Molecular bases for the constitutive photomorphogenic phenotypes in Arabidopsis

The transition from skotomorphogenesis to photomorphogenesis is regulated in part by the COP1/SPA complex and phytochrome-interacting factors (PIFs) in Arabidopsis. The constitutive photomorphogenic (cop) phenotypes of cop1 and spaQ mutants have been shown to result from a high abundance of positively acting transcription factors. Here, we show that the four major PIF proteins are unstable in copl mutants and that overexpression of PIF1, PIF3, P1F4 and PIF5 suppresses copi phenotypes in the dark. A comparison of the transcriptome data among cop I, spaQ and pifQ reveals remarkably overlapping gene expression profiles with preferential regulation of PIF direct target genes. Additionally, HFR1 strongly inhibits the in vivo binding and transcriptional activation activity of PIF1 in the dark. Taken together, these data suggest that the cop phenotypes of the copl and spaQ mutants are due to a combination of the reduced level of PIFs, increased levels of positively acting transcription factors (e.g. HY5/HFR1) and the HFR1-mediated inhibition of PIF-targeted gene expression in the dark.