Phytochromes are red and far-red light photoreceptors that regulate various aspects of plant development including seed germination, seedling photomorphogenesis, and shade avoidance. Phytochromes regulate light responses partly by inhibiting phytochrome-interacting factors (PIFs), a set of bHLH transcription factors that negatively regulate various light responses. When 4 negative phytochrome-interacting protein genes (PIF3, PIF4, PIL5, and PIL6) were mutated, the resulting quadruple mutant seedlings displayed constitutive photomorphogenic phenotypes, including short hypocotyls, and open cotyledons in the dark. Microarray analysis further confirmed that the dark-grown quadruple mutant has a gene expression pattern similar to that of red light-grown wild-type. Together, my data indicate that 4 phytochrome-interacting proteins are required for skotomorphogenesis and phytochromes activate photomorphogenesis by inhibiting these factors.
One of the less understood roles of phytochromes is the inhibition of hypocotyl negative gravitropism, which refers to the loss of hypocotyl gravitropism and resulting random growth direction in red or far-red light. This light response allows seedlings to curve toward blue light after emergence from the soil and enhances seedling establishment in the presence of mulch. Phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF3, PIF4, PIL5, PIL6) as shown by hypocotyl agravitropism of dark-grown pif1 pif3 pif4 pif5 quadruple mutants. I show that phytochromes inhibit negative gravitropism by converting starch-filled gravity-sensing endodermal amyloplasts to other plastids with chloroplastic or etioplastic features in red or far-red light, whereas PIFs promote negative gravitropism by activating the development of endodermal amyloplasts in the dark. By analyzing transgenic plants expressing PIF1 with an endodermis-specific SCARECROW promoter, I further show that endodermal PIF1 is suf...