data. Supporting Evidence: PMID:21753751 ELF3, ELF4 and LUX are required for the proper expression of the growth-promoting transcription factors encoded by PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 PMID:22327739 we determined association of ELF3 to a conserved region of the PRR9 promoter |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IDA PMID:21236673 LUX ARRHYTHMO encodes a nighttime repressor of circadian gen... | ACCEPT | Summary: ComplexPortal annotation of the evening complex. Helfer et al. 2011 showed that LUX directly represses PRR9; ELF3 is part of this nighttime repressor complex and binds the PRR9 promoter. Reason: EC-level repression is experimentally established, with ELF3 as an essential member. Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9) PMID:22327739 we determined association of ELF3 to a conserved region of the PRR9 promoter |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:10571046 Isolation of a gene from Arabidopsis thaliana related to nem... | MODIFY | Summary: The original PYK20 report assumed a transcription-factor role from the glutamine-rich domain alone. ELF3 has no DNA-binding domain; it represses transcription as the scaffold of the evening complex, in which LUX supplies the DNA binding. Reason: DNA-binding transcription factor activity is incorrect for ELF3. Its contribution to transcription is as a non-DNA-binding corepressor subunit of the EC, so transcription corepressor activity is the appropriate term. Proposed replacements: transcription corepressor activity Supporting Evidence: PMID:10571046 Based on homologies of the glutamine-rich domain, the biological role of the pyk20 gene product as a transcription factor is assumed. PMID:32165537 LUX possesses a single MYB DBD, whereas ELF3 and ELF4 have no domains known to interact with DNA. PMID:39880018 ELF3 recruits the JUMONJI (JMJ) H3K4me3 demethylases JMJ17 and JMJ18 to the PIF4 and PIF5 loci in the evening to remove their H3K4me3 marks |
| GO:0005515 protein binding | IPI PMID:11402161 ELF3 encodes a circadian clock-regulated nuclear protein tha... | REMOVE | Summary: Yeast two-hybrid and in vitro interaction of ELF3 with phytochrome B (Liu et al. 2001). Generic protein binding conveys no functional information. Reason: Uninformative protein-binding term; removal does not dispute the ELF3-PHYB interaction. Supporting Evidence: PMID:11402161 the ELF3 protein interacts with PHYB in the yeast two-hybrid assay and in vitro |
| GO:0005515 protein binding | IPI PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | MODIFY | Summary: ELF3 binds ELF4 and LUX and is necessary and sufficient to bring them together into the evening complex. This bridging is the defining activity of ELF3, and generic protein binding does not capture it. Reason: Replace uninformative protein binding with protein-macromolecule adaptor activity, which describes ELF3's scaffold role in the EC. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:21753751 ELF3 is both necessary and sufficient to form a complex between ELF4 and LUX PMID:32848244 a large scaffold protein and key component of temperature sensing |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: ELF3 is nucleus-localized. Reason: Experimentally confirmed. Supporting Evidence: PMID:11402161 the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation |
| GO:0005634 nucleus | IDA PMID:11402161 ELF3 encodes a circadian clock-regulated nuclear protein tha... | ACCEPT | Summary: ELF3 accumulates in the nucleus rhythmically (Liu et al. 2001). Reason: Direct experimental localization. Later work shows that the cellular and sub-nuclear localization of ELF3 shifts with red and blue light (Ronald et al. 2022), but the nucleus remains its site of action. Supporting Evidence: PMID:11402161 the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation PMID:35191492 we determined that the cellular and sub-nuclear localization of ELF3 is responsive to red (RL) and blue light |
| GO:0005634 nucleus | IDA PMID:19061637 COP1 and ELF3 control circadian function and photoperiodic f... | ACCEPT | Summary: ELF3 interacts with COP1 in the nucleus (Yu et al. 2008). Reason: Consistent with established nuclear localization. Supporting Evidence: PMID:11402161 the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation |
