Table 1.
Overview of All 154 Identified Proteins in This Study
| Name and Functional Information | AGI | Triton X-114 2-DE | Na2CO3 2-DE | Acetone 1-DE | C/M 9:1 L 1-DE | C/M 9:1 U 1-DE | C/M 1:1 1-DE | C/M rest 1-DE | C/M 9:1 U+L 1-DE | C/M 1:1 RP-HPLC | Ref 1 | Ref 2 | Refs 3,4 | Ref 5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MITOCHONDRIAL (PREDICTED OR EXPERIMENTAL) | ||||||||||||||
| Similar to ATP synthase D chain | At3g52300 | 21-23 | x | |||||||||||
| Cytochrome c oxidase subunit 6b | At1g22450 | 89 | x | |||||||||||
| Cytochrome c oxidase sub Vb | At3g15640 | x | ||||||||||||
| DegP11 protease | At3g16540 | x | ||||||||||||
| NO PREDICTED cTP OR mTP | ||||||||||||||
| Expressed protein | At4g39730 | 52,53 | ||||||||||||
| OEP6 | At3g63160 | x | x,# | x | ||||||||||
| OM24 | At3g52230 | x | # | x | ||||||||||
| Fatty acid elongase-like prot | At3g23840 | x | ||||||||||||
| Organic anion transporter-like p | At3g20660 | x | ||||||||||||
| Carbonic anhyd homol | At4g20990 | x | ||||||||||||
| cTP ‘STROMA’ | ||||||||||||||
| RUBISCO activase | At2g39730 | x | x | x,# | x | |||||||||
| lipoxygenase AtLOX2 | At3g45140 | x | x | |||||||||||
| Cpn21 | At5g20720 | 44 | Table 1 | x | ||||||||||
| 30 S ribsomal protein S6 | At1g64510 | 53 | x | |||||||||||
| 30S Ribosomal p S5 Isolog L13 | At2g33800 | x | Table 2 | |||||||||||
| 50S ribosomal protein L12-A | At3g27830 | 7(1),30(8) | 31(3),32(4),52(5),53(6),56(7) | x(1) | x(1) | |||||||||
| 50S ribosomal protein L12-C | At3g27850 | 7(1),30(8) | 31(3),32(4),52(5),53(6),56(7) | x(1) | x | x(1) | Table 2 | |||||||
| RNA binding protein CP29 B′ | At2g37220 | 48 | 35-39 | Table 2 | x | |||||||||
| RNA binding protein CP31 | At4g24770 | Table 2 | x | |||||||||||
| PSRP-2 small | At3g52150 | 42 | 17,20,118,120 | Table 2 | x | |||||||||
| PSRP-3 small | At1g68590 | 18 | ||||||||||||
| PSRP-5 large | At3g56910 | 8 | x | |||||||||||
| NEW cTP PROTEIN | ||||||||||||||
| Putative protein - also in CN-PAGE -stroma | At5g14910 | 44 | x | |||||||||||
| Similar to unknown protein (pir‖S75584) | At5g58260 | x | x | |||||||||||
| Putative protein | At4g13200 | x | x | |||||||||||
| Expressed protein | At5g42765 | x | ||||||||||||
| Expressed protein - Rieske [2Fe-2S] domain | At1g71500 | x | x | |||||||||||
| Expressed protein | At2g26340 | x | ||||||||||||
| ycf37 Synechocystis -stromal predicted | At2g23670 | 3,4,5 | 70 | x | ||||||||||
| Stromal predicted - DnaJ central domain (4 repeats) | At2g34860 | x | ||||||||||||
| Expressed protein | At5g44650 | 32 | x | |||||||||||
| Thylakoid phosphoprotein | At3g47070 | 203 | x | x | x | |||||||||
| Expressed protein | At2g46820 | x | x | x | x | x | ||||||||
| Expressed protein - Rhodanese-like domain | At4g01050 | x | x | x | ||||||||||
| Putative protein | At5g55710 | x | ||||||||||||
| Putative protein | At4g22890 | x | ||||||||||||
| Expressed protein | At1g74730 | x | x | |||||||||||
