LUX ARRHYTHMO (LUX; also PHYTOCLOCK 1, PCL1) is a nuclear GARP-family single-MYB-domain transcription factor and the DNA-binding subunit of the evening complex (EC) of the Arabidopsis circadian clock, made up of LUX, ELF3 and ELF4. LUX binds the LUX binding site (LBS; consensus GAT(A/T)CG) through its MYB DNA-binding domain and recruits ELF3, and through ELF3 also ELF4, to target promoters. At dusk and in the early night the EC represses the morning-loop gene PRR9, LUX itself (a negative autoregulatory loop), and growth regulators such as PIF4 and PIF5, which couples the oscillator to diurnal gating of hypocotyl growth. LUX expression is circadian, peaking in the evening, and is repressed in the morning by CCA1 and LHY through evening elements in its promoter. lux loss-of-function mutants are arrhythmic in continuous light and darkness, have elongated hypocotyls and flower early. The EC's DNA binding is temperature-dependent, which contributes to thermoresponsive growth.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000122 negative regulation of transcription by RNA polymerase II | IDA PMID:21236673 LUX ARRHYTHMO encodes a nighttime repressor of circadian gen... | ACCEPT | Summary: LUX directly represses PRR9 and its own promoter at night (Helfer et al. 2011). Reason: Direct experimental evidence; core. Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site PMID:21236673 We also show that LUX binds to its own promoter, defining a new negative autoregulatory feedback loop within the core clock. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: Domain-based DNA-binding call; LUX binds DNA directly with high affinity, and a crystal structure of the MYB domain bound to DNA is available. Reason: Correct. Supporting Evidence: PMID:32165537 To confirm the affinity of LUX–DNA interactions, DNA sequences with variations of the LUX binding site (LBS) were tested against varying protein concentrations using electrophoretic mobility shift assays (EMSAs). |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: LUX is a sequence-specific MYB/GARP-domain transcription factor that binds the LBS and represses its targets, including PRR9 and its own promoter. All of its well-characterized activity is repressive. Reason: The function is sound, but the repressor child term (RNA polymerase II-specific) more precisely describes LUX activity in the evening complex. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN007881368 · PANTHER:PTN007881368 SUPPORTS TRANSFER Node-level DNA-binding TF activity is sound; LUX's characterized activity is specifically repressive. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site PMID:21236673 We also show that LUX binds to its own promoter, defining a new negative autoregulatory feedback loop within the core clock. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the MYB/GARP DNA-binding domain; correct for LUX. Reason: Correct in essence; the repressor child term better describes LUX, consistent with the IBA review. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: Sequence-similarity call of transcription-factor activity from the genome-wide TF family survey; since confirmed experimentally (DNA-binding specificity and promoter repression). Reason: Correct in essence and confirmed experimentally; refine to the repressor child term. Proposed replacements: DNA-binding transcription repressor activity, RNA polymerase II-specific Supporting Evidence: PMID:21236673 We determined the in vitro DNA-binding specificity for LUX by using universal protein binding microarrays |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: LUX is nuclear. Reason: Experimentally confirmed. Supporting Evidence: PMID:21753751 LUX targets the complex to the promoters of PIF4 and PIF5 in vivo |
| GO:0005634 nucleus | IDA PMID:16164597 PHYTOCLOCK 1 encoding a novel GARP protein essential for the... | ACCEPT | Summary: PCL1/LUX localizes to the nucleus (Onai & Ishiura 2005, UniProt curation). Reason: Correct. Supporting Evidence: PMID:16164597 the PCL1 gene encodes a novel DNA binding protein belonging to the GARP protein family and is essential for a functional clock oscillator in A. thaliana |
| GO:0005634 nucleus | IDA PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | ACCEPT | Summary: Evening-complex components, including LUX, 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:21753751 LUX targets the complex to the promoters of PIF4 and PIF5 in vivo |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction; experimentally confirmed. Reason: Correct. Supporting Evidence: PMID:21753751 LUX targets the complex to the promoters of PIF4 and PIF5 in vivo |
