Table 1.
Fifty-nine proteins that are enriched in the CLPC1-TRAP compared with CLPC1-WTa
| Protein identifier | Montandon et al. (2019) enriched in ClpC1-TRAPb | Protein annotation | Function | Observed in # bio reps of TRAP (out of 3) | Total AdjSPC (all 18 exp.) | AdjSPC WT (all) | AdjSPC TRAP (all) | Average TRAP/WT (based on NadjSPC)c | p-valued |
|---|---|---|---|---|---|---|---|---|---|
| ATCG00190.1 | rpoB RNA polymerase (PEP) beta | DNA–RNA | 3 | 35 | 3 | 32 | 12.6 | 0.01500 | |
| ATCG00180.1 | rpoC1 RNA polymerase (PEP) beta | DNA–RNA | 3 | 41 | 3 | 38 | 16.4 | 0.00820 | |
| AT5G46580.1 | pentatricopeptide repeat (PPR) protein SOT1 | DNA–RNA | 3 | 82 | 15 | 67 | 4.0 | 0.02370 | |
| AT5G26742.1 | DEAD box RNA helicase (RH3) (EMB1138; globular stage) | DNA–RNA | 3 | 244 | 21 | 223 | 12.6 | 0.00010 | |
| AT4G36390.1 | tRNA/rRNA methyltransferase | DNA–RNA | 3 | 29 | 2 | 27 | 14.9 | 0.01470 | |
| AT4G31210.1 | DNA-directed topoisomerase—dually targeted mitochondria & plastid | DNA–RNA | 3 | 30 | 4 | 26 | 9.2 | 0.02230 | |
| AT4G09730.1 | DEAD box RNA helicase, RH39 (nara12) 23S rRNA processing | DNA–RNA | 3 | 27 | 1 | 26 | 26.4 | 0.01710 | |
| AT3G48500.1 | nucleoid protein (pTAC10) | DNA–RNA | 3 | 54 | 6 | 48 | 10.8 | 0.00770 | |
| AT3G10270.1 | DNA gyrase B1—dual targeted plastids and mitochondria | DNA–RNA | 3 | 24 | 4 | 20 | 6.7 | 0.04090 | |
| AT3G04260.1 | SAP domain–containing protein (pTAC3) | DNA–RNA | 3 | 58 | 5 | 53 | 9.9 | 0.00910 | |
| AT3G02060.1 | DEAD/DEAH box helicase | DNA–RNA | 3 | 18 | 0 | 18 | 13.9 | 0.02500 | |
| AT2G39670.1 | tRNA/rRNA methyltransferase | DNA–RNA | 2 | 21 | 0 | 21 | 16.5 | 0.01910 | |
| AT1G74850.1 | pentatricopeptide (PPR) repeat (pTAC2) | DNA–RNA | 3 | 25 | 0 | 25 | 19.7 | 0.01400 | |
| AT1G30680.1 | DNA primase-helicase (dual chloro-mito) | DNA–RNA | 3 | 37 | 2 | 35 | 17.1 | 0.01060 | |
| AT1G02150.1 | pentatricopeptide repeat (PPR) protein (6 or 7 repeats). Coexpresses with RNAse E/G At2g04270 | DNA–RNA | 3 | 123 | 26 | 97 | 3.7 | 0.01700 | |
| AT5G67030.1 | zeaxanthin epoxidase (ZEP) | metabolism | 3 | 62 | 13 | 49 | 3.2 | 0.04950 | |
| AT5G64840.1 | ABC transporter family protein (ATGCN5) | metabolism | 3 | 49 | 2 | 47 | 15.6 | 0.00750 | |
| AT5G60600.1 | 4-hydroxy-3-methylbutyl diphosphate synthase (HDS) | metabolism | 3 | 199 | 34 | 165 | 4.8 | 0.00400 | |
| AT5G52920.1 | pyruvate kinase-2 (typically homotetramer) | metabolism | 3 | 31 | 5 | 26 | 5.7 | 0.04290 | |
| AT5G45930.1 | Mg-protoporphyrin IX chelatase - CHLI-2 | metabolism | 3 | 24 | 3 | 21 | 8.3 | 0.03680 | |
| AT5G13110.1 | glucose-6-phosphate dehydrogenase 2 (G6PD2) | metabolism | 3 | 26 | 3 | 22 | 7.2 | 0.04170 | |
| AT4G30720.1 | pigment defective 327 (PDE327) - oxidoreductase | metabolism | 3 | 43 | 9 | 34 | 4.1 | 0.05010 | |
| AT4G22240.1 | fibrillin 1b (FBN1b) | metabolism | 3 | 32 | 0 | 32 | 25.1 | 0.00790 | |
| AT4G21990.1 | 8 | 5′-adenylylsulfate reductase-3 (APR3) | metabolism | 3 | 81 | 4 | 77 | 24.7 | 0.00120 |
| AT4G15560.1 | 1-deoxy-D-xylulose 5-phosphate synthase (DXS1) | metabolism | 3 | 66 | 8 | 58 | 6.4 | 0.01250 | |
| AT4G11570.1 | 6 | ARPP phosphatase cpFHy2 or PYRP2 (high in clpc1, clps1) | metabolism | 3 | 84 | 0 | 84 | 68.9 | 0.00040 |
| AT4G04610.1 | 8 | 5′-adenylylsulfate reductase-1 (APR1) | metabolism | 3 | 218 | 24 | 194 | 8.5 | 0.00040 |
