There are typographical errors in Table 1. Some of the sub-rows were separated into individual rows, when they should be included in prior rows. Please see the corrected table here.
Table 1. Percentage abundance of selected protein groups upon TbUsp7 and TbVdu1 RNAi derived from normalised SILAC ratios.
| Annotation | Protein group | Protein abundance upon RNAi (percent relative to non-induced) | Predicted features | Predicted Trans-membrane domain | PredictedN-terminal signal | Number of lysines in cytoplasmic domain | Predicted GPI-anchor | Sequence length(inclusive signal seq.) | ||
|---|---|---|---|---|---|---|---|---|---|---|
| TbUsp7 26h | TbUsp7 48h | TbVdu1 48h | ||||||||
| USP7 | Tb927.9.14470 | 28 * | 13 * | 101 (+/- 3) | USP7_C2 superfamily | No | No | NA | NA | 1161 |
| VDU1 | Tb927.11.12240 | ND | 105 * | ND | Peptidase_C19 superfamily | No | No | NA | NA | 790 |
| ISG75 | Tb927.5.390 | 43 (+/- 4) | 40 (+/- 34) | 52 (+/- 5) | ISG65-75 superfamily | 468–490 | Yes | 5 | NA | 522 |
| Tb927.5.400 | 468–490 | 4 | 522 | |||||||
| Tb927.5.350 | 468–490 | 4 | 522 | |||||||
| Tb927.5.360 | 42 (+/- 3) | 39 (+/- 26) | 53 (+/- 4) | ISG65-75 superfamily | 469–491 | Yes | 5 | NA | 523 | |
| Tb927.5.370 | ND | ND | 64 (+/- 23) * | ISG65-75 superfamily | 469–491 | Yes | 5 | NA | 523 | |
| ISG65 | Tb927.2.3280 | 96 (+/- 2) | 117 (+/-5) | 69 (+/- 8) | ISG65-75 superfamily | 386–408 | Yes | 4 | NA | 436 |
| Tb927.2.3290 | 388–410 | 4 | 436 | |||||||
| Tb927.2.3300 | 388–410 | 4 | 436 | |||||||
| Tb927.2.3310 | 388–410 | 3 | 436 | |||||||
| Tb927.2.3320 | 97 (+/- 2) | 109 (+/- 41) | 45 (+/- 2) | ISG65-75 superfamily | 387–409 | Yes | 3 | NA | 437 | |
| Tb927.2.3270 | 90 (+/- 2) | 105 (+/- 22) | 62 (+/- 8) | ISG65-75 superfamily | 388–410 | Yes | 4 | NA | 436 | |
| Tb11.v5.0231 | 469–491 | 5 | 523 | |||||||
| Tb11.v5.0731 | 388–410 | 2 | 430 | |||||||
| ISG-related | Tb927.5.630 | 75 (+/- 3) | 79 (+/- 16) | 76 (+/- 11) | ISG65-75 superfamily | 349–372 | Yes | 4 | NA | 401 |
| ISG64 | Tb927.5.1390* | 92 (+/- 3) | 98 (+/- 2) | 87 (+/- 19) | ISG65-75 superfamily | 376–398 | Yes | 4 | NA | 434 |
| Tb927.5.1410 | 377–399 | 4 | 435 | |||||||
| Tb927.5.1430 | 97 (+/- 9) | 107 (+/- 5) | 94 (+/- 20) | ISG65-75 superfamily | 376–398 | Yes | 4 | NA | 434 | |
| MBAP1 | Tb927.11.13130 | 50 (+/- 1) | 29 (+/- 2) | 101 (+/- 11) | acidic phosphatase [33] | 459–481 | Yes | 2 | No | 524 |
| putative type I membrane protein 1 | Tb927.7.470 | 38 (+/- 1) | 32 * | 85 (+/- 4) | 182–204 | Yes | 4 | No | 297 | |
| putative type I membrane protein 2 | Tb927.9.11480 | 45 (+/- 4) | 34 (+/- 3) | 87 (+/- 2) | 512–537 | Yes | 1 | No | 561 | |
| putative type IV membrane protein | Tb927.11.7550 | 51 (+/- 2) | 38 * | 97 (+/- 7)* | 49–71,112–134,141–163,190–212 | No | 3 | No | 221 | |
| VAMP7B | Tb927.5.3560 | 70 (+/- 3) | 62 (+/- 12) | 81 (+/- 21) | Vesicle-associated membrane protein | 184–206 | No | No | No | 796 |
| TPR-repeat protein | Tb927.11.810 | 46 * | 55 (+/- 4) | 97 (+/- 4) | Tetratrico peptide repeat [42] | No | No | No | No | 216 |
| ESAG5 | Tb11.v5.0826 | 142 (+/- 2) | 170 (+/- 26) | 132 (+/- 12) | potential lipid or lipo-polysaccha ride binding [36,37] | No | Yes | NA | No | 464 |
| Tb927.7.6860 | 480 | |||||||||
| ESAG6 | Tb927.7.3250 | 132 (+/- 17) | 202 (+/-56) | 101 (+/- 43)* | Transferrin receptor | No | Yes | NA | Yes | 397 |
| ESAG7 | Tb927.7.3260 | No | Yes | NA | No | 339 | ||||
| ESAG2 | Tb927.11.14620 | 114 (+/- 8) | 115 (+/- 21) | 85 (+/- 3) | No | Yes | NA | Yes | 458 | |
| VSG-related protein | Tb927.7.180 | 126 (+/- 17) | 139 * | 117 (+/- 4)* | VSG-related | No | Yes | NA | No | 437 |
Values represent average percentage protein abundance relative to uninduced cells ± standard deviation. TbUsp7 and TbVdu1 RNAi samples were analysed at indicated time points in experimental duplicate and triplicate, respectively. Asterisks mark proteins not quantified in all replicates. Polypeptide features predicted using TMHMM2 for trans-membrane domains [39], signalP for N-terminal ER-targeting signal [40], PredGPI for GPI-anchor addition C-terminal signal sequence [41] and TPRpred for tetratrico peptide repeats [42]. Predictions are given as Yes, No responses or sequence positions (inclusive signal sequence) using default parameters. In most cases the topology of the protein is experimentally known or predictable based on close homology of experimentally derived information. All protein hits shown have been inspected for their genomic context and integrity. Protein groups consist of indistinguishable paralogs, sharing identical quantified peptides. For the complete quantification data see S1 Table. NA; not applicable, ND; not detected.
Reference
- 1. Zoltner M, Leung KF, Alsford S, Horn D, Field MC (2015) Modulation of the Surface Proteome through Multiple Ubiquitylation Pathways in African Trypanosomes. PLoS Pathog 11(10): e1005236 doi:10.1371/journal.ppat.1005236 [DOI] [PMC free article] [PubMed] [Google Scholar]