Fig. 2: Simultaneous measurements of spatial and temporal kinetics under UPR. | Nature Communications

Fig. 2: Simultaneous measurements of spatial and temporal kinetics under UPR.

From: Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions

Fig. 2

a Bar graphs of expression ratios of known ER stress markers upon 8 and 16 h of thapsigargin (Thps.) (n = 6 normal; n = 3 thapsigargin). *: P < 0.01; **: P < 0.001; ***: P d < 0.0001; limma multiple-testing corrected (FDR adjusted) P (two-sided). Error bars: expression ratios ± s.d. b PC1 and PC2 of proteins spatial map showing the localization of confidently allocated proteins in normal and thapsigargin-treated AC16 cells. Data point: protein; color: subcellular compartment classification. c Distribution of light (unlabeled) protein features in each of the 12 subcellular compartments (n = 3); fill color represents whether the protein is also annotated to the same subcellular compartment in UniProt Gene Ontology Cellular Component terms. d Histograms of determined log10 protein turnover rates in control and thapsigargin cells (n = 3). Text overlay: median half-life. e Boxplot of log2 turnover rate ratios in thapsigargin /normal cells for proteins localized to the ER (blue) (T) or not (F); or the Golgi (GA; green). P values: Mann–Whitney test (two-sided). A Bonferroni corrected threshold of 0.05/13 is considered significant. Center line: median; box limits: interquartile range; whiskers: 1.5x interquartile range; n = 286, 2234, 62, 2458 proteins over 3 independent experiments per group. f First-order protein kinetic curves in normal (gray), and thapsigargin treated (red) AC16 cells of 4 known ER stress markers with elevated turnover (HSPA5, RCN3, HSP90B1, PDIA4). Point: best-fit k; line: first-order kinetic curve of k; bands: fitting s.e. g Turnover rate ratios (thapsigargin vs. normal) of top proteins with elevated temporal kinetics in UPR. Color: compartment; P.adj: Mann–Whitney test (two-sided) with Benjamini-Hochberg multiple-testing correction. Dashed line: 1:1 ratio; point: median ratio; range: median ± MAD/median of ratios; n=number of peptide observations (parenthesis) over 3 biologically independent samples per group. h Gene set enrichment analysis (GSEA) of turnover rate ratios in thapsigargin treatment. Color: multiple-testing corrected (FDR adjusted) P in GSEA (two-sided); x-axis: normalized enrichment score (NES). Size: proteins in the gene set.

Back to article page