Table 2.
Proteins Co-Purified by PCH1 AP-MS in elf4-2 and elf3-2, compared to WT. Proteins co-purified with PCH1 were identified from affinity purification coupled with mass spectrometry (AP-MS) analyses using 12L:12D grown, 10-day-old PCH1ox3 plants in either elf4-2 or elf3-2 mutant backgrounds harvested at ZT12.
| AGI number | Protein name | ELF3 AP-MSb | Exclusive unique peptide count/Percent coveragea | ||||||
|---|---|---|---|---|---|---|---|---|---|
| PCH1ox3 in WTc | PCH1ox3 in elf4-2 | PCH1ox3 in elf3-2 | |||||||
| rep1 | rep2 | rep3 | rep1 | rep2 | rep1 | rep2 | |||
| At2g16365 | PCH1d | Y | 30/73% | 41/85% | 37/79% | 29/77% | 34/78% | 42/82% | 36/82% |
| At2g18790 | phyB | Y | 46/69% | 47/65% | 41/60% | 47/70% | 31/46% | 42/63% | 40/56% |
| At5g35840 | phyC | Y | 31/44% | 23/28% | 25/29% | 30/43% | 13/16% | 20/28% | 15/18% |
| At4g16250 | phyD | Y | 22/47% | 19/34% | 20/38% | 20/42% | 12/25% | 20/37% | 16/30% |
| At4g18130 | phyE | Y | 41/55% | 40/52% | 45/60% | 42/57% | 37/50% | 43/55% | 40/53% |
| At1g09570 | phyA | Y | 31/46% | 36/49% | 35/45% | 32/47% | 24/34% | 34/49% | 27/38% |
| At2g37678 | FHY1 | N | 2/22% | 2/21% | 4/28% | —e | 3/21% | —e | 3/21% |
| At3g42170 | DAYSLEEPER | Y | 5/13% | — | 4/11% | 3/7% | 5/11% | 2/5% | —e |
| At1g09340 | CRB | Y | —e | —e | 4/17% | 2/9% | 5/22% | 3/13% | 3/13% |
| At5g43630 | TZP | Y | 9/15% | 6/12% | 12/23% | 4/7% | —e | 12/21% | 2/3% |
| At2g32950 | COP1 | Y | 7/15% | 8/16% | 8/18% | 3/7% | —e | 12/25% | 7/11% |
| At2g46340 | SPA1 | Y | 8/14% | 5/7% | 8/12% | 5/10% | 2/4% | 17/26% | 7/11% |
| At2g25930 | ELF3 | Y | 6/12% | 11/25% | 12/26% | 4/9% | 3/6% | — | — |
| At2g40080 | ELF4 | Y | —e | 4/60% | 3/42% | — | — | — | —e |
| At3g46640 | LUX | Y | 2/6% | —e | 4/15% | —e | — | — | — |
| At3g03940 | MLK2 | Y | —e | 2/6% | 2/6% | — | — | 2/4% | — |
| At1g15750 | TPL | N | —e | 3/3% | 4/5% | 2/3% | 3/3% | 4/5% | 4/5% |
| At1g47128 | RD21a | Y | —e | 3/8% | 2/4% | —e | 2/8% | 3/8% | —e |
| Also see Table 1—source data 1 | |||||||||
a All listed proteins match 99% protein threshold, minimum number peptides of 2 and peptide threshold as 95%. Proteins not matching the criteria were marked with "—".
b ELF3 AP-MS (Huang et al., 2015) was used for comparison.
c PCH1ox3 in WT is as shown in Table 1, for comparison with PCH1ox3 in elf4-2 and elf3-2.
d percent coverage for PCH1 is calculated using protein encoded by At2g16365.2.
e only one exclusive unique peptide was detected.