Table 2. Biotinylated proteins in cilia of cells expressing BirA*-tagged Ccdc113 or Ccdc96 identified using mass spectrometry.
| Protein name | Number in TGD | Ccdc113-BirA* | BirA* Ccdc113 | Ccdc96-BirA* | BirA* Ccdc96 | ||
|---|---|---|---|---|---|---|---|
| Exp 1 | Exp 2 | Exp 1 | Exp 1 | Exp 2 | Exp 1 | ||
| Ccdc113 | TT_00312810 | 41/16 | 25/14 | 7/7 | 83/22 | 41/16 | 0/0 |
| Ccdc96 | TT_00529650 | 2/2 | 3/3 | 9/9 | 77/23 | 31/17 | 4/4 |
| Fap57A | TT_00105300 | 45/25 | 67/34 | 0 | 177/47 | 52/32 | 0 |
| Fap57B | TT_00052490 | 0 | 0 | 0 | 0 | 0 | 0 |
| Fap57C | TT_00214710 | 6/6 | 1/1 | 0 | 36/16 | 6/5 | 0 |
| actin | TT_00190950 | 5/3 | 3/2 | 2/2 | 14/7 | 6/5 | 2/2 |
| Drc1 | TT_01345750 | 1/1 | 2/1 | 0 | 32/16 | 6/5 | 0 |
| Drc2 | TT_00971830 | 0 | 0 | 0 | 31/10 | 0 | 0 |
| Drc3 | TT_00316370 | 0 | 0 | 0 | 24/10 | 8/6 | 0 |
| Drc4a | TT_00857910 | 1/1 | 0 | 0 | 29/10 | 6/4 | 0 |
| Drc4b | TT_00649240 | 0 | 0 | 1/1 | 21/9 | 7/5 | 0 |
| Fap251 | TT_ 01262850 | 0 | 2/2 | 0 | 0 | 2/2 | 0 |
Table shows the numbers (X/Y) of all the identified peptides (X) and unique peptide sequences (Y). TGD–Tetrahymena Genome Database. Complete data are presented in S5 and S6 Tables. In the case of BirA*-HA-Ccdc96 experiment, actin was also identified in a control sample (2/2; S6 Table). Note that in Ccdc96-HA-BirA* expressing cells biotinylated proteins were identified by a significantly higher number of peptides compared to cells expressing Ccdc113-HA-BirA*. This could be due to: (i) the different distance between BirA* and neighboring proteins; (ii) a more or less exposed position of BirA* (the protein end can be hidden between other proteins); (iii) the conformation of the protein end to which the BirA* ligase is fused; we do not know yet where N- and C-termini of Ccdc96 and Ccdc113 are positioned; (iv) the level of the assortment of the transgene enabling expression of the BirA* tagged protein.