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.