Table I. Selected IP-MS results from LKP2, FKF1, and ZTL decoys.
At left, the LKP2 and FKF1 decoy immunoprecipitations were harvested at ZT18 under long-day conditions and from the ZTL decoy immunoprecipitation at ZT18 under 12-h-light/12-h-dark conditions. Corresponding full interactor lists are available in Supplemental Table S3. At right, IP-MS results are shown from ZTL decoy immunoprecipitations at 3 h before (ZT9) and after (ZT15) dusk under 12-h-light/12-h-dark diurnal conditions and at 3 h after subjective dusk in continuous light (ZT15-LL). Corresponding full interactor lists are available in Supplemental Table S5.
| Locus | Protein Name | Total Spectral Counts (SAINT Score, SAINT P Value)a | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| LKP2 Decoy ZT18 (LD) | FKF1 Decoy ZT18 (LD) | ZTL Decoy ZT18 (LD) | Wild Typeb | 35S:: FLAG-His-GFPc | ZTL Decoy ZT9 (LD) | ZTL Decoy ZT15 (LD) | ZTL Decoy ZT15 (LL) | Wild Typeb | 35S:: FLAG-His-GFPc | ||
| Bait | |||||||||||
| AT2G18915 | LKP2 | 1,412 | 29 (1*) | 82 (1**) | 0 | 0 | 75 (1**) | 70 (1**) | 74 (1**) | 0 | 0 |
| AT1G68050 | FKF1 | 0 | 2,855 | 0 | 128 | 0 | 0 | 0 | 0 | 0 | 0 |
| AT5G57360 | ZTL | 34 (1*) | 108 (1**) | 439 | 0 | 0 | 466 | 565 | 503 | 0 | 10 |
| Regulatory partners | |||||||||||
| AT1G22770 | GI | 129 (1**) | 265 (1**) | 218 (1**) | 0 | 0 | 250 (1**) | 300 (1**) | 387 (1**) | 0 | 0 |
| AT5G56010 | HSP90.3 | 221 (1**) | 314 (1**) | 466 (1**) | 0 | 0 | 299 (0.5) | 357 (0.5) | 368 (0.5) | 0 | 0 |
| AT5G56000 | HSP90.4 | 192 (1*) | 266 (1*) | 380 (1**) | 6 | 3 | 11 (0.07) | 79 (0.5) | 6 (0) | 18 | 0 |
| Transcription factors | |||||||||||
| AT5G61380 | TOC1 | 74 (1**) | 0 | 28 (1*) | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AT5G24470 | PRR5 | 55 (1**) | 0 | 0 | 0 | 0 | 0 | 0 | 9 (0.5) | 0 | 0 |
| AT5G39660 | CDF2 | 0 | 6 (1) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AT1G72010 | TCP22 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 41 (0.5) | 0 | 0 |
| AT5G08330 | CHE (TCP21) | 0 | 0 | 0 | 0 | 0 | 0 | 25 (0.5) | 17 (0.5) | 0 | 0 |
| AT5G52660 | RVE6 | 6 (1) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Transcription regulators | |||||||||||
| AT3G26640 | LWD2 | 0 | 0 | 0 | 0 | 0 | 26 (0.5) | 37 (0.5) | 34 (0.5) | 0 | 0 |
| AT3G20810 | JMJD5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 24 (0.5) | 0 | 0 |
| AT1G15750 | TPL | 0 | 11 (0.98) | 0 | 9 | 0 | 62 (1**) | 0 | 8 (0.5) | 0 | 0 |
| AT2G19520 | FVE (MSI4) | 0 | 5 (1) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Deubiquitinating enzymes | |||||||||||
| AT5G06600 | UBP12 | 97 (1) | 23 (0) | 162 (1) | 56 | 0 | 156 (0.98*) | 240 (1*) | 193 (0.99*) | 25 | 22 |
| AT3G11910 | UBP13 | 48 (0.99) | 0 | 136 (1) | 34 | 0 | 89 (1*) | 112 (1*) | 89 (1*) | 0 | 0 |
The SAINT scores represent the confidence of protein interactions. The score is from 1 to 0, in which 1 suggests a higher confidence interaction. The SAINT P values are represented by asterisks (*, P ≤ 0.05 and **, P ≤ 0.01). bThe spectral counts of CCA1p:Luciferase and Col-0 were summed to generate the total spectral counts in the Wild Type column. cThe spectral counts from two biological replicates of 35S::FLAG-His-GFP were summed to generate the total spectral counts in the 35S::FLAG-His-GFP column.