Fig. 1.

Phytochromes activate PhAPGs by promoting the assembly of the PEP. a Images of embryonic leaves from 4-d-old Col-0, phyB-9 (phyB), phyA-211/phyB-9 (phyAB), and phyA/phyB/phyC/phyD/phyE (phyABCDE) seedlings grown in either darkness or 10 μmol m⁻² s⁻¹ R light. b Total chlorophyll levels in seedlings shown in (a). Different letters denote statistically significant differences in chlorophyll content (ANOVA, Tukey’s HSD, p ≤ 0.001). c Images of embryonic leaves of 4-d-old Col-0 and phyAB seedlings from the indicated time points after dark-grown seedlings were illuminated with 10 μmol m⁻² s⁻¹ R light. d Total chlorophyll levels in Col-0 and phyAB seedlings during the dark-to-light transition described in (c). *** Indicates a statistically significant difference between Col-0 and phyAB (Student’s t-test, p ≤ 0.001). e, f qRT-PCR results showing the transcript levels of representative PEP- and NEP-dependent genes in 4-d-old indicated lines grown in either darkness or 10 μmol m⁻² s⁻¹ R light (e) or during the dark-to-light transition described in (c) (f). The transcript levels were calculated relative to those of PP2A. Fold changes are shown only for the samples exhibiting greater than twofold changes compared with the values of dark-grown Col-0 (***, Student’s t-test, p ≤ 0.001). g, h Immunoblots showing the levels of the PEP complex as well as rpoB and HMR proteins in 4-d-old indicated lines (g) or during the dark-to-light transition (h). Total protein was isolated under either native or denaturing conditions and resolved by blue-native PAGE or SDS-PAGE, respectively. PEP complex on blue-native gels and denatured rpoB and HMR separated by SDS-PAGE were detected by immunoblots using antibodies against rpoB and HMR. RPN6 was used as a loading control. For (b), (c), (e), and (f), error bars represent SD of three biological replicates. The source data underlying the chlorophyll measurements in (b) and (d), the qRT-PCR analysis in (e) and (f), and immunoblots in (g) and (h) are provided in the Source Data file