Arabidopsis core circadian oscillator (CCA1/LHY - PRR - evening complex - ZTL)

The core circadian oscillator of Arabidopsis thaliana is a network of interlocked transcriptional repressor loops that generates a roughly 24 h rhythm in the nucleus. It is reinforced by timed, light-gated proteolysis. At dawn, the single-MYB transcription factors CCA1 and LHY peak and repress evening-phased clock genes (TOC1, ELF4, LUX, ELF3) through evening elements in their promoters. Through the day, the pseudo-response regulators PRR9, PRR7, PRR5 and finally TOC1 (PRR1) accumulate in sequential waves. Each binds target promoters through its C-terminal CCT domain and represses CCA1 and LHY, recruiting TOPLESS/TPR corepressors with histone deacetylase, so that CCA1/LHY expression stays low until the end of the night. At dusk the evening complex (EC) assembles: the scaffold ELF3 bridges the DNA-binding MYB protein LUX and the small protein ELF4. The EC represses PRR9, PRR7, GI and LUX itself through the LUX binding site, closing the evening-to-morning connection and gating growth genes (PIF4/PIF5) to the end of the night. Post-translational control sets the pace. The LOV-domain F-box photoreceptor ZEITLUPE (ZTL), as the substrate adaptor of an SCF E3 ligase, targets phosphorylated TOC1 and PRR5 for proteasomal degradation, mainly in the dark. GIGANTEA binds ZTL in a blue-light-enhanced manner and stabilizes it during the day, so ZTL activity rises at dusk. Light input through phytochromes and cryptochromes, temperature input (sensed partly by the ELF3 prion-like domain), and output pathways such as photoperiodic flowering (GI-CO-FT, CDFs) are outside this module's boundary except where a component acts directly within the oscillator loops.

MODULE:plant_circadian_clock_oscillatorDRAFTCONCRETEBiological Processmodules/plant_circadian_clock_oscillator.yaml
circadian rhythmGO:0007623
PMID:20233950
PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock.
PRR9, PRR7 and PRR5 repress CCA1 and LHY and bind their promoters, forming the daytime negative arm of the CCA1/LHY-PRR loop.
Here, we demonstrate that PRR9, PRR7, and PRR5 act as transcriptional repressors of CCA1 and LHY.
PMID:11100772
Circadian waves of expression of the APRR1/TOC1 family of pseudo-response regulators in Arabidopsis thaliana: insight into the plant circadian clock.
PRR transcripts accumulate in sequential waves after dawn.
the APRR-mRNAs started accumulating sequentially after dawn with 2-3 h intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1
PMID:21753751
The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth.
The evening complex consists of ELF3, ELF4 and LUX, with ELF3 bridging ELF4 and LUX.
ELF3 is both necessary and sufficient to form a complex between ELF4 and LUX
PMID:21236673
LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.
LUX directly represses PRR9, linking the evening and morning loops.
LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit
PMID:18562312
Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins.
Within the PRR family, only TOC1 and PRR5 are SCF-ZTL proteolytic substrates.
together with TOC1, PRR5 is the only other likely proteolytic substrate of the E3 ubiquitin ligase SCF(ZTL) within this PRR family
PMID:23267111
Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription.
PRR5, PRR7 and PRR9 recruit TPL/TPR corepressors at the CCA1 and LHY promoters.
interact with these three PRR proteins at the CCA1 and LHY promoters to repress transcription and alter circadian period
6Nodes
5Parts
0Variant Sets
0Variants
12Annotons
7Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:plant_circadian_clock_oscillator deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

12 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (12 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
cca1_myb_tf CCA1
UniProtKB:P92973
Gene 		DNA-binding transcription factor activity
GO:0003700 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lhy_myb_tf LHY
UniProtKB:Q6R0H1
Gene 		DNA-binding transcription factor activity
GO:0003700 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prr9_repressor PRR9
UniProtKB:Q8L500
Gene 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prr7_repressor PRR7
UniProtKB:Q93WK5
Gene 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prr5_repressor PRR5
UniProtKB:Q6LA42
Gene 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
toc1_repressor TOC1
UniProtKB:Q9LKL2
Gene 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lux_dna_binding_subunit LUX
UniProtKB:Q9SNB4
Gene 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
elf3_scaffold ELF3
UniProtKB:O82804
Gene 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
elf4_corepressor ELF4
UniProtKB:O04211
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ztl_substrate_adaptor ZTL
UniProtKB:Q94BT6
Gene 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ztl_photoreceptor ZTL
UniProtKB:Q94BT6
Gene 		blue light photoreceptor activity
GO:0009882 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gi_ztl_stabilizer GI
UniProtKB:Q9SQI2
Gene 		ubiquitin protein ligase binding
GO:0031625 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

