Arabidopsis, protein turnover, plastid, leaf growth and development-15N fully labelling as reference

In order to characterize plant protein degradation rates and understand their determinants as they relate to plant growth rate, we have applied 15N labelling approaches in leaves of the Arabidopsis rosette. We found a series of leaves in Arabidopsis plants for which the proteome was stable over time and degradation rates of individual proteins could thus be measured by considering the dilution of total protein abundance through growth. By progressively labelling new peptides with 15N and measuring the decrease in the abundance of over 60,000 peptides with natural isotope abundance profiles we determined the degradation rate of 1228 proteins. The exponential constant of the decay rate (KD) for each protein calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth showed a wide distribution, ranging from 0 to 2 per day. This showed Arabidopsis protein half-lives vary from several hours to several months. In assessing intrinsic factors to explain these protein degradation rates, little effect of the N-end amino acid of proteins or of protein aggregation propensity were found, however protein complex membership and specific protein domains were strong predictors of degradation rate. We found new rapidly degrading subunits in a variety of protein complexes in plastids, identified the set of plant proteins whose degradation rate changes in different leaves of the rosette and correlated with leaf growth rate, and calculated the protein turnover energy costs in different leaves and their key determinants within the proteome.