Separate sites of action for cry1 and phot1 blue-light receptors in the Arabidopsis hypocotyl

Rapid cell expansion pushes the Arabidopsis hypocotyl (juvenile stem) through the soil until blue light, acting first through phototropin 1 (phot1) and then through cryptochrome 1 (cry1), suppresses elongation to produce a length characteristic of established, photosynthetically capable seedlings. To determine where these two different blue-light receptors act to suppress hypocotyl elongation, we measured relative elemental growth rate, specifically along the hypocotyl midline at 5-min intervals before and during blue light, using a machine-learning-based image analysis pipeline designed specifically for this kinematic analysis of growth. In darkness, hypocotyl material expanded most rapidly (approximately 4% h^-1) in a broad zone approximately 1 mm below the apical terminus of the hypocotyl (cotyledonary node). Blue light, acting through phot1, rapidly inhibited expansion in this zone, while simultaneously stimulating unexpanded cells in a very narrow, more apical region. Nuclear cry1, and not its cytoplasmic pool, counteracted the phot1-initiated expansion of the small cells in this apical region, preventing them from entering the more basal elongation zone. In a cry1 mutant, expansion of these apical cells proceeded unchecked, reaching rates as high as 6% h^-1 to produce the iconic cry1 long-hypocotyl phenotype. The new spatial information shows where to focus future cell and molecular studies of cry1 and phot1 signaling mechanisms and, ecologically, indicates that a seedling may use an apical reservoir of elongation potential to reenter a lit environment should a natural darkening event such as soil disturbance deactivate cry1.