1 negative regulator(s) described as feedback but with no upstream edge (loop cut):

  • morning_myb_loop ⊣ toc1_evening_repressor [input]
    morning_myb_loop is a negative regulator with no upstream edge (not described as feedback)
  • prr_repressor_wave ⊣ morning_myb_loop [input]
    prr_repressor_wave is a negative regulator with no upstream edge (not described as feedback)
  • toc1_evening_repressor ⊣ morning_myb_loop [cut]
    toc1_evening_repressor is described as feedback/induced but has no incoming activating edge: the loop is cut (it reads as a free input in a Boolean translation)
  • evening_complex ⊣ prr_repressor_wave [input]
    evening_complex is a negative regulator with no upstream edge (not described as feedback)
  • ztl_proteolysis ⊣ toc1_evening_repressor [input]
    ztl_proteolysis is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (11/11 grounded genes reviewed)

11 complete review(s) · 6 with deep research · 0 missing review · 5 reviewed but lacking deep research

Gene Review Complete Deep research
CCA1 P92973 ✓ ✓ ✓
ELF3 O82804 ✓ ✓ ✗
ELF4 O04211 ✓ ✓ ✓
GI Q9SQI2 ✓ ✓ ✓
LHY Q6R0H1 ✓ ✓ ✓
LUX Q9SNB4 ✓ ✓ ✗
PRR5 Q6LA42 ✓ ✓ ✗
PRR7 Q93WK5 ✓ ✓ ✗
PRR9 Q8L500 ✓ ✓ ✗
TOC1 Q9LKL2 ✓ ✓ ✓
ZTL Q94BT6 ✓ ✓ ✓

Details

Context
Arabidopsis thalianaNCBITaxon:3702
nucleusGO:0005634
Arabidopsis core circadian oscillatorBiological Processplant_circadian_clock_oscillator

Interlocked transcriptional repressor loops (morning MYB factors, sequential PRR repressors, evening complex) plus SCF-ZTL proteolysis of TOC1/PRR5, which together generate and pace the plant circadian rhythm.

circadian rhythmGO:0007623
Context
Arabidopsis thalianaNCBITaxon:3702
nucleusGO:0005634

No production GO-CAM in gocams/index.tsv contains these Arabidopsis clock genes (checked 2026-10-06), so no gocam_associations are given. ZTL is grounded on the canonical Swiss-Prot entry UniProtKB:Q94BT6 (ADO1_ARATH, At5g57360). The genes/ARATH/ZTL review was re-grounded from the TrEMBL alternative gene model F4KAN2 (identical over residues 1-596, differing only at the C-terminus) to Q94BT6 on 2026-10-06 (see ZTL-notes.md). The RVE8/LNK activators, CHE, PRR3, and the light (PHY/CRY) and temperature input pathways are omitted from this core boundary. Photoperiodic flowering outputs (GI-FKF1-CDF-CO-FT) are a separate module. PANTHER family ids are not asserted.

