DOI: 10.5061/dryad.q3h85
title: Data from: Protein degradation rate in Arabidopsis thaliana leaf growth and development

description: 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 &gt;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.
description: TPC2016-00768-LSBR1_Supplemental_Data_Set_1Supplemental Data 1 Growth rates of Arabidopsis leaf 3, leaf 5 and leaf 7.TPC2016-00768-LSBR1_Supplemental_Data_Set_2Supplemental Data 2. Protein degradation rates of 1228 proteins and statistical analysis across samples.TPC2016-00768-LSBR1_Supplemental_Data_Set_3Supplemental Data 3. Ratios of specific protein abundances relative to a 15N fully labelled reference.TPC2016-00768-LSBR1_Supplemental_Data_Set_4Supplemental Data 4. The correlation of intrinsic properties of proteins with their protein degradation ratesTPC2016-00768-LSBR1_Supplemental_Data_Set_5Supplemental Data 5. Comparison of protein degradation rate (KD) and protein abundance between selected proteins in leaf 3 and leaf 7.TPC2016-00768-LSBR1_Supplemental_Data_Set_6Supplemental Data 6. Comparison of protein degradation rate (KD) and leaf growth rates in leaf 3, leaf 5 and leaf 7TPC2016-00768-LSBR1_Supplemental_Data_Set_7Supplemental Data 7. Calculation of ATP costs for protein synthesis and degradation in leaf 3, leaf 5 and leaf 7.TPC2016-00768-LSBR1_Supplemental_Data_Set_8Supplemental Data 8. Comparison of protein degradation rate and protein abundance for selected proteins of interest.TPC2016-00768-LSBR1_Supplemental_Data_Set_9Supplemental Data 9. Determination of protein abundance fold change relative to a 15N reference in 36 individual leaf samples.TPC2016-00768-LSBR1_Supplemental_Data_Set_10Supplemental Data 10. The peptide identification data for each time point for peptides at T=0 days in the spiked in 15N reference experimentTPC2016-00768-LSBR1_Supplemental_Data_Set_11Supplemental Data 11. The peptide identification data for each time point for peptides at T=1 day in the spiked in 15N reference experiment.TPC2016-00768-LSBR1_Supplemental_Data_Set_12Supplemental Data 12. The peptide identification data for each time point for peptides at T=3 days in the spiked in 15N reference experimentTPC2016-00768-LSBR1_Supplemental_Data_Set_13Supplemental Data 13. The peptide identification data for each time point for peptides at T=5 days in the spiked in 15N reference experimentTPC2016-00768-LSBR1_Supplemental_Data_Set_14Supplemental Data 14. Determination of labelled protein fraction (LPF) for peptides by 15N progressively labelling in 27 individual leaf samples.TPC2016-00768-LSBR1_Supplemental_Data_Set_15Supplemental Data 15. The peptide identification data for 15N progressively labelled peptides at all time points.