TABLE 2:
Polypeptide ratios in WT and d1blic (RNAi-A) flagella determined by iTRAQ analysis.
| Experiment 1 | Experiment 2 | ||||||
|---|---|---|---|---|---|---|---|
| Polypeptide | Chlamydomonas genome ID (V5.5) | Peptides | WT/WT | d1blic/WT | Peptides | WT/WT | d1blic/WT |
| Decreased | |||||||
| Retrograde motor | |||||||
| DHC1b | Cre06.g250300 | 89 (241) | 1.01 | 0.39, 0.34 | 191 (248) | 1.04 | 0.27, 0.29 |
| FAP133/D1bIC2 | Cre02.g110950 | 4 (7) | 1.00 | 0.61, 0.51 | 11 (13) | 1.05 | 0.35, 0.36 |
| FAP163/D1bIC1 | Cre10.g428664 | 7 (10) | 0.97 | 0.44, 0.51 | 17 (18) | 1.02 | 0.37, 0.36 |
| D1bLIC | Cre09.g398882 | 11 (32) | 1.00 | 0.31, 0.29 | 18 (25) | 1.07 | 0.32, 0.29 |
| Anterograde motor | |||||||
| FLA10 | Cre17.g730950 | 14 (37) | 1.02 | 0.81, 0.70 | 56 (55) | 1.07 | 0.48, 0.48 |
| FLA8 | Cre12.g522550 | 17 (36) | 1.03 | 0.82, 0.88 | 46 (57) | 1.07 | 0.53, 0.52 |
| KAP | Cre10.g449250 | 10 (26) | 1.00 | 0.84, 0.66 | 31 (35) | 1.01 | 0.47, 0.48 |
| Other | |||||||
| RSP17 | Cre07.g340400 | 20 (52) | 1.02 | 0.35, 0.35 | 36 (48) | 1.04 | 0.42, 0.34 |
| WNK1 | Cre17.g700133 | 6 (14) | 1.00 | 0.61, 0.65 | 6 (7) | 1.07 | 0.31, 0.33 |
| FAP24 | Cre02.g081050 | 12 (34) | 1.02 | 0.70, 0.46 | 35 (35) | 1.01 | 0.45, 0.52 |
| PKD2 | Cre17.g715300 | 13 (39) | 1.03 | 0.71, 0.48 | 32 (34) | 1.05 | 0.75, 0.73 |
| FAP5 | Cre16.g687966 | 34 (126) | 1.00 | 0.74, 0.61 | 57 (67) | 1.06 | 0.34, 0.36 |
| FAP208 | Cre11.g482001 | 43 (116) | 1.04 | 0.77, 0.71 | 82 (108) | 1.05 | 0.37, 0.36 |
| TPR protein | Cre17.g747247 | 58 (121) | 1.02 | 0.79, 0.64 | 109 (123) | 1.05 | 0.41, 0.41 |
| FAP26 | Cre04.g215250 | 21 (42) | 1.02 | 0.87, 0.58 | 45 (48) | 1.04 | 0.77, 0.72 |
| FAP48/IP3R | Cre16.g665450 | 61 (199) | 1.00 | 0.92, 0.78 | 122 (139) | 1.03 | 0.79, 0.79 |
| Increased | |||||||
| IFT complex A | |||||||
| IFT144 (FAP66) | Cre13.g572700 | 56 (176) | 1.02 | 1.56, 1.28 | 92 (101) | 1.00 | 1.93, 1.82 |
| IFT140 | Cre08.g362650 | 50 (159) | 1.04 | 1.62, 1.36 | 99 (99) | 0.99 | 1.90, 1.83 |
| IFT139 (FAP60) | Cre06.g268800 | 68 (214) | 1.02 | 1.56, 1.45 | 99 (98) | 0.99 | 1.89, 1.77 |
| IFT121 (FAP118) | Cre11.g475000 | 42 (118) | 1.04 | 1.55, 1.40 | 62 (61) | 0.99 | 2.09, 1.99 |
| IFT43 | Cre06.g251200 | 4 (9) | 0.96 | 1.43, 1.00 | 17 (22) | 1.01 | 1.78, 1.66 |
| IFT complex B | |||||||
| IFT172 | Cre17.g703900 | 86 (244) | 1.04 | 1.59, 1.44 | 171 (158) | 0.98 | 1.76, 1.67 |
| IFT88 | Cre07.g335750 | 36 (115) | 1.05 | 1.59, 1.76 | 71 (86) | 0.99 | 1.80, 1.70 |
| IFT81 | Cre17.g723600 | 38 (123) | 1.02 | 1.60, 1.66 | 68 (88) | 1.03 | 1.71, 1.58 |
| IFT80 | Cre03.g204150 | 29 (80) | 1.01 | 1.58, 1.21 | 41 (42) | 0.99 | 1.83, 1.85 |
| IFT74/72 | Cre01.g027950 | 41 (149) | 1.02 | 1.61, 1.56 | 88 (101) | 1.00 | 1.82, 1.70 |
| IFT70/TPR5 | Cre07.g342200 | 26 (77) | 1.03 | 1.57, 1.78 | 45 (59) | 1.00 | 1.84, 1.85 |
| IFT57 | Cre10.g467000 | 18 (60) | 1.00 | 1.61, 1.82 | 36 (38) | 0.98 | 1.74, 1.55 |
