Abstract
Plant seedlings germinating under the soil are challenged by rough soil grains that can induce physical damage and sudden exposure to light, which can induce photobleaching. Seedlings overcome these challenges by developing apical hooks and by suppressing chlorophyll precursor biosynthesis. These adaptive responses are, respectively, regulated by the phytochrome and ethylene signaling pathways via the PHYTOCHROME-INTERACTING FACTORs (PIFs) and the ETHYLENE INSENSITIVE 3 (EIN3)/EIN3-LIKE transcription factors. Although many processes downstream of phytochrome and ethylene signaling are similar, it remains unclear if and where these pathways converge. Here, we show PIFs and EIN3 induce similar changes in the transcriptome without robustly regulating each other’s signaling pathways. PIFs and EIN3 target highly overlapped gene promoters and activate subsets of the co-target genes either interdependently or additively to induce plant responses. For chlorophyll biosynthesis, PIFs and EIN3 target and interdependently activate the expression of HOOKLESS1. HOOKLESS1, in turn, represses chlorophyll synthesis genes to prevent photobleaching. Thus, our results indicate an integration of the phytochrome and ethylene signaling pathways at the level of transcriptional gene regulation by two core groups of transcription factors, PIFs and EIN3.
Highlights
Plants use light as an energy source and as a signal that allows them to monitor their environment and neighboring plants
The pifq mutant and the ethylene-related mutants etr1, ein2, and ein3 show open cotyledons in the dark and excessive photobleaching when transferred to the light (Supplementary Figure S1)
We found ACC up-regulated genes tend to be significantly down-regulated in the pifq mutant, while ACC down-regulated genes tend to be significantly up-regulated in the pifq mutant (Figure 1B)
Summary
Plants use light as an energy source and as a signal that allows them to monitor their environment and neighboring plants. Plants have multiple types of photoreceptors including phytochromes, cryptochromes, phototropins, zeitlupes, and UVR8. This photoreceptor diversity allows plants to detect a broad spectrum of light stimuli and respond with a wide range of developmental and physiological processes. Light exposure induces a conformational change to the active Pfr form, which translocates to the nucleus (Sakamoto and Nagatani, 1996; Kircher et al, 1999; Yamaguchi et al, 1999). Active phytochromes interact with various phytochrome-interacting factors to trigger the global gene expression changes that direct appropriate light responses (Castillon et al, 2007; Bae and Choi, 2008; Leivar and Quail, 2011)
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