Data from: Protein degradation rate in Arabidopsis thaliana leaf growth and development

Dataset

Description

TPC2016-00768-LSBR1_Supplemental_Data_Set_1.xlsx (66.25 Kb):
Supplemental Data 1 Growth rates of Arabidopsis leaf 3, leaf 5 and leaf 7.

TPC2016-00768-LSBR1_Supplemental_Data_Set_2.xlsx (1.737 Mb):
Supplemental Data 2. Protein degradation rates of 1228 proteins and statistical analysis across samples.

TPC2016-00768-LSBR1_Supplemental_Data_Set_3.xlsx (1.667 Mb):
Supplemental Data 3. Ratios of specific protein abundances relative to a 15N fully labelled reference.

TPC2016-00768-LSBR1_Supplemental_Data_Set_4.xlsx (345.5 Kb):
Supplemental Data 4. The correlation of intrinsic properties of proteins with their protein degradation rates.

TPC2016-00768-LSBR1_Supplemental_Data_Set_5.xlsx (87.26 Kb):
Supplemental 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_6.xlsx (262.4 Kb):
Supplemental Data 6. Comparison of protein degradation rate (KD) and leaf growth rates in leaf 3, leaf 5 and leaf 7.

TPC2016-00768-LSBR1_Supplemental_Data_Set_7.xlsx (655.3 Kb):
Supplemental 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_8.xlsx (111.6 Kb):
Supplemental Data 8. Comparison of protein degradation rate and protein abundance for selected proteins of interest.

TPC2016-00768-LSBR1_Supplemental_Data_Set_9.xlsx (12.15 Mb):
Supplemental Data 9. Determination of protein abundance fold change relative to a 15N reference in 36 individual leaf samples.

TPC2016-00768-LSBR1_Supplemental_Data_Set_10.xlsx (41.61 Mb):
Supplemental Data 10. The peptide identification data for each time point for peptides at T=0 days in the spiked in 15N reference experiment.

TPC2016-00768-LSBR1_Supplemental_Data_Set_11.xlsx (40.08 Mb):
Supplemental 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_12.xlsx (39.32 Mb):
Supplemental Data 12. The peptide identification data for each time point for peptides at T=3 days in the spiked in 15N reference experiment.

TPC2016-00768-LSBR1_Supplemental_Data_Set_13.xlsx (47.55 Mb):
Supplemental Data 13. The peptide identification data for each time point for peptides at T=5 days in the spiked in 15N reference experiment.

TPC2016-00768-LSBR1_Supplemental_Data_Set_14.xlsx (5.241 Mb):
Supplemental 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_15.xlsx (22.56 Mb):
Supplemental Data 15. The peptide identification data for 15N progressively labelled peptides at all time points.

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.
Date made available31 Jan 2017
PublisherDryad Digital Repository

Keywords

  • Protein degradation
  • leaf protein turnover
  • 15N labelling
  • Arabidopsis

Cite this

Li, L. (Creator), Nelson, C. J. (Creator), Trosch, J. (Creator), Castleden, I. R. (Creator), Huang, S. (Creator), Millar, A. H. (Creator)(31 Jan 2017). Data from: Protein degradation rate in Arabidopsis thaliana leaf growth and development. Dryad Digital Repository. 10.5061/dryad.q3h85