Table 1. MS analysis of the proteins... | Rockefeller University Press

Table 1.

MS analysis of the proteins associated with the PF16-related complex within the ciliary CA

Protein	Molecular weight (kD)	Phytozome gene number	Unique peptides in different strains (n)^a						Quantification ratio^a
Protein	Molecular weight (kD)	Phytozome gene number	WT	pf16	fap76-1	fap81	fap92	fap216	pf16/WT	fap76-1/WT	fap81/WT	fap92/WT	fap216/WT
Proteins traditionally assigned to the C1 microtubule^b
PF16 (C1)	50	Cre09.g394251	25	0	21	26	26	27	0	0.86	0.89	1.18	1.08
PF6 (C1a)	237	Cre10.g434400	99	47	98	103	107	100	0.03	0.57	0.95	1.09	1.02
FAP101/C1a-86 (C1a)	86	Cre02.g112100	24	7	24	25	23	24	0.02	0.72	0.61	1.17	0.93
FAP119/C1a-34 (C1a)	34	Cre06.g256450	13	8	11	12	13	13	0.04	0.54	0.73	1.4	1.01
FAP114/C1a-32 (C1a)	32	Cre09.g389282	16	6	16	15	17	15	0.08	0.84	0.6	0.91	0.98
FAP227/C1a-18 (C1a)	20	Cre17.g729850	17	6	17	17	16	18	0.04	1.08	0.6	0.96	0.96
PP1C (C1)	35	Cre06.g292550	14	9	15	14	15	13	0.2	0.52	0.94	0.96	0.28
FAP221 (C1d)	104	Cre11.g476376	40	36	38	40	45	45	0.47	0.67	1.05	1.17	0.84
FAP54 (C1d)	318	Cre12.g518550	108	80	95	119	106	115	0.36	0.54	1.13	0.92	0.92
Novel PF16-associated proteins^c
FAP76	162	Cre09.g387689	60	22	11	52	64	63	0.05	0	0.72	0.89	1.09
FAP81	172	Cre06.g296850	54	2	50	0	56	52	0	0.49	0	1.3	1.01
FAP92	150	Cre13.g562250	51	5	41	38	50	52	0	0.31	0.37	0.88	1.03
FAP216	79	Cre12.g497200	23	2	21	5	24	0	0	0.69	0.07	1.14	0
FAP105	31	Cre12.g511750	27	0	29	27	28	27	0	0.87	1.07	1.23	1.24
FAP108	22	Cre06.g297200	11	11	8	11	12	11	0.79	9.98	0.87	0.77	1.63
FAP305/MOT17	28	Cre11.g482300	12	12	12	13	13	11	0.06	0.59	2.44	1.65	0.77
FAP412	57	Cre12.g497450	24	0	29	24	25	24	0	0.71	1.24	1.38	0.99

Protein	Molecular weight (kD)	Phytozome gene number	Unique peptides in different strains (n)^a						Quantification ratio^a
Protein	Molecular weight (kD)	Phytozome gene number	WT	pf16	fap76-1	fap81	fap92	fap216	pf16/WT	fap76-1/WT	fap81/WT	fap92/WT	fap216/WT
Proteins traditionally assigned to the C1 microtubule^b
PF16 (C1)	50	Cre09.g394251	25	0	21	26	26	27	0	0.86	0.89	1.18	1.08
PF6 (C1a)	237	Cre10.g434400	99	47	98	103	107	100	0.03	0.57	0.95	1.09	1.02
FAP101/C1a-86 (C1a)	86	Cre02.g112100	24	7	24	25	23	24	0.02	0.72	0.61	1.17	0.93
FAP119/C1a-34 (C1a)	34	Cre06.g256450	13	8	11	12	13	13	0.04	0.54	0.73	1.4	1.01
FAP114/C1a-32 (C1a)	32	Cre09.g389282	16	6	16	15	17	15	0.08	0.84	0.6	0.91	0.98
FAP227/C1a-18 (C1a)	20	Cre17.g729850	17	6	17	17	16	18	0.04	1.08	0.6	0.96	0.96
PP1C (C1)	35	Cre06.g292550	14	9	15	14	15	13	0.2	0.52	0.94	0.96	0.28
FAP221 (C1d)	104	Cre11.g476376	40	36	38	40	45	45	0.47	0.67	1.05	1.17	0.84
FAP54 (C1d)	318	Cre12.g518550	108	80	95	119	106	115	0.36	0.54	1.13	0.92	0.92
Novel PF16-associated proteins^c
FAP76	162	Cre09.g387689	60	22	11	52	64	63	0.05	0	0.72	0.89	1.09
FAP81	172	Cre06.g296850	54	2	50	0	56	52	0	0.49	0	1.3	1.01
FAP92	150	Cre13.g562250	51	5	41	38	50	52	0	0.31	0.37	0.88	1.03
FAP216	79	Cre12.g497200	23	2	21	5	24	0	0	0.69	0.07	1.14	0
FAP105	31	Cre12.g511750	27	0	29	27	28	27	0	0.87	1.07	1.23	1.24
FAP108	22	Cre06.g297200	11	11	8	11	12	11	0.79	9.98	0.87	0.77	1.63
FAP305/MOT17	28	Cre11.g482300	12	12	12	13	13	11	0.06	0.59	2.44	1.65	0.77
FAP412	57	Cre12.g497450	24	0	29	24	25	24	0	0.71	1.24	1.38	0.99

Missing or significantly reduced unique peptide numbers (less than half of WT) or ratios (<0.2) are highlighted in bold; MS analysis of pf16 and fap76-1 was originally from Zhao et al. (2019); quantification ratios of pf16/WT and fap76-1/WT were estimated by the IBAQ method (Schwanhäusser et al., 2011); fap81/WT, fap92/WT, and fap216/WT were estimated by the MIC sin value (Trudgian et al., 2011).

Proteins traditionally assigned to the C1 microtubule in general (C1) or specifically to the C1a or C1d projection, as indicated.

Proteins that were identified in sucrose gradient analyses of pf28 and pf28;pf16 samples and also predicted to be associated with C1 (Zhao et al., 2019) are included here.

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