| GO:0005634 nucleus | IDA PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | ACCEPT | Summary: Evening-complex components, including ELF3, are nuclear (ComplexPortal). Reason: Correct. Supporting Evidence: PMID:21753751 LUX targets the complex to the promoters of PIF4 and PIF5 in vivo |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus; experimentally confirmed. Reason: Correct. Supporting Evidence: PMID:11402161 the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction; experimentally confirmed. Reason: Correct. Supporting Evidence: PMID:11402161 the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation |
| GO:0005667 transcription regulator complex | IBA GO_REF:0000033 | ACCEPT | Summary: ELF3 is a core subunit of the evening complex (ELF3-ELF4-LUX), a transcription regulator complex. Reason: Experimentally established complex membership. Supporting Evidence: PMID:21753751 Here we identify a protein complex (called the evening complex)--composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth |
| GO:0005667 transcription regulator complex | IDA PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | ACCEPT | Summary: Nusinow et al. 2011 identified the ELF4-ELF3-LUX evening complex, with ELF3 bridging ELF4 and LUX. Reason: Direct experimental evidence of complex membership; core. Supporting Evidence: PMID:21753751 Here we identify a protein complex (called the evening complex)--composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth PMID:21753751 ELF3 is both necessary and sufficient to form a complex between ELF4 and LUX |
| GO:0007623 circadian rhythm | IMP PMID:11402162 ELF3 modulates resetting of the circadian clock in Arabidops... | ACCEPT | Summary: elf3 is arrhythmic in continuous light, and ELF3 modulates resetting of the clock by light during the subjective night (Covington et al. 2001). Reason: Direct genetic evidence for a clock role; core. Supporting Evidence: PMID:11402162 ELF3 antagonizes light input to the clock during the night |
| GO:0009409 response to cold | IEP PMID:10571046 Isolation of a gene from Arabidopsis thaliana related to nem... | KEEP AS NON CORE | Summary: PYK20/ELF3 transcript levels are reduced by temperature stress. ELF3 does have a genuine temperature-sensing role (via its prion-like domain), but this IEP row reflects a transcript change only. Reason: Expression response; non-core. Supporting Evidence: PMID:10571046 IAA and kinetin treatment increased the level of the pyk20 transcript in the plant, whereas ABA treatment and temperature stress reduced the pyk20 transcript level. |
| GO:0009585 red, far-red light phototransduction | IMP PMID:11402161 ELF3 encodes a circadian clock-regulated nuclear protein tha... | KEEP AS NON CORE | Summary: ELF3 interacts with PHYB and requires PHYB function in early morphogenesis, consistent with a role in red-light signalling. Reason: Supported light-signalling role; secondary to the EC/clock function. Supporting Evidence: PMID:11402161 ELF3 requires PHYB function in early morphogenesis but not for the regulation of flowering time |
| GO:0009649 entrainment of circadian clock | IBA GO_REF:0000033 | ACCEPT | Summary: ELF3 gates light input to the clock at night and is needed for entrainment by temperature cycles. Reason: Experimentally supported (IMP). Supporting Evidence: PMID:11402162 ELF3 antagonizes light input to the clock during the night PMID:20133619 ELF3 is broadly required for circadian clock function regardless of light conditions |
| GO:0009649 entrainment of circadian clock | IMP PMID:20133619 Ambient temperature response establishes ELF3 as a required ... | ACCEPT | Summary: Etiolated elf3-1 seedlings fail to show entrainment by thermocycles, and ELF3 is required for clock function regardless of light conditions (Thines & Harmon 2010). Reason: Direct genetic evidence, since confirmed by Zhu et al. 2022: without ELF3 the oscillator cannot respond to temperature changes, and this ELF3 role appears not to require the rest of the evening complex. Supporting Evidence: PMID:20133619 ELF3 is broadly required for circadian clock function regardless of light conditions PMID:34698833 ELF3 is essential for delivering temperature input to the clock |
| GO:0009733 response to auxin | IEP PMID:10571046 Isolation of a gene from Arabidopsis thaliana related to nem... | MARK AS OVER ANNOTATED | Summary: Increased PYK20 transcript after IAA treatment in a single northern-blot study; there is no evidence that ELF3 functions in auxin responses. Reason: A single transcript-level change is not informative about ELF3 function. Supporting Evidence: PMID:10571046 IAA and kinetin treatment increased the level of the pyk20 transcript in the plant, whereas ABA treatment and temperature stress reduced the pyk20 transcript level. |
