Day and night isotope labelling reveal metabolic pathway specific regulation of protein synthesis rates in Arabidopsis

• Published in: The Plant journal : for cell and molecular biology Vol. 109; no. 4; pp. 745 - 763
• Main Authors: Duncan, Owen, Millar, A. Harvey
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.02.2022
• Subjects: Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; ATP; Biodegradation; Carbon - metabolism; Carbon Dioxide - metabolism; Degradation; deuterium labelling; diurnal regulation; Energy budget; Gene Expression Regulation, Plant; Homeostasis; Isotope Labeling; Labeling; Leaves; Maintenance management; Metabolic Networks and Pathways; Metabolic pathways; Metabolism; Night; photosynthetic machinery; Photosystem; Plant Leaves - metabolism; Protein Biosynthesis; protein degradation; Protein synthesis; Proteins; Proteolysis; Proteomes; Arabidopsis thaliana; protein synthesis; diurnal regulation; deuterium labelling; photosynthetic machinery; protein degradation
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15661

Summary 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 the output of the translation process and to estimate the ATP investment involved, the individual rates of protein synthesis and degradation of hundreds of different proteins need to be measured simultaneously. We quantified protein synthesis and degradation through pulse labelling with heavy hydrogen in Arabidopsis thaliana rosettes to allow such an assessment of ATP investment in leaf proteome homeostasis on a gene‐by‐gene basis. Light‐harvesting complex proteins were synthesised and degraded much faster in the day (approximately 10:1), while carbon metabolism and vesicle trafficking components were translated at similar rates day or night. Few leaf proteins changed in abundance between the day and the night despite reduced protein synthesis rates at night, indicating that protein degradation rates are tightly coordinated. The data reveal 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. Significance Statement Advances in collection and processing of stable isotope incorporation data have allowed characterisation of differential protein synthesis rates over the diurnal cycle in the model plant Arabidopsis. This reveals both global and specific programmes determining protein synthesis rates for the enzymatic machinery of core biochemical pathways.