Table 2.
Summary of the features the CLPC1-trapped proteins without known functions and their Arabidopsis homologs
| Protein id | Abbreviated name | This study in Table 1 or prior studya,b | Curated location (PPDB) | Predicted locationc | Total AdjSPC (this study)d | Average CLPC1-TRAP/CLPC1-WTe | Conclusion coevolution ERC (Fig. 5) (in bold, most pronounced) | Conclusions from mRNA coexpression (Figs. 6 and 7) (in bold, most pronounced) | PeptideAtlas # experiments (Fig. 8) | Conclusion for protein abundance and CLPC1 interaction and trapping |
|---|---|---|---|---|---|---|---|---|---|---|
| AT1G23180.1 | ARM | Table 1 | plastid | C | 78 | 16.6 | coevolution of ARM with EXE2 and with CLP core and CLPC1/2 | in module enriched for plastid proteostasis | 108 | Abundant protein and enriched in trap |
| AT1G33780.1 | DUF179-1 | plastid stroma | C | 217 | 1.3 | coevolution with UVR2/3 and DUF760-1 | some connectivity | 90 | Abundant interactor to ClpC1, independent of trapping | |
| AT3G19780.1 | DUF179-2 | unknown | S | 0 | nd | Coevolution of DUF760-3, DUF760-7 and DUF179-2 | poor connectivity | 38 | Moderately abundant, but not a ClpC1 interactor. Perhaps not located in the plastid | |
| AT3G29240.1 | DUF179-3 | Table 1 (b3) | plastid stroma | C | 427 | 4.6 | coevolution with DUF179-2 | module enriched for UBI/ATG degradation | 35 | Moderately abundant interactor, enriched in trap |
| AT5G52960.1 | DUF3143 | a,b13 | plastid stroma | C | 19 | 2.4 | DUF760-2, DUF760-3 and DUF3143 showed many connections to the tight CLPPRT cluster | 74 | Abundant, but not a strong ClpC1 interactor | |
| AT1G32160.1 | DUF760-1 (clade 1) | Table 1 | plastid | C | 23 | 4.4 | Coevolution with DUF179–1 and CLPT1/2 | small module of UVR1, DUF760-1, DUF760-5, DUF760-7, DUF760-8. Direct edges between DUF760-1, DUF760-7, DUF760-8 and HUGZ-1 | 115 | Abundant, but not a strong ClpC1 interactor, but enriched in trap |
| AT1G48450.1 | DUF760-2 (clade 1) | Table 1 (b1) | plastid | C | 600 | 32.1 | DUF760-2, DUF760-3, and DUF3143 showed many connections to the tight CLPPRT cluster | 18 | Low abundance, highly enriched in trap | |
| AT1G63610.1 | DUF760-3 (clade 2) | b4 | plastid | C | 821 | 2.1 | Coevolution of DUF760-3, DUF760-7 and DUF179-2 | DUF760-2, DUF760-3, and DUF3143 showed many connections to the tight CLPPRT cluster; direct edge with HugZ-3 | 105 | Abundant, ClpC1 interactor, not strongly dependent on trapping |
| AT2G14910.1 | DUF760-4 (clade 2) | Table 1 (b5) | plastid | C | 103 | 43.0 | some connectivity | 12 | Low abundance, highly enriched in trap | |
| AT3G07310.1 | DUF760-5 (clade 3) | unknown | M | 6 | 4.5 | module of UVR1, DUF760-1, DUF760-5; direct edges with UVR1,3 and DUF760-8 | 3 | Very low abundance, enriched in trap | ||
| AT3G17800.1 | DUF760-6 (clade 1) | Table 1 (b2) | plastid | C | 180 | 142.2 | small module of CLPD and DUF760-6 | 36 | Moderately abundant interactor, highly enriched in trap | |
| AT5G14970.1 | DUF760-7 (clade 2) | unknown | C | 13 | 10.9 | Coevolution with DUF760-3, DUF179-2 and CLPD | small module of UVR1, DUF760-1, DUF760-5, DUF760-7, DUF760-8. Direct edges between DUF760-1, DUF760-7, DUF760-8, and UVR1 | 2 | Very low abundance, enriched in trap | |
| AT5G48590.1 | DUF760-8 (clade 3) | unknown | C | 0 | nd | small module of UVR1, DUF760-1, DUF760-5, DUF760-7, DUF760-8. Direct edges between DUF760-1, DUF760-7, DUF760-8 and HUGZ-1 | 0 | protein not detected; pseudogene? | ||
| AT4G33630.1 | EXE1 | Table 1 | thylakoid | C | 194 | 178.5 | some connectivity | 84 | Abundant interactor highly enriched in trap | |
| AT1G27510.1 | EXE2 | Table 1 (b9) | thylakoid | C | 233 | 215.7 | Coevolution with ARM | direct edges with DUF760-2 and ClpX2 | 74 | Abundant interactor highly enriched in trap |
| AT5G24060.1 | HugZ-1 | Table 1 (b16) | plastid | C | 97.7 | 83.5 | Coevolution with CLPP3,4,5 and EXE1 | Direct edges between DUF760-1, DUF760-7, DUF760-8 and HUGZ-1. HugZ1- direct edge to CLPP3 and CLPP5 | 65 | Abundant interactor to ClpC1, highly enriched in trap |
| AT3G49140.1 | HugZ-2 | plastid | C | 11.3 | 10.9 | Coevolution with CLPP3,4,5 and EXE1 | direct edge with DUF760-3 | 108 | Abundant, but not a strong ClpC1 interactor, but enriched in trap | |
| AT3G59300.1 | HugZ-3 | plastid | C | 9 | 9.4 | coevolution with CLPF and CLPP1, P3, R2, R4,T1/2, CLPS1, DUF760-3 and ARM | poor connectiviy | 6 | Very low abundance, enriched in trap | |
| AT3G09250.1 | UVR1 | plastid stroma | C | 0 | nd | small module of UVR1, DUF760-1, DUF760-5, DUF760-7, DUF760-8; direct edges of UVR1 to DUF760-4,7, CLPP3,5 | 59 | Abundant, but not a ClpC1 interactor | ||
| AT1G75380.1 | UVR2 | Table 1 | plastid | C | 34 | 28.4 | Coevolution with DUF179–1 | UBI/ATG degradation module of UVR2, UVR3 and DUF760-5. Direct edge between UVR2 and UVR3 | 50 | moderately abundant interactor, highly enriched in trap |
| AT1G19660.1 | UVR3 | Table 1 | plastid | C | 20 | 16.1 | Coevolution with DUF179-1 | UBI/ATG degradation module of UVR2, UVR3 and DUF760-5. Direct edge between UVR2 and UVR3 | 45 | Moderately abundant interactor, enriched in trap |
| AT5G66050.1 | UVR4 | Table 1 | plastid | C | 60 | 46.7 | poor connectivity | 8 | Low abundance, highly enriched in trap |
a
ClpS1 interactor, Nishimura et al. (2013).
b
Trapped in ClpC1, Montandon et al. (2019); # indicates abundance rank.
c
Predicted subcellular location by TargetP. C, chloroplast; M, mitochondria; S, secreted with signal peptide.
d
Total AdjSPC, adjusted matched MS/MS spectra.
e
Average TRAP/WT NadjSPC (input 1.10–5 for zero).