| AT4G04020.1 | fibrillin 1a (FBN1a) | metabolism | 3 | 74 | 14 | 60 | 3.7 | 0.02860 | |
| AT3G44720.1 | arogenate dehydratase 4 (ADT4) | metabolism | 3 | 34 | 1 | 33 | 50.3 | 0.00730 | |
| AT3G21200.1 | GluTR binding protein (GBP or PGR7) | metabolism | 3 | 24 | 3 | 21 | 5.2 | 0.06020 | |
| AT3G10970.1 | 7 | PYRP2-related Haloacid dehalogenase (HAD) hydrolase | metabolism | 2 | 54 | 0 | 54 | 43.1 | 0.00200 |
| AT3G07630.1 | arogenate dehydratase 2 (ADT2) | metabolism | 3 | 25 | 4 | 21 | 4.3 | 0.07420 | |
| AT2G44530.1 | ribose-phosphate pyrophosphokinase | metabolism | 3 | 38 | 5 | 33 | 4.8 | 0.04410 | |
| AT2G35390.1 | ribose-phosphate pyrophosphokinase 1/phosphoribosyl diphosphate synthetase 1 (PRSI) | metabolism | 3 | 28 | 3 | 25 | 8.5 | 0.03000 | |
| AT2G29630.1 | thiamine biosynthesis (thiC family) | metabolism | 3 | 40 | 5 | 35 | 5.7 | 0.02780 | |
| AT1G62180.1 | 8 | 5′-adenylylsulfate reductase-2 (APR2) | metabolism | 3 | 270 | 26 | 245 | 10.2 | 0.00010 |
| AT1G36180.1 | acetyl-CoA carboxylase - ACC2 | metabolism | 3 | 147 | 0 | 147 | 137.4 | 0.00000 | |
| AT5G51110.1 | Rubisco assembly factor 2 (RAF2) | proteostasis | 2 | 33 | 8 | 25 | 3.4 | 0.09030 | |
| AT5G51070.1 | CLPD | proteostasis | 3 | 575 | 111 | 464 | 3.8 | 0.00040 | |
| AT5G42390.1 | stromal processing peptidase (SPP) | proteostasis | 2 | 63 | 10 | 53 | 5.6 | 0.02050 | |
| AT5G20720.1 | CPN20 | proteostasis | 3 | 89 | 9 | 80 | 10.3 | 0.00230 | |
| AT4G25370.1 | CLPT1 | proteostasis | 3 | 24 | 0 | 24 | 18.3 | 0.01590 | |
| AT4G12060.1 | CLPT2 | proteostasis | 3 | 38 | 6 | 32 | 5.4 | 0.03320 | |
| AT3G48870.1 | CLPC2 | proteostasis | 3 | 1527 | 170 | 1356 | 6.3 | 0.00000 | |
| AT2G44650.1 | 10 | CPN10–1 | proteostasis | 3 | 19 | 0 | 19 | 17.3 | 0.01810 |
| AT2G03390.1 | CLPF (adaptor) | proteostasis | 3 | 76 | 10 | 66 | 5.6 | 0.01250 | |
| AT1G35340.1 | LON-domain protein 2 (LON-like2) | proteostasis | 3 | 25 | 3 | 22 | 7.9 | 0.03690 | |
| AT5G66050.1 | UVR4 (DUF151 and UVR domain) | unknown | 3 | 60 | 0 | 60 | 46.7 | 0.00150 | |
| AT5G24060.1 | 16 | HugZ-1 | unknown | 3 | 98 | 0 | 98 | 83.5 | 0.00020 |
| AT4G33630.1 | Executer 1 (EXE1) | unknown | 3 | 194 | 0 | 194 | 178.5 | 0.00000 | |
| AT3G29240.1 | 3 | DUF179–3 | unknown | 3 | 427 | 73 | 354 | 4.6 | 0.00050 |
| AT3G17800.1 | 2 | DUF760–5 | unknown | 3 | 180 | 1 | 179 | 142.2 | 0.00000 |
| AT2G14910.1 | 5 | DUF760–4 | unknown | 3 | 103 | 2 | 101 | 43.0 | 0.00040 |
| AT1G75380.1 | UVR2 (DUF151 and UVR domain) | unknown | 2 | 34 | 1 | 33 | 28.4 | 0.01070 | |
| AT1G48450.1 | 1 | DUF760–2 | unknown | 3 | 600 | 16 | 584 | 32.1 | 0.00000 |
| AT1G32160.1 | DUF760–1 | unknown | 2 | 23 | 4 | 19 | 4.4 | 0.08430 | |
| AT1G27510.1 | 9 | Executer 2 (EXE2) | unknown | 3 | 233 | 0 | 233 | 215.7 | 0.00000 |
| AT1G23180.1 | armadillo repeat protein (ARM) | unknown | 3 | 78 | 4 | 74 | 16.6 | 0.00220 | |
| AT1G19660.1 | UVR3 (DUF151 and UVR domain) | unknown | 2 | 20 | 0 | 20 | 16.1 | 0.01990 |
a
At least 3-fold ratio of CLPC1-TRAP/CLPC1-WT based NadjSPC. All proteins have at least three independent peptides (different aa sequences). All proteins are localized to the plastid.
b
Montandon et al., 2019 JPR. Table 2 - enriched in ClpC1-TRAP - rank (1–17; 1 is most enriched).
c
trap/wt NadjSPC (input 1.10–5 for zero; this only happened for wt).
d
p-Value (normalized to ClpC1) (based on GLEE pVal NadjSPC).