| Putative protein - Synech.pir‖S76575 - YGGT family | At5g36120 | x | ||||||||||||
| Expressed protein | At4g01150 | x | x | x | x | x | ||||||||
| Expressed protein | At1g52220 | x | x | |||||||||||
| Putative protein | At3g51510 | x | ||||||||||||
| Expressed protein | At3g17930 | x | ||||||||||||
| Hypothetical protein | At1g73885 | x | ||||||||||||
| Putative protein | At5g23060 | x | ||||||||||||
| Expressed protein | At5g08050 | x | x | x | ||||||||||
| Hp 17 | At1g42960 | x | # | |||||||||||
| Expressed protein - Rubredoxin and PDZ domain | At5g17170 | x | x | |||||||||||
| Putative protein | At5g16660 | x | x | |||||||||||
| Rubredoxin - homolog in Synechococcus | At1g54500 | x | x | |||||||||||
| PHOTOSYSTEM II | ||||||||||||||
| psbA D1 | Atcg00020 | x | x | x | ||||||||||
| psbB CP47 | Atcg00680 | x | x | x | x | |||||||||
| psbC CP43 | Atcg00280 | x | x | x | x | |||||||||
| psbD D2 | Atcg00270 | x | x | x | x | x | ||||||||
| psbE cytb559a | Atcg00580 | x | x | x | x | x | x | |||||||
| psbF cytb559b | Atcg00570 | x | x | x | x | |||||||||
| psbH-phospho | Atcg00710 | x | x | x | x | x | ||||||||
| psbL | Atcg00560 | x | ||||||||||||
| psbO OEC33 | At5g66570 | 10,13-16(25),39,40 | 12(1),13(2),91,95,117 | x(2) | x | x(2) | Table 1 | x | ||||||
| psbO OEC33-like | At3g50820 | 10,13-16(25) | 12(1),13(2) | x(2) | x | x(2) | Table 1 | x | ||||||
| psbP OEC23 Tat ITP | At2g30790 | x(3) | x | |||||||||||
| psbP OEC23 Tat ITP | At1g06680 | 92-94 | x,x(3) | Table 1 | x | x | ||||||||
| OEC23-like Tat ITP | At4g15510 | 19 | Table 1 | x | ||||||||||
| OEC23-like Tat ITP | At2g39470 | x | Table 1 | |||||||||||
| OEC23-like Tat ITP | At1g76450 | 65 | Table 1 | x | ||||||||||
| psbQ OEC16 Tat ltp | At4g21280 | 212-215,218 | x | Table 1 | x | |||||||||
| psbQ OEC16-like Tat ITP | At4g05180 | 212,215 | x | x | Table 1 | x | ||||||||
| PsbQ domain TAT ITP | At1g14150 | x | ||||||||||||
| PsbQ domain Tat ITP | At3g01440 | x | ||||||||||||
| psbR | At1g79040 | x | x | |||||||||||
| psbS | At1g44575 | x | x | x | x | |||||||||
| psbT/ycf8 | Atcg00690 | x | ||||||||||||
| psbTn-2 | At1g51400 | x | x | |||||||||||
| psbW - ‘LTP’ but spontaneous | At2g30570 | x | ||||||||||||
| psbW -like | At4g28660 | 2 | ||||||||||||
| psbX- ITP but spontaneous | At2g06520 | x | x | |||||||||||
| psbY1+2 | At1g67740 | x | ||||||||||||
| psbZ'ycf9 | Atcg00300 | x | ||||||||||||
| PSII Lumen Tat ITP | At1g03600 | 68,206,207 | x | x | Table 1 | |||||||||
| LHCII PROTEINS | ||||||||||||||
| LHCII-1.1 - 100% identical to lhcb-1.2,3-mature | At1g29910 | x(1) | x(3) | x(1) | x(5) | x(4) | x(1) | |||||||
| LHCII-1.2 - 100% identical to lhcb-l.l,3-mature | At1g29920 | x(1) | x(3) | x(1) | x(5) | x,x(4) | x(1) | |||||||
| LHCII-1.3 - 100% identical to lhcb-1.1,2 -mature | At1g29930 | x(1) | x(3) | x(1) | x(5) | x(4) | x(1) | |||||||
| LHCII-1.4 | At2g34430 | x(2) | x,x(2) | x,x(2) | x,x(2) | x(4) | x(2) | x | x | |||||
| LHCII-1.5 | At2g34420 | x(2) | x(2) | x(2) | x(2) | x(4) | x(2) | |||||||
