Large scale measurement of protein synthesis rates over the diurnal cycle reveal pathway specific regulation of translation

Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess aggregate protein translation and degradation for specific proteins and to estimate the ATP investment involved, the individual rates of synthesis and degradation of hundreds of different proteins were measured in Arabidopsis thaliana rosettes. This quantification of translation control through incorporation of heavy hydrogen into newly synthesised protein confirmed that most protein synthesis occurs during the day hours (~3:1 day:night), but revealed it was highly divergent across functional categories. Proteins involved in photosynthesis, especially components of the light harvesting complexes, were synthesized much faster in the day (~10:1), while the protein components of carbon metabolism and vesicle trafficking were translated at similar rates day or night. Comparison of aggregate translation with a range of comparable studies using polysomal loading of transcripts or transcript abundance suggests that translational control is a major contributor to effective gene expression over the diurnal cycle. Diurnal protein degradation rate was observed to be tightly coordinated with protein synthesis rate as few leaf proteins changed in abundance despite reduced translation rates during the night. The direct, quantitative and aggregate analysis of protein synthesis provides an integration of transcriptional, post-transcriptional and translational control of leaf proteome homeostasis and an opportunity to assess the ATP investments involved. The data reveals how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule. One sentence summaryAdvances in collection and processing of stable isotope incorporation data has allowed characterisation of differential protein synthesis rates over the diurnal cycle which reveal both global and specific translational regulation programs of core biochemical pathways.