Article Figures & Data
Figures
- Fig. 1.
A, heatmap showing the HCL-ST clustering of Log2 fold changes in phosphopeptide abundance during the differentiation time-course. Cluster numbers assigned by MeV are shown to the left. B, graphical representation of abundance changes for peptides assigned to each cluster, with the mean values for each cluster represented as a pink line.
- Fig. 2.
A, Log2 fold abundance changes for phosphopeptides that display transient phosphorylation during differentiation. The numbers after the “_” indicate the residue number of the phosphorylation site(s) in the respective protein. B, phosphopeptides that display transient dephosphorylation.
- Fig. 3.
The number of phosphopeptides per protein in the time-course experiment. Different colors indicate whether different phosphopeptides from the same protein show the same (blue) or different (red, green, or purple) kinetics.
- Fig. 4.
Initiation of peptide phosphorylation and dephosphorylation events at different phases of differentiation.
- Fig. 5.
Log2 fold-change values for the 319 phosphopeptides that were detected in all three conditions of the signal-dependent phosphorylation experiment (supplemental Table S2). The values for each phosphopeptide after 2.5 h of exposure to 37 °C (red), pH (blue), and both (green) are represented by different positions along the x-axis of the graph. “Full response” indicates a change when exposed to both signals; “partial response” indicates a change when exposed to the temperature or pH signal alone. Changes that occurred in response to only temperature or pH are indicated at the top by “temp” or “pH,” “temp & pH” indicates a change in response to both temperature and pH separately, and “temp+pH” indicates a change in response to only the complete signal (both temperature and pH together).
- Fig. 6.
A, phosphopeptides that showed >2-fold change in phosphorylation only in response to the full signal. B, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by temperature. C, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by pH. D, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by temperature and pH separately. Values are presented as Log2 fold change from promastigotes.
- Fig. 7.
A, protein kinases and phosphatase that were phosphorylated during phase I and remained phosphorylated throughout differentiation. B, protein kinases and a phosphatase that were transiently phosphorylated. C, phosphorylation kinetics of different sites in the multiply phosphorylated protein kinase A regulatory subunit like-protein (PKAR'). Values are presented as Log2 fold change from promastigotes.
Tables
- Table I Classes of proteins that were enriched for phosphorylation changes at different time points
Trend of phosphorylation Time point 2.5 h 5 h 10 h 15 h 24 h Amastigotes (120 h) Up Protein kinase Metabolism Translation Chaperone Chaperone Metabolism Protein kinase Down Ribosomal Ribosomal transporter Ribosomal transporter Ribosomal transporter Phase I Phase II Phase III Phase IV “Up” denotes an increase in phosphorylation, and “down” denotes an increase in dephosphorylation.
- Table II Summary of log2 fold-change values for the 317 phosphopeptides that were detected in all three conditions of the signal-dependent phosphorylation experiment (supplemental Table S2 and Fig. 5)
A, abundance changes were coded as “up” or “down” if they changed by more than 1.34-fold (log2 ≥ 0.42), and each phosphopeptide was manually assigned to 1 of 27 possible patterns. Pattern Code Temperature pH pH + temperature Count 1 UUU Up Up Up 20 2 NUU – Up Up 20 3 DUU Down Up Up 2 4 UNU Up – Up 25 5 NNU – – Up 56 6 DNU Down – Up 4 7 UDU Up Down Up 2 8 NDU – Down Up 13 9 DDU Down Down Up 1 10 UUN Up Up – 4 11 NUN – Up – 8 12 DUN Down Up – 0 13 UNN Up – – 16 14 NNN – – – 85 15 DNN Down – – 10 16 UDN Up Down – 4 17 NDN – Down – 24 18 DDN Down Down – 11 19 UUD Up Up Down 0 20 NUD – Up Down 1 21 DUD Down Up Down 0 22 UND Up – Down 0 23 NND – – Down 3 24 DND Down – Down 3 25 UDD Up Down Down 0 26 NDD – Down Down 4 27 DDD Down Down Down 1 Up 71 55 143 No change 214 202 162 Down 32 60 12 B, these patterns were used to ascribe a signal-dependent response to each phosphopeptide. Response Signal Pattern(s) Number of peptides Full Temperature alone 4 + 7 + 21 + 24 30 155 pH only 2 + 3 + 25 + 26 26 Temperature and pH 1 + 27 21 Temperature + pH 5 + 6 + 8 + 9 + 19 + 20 + 22 + 23 78 Partial Temperature only 13 + 15 26 77 pH only 11 + 17 32 Temperature and pH only 10 + 12 + 16 + 18 19 No change None 14 85 85
Supplemental Data
Files in this Data Supplement:
- Supplemental figure S1 - LinJ.05.0140 phosphopeptides.
- Supplemental figure S2 - Initiation of phosphorylation/dephosphorylation events at different time-points during differentiation.
- Legends for supplemental data - Legends for supplemental tables and figures
- Supplemental Table S1 - Leishmania donovani phosphopeptide abundance during promastigote-to-amastigote differentiation.
- Supplemental Table S2 - Signal-dependent phosphopeptide abundance at 2.5 hours of Leishmania donovani differentiation.
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