| GO:0009737 response to abscisic acid | IEP PMID:10571046 Isolation of a gene from Arabidopsis thaliana related to nem... | MODIFY | Summary: This row rests on decreased PYK20 transcript after ABA treatment in a single study. Later work gives a functional link: ELF3, ELF4 and LUX attenuate ABA signalling during seed germination by physically interacting with ABI3 and ABI5 and repressing their function and accumulation (Tang et al. 2025). Reason: The transcript change alone would not justify the term. Tang et al. 2025, however, shows that ELF3 acts upstream of ABA signalling as a negative regulator, so the claim is sound but better stated as negative regulation of abscisic acid-activated signaling pathway. This rests on the cached abstract only. The abstract names ELF3 in both the physical-interaction and the ABI3/ABI5 repression statements; what it does not state is whether the elf3 single mutant alone shows the ABA germination phenotype. Proposed replacements: negative regulation of abscisic acid-activated signaling pathway Supporting Evidence: PMID:10571046 IAA and kinetin treatment increased the level of the pyk20 transcript in the plant, whereas ABA treatment and temperature stress reduced the pyk20 transcript level. PMID:40737553 the evening complex (EC) components EARLY FLOWERING 3 (ELF3), ELF4, and LUX ARRHYTHMO (LUX) attenuate ABA signaling PMID:40737553 ELF3, ELF4, and LUX repress the function and accumulation of ABI3 and ABI5 |
| GO:0009826 unidimensional cell growth | IMP PMID:10759510 Independent action of ELF3 and phyB to control hypocotyl elo... | KEEP AS NON CORE | Summary: elf3 mutants have elongated hypocotyls and petioles. Through the EC, ELF3 represses PIF4/PIF5 to gate hypocotyl cell elongation. Reason: Supported output phenotype; non-core. Supporting Evidence: PMID:10759510 Like phyB mutants, elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. PMID:21753751 ELF3, ELF4 and LUX are required for the proper expression of the growth-promoting transcription factors encoded by PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 |
| GO:0009909 regulation of flower development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: elf3 mutants flower early, regardless of photoperiod. This is an output of clock/EC dysfunction and of the GI/CO/FT pathway rather than a direct floral-development activity. Reason: Supported downstream phenotype; non-core (photoperiodic flowering is treated as a separate output module). Supporting Evidence: PMID:10759510 Like phyB mutants, elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. |
| GO:0009909 regulation of flower development | IMP PMID:10759510 Independent action of ELF3 and phyB to control hypocotyl elo... | KEEP AS NON CORE | Summary: elf3 mutants flower early (Reed et al. 2000). Reason: Genetic output phenotype; non-core. Supporting Evidence: PMID:10759510 Like phyB mutants, elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. |
| GO:0010031 circumnutation | IMP PMID:15908440 Circadian rhythm of circumnutation in inflorescence stems of... | KEEP AS NON CORE | Summary: elf3 abolishes the circadian rhythm of circumnutation speed in LL, which reflects the clock's control of this output. Reason: Clock output phenotype; non-core. Supporting Evidence: PMID:15908440 elf3 causes an arrhythmic phenotype in circumnutation speed in LL |
| GO:0010119 regulation of stomatal movement | IMP PMID:21737277 FLOWERING LOCUS T regulates stomatal opening. | KEEP AS NON CORE | Summary: A null elf3 allele (scs1-1) in a phot1 phot2 background causes open stomata with increased guard-cell FT expression. The effect is downstream of ELF3 repression of FT. Reason: Genetic phenotype via an output gene; non-core. Supporting Evidence: PMID:21737277 the flowering time genes ELF3 and FT are involved in the regulation of H(+)-ATPase by blue light in guard cells |
| GO:0042752 regulation of circadian rhythm | IDA PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | ACCEPT | Summary: The evening complex regulates the circadian clock and its growth outputs (ComplexPortal). Reason: Core clock role, consistent with arrhythmia of elf3. Supporting Evidence: PMID:21753751 Here we identify a protein complex (called the evening complex)--composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth PMID:20133619 ELF3 is broadly required for circadian clock function regardless of light conditions |
