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. 2019 Apr 8;15(4):e8689. doi: 10.15252/msb.20188689

Figure 5. TRAPP reveals the dynamics of RBPome upon stress.

Figure 5

  1. Volcano plot showing Log2 protein abundance fold change in RBPome plotted against – Log10 P‐value. Black points represent proteins showing no statistically significant change upon sorbic acid exposure in PAR‐TRAPP, while proteins changing significantly (P‐value adjusted < 0.05) are labelled with blue. Only proteins observed as RNA interacting in PAR‐TRAPP were included in the analysis.
  2. Scatter plot of Log2 SILAC ratios +Sorbic/−Sorbic for Saccharomyces cerevisiae proteins, quantified with PAR‐TRAPP. Grey points represent proteins showing no statistically significant change upon sorbic acid exposure in PAR‐TRAPP, while proteins changing significantly (P‐value adjusted < 0.05) are labelled with other colours. Only proteins observed as RNA interacting in PAR‐TRAPP were included in the analysis, except for proteins in the category “protein of intermediary metabolism extended”, for which this criterion was dropped. Proteins annotated with GO term categories “RNA binding”, “translation”, “translation initiation”, “P‐body” and “small molecule metabolism” are displayed together with proteins annotated in literature‐curated lists: “ribosome biogenesis 40S”, “ribosome biogenesis 60S” (Woolford & Baserga, 2013). Proteins belonging to categories “protein of intermediary metabolism” and “protein of intermediary metabolism extended” are yeast enzymes and transporters of intermediary metabolism, obtained from YMDB and further filtered to remove aminoacyl‐tRNA synthetases. “P‐body core” category contains proteins identified as core components of P‐bodies in yeast (Buchan et al, 2010). Numbers label the following protein on the chart: 1 – Rtc3; 2 – Tif3; 3 – Rpg1; 4 – Tif35; 5 – Gcd11; 6 – Rlp24; 7 – Ssd1; 8 – Rbp7; 9 – Nmd3.
  3. Volcano plot showing Log2 fold change in protein abundance upon sorbic acid exposure plotted against – Log10 P‐value. Black points represent proteins showing no statistically significant change in abundance upon sorbic acid exposure (P‐value adjusted > 0.05).
  4. The cytoplasmic phase of large subunit maturation in yeast (Lo et al, 2010). Proteins altered in abundance in PAR‐TRAPP data upon sorbic acid exposure are indicated with arrows. Blue arrow denotes decrease, while red arrows indicate increase in PAR‐TRAPP recovery upon stress. For proteins passing the statistical significance cut‐off (P‐value adjusted < 0.05), fold change is indicated.