| GO:0005667 transcription regulator complex | IDA PMID:21753751 The ELF4-ELF3-LUX complex links the circadian clock to diurn... | ACCEPT | Summary: LUX is the DNA-binding subunit of the ELF4-ELF3-LUX evening complex. Reason: Direct evidence; 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 |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: Domain-based regulation-of-transcription call; correct for LUX. Reason: Correct, general. Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Author statement from the genome-wide TF family survey; correct for LUX. Reason: Correct, general. Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: LUX regulates transcription of target genes from Pol II promoters (PRR9, LUX, PIF4/PIF5). Reason: Correct; more specifically repression. Supporting Evidence: PMID:21236673 LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit, through association with the newly discovered DNA binding site |
| GO:0007623 circadian rhythm | IBA GO_REF:0000033 | ACCEPT | Summary: LUX is a core clock component; lux mutants are arrhythmic. Reason: Core. Supporting Evidence: PMID:16006522 This screen identified five mutant alleles of a clock gene, LUX ARRHYTHMO (LUX), that significantly affect amplitude and robustness of rhythms in both constant white light and dark conditions. |
| GO:0007623 circadian rhythm | IEP PMID:16164597 PHYTOCLOCK 1 encoding a novel GARP protein essential for the... | ACCEPT | Summary: PCL1/LUX transcript cycles with a circadian rhythm in LL and DD. Reason: Expression evidence consistent with the established core clock role. Supporting Evidence: PMID:16164597 PCL1 expression showed circadian rhythm in both constant light and constant dark |
| GO:0007623 circadian rhythm | IMP PMID:16006522 LUX ARRHYTHMO encodes a Myb domain protein essential for cir... | ACCEPT | Summary: lux mutant alleles strongly affect the amplitude and robustness of rhythms in LL and DD (Hazen et al. 2005). Reason: Direct genetic evidence; core. Supporting Evidence: PMID:16006522 This screen identified five mutant alleles of a clock gene, LUX ARRHYTHMO (LUX), that significantly affect amplitude and robustness of rhythms in both constant white light and dark conditions. |
| GO:0010468 regulation of gene expression | IMP PMID:23638299 Accurate timekeeping is controlled by a cycling activator in... | KEEP AS NON CORE | Summary: Hsu et al. 2013 show that RVE8 expression is reduced in lux and other clock mutants. The very general regulation-of-gene-expression term reflects an indirect, clock-mediated effect. Reason: Supported but uninformative and likely indirect; non-core. Supporting Evidence: PMID:23638299 RVE8 expression is significantly reduced in all of these clock mutants in LD (Figure 6A), indicating that TOC1, LUX and CCA1 directly or indirectly regulate RVE8 expression. |
| 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, with LUX as its DNA-binding subunit, regulates the circadian clock and its growth outputs. Reason: 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:16006522 This screen identified five mutant alleles of a clock gene, LUX ARRHYTHMO (LUX), that significantly affect amplitude and robustness of rhythms in both constant white light and dark conditions. |
| GO:0042753 positive regulation of circadian rhythm | IMP PMID:16164597 PHYTOCLOCK 1 encoding a novel GARP protein essential for the... | KEEP AS NON CORE | Summary: pcl1 null mutants are arrhythmic. UniProt curated this as positive regulation of circadian rhythm. LUX is better described as a component of the oscillator (circadian rhythm), but the requirement for rhythm generation is genuine. Reason: The term captures the loss-of-rhythm phenotype; retained but the core role is captured by circadian rhythm and regulation of circadian rhythm. Supporting Evidence: PMID:16164597 pcl1 null mutations caused arrhythmia in multiple circadian outputs |
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Download this section (compressed HTML)Q: How does ELF3 binding reduce LUX DNA-binding affinity while ELF4 restores it, and is this switch the basis of the temperature sensitivity of EC occupancy?
Q: Does the LUX paralog NOX/BOA partially substitute for LUX within the evening complex, and at which targets?
Experiment: Genome-wide LUX ChIP-seq in elf3 and elf4 backgrounds at different temperatures, compared with in vitro LUX/LUX-ELF3/EC binding to the same sites.
Hypothesis: LUX occupancy in vivo depends on the ELF3-ELF4 composition of the complex in a temperature-dependent way.
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