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).