Connections

morning_myb_loop -> toc1_evening_repressor Negatively Regulates
CCA1/LHY bind the evening element of the TOC1 promoter and repress it at dawn.
morning_myb_loop -> evening_complex Negatively Regulates
CCA1/LHY repress the evening-phased EC genes (ELF4, LUX, ELF3) through evening elements.
PMID:16006522
CCA1 and LHY bind the evening element in the LUX promoter.
We demonstrate that CCA1 and LHY bind to the evening element motif in the LUX promoter, which strongly suggests that these proteins repress LUX expression, as they do TOC1.
prr_repressor_wave -> morning_myb_loop Negatively Regulates
PRR9, PRR7 and PRR5 bind and repress the CCA1 and LHY promoters during the day.
PMID:20233950
PRR9/7/5 associate with CCA1/LHY promoters in vivo.
PRR9, PRR7, and PRR5 associate with the CCA1 and LHY promoters in vivo, coincident with the timing of decreased CCA1 and LHY expression
toc1_evening_repressor -> morning_myb_loop Negatively Regulates
TOC1 represses CCA1 and LHY at dusk and through the night.
evening_complex -> prr_repressor_wave Negatively Regulates
The EC, via LUX binding sites, represses PRR9 (and PRR7) during the early night, allowing CCA1/LHY to rise toward dawn.
PMID:21236673
LUX directly represses PRR9.
LUX directly regulates the expression of PSEUDO RESPONSE REGULATOR9 (PRR9), a major component of the morning transcriptional feedback circuit
ztl_proteolysis -> toc1_evening_repressor Negatively Regulates
SCF-ZTL degrades TOC1 in the dark.
PMID:18562312
TOC1 and PRR5 are SCF-ZTL substrates.
together with TOC1, PRR5 is the only other likely proteolytic substrate of the E3 ubiquitin ligase SCF(ZTL) within this PRR family
ztl_proteolysis -> prr_repressor_wave Negatively Regulates
SCF-ZTL degrades PRR5, but not PRR9 or PRR7.
PMID:17693530
ZTL targets PRR5 for proteasomal degradation.
ZTL targets PRR5 for degradation by 26S proteasomes in the circadian clock and in early photomorphogenesis
Part 1: morning loop (dawn MYB repressors)
CCA1/LHY morning loopRegulatory Stepmorning_myb_loop

Partially redundant single-MYB (RVE-type) transcription factors that peak at dawn, bind evening elements and repress evening-phased clock genes including TOC1, ELF4 and LUX.

Annotons

CCA1: dawn MYB transcription factor
cca1_myb_tf
Participant: Gene Product: CCA1
Gene Product:
CCA1UniProtKB:P92973

Function

DNA-binding transcription factor activityGO:0003700

Processes

circadian rhythmGO:0007623

Locations

nucleusGO:0005634

Binds evening elements and represses evening-phased oscillator genes at dawn.

LHY: dawn MYB transcription factor
lhy_myb_tf
Participant: Gene Product: LHY
Gene Product:
LHYUniProtKB:Q6R0H1

Function

DNA-binding transcription factor activityGO:0003700

Processes

regulation of circadian rhythmGO:0042752

Locations

nucleusGO:0005634

Partially redundant with CCA1 in dawn repression of evening genes.

Part 2: daytime PRR repressor wave
PRR9 -> PRR7 -> PRR5 sequential repressorsRegulatory Stepprr_repressor_wave

Pseudo-response regulators expressed in successive waves from morning (PRR9) through midday (PRR7) to afternoon/evening (PRR5). Each represses CCA1 and LHY through its CCT domain with TPL/TPR corepressors, keeping the morning genes off until the end of the night. The three are partially redundant: the prr9 prr7 prr5 triple mutant is arrhythmic.

Annotons

PRR9: morning CCT-domain repressor
prr9_repressor
Participant: Gene Product: PRR9
Gene Product:
PRR9UniProtKB:Q8L500

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Processes

circadian rhythmGO:0007623

Locations

nucleusGO:0005634

Earliest PRR; light-induced, represses CCA1/LHY in the morning.

PRR7: midday CCT-domain repressor
prr7_repressor
Participant: Gene Product: PRR7
Gene Product:
PRR7UniProtKB:Q93WK5

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Processes

circadian rhythmGO:0007623

Locations

nucleusGO:0005634

Midday PRR; represses CCA1/LHY and morning output genes.

PRR5: afternoon CCT-domain repressor
prr5_repressor
Participant: Gene Product: PRR5
Gene Product:
PRR5UniProtKB:Q6LA42

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Processes

circadian rhythmGO:0007623

Locations

nucleusGO:0005634

Afternoon PRR; represses CCA1/LHY and output genes, heterodimerizes with TOC1, and is an SCF-ZTL substrate.

