Data from: Protein degradation rate in Arabidopsis thaliana leaf growth and development

We have applied 15N labeling approaches to leaves of the Arabidopsis thaliana rosette to characterize their protein degradation rate and understand its determinants. The progressive labeling of new peptides with 15N and measuring the decrease in the abundance of >60,000 existing peptides over time allowed us to define the degradation rate of 1228 proteins in vivo. We show that Arabidopsis protein half-lives vary from several hours to several months based on the exponential constant of the decay rate for each protein. This rate was calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth. Protein complex membership and specific protein domains were found to be strong predictors of degradation rate, while N-end amino acid, hydrophobicity or aggregation propensity of proteins were not. We discovered rapidly degrading subunits in a variety of protein complexes in plastids and identified the set of plant proteins whose degradation rate changed in different leaves of the rosette and correlated with leaf growth rate. From this information, we have calculated the protein turnover energy costs in different leaves and their key determinants within the proteome.我们针对拟南芥（Arabidopsis thaliana）莲座叶应用15N同位素标记法（15N labeling），以解析其叶片蛋白质的降解速率并阐明其决定因素。通过对新合成肽段（peptide）进行15N逐步标记，并动态监测超过60000种现存肽段的丰度衰减趋势，我们成功在体内确定了1228种蛋白质的降解速率。研究表明，基于每种蛋白质的降解速率指数常数，拟南芥蛋白质的半衰期可从数小时跨度至数月。该降解速率通过计算每种肽段的相对同位素丰度，以及生长过程中蛋白质丰度的倍数变化得以求得。研究发现，所属蛋白质复合物成员身份与特定蛋白质结构域是蛋白质降解速率的强预测因子，而蛋白质的N端氨基酸、疏水性或聚集倾向则并非如此。我们在质体（plastids）的多种蛋白质复合物中发现了快速降解的亚基，并鉴定出在莲座叶不同叶片中降解速率发生改变、且与叶片生长速率相关的植物蛋白质集合。基于上述研究数据，我们计算了不同叶片中的蛋白质周转能量消耗，及其在蛋白质组（proteome）中的关键决定因素。