Fig. 3: TMT proteomics identifies FAP106-dependent, lineage-specific MIP proteins.
From: FAP106 is an interaction hub for assembling microtubule inner proteins at the cilium inner junction
A Demembranated flagella were purified from 29-13 (Ctrl) or FAP106 KD parasites grown in tetracycline to induce knockdown. Volcano plot shows significance using a moderated two-sided t-test with Benjamini–Hochberg adjustment for multiple comparisons (−Log10 Adjusted p value) vs. relative abundance in FAP106 KD/Ctrl (Log2 Fold-Change) for all proteins quantified by TMT proteomics of two independent biological samples. Proteins meeting the filtering criteria (≥2-fold decrease, adjusted p value ≤ 0.06; Table 2) are indicated by red dots; text labels indicate known proteins (red) and putative MIP candidates (green). Source data are provided in the Source Data file and Supplementary Data 1. Asterisks indicate proteins independently identified as putative B-tubule MIP candidates in a separate proximity labeling approach (Supplementary Fig. 6 and Supplementary Data 2). B Cross-sectional illustration of the DMT as viewed from the flagellum tip, showing the positions of MIP structures lost in FAP106 KD, with known MIPs colored and unknown densities in gray, as observed by cryoET (Fig. 2). A- and B-tubules are indicated (At, Bt) and protofilaments are numbered. C Motility analysis showing mean squared displacement (MSD) of 29-13 (Ctrl) and MC KD parasites from ≥2 independent biological replicates. Dotted lines indicate the upper and lower bounds of the standard error of the mean. Ctrl N = 1761; MC3 KD N = 627; MC5 KD N = 753; MC8 KD N = 709, MC15 KD N = 751. Individual replicates are shown in Supplementary Fig. 7A. D Graph shows the mean ± standard deviation of flagellum lengths as measured by anti-paraflagellar rod (PFR) immunofluorescence microscopy on detergent-extracted cytoskeletons prepared from the indicated KD parasites or their respective mNeonGreen (NG)-tagged parental cell lines (Ctrl). N = 50 flagella for each, except N = 45 flagella for MC15-NG. Unpaired, two-tailed t-test: MC3-NG vs. MC3 KD p = 0.14, MC5-NG vs. MC5 KD p = 0.72, MC8-NG vs. MC8 KD p = 0.005 and MC15-NG vs. MC15 KD p = 0.0008. Source data and means are provided as a Source Data file.
