Table II.
Putative vacuolar membrane proteins sorted according to the number of their putative TMDs
AGI Acc. No., Arabidopsis Genome Initiative accession number; AGIs in italics correspond to other possible proteins matching with the same peptides or part of them, AGIs in bold correspond to novel localized membrane proteins. TMD, Putative transmembrane domains were assumed according to the Aramemnon database (http://aramemnon.botanik.uni-koeln.de/) and the MIPS database (http://mips.gsf.de/). Loc., Subcellular localization predictions according to the Aramemnon database [CL, Chloroplast; ED, endosomes; MT, mitochondria; PM, plasma membrane; (PM), novel plasma membrane protein; PR, peroxisomes; T, tonoplast; (T), novel tonoplast protein; U, unknown]. PP, Protein-Prophet scores above 0.9 were accepted; at this cutoff, the rate of false-positive protein identifications is less than 10%; l, lower PP score but additional localization experiments (in bold); kD, predicted Mr in kD; tonoplast fraction treated with KI, potassium iodide; NaOH, sodium hydroxide; C/M pH 6, treatment with sodium phosphate buffer at pH 6 followed by C/M; numbers in parentheses mean the number of gel slices. The fraction in which each protein was identified is indicated by the unique number of peptides. Ref, Indicates Arabidopsis homolog(s) found by: a, Carter et al. (2004); b, Endler et al. (2006); c, Sazuka et al. (2004); d, Shimaoka et al. (2004); e, Szponarski et al. (2004); and f, Jaquinod et al. (2007).
| AGI Acc. No. | Protein Function | TMD | Loc. | PP | kD | pI | KI (8) | Ac (8) | NaOH (4) | NaOH (10) | C/M (4) | C/M pH6 (4) | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| At1g16780 | Vacuolar proton-translocating pyrophosphatase | 16 | T | 1 | 85.3 | 5.4 | 3 | 1 | d | ||||
| At1g78920 | Vacuolar proton-translocating pyrophosphatase (AtAVP2) | 16 | T | 1 | 85.1 | 5.4 | 2 | d | |||||
| At3g62700 | Multidrug resistance-related protein (AtMRP14) | 16 | U | 1 | 172.1 | 8.7 | 2 | 7 | 2 | a, b, d, e, f | |||
| At2g47800 | |||||||||||||
| At3g07160 | Callose synthase (1,3-β-glucan synthase) family | 15 | U | 1 | 222.1 | 8.6 | 4 | ||||||
| At1g15690 | V-PPase (AtAVP-3) | 14 | T | 1 | 80.8 | 4.9 | 9 | 21 | 21 | 2 | 4 | a, b, c, d, e, f | |
| At1g01790 | Potassium efflux antiporter, putative (AtKEA1) | 12 | U | 1 | 65.0 | 6.5 | 3 | ||||||
| At3g28860 | Multidrug resistance protein (AtMDR11) | 12 | U | 1 | 136.8 | 8.4 | 4 | 4 | |||||
| At4g38350 | Patched protein family | 12 | U | 1 | 116.1 | 5.1 | 4 | a, d, e, f | |||||
| At1g16390 | Organic cation transporter related | 11 | (T) | 1 | 57.4 | 5.9 | 1 | ||||||
| At3g49310 | Expressed protein | 11 | U | 0.93 | 50.7 | 6.7 | 1 | f | |||||
| At1g64650 | |||||||||||||
| At4g27720 | Expressed protein | 11 | U | 0.93 | 50.9 | 7.2 | 1 | 1 | |||||
| At1g27770 | Ca2+-ATPase 1 (AtACA1) | 10 | ER | 1 | 103.7 | 5.4 | 2 | ||||||
| At1g29310 | Flower pigmentation protein | 10 | U | 0.97 | 52.2 | 9.3 | 3 | 3 | |||||
