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.

我们采用15N标记技术处理拟南芥（Arabidopsis thaliana）莲座叶丛的叶片，以表征其蛋白质降解速率并解析其调控决定因素。通过对新合成肽段进行持续性15N标记，并随时间定量检测超过60000种现存肽段的丰度下降情况，我们得以在活体条件下确定1228种蛋白质的降解速率。研究表明，基于每种蛋白质降解速率的指数常数，拟南芥蛋白质的半衰期从数小时到数月不等。该降解速率可通过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计算得到。我们发现，蛋白质复合物组成成员与特定蛋白质结构域是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有效的预测因子。我们在质体中的多种蛋白质复合物中发现了快速降解的亚基，并鉴定出一组在莲座叶丛不同叶片中降解速率发生变化、且与叶片生长速率相关的植物蛋白质。基于上述数据，我们计算了不同叶片中的蛋白质周转能量消耗，以及蛋白质组内影响该消耗的关键决定因素。