| IFT56 (DYF13) | Cre11.g467616 | 25 (50) | 1.00 | 1.59, 1.33 | 27 (48) | 0.95 | 1.94, 2.04 |
| IFT54 (FAP116) | Cre11.g467739 | 14 (57) | 1.00 | 1.62, 1.76 | 59 (68) | 1.03 | 1.78, 1.68 |
| IFT52 (BLD1) | Cre04.g219250 | 22 (60) | 0.98 | 1.66, 1.45 | 58 (66) | 1.00 | 1.80, 1.80 |
| IFT46 (FAP32) | Cre05.g241637 | 20 (51) | 0.99 | 1.63, 1.30 | 34 (41) | 1.01 | 1.77, 1.66 |
| IFT27 (FAP156) | Cre01.g047950 | 8 (24) | 0.99 | 1.53, 1.67 | 8 (16) | 0.93 | 1.56, 1.44 |
| IFT25 (FAP232) | Cre10.g450350 | 7 (18) | 0.97 | 1.73, 0.88 | 6 (7) | 0.98 | 1.92, 1.95 |
| IFT22/RabL5 | Cre01.g039200 | 9 (16) | 1.03 | 1.49, 0.91 | 22 (21) | 0.97 | 1.60, 1.43 |
| IFT20 | Cre02.g089950 | 9 (27) | 0.99 | 1.60, 1.33 | 19 (21) | 1.05 | 1.75, 1.64 |
| FAP22 (qilin) | Cre17.g721250 | 14 (70) | 0.98 | 1.78, 1.74 | 35 (41) | 1.00 | 1.96, 1.78 |
| BBSome | |||||||
| BBS1 | Cre17.g741950 | 6 (12) | 1.00 | 1.64, 1.23 | 5 (4) | 0.95 | 1.94, 1.89 |
| BBS3 | Cre06.g257250 | 8 (14) | 1.00 | 1.63, 1.18 | 5 (5) | 0.96 | 2.01, 2.01 |
| BBS3 | Cre16.g664500 | 1 (3) | 0.88 | 1.94, 2.28 | 11 (14) | 0.97 | 1.85, 1.72 |
| BBS4 | Cre12.g548650 | 3 (5) | 1.00 | 1.31, 1.25 | 5 (4) | 1.04 | 1.96, 1.94 |
| BBS5 | Cre06.g267550 | 1 (3) | 1.09 | 1.39, 0.95 | 1 (1) | 1.00 | 0.68, 0.94 |
| BBS7 | Cre01.g043750 | 6 (16) | 1.01 | 1.68, 1.34 | 10 (11) | 0.98 | 2.06, 1.80 |
| BBS8 | Cre16.g666500 | 2 (7) | 1.02 | 1.52, 2.03 | 2 (2) | 1.01 | 2.17, 2.16 |
| BBS9 | Cre04.g219700 | 2 (8) | 0.92 | 1.50, 1.26 | 3 (2) | NQ | NQ |
| Other | |||||||
| FAP256 | Cre10.g431150 | 10 (23) | 0.98 | 1.29, 1.39 | 14 (17) | 0.95 | 1.49, 1.34 |
| RB47 | Cre01.g039300 | 6 (9) | 0.98 | 1.31, 1.51 | 6 (8) | 1.00 | 2.3, 2.12 |
| tRNA synthetase | Cre02.g143200 | 4 (6) | 1.09 | 1.42, 1.72 | 14 (13) | 1.04 | 1.32, 1.18 |
| HSP90A | Cre09.g386750 | 6 (12) | 1.00 | 1.42, 1.46 | 8 (13) | 1.00 | 1.47, 1.38 |
| ABC4 | Cre04.g222700 | 13 (19) | 1.01 | 1.44, 1.35 | 42 (48) | 1.06 | 1.32, 1.25 |
| GDP-d-mannose phosphorylase | Cre16.g672800 | 3 (3) | 0.94 | 1.61, 1.56 | 2 (4) | 0.99 | 1.63, 1.50 |
| GST | Cre16.g682725 | 4 (10) | 1.02 | 1.71, 1.83 | 6 (7) | 1.03 | 1.47, 1.70 |
| FAP295 | Cre16.g663200 | 41 (138) | 1.03 | 1.79, 1.71 | 44 (61) | 1.02 | 1.89, 1.71 |
| PRX2 | Cre02.g114600 | 17 (56) | 1.00 | 1.95, 2.54 | 33 (47) | 0.98 | 1.57, 1.45 |
| FAP179/GST | Cre17.g742300 | 17 (45) | 1.02 | 2.08, 2.42 | 21 (24) | 0.93 | 3.35, 3.30 |
| ICL1 | Cre06.g282800 | 25 (102) | 1.09 | 2.62, 2.62 | 93 (86) | 0.97 | 2.53, 2.30 |
| Unknown | Cre05.g239500 | 25 (45) | 1.02 | 2.30, 1.68 | 32 (38) | 0.89 | 5.52, 5.19 |
Peptides refers to the number of peptides identified at 95% confidence and the number of peptides used for iTRAQ quantification. Both WT and mutant samples were analyzed in duplicate. WT/WT ratios typically varied <10%. Mutant/WT ratios that were statistically significant (p < 0.05) are shown in bold type. NQ = not quantified.