| LHCII-2.1 | At2g05100 | x(3) | x(5) | x(3) | x(7) | x(4) | ||||||||
| LHCII-2.2 | At2g05070 | x(3) | x(5) | x(3) | x(7) | x,x(4) | ||||||||
| LHCII-2.4 | At3g27690 | x(3) | x(5) | x(3) | x(7) | x,x(4) | x | |||||||
| LHCII-3 | At5g54270 | x | x | x | x | x | x | |||||||
| LHCII-4.1-CP29 | At5g01530 | x | x | x | x | x | ||||||||
| LHCII-4.2 - CP29 | At3g08940 | x | x | x | x | x | ||||||||
| LHCII-4.3 -CP29 | At2g40100 | x | x | x | ||||||||||
| LHCII-5 - CP26 | At4g10340 | x | x | x | x | x | x | |||||||
| LHCII-6 - CP24 | At1g15820 | x | x | x | x | x | x | x | ||||||
| cytb6f COMPLEX | ||||||||||||||
| petA - cytochrome f (cleavable LTP of 35 aa) | Atcg00540 | x | x | x | ||||||||||
| petB - Cytochrome b6 | Atcg00720 | x | x | x | x | |||||||||
| petC - Rieske Fe-S protein - LTP | At4g03280 | 1#,31,32# | x | x | x | x | ||||||||
| petD - subIV | Atcg00730 | x | x | x | x | |||||||||
| ELECTRON TRANSPORT | ||||||||||||||
| FNR-1 | At5g66190 | 10,89 | x | x | Table 2 | x | # | x | ||||||
| FNR-2 | At1g20020 | x | x | |||||||||||
| PHOTOSYSTEM I | ||||||||||||||
| psaA - subunit Ia | Atcg00350 | x | ||||||||||||
| psaB - subunit Ib | Atcg00340 | x | x | x | ||||||||||
| psaC - subunit VII - stromal side | Atcg01060 | x | x | x | x | |||||||||
| psaD-1 subunit II - stromal side-tight | At1g03130 | x(1) | Table 2 | x | ||||||||||
| psaD-2 subunit II - stromal side-tight | At4g02770 | x(1) | x | |||||||||||
| psaE-1 subunit IV - stromal side | At4g28750 | 210 | x(4) | x | x | x | Table 2 | |||||||
| psaE-2 subunit IV - stromal side | At2g20260 | x(4) | x | x | ||||||||||
| psaF- subunit III - LTP - hydrophobic | At1g31330 | x | x | x | x | x | x | |||||||
| psaG - subunit V - stromal side | At1g55670 | x | x | x | x | x | x | x | x | |||||
| psaH-1 - subunit VI | At3g16140 | x,x(5) | x | x | x(8) | x | x | |||||||
| psaH-2 - subunit VI | At1g52230 | x(5) | x | x | x(8) | x | ||||||||
| psaJ - subunit VIII | Atcg00630 | x | x | |||||||||||
| psaK - subunit X | At1g30380 | x | x | x | ||||||||||
| psaL - subunit XI (also named V) | At4g12800 | x | x | x | x | x | x | |||||||
| psaN -TAT LTP | At5g64040 | 201,202 | x | x | x | x | x | Table 1 | ||||||
| LHCI-1-1 - LHCI-730 | At3g54890 | x | x | x | x | x | x | |||||||
| LHCI-2.1 - LHCI-680B | At3g61470 | x | x | x | x | |||||||||
| LHCI-3 - LHCI-680A CAB4 | At1g61520 | x | x | x | x | x | x | x | ||||||
| LHCI-4 - LHCI-730 | At3g47470 | x | x | x | x | x(5) | x | x | ||||||
| LHCI-5 - new | At1g45474 | x(5) | ||||||||||||
| CFO-CF1 | ||||||||||||||
| CFO-I - atpF | Atcg00130 | x | x | x | x | |||||||||
| CFO-II - atpG | At4g32260 | 30 | 56 | x | x | x | x | x | x | |||||
| CFO-III - atpH | Atcg00140 | x | x | x | ||||||||||
| CFO-IV - atpI | Atcg00150 | x | ||||||||||||
| CF1b - atpB | Atcg00480 | 122-126 | x,x(3) | x | Table 2 | x | ||||||||
| Atcg00120 | 110,111,122-125 | x | x | x | Table 2 | x | ||||||||
| CF1a - atpA | ||||||||||||||
