Gene: TOC1 / APRR1 / PRR1 (At5g61380), UniProt Q9LKL2, Arabidopsis thaliana (NCBITaxon:3702).
Reviewer journal for the GO annotation review.
TOC1 (TIMING OF CAB EXPRESSION 1; also APRR1 / PRR1) is the founding member of the
Arabidopsis pseudo-response regulator (PRR) family and a core evening-phased
component of the plant circadian clock. It is a nuclear, DNA-binding transcriptional
repressor that occupies the promoters of the morning genes CCA1 and LHY and
represses their expression, completing the central transcriptional feedback loop in
which morning-expressed CCA1/LHY in turn directly repress TOC1 transcription.
Domain architecture: an N-terminal pseudo-receiver (PR / psREC) domain (~aa 20–138)
and a C-terminal CCT domain (CONSTANS, CO-like, TOC1; ~aa 533–575).
Although TOC1 has a receiver-domain-like fold, it is a pseudo-response regulator:
UniProt CAUTION: "Lacks the phospho-accepting Asp (here Glu-71), present in the
receiver domain, which is one of the conserved features of the two-component response
regulators (ARRs) family." [Q9LKL2 UniProt]
GO:0000160 "phosphorelay signal transduction system" is defined as a His-kinase
autophosphorylation → Asp phosphotransfer → response regulator cascade (QuickGO API,
2026-06-14). GO:0009736 "cytokinin-activated signaling pathway" is the cytokinin
two-component cascade ending in transcription (QuickGO API). TOC1 lacks the catalytic
Asp and is not part of cytokinin signaling; both IEA annotations are over-propagations
from the receiver-domain InterPro/ARBA signatures and are biologically incorrect for
TOC1. There is no experimental evidence linking TOC1 to cytokinin signaling.
TOC1 binds the T1ME element (TGTG core), and also ME and HUD motifs.
The 2009 CHE paper (PMID:19286557) carries a NOT annotation for GO:0000976
"transcription cis-regulatory region binding" because at that time direct TOC1 DNA
binding could not be detected and TOC1 was thought to lack DNA-binding domains:
The 2009 study used the CHE/TCP-binding region of the CCA1 promoter and concluded TOC1
is recruited to that specific promoter region via CHE (a TCP transcription factor),
rather than binding it directly. In 2012, Gendron et al. (PMID:22315425) showed with
purified protein that full-length TOC1 does bind DNA directly through its CCT domain,
and that DNA binding is necessary for repression. The 2012 finding refines, but does not
fully overturn, the 2009 result: TOC1 binds T1ME/G-box/ME-type elements directly, while
its association with the specific TCP-binding-site region of the CCA1 promoter may be
CHE-mediated. The negated GO:0000976 annotation is therefore retained (it reflects a
genuine published negative result about a specific promoter region), but the positive
DNA-binding and DNA-binding-TF activity annotations from 2012 are the well-supported
current view.
TOC1/PRRs also directly bind and repress PIF4 and PIF5 promoters to control
photoperiodic hypocotyl growth:
The IDA GO:0003677 DNA-binding annotation to PMID:32165445 is supported by the EMSA
evidence (PRRs binding G-box cis-elements of CCA1/PIF4/PIF5 promoters).
PMID:23638299 (RVE8 paper, IMP for regulation of gene expression) shows TOC1 expression
itself is activated by RVE8 and that TOC1 represses morning genes; the loss-of-clock-
function genetic context supports TOC1's role in regulation of gene expression.
UniProt: SUBCELLULAR LOCATION: Nucleus (PROSITE-ProRule CCT NLS + PubMed:18562312).
Multiple independent IDA/TAS/ISM nucleus annotations.
TOC1 interacts with many partners; these IntAct-derived "protein binding" annotations
are individually true but uninformative as molecular function:
- PIF/PIL bHLH factors (PIF1, PIL2, PIF3, PIF4, PIL5, PIL6) [UniProt SUBUNIT; PMID:11828029 IntAct partner Q8L5W8 = PIL1].
- ADO1/ZTL (ZEITLUPE) F-box photoreceptor — targets TOC1 for SCF(ZTL) degradation
[PMID:14654842; PMID:17704763]; ADO2/LKP2 PMID:15310821.
- PRR3/APRR3 — protects TOC1 from ZTL degradation in the vasculature PMID:18055606.
- PRR5 — promotes TOC1 nuclear import, phosphorylation, subnuclear foci PMID:20407420.
- TCP21/CHE — recruits TOC1 to the CCA1 promoter PMID:19286557.
- Large-scale interactome / phytohormone network screens [PMID:21798944; PMID:28650476;
PMID:32612234].
TOC1 is phosphorylated during the day and degraded by SCF(ZTL)/26S proteasome; PRR3 and
PRR5 modulate its stability and nuclear accumulation.
This is a downstream circadian output phenotype of clock disruption, not a core TOC1
molecular function — best kept as non-core.