| At2g34250 | |||||||||||||
| At1g53210 | Drought-induced protein, putative | 10 | U | 1 | 63.4 | 5.0 | 2 | 3 | 3 | a, e, f | |||
| At2g07560 | P-ATPase (AtAHA6) | 10 | PM | 1 | 105.0 | 6.1 | 5 | ||||||
| At2g18960 | P-ATPase (AtAHA1) | 10 | PM | 0.98 | 104.2 | 6.7 | 2 | 4 | 1 | 6 | a, c, f | ||
| At4g30190 | |||||||||||||
| At2g41560 | Ca2+-ATPase 4 (AtACA4) | 10 | T | 1 | 112.7 | 5.9 | 2 | a, b, f | |||||
| At3g57330 | Ca2+-ATPase 11 (AtACA11) | 10 | T | 1 | 111.9 | 6.3 | 3 | a, b, d, e, f | |||||
| At4g35300 | Monosaccharide transporter, putative | 10 | U | 0.97 | 79.7 | 5.4 | 1 | 1 | a, b, f | ||||
| At1g10950 | Endomembrane protein 70, putative | 9 | ER | 0.98 | 66.9 | 7.7 | 2 | 2 | |||||
| At3g13772 | Endomembrane protein 70, putative | 9 | ER | 0.92 | 73.6 | 8.2 | 1 | f | |||||
| At1g55130 | |||||||||||||
| At2g01970 | Endomembrane protein 70, putative | 9 | ER | 0.95 | 68.0 | 7.1 | 2 | ||||||
| At5g45370 | Nodulin N21 family protein | 9 | (T) | 1 | 38.4 | 8.5 | 1 | ||||||
| At3g45870 | |||||||||||||
| At4g19185 | |||||||||||||
| At5g46110 | Phosphate/triose-P translocator (AtTPT) | 9 | CL | 0.99 | 44.6 | 10.3 | 2 | 2 | |||||
| At1g06470 | Integral membrane protein, putative | 8 | (T) | 1 | 46.4 | 4.7 | 1 | ||||||
| At2g25520 | |||||||||||||
| At4g32390 | |||||||||||||
| At5g11230 | |||||||||||||
| At5g25400 | |||||||||||||
| At5g54800 | Glc-6-P/phosphate translocator (AtGPT1) | 7 | CL | 1 | 42.3 | 10.1 | 2 | ||||||
| At1g01620 | Plasma membrane intrinsic protein 1c (AtPIP1.3) | 6 | PM | 1 | 30.6 | 9.1 | 1 | c | |||||
| At1g17840 | White-brown complex homolog, putative (AtWBC11) | 6 | (PM) | l | 78.4 | 8.8 | 1 | ||||||
| At2g16850 | Plasma membrane intrinsic protein 3b (AtPIP2.8) | 6 | PM | 1 | 29.5 | 9.1 | 1 | 1 | 1 | ||||
| At2g21410 | V-ATPase subunit a2 (AtVHA-a2) | 6 | T | 1 | 93.1 | 5.2 | 7 | 8 | 15 | a, b, c, d, f | |||
| At2g39010 | Plasma membrane intrinsic protein 2e (AtPIP2.6) | 6 | PM | 0.98 | 31.1 | 8.3 | 1 | 1 | 1 | c | |||
| At2g45960 | Plasma membrane intrinsic protein 1b (AtPIP1.2) | 6 | PM | 1 | 30.5 | 9.3 | 1 | 5 | 1 | 1 | a, c | ||
| At3g26520 | Tonoplast intrinsic protein 2 γ (AtTIP1.2) | 6 | T | 1 | 25.8 | 4.7 | 1 | 1 | 1 | 1 | 1 | a, b, f | |
| At3g61430 | Plasma membrane intrinsic protein 1a (AtPIP1.1) | 6 | PM | 1 | 30.7 | 9.3 | 2 | 2 | 1 | 7 | 1 | a, c | |
| At4g35100 | Plasma membrane intrinsic protein 3a (AtPIP2.7) | 6 | PM | 1 | 29.7 | 9.1 | 3 | 4 | 2 | 2 | 2 | 2 | c, d |
| At4g39080 | V-ATPase subunit a3 (AtVHA-a3) | 6 | T | 1 | 92.8 | 5.8 | 4 | 8 | 1 | 11 | 1 | 1 | a, b, c, d, e, f |
| At1g09330 | Expressed protein | 4 | U | 0.97 | 21.2 | 9.2 | 1 | ||||||
| At1g44575 | Chloroplast precursor (AtPSBS) | 4 | CL | 0.99 | 28.0 | 10.0 | 2 | a | |||||
| At1g61250 | Secretory carrier membrane protein family | 4 | U | 1 | 32.6 | 9.0 | 1 | ||||||
| At2g26650 | Potassium channel (AtAKT1) | 4 | PM | 0.92 | 97.0 | 7.3 | 2 | ||||||
| At4g14230 | CBS domain-containing protein related | 4 | U | 0.93 | 43.8 | 5.3 | 1 | ||||||