| CF1e - atpE | Atcg00470 | 20,87 | x | x | x | x | Table 2 | |||||||
| CF1y - atpC | At4g04640 | 89 | x | x | Table 2 | x | ||||||||
| CF1d - atpD | At4g09650 | 31,41 | 32,33,114-116 | x | x | x | x | x | Table 2 | x | ||||
| ALTERNATIVE ELECTRON FLOW | ||||||||||||||
| NDH E (4L) | Atcg01070 | x | x | |||||||||||
| NDHI | Atcg01090 | x | ||||||||||||
| PGR5 | At2g05620 | x | ||||||||||||
| TRANSLOCATION AND ASSEMBLY | ||||||||||||||
| SecE | At4g14870 | |||||||||||||
| HCF136 Tat Itp | At5g23120 | 6,98,103,110 | x | Table 1 | x | |||||||||
| STRESS DEFENSE AND OTHERS | ||||||||||||||
| Fibrillin | At2g35490 | 9 | 1 | x | Table 2 | |||||||||
| Fibrillin | At3g23400 | 12-15,39 | x | Table 2 | x | |||||||||
| Fibrillin | At4g22240 | 11,36,38 | x(9) | Table 2 | x | |||||||||
| Fibrillin | At4g04020 | 10,35,37 | 12 | x,x(9) | Table 2 | x | ||||||||
| Fibrillin | At3g26070 | x(2) | ||||||||||||
| Fibrillin | At3g26080 | x(2) | ||||||||||||
| Thioredoxin m2 | At4g03520 | 46 | 68,78 | Table 1 | ||||||||||
| Thioredoxin m4 | At3g15360 | 77,87 | Table 1 | x | ||||||||||
| Asc-perox lumen Tat Itp | At4g09010 | x | Table 1 | x | ||||||||||
| Ferritin 1 | At5g01600 | 19 | ||||||||||||
| Ohp1 or Lil2/Hlip/Scp | At5g02120 | x | ||||||||||||
| Ohp2 | At1g34000 | x | x | x | ||||||||||
| THYLAKOID PROTEASES AND PEPTIDASE | ||||||||||||||
| FtsH2 (Var2) | At2g30950 | 50*,68* | x(4) | x | x | |||||||||
| FtsH8 | At1g06430 | x(4) | x | |||||||||||
| FtsH5 | At5g42270 | x | x | |||||||||||
| NEW LUMENAL PROTEINS AND ISOMERASES | ||||||||||||||
| Isomerases TAT ITP | At3g10060 | 53 | Table 1 | |||||||||||
| Isomerases | At4g39710 | x | Table 1 | |||||||||||
| Isomerases | At3g15520 | 6,9 | x | |||||||||||
| Thylakoid lumen 18.3 kD -ambiguous - Duf477 | At1g54780 | x | x | Table 1 | x | |||||||||
| Thylakoid lumen protein TL16.5 | At4g02530 | 6 | 26,28,57,80 | x | Table 1 | x | ||||||||
| Pentapeptide repeat TL17.4 | At5g53490 | 25 | Table 1 | x | ||||||||||
| Thylakoid lumen pentapeptide repeat | At1g12250 | 112,113 |
Proteins are classified per location or function. Indicated is in which fraction(s) the proteins were identified. Details concerning identification, functional domains, and other parameters can be found in the Tables 1, 2, and 3 in the supplemental data online and in the PPDB. Proteins (76 in total) indicated in bold text are integral membrane proteins. Numbers in parentheses indicate that some of the MS data match to a paralogue; these paralogue pairs are connected by the same integer within each column. The explanation for each fraction is self-explanatory. In addition, the identified proteins were cross-checked with our recent proteome study on the thylakoid-lumenal enriched proteome from Peltier et al. (2002) (ref. 1), the study on the lumenal proteome from Schubert et al. (2002) (ref. 2), and studies of the A. thaliana choroplast envelope from Ferro et al. (2002, 2003) (refs. 3 and 4) and from Froehlich et al. (2003) (ref. 5).