Supplemental Figure 3: Hierarchical heat map of significantly changing diurnal phosphopeptides at the L-D transition.
The hierarchical heat map was generated using the R package Pheatmap and Euclidean distance. Standardized relative log2 FC in phosphopeptide abundance is shown along with the corresponding AGI and phosphopeptide with phosphorylation site probabilities. GO terms of proteins in the heatmap clusters are shown on the right together with their predicted subcellular localization (SUBAcon). The segments of the circles represent the nucleus (red), cytosol (orange), plastid (green), mitochondria (blue), plasma membrane (purple) and other (black) localizations. The numbers below each pie chart represent the number of unique protein identifications. The time points of sampling for phosphoprotein analysis were 30 min before dark (BD30), 10 min after dark (AD10) and 30 min after dark (AD30).
Supplemental Figure 4: Diurnal phosphorylation of nitrate reductase 1 (NIA1) and 2 (NIA2). (A-B) Diurnal fluctuations of NIA1 and 2 mRNA and protein levels, and phosphorylation status. Relative changes in mRNA and protein levels were assessed over 24 h. Transcript data was extracted from Diurnal DB (http://diurnal.mocklerlab.org/). Relative changes in protein phosphorylation were measured at the D-L and L-D transitions only (see Materials and Methods). (C) Model of NIA2 protein structure including molybdenum cofactor (MoCo), dimerization (Dimer), cytochrome b5 (Cyt B), FAD and NADH binding domains in addition to hinge regions 1 and 2. Phosphorylation of the three annotated phosphorylation sites in NIA2 shown as circles is light-dependent (yellow), dark-dependent (blue) and nitric oxide-induced (white; Wang et al; 2011).