| At4g14240 | |||||||||||||
| At4g39220 | ER protein-retrieval protein (AtRER1A) | 4 | ER | 0.98 | 22.0 | 9.4 | 2 | ||||||
| At1g19910 | V-ATPase subunit c2 (AtVHA-c2) | 3 | T | 1 | 16.7 | 8.7 | 1 | 2 | 6 | 3 | 4 | a, b, c, d, f | |
| At1g75630 | |||||||||||||
| At2g16510 | |||||||||||||
| At4g34720 | |||||||||||||
| At4g38920 | |||||||||||||
| At1g32210 | Defender against cell death protein | 3 | U | 0.97 | 12.7 | 8.5 | 2 | ||||||
| At1g32400 | Senescence-associated protein family | 3 | U | 0.97 | 31.6 | 5.1 | 2 | a, d | |||||
| At1g72960 | Root hair defective | 3 | U | 0.97 | 83.8 | 5.5 | 1 | ||||||
| At3g08580 | Mitochondrial adenylate translocator (AtAAC1) | 3 | MT | 1 | 41.5 | 10.3 | 3 | 2 | 20 | 1 | a, d, f | ||
| At3g10915 | RING zinc finger protein, putative | 3 | U | 0.98 | 25.1 | 9.5 | 2 | ||||||
| At3g45600 | Senescence-associated protein family | 3 | U | 1 | 31.9 | 8.7 | 1 | 1 | |||||
| At4g21150 | Expressed protein | 3 | U | 1 | 74.7 | 7.6 | 2 | f | |||||
| At4g23630 | Expressed protein | 3 | U | 1 | 30.5 | 8.6 | 6 | 2 | a | ||||
| At1g64090 | |||||||||||||
| At4g11220 | |||||||||||||
| At5g41600 | |||||||||||||
| At4g28390 | Mitochondrial adenylate translocator (AtAAC3) | 3 | MT | 1 | 40.7 | 10.3 | 1 | 3 | 1 | ||||
| At4g28770 | Senescence-associated protein, putative | 3 | (T) | 0.97 | 31.0 | 4.7 | 1 | 1 | a, d, f | ||||
| At5g13490 | Mitochondrial adenylate translocator (AtAAC2) | 3 | MT | 1 | 41.7 | 10.3 | 2 | 2 | 1 | 2 | 3 | f | |
| At5g46800 | Mitochondrial Arg-Orn translocator (AtBOU) | 3 | MT | 0.93 | 31.0 | 10.0 | 1 | ||||||
| At1g06950 | Chloroplast inner envelope protein (AtTic110) | 2 | CL | 1 | 19.8 | 5.2 | 2 | 6 | 2 | ||||
| At1g08480 | Expressed protein | 2 | U | 1 | 15.8 | 6.8 | 2 | a, f | |||||
| At1g15820 | Chlorophyll a/b-binding protein (AtLHCb6) | 2 | CL | 1 | 27.5 | 7.7 | 1 | 2 | 2 | 1 | a | ||
| At1g65820 | Microsomal glutathione S-transferase, putative | 2 | U | 1 | 16.6 | 9.3 | 2 | 3 | 1 | a, d | |||
| At2g07698 | Expressed protein | 2 | U | 1 | 85.9 | 5.2 | 7 | 4 | 11 | a, d, f | |||
| At2g40800 | Expressed protein | 2 | U | 0.98 | 41.7 | 10.4 | 2 | 2 | e | ||||
| At3g56430 | |||||||||||||
| At3g08640 | CCT motif-containing protein (AtCIL) | 2 | U | 0.97 | 35.2 | 9.0 | 1 | ||||||
| At5g01500 | Expressed protein | 2 | U | 1 | 45.1 | 10.4 | 5 | ||||||
| At5g19760 | Mitochondrial dicarboxylate/ tricarboxylate carrier (AtDTC) | 2 | MT | 1 | 31.9 | 9.6 | 2 | 2 | 4 | 6 | a, f | ||
| At5g24650 | Expressed protein | 2 | U | 1 | 27.8 | 10.3 | 5 | 3 | 1 | e, f | |||
| At5g25940 | Nodulin-like protein | 2 | U | 1 | 12.3 | 11.0 | 3 | ||||||
| At5g40820 | FAT domain-containing phosphatidylinositol 3- and 4-kinase family | 2 | U | 0.92 | 302.4 | 7.0 | 2 | ||||||
| At1g04630 | Expressed protein | 1 | U | 1 | 16.1 | 9.6 | 3 | ||||||
| At2g33220 | |||||||||||||
| At1g04750 | R-SNARE synaptobrevin, putative (AtVAMP721) | 1 | ED | 1 | 16.1 | 10.0 | 4 | f | |||||
