Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome

Abstract

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high‐resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light‐to‐dark and dark‐to‐light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light–dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin‐dependent kinases among the primary light–dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.

The Circadian Clock Gene Circuit Controls Protein and Phosphoprotein Rhythms in Arabidopsis thaliana

“…Interestingly, nitrate reductases have been reported as classical SnRK1 targets in other species ( 48 ). In light–dark cycles, NIA1 and NIA2 protein abundances are rhythmic ( 25 ), while in our analysis under constant light NIA1 protein was not detected in the global analysis and NIA2 protein abundance changed significantly ( supplemental Fig. S4 B ) but not in phase with the phosphosites, suggestive of regulated (de)phosphorylation.…”

“…NIA2 protein abundances are rhythmic(25), while in our analysis under constant light NIA1 protein was not detected in the global analysis and NIA2 protein abundance changed significantly (FigureS4B) but not in phase with the phosphosites, suggestive of regulated (de)phosphorylation. Another indication of increased SnRK1 activity at subjective dawn are rhythms in phosphopeptides and abundance of the protein FCS-LIKE ZINC FINGER (FLZ)Figure S 7): transcriptional up-regulation of FLZ6 by SnRK1 signalling has previously been…”

“…With mass spectrometer technology becoming more and more advanced, several circadian proteomics studies have been conducted in different species, such as proteomics analyses of J o u r n a l P r e -p r o o f protein abundance time courses (15,(22)(23)(24)(25), proteomics specifically at the day / night transition (25,26) or circadian phosphoproteomics (9,24).…”

The circadian clock gene circuit controls protein and phosphoprotein rhythms inArabidopsis thaliana

“…With mass spectrometer technology becoming more and more advanced, several circadian proteomics studies have been conducted in different species, such as proteomics analyses of protein abundance time courses (15,(22)(23)(24)(25), proteomics specifically at the day / night transition (25,26) or circadian phosphoproteomics (9,24).…”

Post-Translational Mechanisms of Plant Circadian Regulation

“…A large number of the rhythmic phosphosites reported in the Krahmer et al report have not been previously characterized [79]. Additional studies involving systematic quantification of phosphoproteomes using different tissues under diurnal conditions have been published recently [81,82]. Mining these works may provide insights into the connection between rhythmic phosphorylation changes and developmental/metabolic processes, and suggest kinases that are involved in these phosphorylation events.…”