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.

本研究采用15N同位素标记法（15N labeling）处理拟南芥（Arabidopsis thaliana）莲座叶（rosette），以解析其叶片蛋白质的降解速率，并阐明降解速率的决定因素。通过对新合成肽段（peptide）进行15N逐步标记，并随时间监测超过60,000种现存肽段的丰度（abundance）下降情况，本研究得以确定1228种蛋白质在体内（in vivo）的降解速率。研究发现，基于每种蛋白质的衰减速率指数常数，拟南芥蛋白质的半衰期范围为数小时至数月不等。该降解速率通过每种肽段的相对同位素丰度，以及植株生长过程中蛋白质丰度的倍数变化（fold change）计算得到。研究表明，蛋白质复合物组成成员与特定蛋白质结构域（protein domain）是蛋白质降解速率的强力预测因子，而蛋白质的N端氨基酸、疏水性（hydrophobicity）或聚集倾向则无显著预测作用。本研究在质体（plastid）的多种蛋白质复合物中鉴定出快速降解的亚基，并筛选得到一组在莲座叶不同叶片中降解速率发生改变、且与叶片生长速率显著相关的植物蛋白质。基于上述研究结果，本研究计算了不同叶片中的蛋白质周转（protein turnover）能量消耗，以及蛋白质组（proteome）内影响该消耗的关键决定因素。