A cis-carotene derived cleavage product acts downstream of deetiolated 1 to control protochlorophyllide oxidoreductase and prolamellar body formation

Cleavage products of cis-carotenes are reported to regulate nuclear gene expression, carotenoid homeostasis and leaf development in plants. The substrate(s), where and when they accumulate, as well as their physiological and regulatory mechanism remain unknown. The loss-in-function of the carotenoid isomerase (crtiso) mutants perturb prolamellar body (PLB) formation in etioplasts and induce yellow virescent phenotypes in leaves. Here we demonstrate how growing crtiso mutant plants under an extended period of darkness (shorter day length) can trigger the generation of cis-carotenes and perturb plastid development. By use of a forward genetics screen we show how an epistatic interaction between the ζ-carotene isomerase (ziso-155) and Arabidopsis crtiso (ccr2) mutants blocked the biosynthesis of specific cis-carotene substrates, thereby restoring PLB formation in cotyledon etioplasts and chloroplast development in leaves. Chemical inhibition of carotenoid cleavage dioxygenase activity restored PLB formation in ccr2 etioplasts during skotomorphogenesis and chloroplast development in cotyledons following de-etiolation, providing a function for a novel cis-carotene-derived signaling metabolite. The cis-carotene cleavage product acted downstream of a repressor of photomorphogenesis, DET1, to post-transcriptionally regulate PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR), PHYTOCHROME INTERACTING FACTOR3 (PIF3) and ELONGATED HYPOCOTYL5 (HY5) protein levels, the latter of which controls photosynthesis associated nuclear gene expression. We demonstrate that ccr2 and a det1-154 mutant block PLB formation in etioplasts by POR independent and dependent processes respectively, as a ccr2 det1-154 double mutant develops a PLB and green leaves following de-etiolation. We describe a model whereby CRTISO and DET1 control the generation of an intracellular cis-carotene derived cleavage product that fine-tunes plastid development during extended periods of darkness.