| GO:0048573 photoperiodism, flowering | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: ELF3 contributes to photoperiodic control of flowering via the clock and by promoting COP1-mediated GI degradation. Reason: Supported; output-pathway role, non-core to the oscillator function. Supporting Evidence: PMID:19061637 ELF3 acts as a substrate adaptor, enabling COP1 to modulate light input signal to the circadian clock through targeted destabilization of GI |
| GO:0048573 photoperiodism, flowering | IMP PMID:18799658 Diversification of photoperiodic response patterns in a coll... | KEEP AS NON CORE | Summary: Screen of early-flowering mutants for altered photoperiodic response (Pouteau et al. 2008); elf3 alleles show altered daylength responses. Reason: Genetic output phenotype; non-core. Supporting Evidence: PMID:18799658 A high proportion of mutants with altered Pce exhibited abnormal hypocotyl elongation in the dark and altered circadian periods of leaf movements. |
| GO:2000028 regulation of photoperiodism, flowering | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the ELF3 family to regulation of photoperiodism, flowering. Correct as an output role. Reason: Supported by genetics; non-core. Supporting Evidence: PMID:19061637 ELF3 acts as a substrate adaptor, enabling COP1 to modulate light input signal to the circadian clock through targeted destabilization of GI |
| GO:0009266 response to temperature stimulus | IDA PMID:32848244 A prion-like domain in ELF3 functions as a thermosensor in A... | NEW | Summary: ELF3 itself senses ambient temperature: its prion-like domain undergoes reversible, temperature-dependent phase separation in vitro and in planta, which reduces evening-complex activity at warm temperatures. ELF3 performs the sensing step, so it participates in the response rather than merely being required for it. Reason: Direct biophysical and genetic evidence that the ELF3 PrD is a thermosensor; not present in GOA. Supporting Evidence: PMID:32848244 A purified fragment encompassing the ELF3 PrD reversibly forms liquid droplets in response to increasing temperatures in vitro PMID:32165537 In vitro, the full EC is able to act as a direct thermosensor PMID:37399408 This species undergoes LLPS in a pH- and temperature-sensitive manner PMID:35234947 Warm temperatures promoted the formation of nuclear condensates of ELF3 in hypocotyl cells during the afternoon but not in the morning |
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Download this section (compressed HTML)Q: How does phase separation of the ELF3 prion-like domain mechanistically reduce EC occupancy at target promoters: by sequestering ELF3 away from LUX, or by altering the conformation of the bound complex?
Q: Does ELF3's COP1 substrate-adaptor role in GI degradation operate within the evening complex or in a separate, EC-independent pool of ELF3?
Q: Salicylic acid reduces ELF3 condensation yet increases ELF3 binding at the PIF4 promoter. Is the condensed pool of ELF3 the inactive one, and is condensation itself the switch that releases EC repression at warm temperature?
Q: Which partners carry ELF3's EC-independent temperature input to the oscillator, given that the rest of the evening complex appears not to be required?
Q: ELF3Ξ² (from an alternative promoter in intron 2) is not represented in UniProt. Should it be added as an alternative product, and does it have functions beyond antagonising full-length ELF3?
Q: TAIR annotates PHYB, the canonical plant thermosensor, to GO:0009266 response to temperature stimulus, whereas the C. elegans AFD thermoreceptor guanylyl cyclases (gcy-8, gcy-18, gcy-23) carry GO:0016048 detection of temperature stimulus. Should direct plant thermosensors such as PHYB and ELF3 also be annotated to GO:0016048?
Q: ELF3 targets the JMJ17/JMJ18 H3K4me3 demethylases to PIF4 and PIF5 but the JMJs perform the catalysis. Does this targeting role warrant a histone H3K4 demethylation process annotation for ELF3 (the former process term GO:0034720 is obsolete), or is it fully captured by transcription corepressor activity?
Experiment: Temperature-shift ChIP-seq of LUX and ELF3 in lines expressing PrD-deleted or PrD-swapped ELF3 variants, combined with in vitro EC DNA-binding at varying temperatures.
Hypothesis: PrD-driven ELF3 condensation is sufficient to release the EC from target promoters at warm temperature.
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