Phytochrome signaling pathway to turn on photomorphogenesis (WP3662)

Arabidopsis thaliana

The pathways activated by phytochromes in Arbabidopsis thaliana de-repress transcription regulators important for photomorphogenesis induction by inhibiting COP1, DET1, and CSN directly and indirectly through HMR. The inhibition represses function of Cul4 ubiquitin ligases. However, HMR is also involved in degradation Phytochrome A in the same pathway. Phytochromes further degrade PIFs in another pathway through HMR activation to inhibit repression of photomorphogenesis. Interaction of both pathways has been proposed through inhibition of HFR1 by COP1/DET1 to increase protein stability of PIFs. This pathway is based on figure 3 from Chen et al.


AAR&Co , Friederike Ehrhart , Kristina Hanspers , and Eric Weitz


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Arabidopsis thaliana



Pathway Ontology

photosignal transduction pathway


Label Type Compact URI Comment
LAF1 GeneProduct ensembl:AT4G25560
HY5 GeneProduct ensembl:AT5G11260
CSN GeneProduct ensembl:AT3G61140 CSN Not Specified
PIF1 GeneProduct ensembl:AT2G20180 PIF Not Specified
COP1 GeneProduct ensembl:AT2G32950
COP10 GeneProduct ensembl:AT3G13550
HFR1 GeneProduct ensembl:AT1G02340
PHYA GeneProduct ensembl:AT1G09570
SPA GeneProduct ensembl:AT2G46340 SPA Not Specified
DET1 GeneProduct ensembl:AT4G10180
DDB1 GeneProduct ensembl:AT4G05420 DDB1 Not Specified
CUL4 GeneProduct ensembl:AT5G46210
HMR GeneProduct ensembl:AT2G34640
CUL4 GeneProduct ensembl:AT5G46210
DDB1 GeneProduct ensembl:AT4G05420 DDB1 Not Specified
PHYB GeneProduct ensembl:AT2G18790
PHYC GeneProduct ensembl:AT5G35840
PHYE GeneProduct ensembl:AT4G18130
PHYD GeneProduct ensembl:AT4G16250
PIF3 GeneProduct ensembl:AT1G09530 PIF Not Specified
PIF4 GeneProduct ensembl:AT2G43010 PIF Not Specified
PIF5 GeneProduct ensembl:AT3G59060 PIF Not Specified
PIF6 GeneProduct ensembl:AT3G62090 PIF Not Specified
HMR GeneProduct ensembl:AT2G34640
PIF7 Protein uniprot:Q570R7 PIF Not Specified


  1. Phytochrome signaling mechanisms and the control of plant development. Chen M, Chory J. Trends Cell Biol. 2011 Nov;21(11):664–71. PubMed Europe PMC Scholia