| At2g33120 | |||||||||||||
| At1g34610 | Ulp1 protease family | 1 | U | 0.96 | 111.4 | 6.0 | 2 | ||||||
| At3g09170 | |||||||||||||
| At1g42960 | Expressed protein | 1 | U | 1 | 17.8 | 8.7 | 1 | ||||||
| At1g53840 | Pectinesterase family | 1 | U | 1 | 64.1 | 8.5 | 1 | 1 | f | ||||
| At1g63830 | Expressed protein | 1 | U | 0.99 | 25.7 | 5.7 | 2 | ||||||
| At5g41390 | |||||||||||||
| At1g70680 | Ca2+-binding EF-hand common family protein | 1 | U | 1 | 21.5 | 9.3 | 2 | ||||||
| At1g70770 | Expressed protein | 1 | U | 0.90 | 66.9 | 9.3 | 1 | f | |||||
| At1g76400 | Ribophorin I, putative | 1 | U | 0.91 | 68.6 | 8.8 | 1 | ||||||
| At2g27730 | Expressed protein | 1 | U | 1 | 11.9 | 10.3 | 1 | 1 | a | ||||
| At2g33380 | RD20 protein | 1 | U | 1 | 26.6 | 5.0 | 1 | a | |||||
| At2g36650 | Expressed protein | 1 | U | 0.90 | 43.0 | 5.0 | 1 | ||||||
| At3g09740 | Qc-SNARE domain protein (AtSYP71) | 1 | U | 1 | 30.0 | 4.8 | 3 | ||||||
| At3g11820 | Qc-SNARE domain protein (AtSYP121) | 1 | U | 0.95 | 38.0 | 9.4 | 1 | ||||||
| At3g17840 | Receptor-like kinase RLK, putative | 1 | U | 0.96 | 70.4 | 6.5 | 1 | ||||||
| At3g19820 | Cell elongation protein, Dwarf1 | 1 | U | 1 | 65.4 | 8.1 | 8 | 4 | 2 | 11 | a, d, f | ||
| At3g27240 | Cytochrome c, putative | 1 | U | 1 | 33.7 | 6.1 | 4 | d, f | |||||
| At3g48850 | Mitochondrial phosphate transporter, putative (AtPHT3-2) | 1 | MT | 1 | 39.0 | 9.7 | 3 | 1 | 8 | 6 | f | ||
| At5g14040 | |||||||||||||
| At3g48890 | Progesterone-binding protein homolog Atmp2, putative (AtMSBP1) | 1 | U | 0.96 | 25.4 | 4.3 | 1 | 2 | |||||
| At5g52240 | |||||||||||||
| At3g49720 | Expressed protein | 1 | U | 1 | 28.5 | 9.7 | 1 | f | |||||
| At3g49750 | Expressed protein | 1 | U | 1 | 30.0 | 8.1 | 1 | ||||||
| At3g54110 | Mitochondrial uncoupling protein 1 (AtUCP1) | 1 | MT | 1 | 32.7 | 10.1 | 2 | 2 | f | ||||
| At3g60750 | Transketolase, putative | 1 | U | 0.94 | 80.0 | 6.3 | 1 | ||||||
| At3g62360 | Expressed protein | 1 | U | 1 | 132.9 | 6.4 | 1 | ||||||
| At3g63410 | Chloroplast inner envelope protein (AtAPG1) | 1 | CL | 1 | 37.9 | 9.5 | 2 | 3 | 1 | f | |||
| At4g21105 | Expressed protein | 1 | U | 0.95 | 7.7 | 10.5 | 2 | f | |||||
| At4g35000 | Peroxisomal ascorbate peroxidase (AtAPX3) | 1 | PR | 0.99 | 31.6 | 7.0 | 2 | e, f | |||||
| At4g37830 | Expressed protein | 1 | U | 1 | 11.2 | 9.5 | 1 | 1 | |||||
| At5g01530 | Light-harvesting chlorophyll a/b-binding protein | 1 | CL | 1 | 31.1 | 6.0 | 2 | a | |||||
| At5g07340 | Calnexin, putative | 1 | ER | 1 | 60.5 | 4.5 | 1 | 1 | f | ||||
| At5g08080 | Qa-SNARE domain protein (AtSYP132) | 1 | U | 0.96 | 34.2 | 6.3 | 2 | ||||||
| At5g16660 | Expressed protein | 1 | U | 1 | 18.2 | 8.7 | 1 | ||||||
| At5g47570 | Expressed protein | 1 | U | 1 | 13.2 | 8.5 | 3 | ||||||
| At5g61790 | Calnexin 1 (CNX1) | 1 | ER | 1 | 60.5 | 4.5 | 1 | 3 | a, e, f | ||||
| At5g66680 | Dolichyl-di-phosphooligosaccharide- protein glycotransferase | 1 | U | 1 | 48.7 | 6.3 | 2 | 2 | a, f |