Part 3: evening PRR repressor (TOC1)
TOC1 (PRR1) evening repressorRegulatory Steptoc1_evening_repressor

TOC1, the last PRR wave, peaks at dusk and binds the CCA1 and LHY promoters through its CCT domain to repress them. With the morning MYBs it forms the original reciprocal feedback loop.

Annotons

TOC1: evening CCT-domain repressor
toc1_repressor
Participant: Gene Product: TOC1
Gene Product:
TOC1UniProtKB:Q9LKL2

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Processes

circadian rhythmGO:0007623

Locations

nucleusGO:0005634

Dusk-phased repressor of CCA1/LHY.

Part 4: evening complex
Evening complex (ELF3-ELF4-LUX)Protein Complexevening_complex

Dusk-phased nuclear repressor complex. LUX provides sequence-specific DNA binding (LBS, GAT(A/T)CG); ELF3 is the scaffold bridging LUX and ELF4; ELF4 restores high-affinity DNA binding of the LUX-ELF3 subcomplex. The EC represses PRR9, PRR7, GI and LUX and the growth regulators PIF4/PIF5 during the early night, and its target occupancy weakens at warm temperature.

transcription regulator complexGO:0005667

Annotons

LUX: MYB DNA-binding subunit
lux_dna_binding_subunit
Participant: Gene Product: LUX
Gene Product:
LUXUniProtKB:Q9SNB4

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Processes

negative regulation of transcription by RNA polymerase IIGO:0000122

Locations

nucleusGO:0005634

Targets the EC to LBS-containing promoters.

ELF3: EC scaffold
elf3_scaffold
Participant: Gene Product: ELF3
Gene Product:
ELF3UniProtKB:O82804

Function

protein-macromolecule adaptor activityGO:0030674

Processes

negative regulation of transcription by RNA polymerase IIGO:0000122

Locations

nucleusGO:0005634

Non-DNA-binding scaffold and corepressor; its prion-like domain makes EC activity temperature-sensitive.

ELF4: EC corepressor subunit
elf4_corepressor
Participant: Gene Product: ELF4
Gene Product:
ELF4UniProtKB:O04211

Function

transcription corepressor activityGO:0003714

Processes

negative regulation of transcription by RNA polymerase IIGO:0000122

Locations

nucleusGO:0005634

Small helical subunit recruited via ELF3; restores EC DNA binding.

Part 5: ZTL-mediated proteolysis of TOC1 and PRR5 (gated by GI and blue light)
SCF-ZTL degradation of TOC1/PRR5Regulatory Stepztl_proteolysis

The LOV/F-box/Kelch photoreceptor ZTL is the substrate adaptor of an SCF E3 ligase that recognizes phosphorylated TOC1 and PRR5 via their pseudo-receiver domains and targets them for 26S proteasomal degradation, mainly in the dark. GIGANTEA binds ZTL in a blue-light-enhanced manner and stabilizes it during the day, so ZTL protein levels oscillate and its activity rises at dusk.

Annotons

ZTL: SCF substrate adaptor for TOC1/PRR5
ztl_substrate_adaptor
Participant: Gene Product: ZTL
Gene Product:
ZTLUniProtKB:Q94BT6

Function

ubiquitin-like ligase-substrate adaptor activityGO:1990756

Processes

SCF-dependent proteasomal ubiquitin-dependent protein catabolic processGO:0031146

Locations

cytosolGO:0005829

Recognizes phosphorylated TOC1/PRR5; LOV domain gates activity by blue light.

ZTL: LOV-domain blue-light photoreceptor
ztl_photoreceptor
Participant: Gene Product: ZTL
Gene Product:
ZTLUniProtKB:Q94BT6

Function

blue light photoreceptor activityGO:0009882

Processes

response to blue lightGO:0009637

Locations

cytosolGO:0005829

FMN-binding LOV domain senses blue light and enhances GI binding.

GI: binds and stabilizes ZTL
gi_ztl_stabilizer
Participant: Gene Product: GI
Gene Product:
GIUniProtKB:Q9SQI2

Function

ubiquitin protein ligase bindingGO:0031625

Processes

regulation of circadian rhythmGO:0042752

Locations

cytoplasmGO:0005737

Blue-light-enhanced ZTL partner that stabilizes ZTL during the day.