Table 1.

Functional Categorization and Characterization of Identified Vacuolar Proteins

LocusDescriptionMWpILocalizationTMDs2-D LC MS/MS1-D SDS-PAGE LC MS/MSTonoplast
Glycosidases
At1g09010.1Glycoside hydrolase family 2, low similarity to mannosidase107,6446.42010x
At1g12240.1Glycosyl hydrolase family 32, β-fructosidase73,8275.30121xx
At1g52400.1Glycosyl hydrolase family 1, β-glucosidase (BG1)60,4427.23SSS101xx
At1g55120.1Glycosyl hydrolase, β-fructofuranosidase67,0505.52SSS110x
At1g62660.1Glycosyl hydrolase family 32, identical to β-fructosidase72,2115.27111x
At1g66270.1Glycosyl hydrolase family 1, β-glucosidase59,6467.02SSS110x
At2g28100.1Glycosyl hydrolase family 29 (α-l-fucosidase)57,1695.13SSS100x
At2g32810.1Glycosyl hydrolase family 35 (β-galactosidase)99,1818.11SSS111x
At3g09260.1Glycosyl hydrolase family 1, β-glucosidase59,7036.91SSS100x
At3g10740.1Glycosyl hydrolase family 51, similar to arabinoxylan arabinofuranohydrolase isoenzyme75,0275.52SSS010x
At3g16850.1Polygalacturonase, putative49,1075.65SSS100xx
At3g26720.1Glycosyl hydrolase family 38 (α-mannosidase)115,2036.70SSS101xx
At3g47050.1Glycosyl hydrolase, family 3, β-d-glucan exohydrolase67,2345.08000x
At3g55260.1Glycosyl hydrolase family 20, similar to β-hexosaminidase61,2126.20SSS300xx
At3g56310.1Glycosyl hydrolase family 27 (α-galactosidase/melibiase)48,3454.52SSS111xx
At3g57260.1Glycosyl hydrolase family 17, similar to glucan endo-1,3-β-glucosidase37,3214.60SSS111x
At3g62110.1Polygalacturonase, putative51,9796.44SSS100x
At3g62750.1Glycosyl hydrolase family 1, β-glucosidase55,1556.72SSS101xx
At4g27830.1Glycosyl hydrolase family 1, β-glucosidase57,0615.32SSS000x
At5g10560.1Glycosyl hydrolase family 3, β-xylosidase87,1686.33CSS000x
At5g11720.1Glycosyl hydrolase family 31, similar to α-glucosidase101,1015.72SSS010xxx
At5g13690.1α-N-Acetylglucosaminidase92,6727.60SSS000x
At5g13980.2Glycosyl hydrolase family 38 (α-mannosidase)115,8856.41SSS000x
At5g25980.1Glycosyl hydrolase family 1, similar to myrosinase precursor53,7796.89SSS111xxx
At5g26000.1Glycosyl hydrolase family 1, myrosinase precursor61,1155.70SSS000xx
Protein Degradation
At1g02305.1Expressed protein (cathepsin B-like Cys protease)40,0166.91SS121x
At1g09850.1Cys protease XBCP348,0566.42SSS100xx
At1g11910.1Asp proteinase-related54,5965.20SSS201xxx
At1g15000.1Ser carboxypeptidase-related49,2055.19SSS010x
At1g36340.1Ubiquitin-conjugating enzyme17,8159.63M000x
At1g47128.1Cys proteinase RD21A50,9495.05SSS110xxx
At1g62290.1Asp protease-related55,7316.27SSS101x
At1g78670.1γ-Glutamyl hydrolase-related398656.17SSS210x
At1g78680.1γ-Glutamyl hydrolase (γ-Glu-X carboxypeptidase/conjugase)38,6257.16SSS210x
At2g35780.1Ser carboxypeptidase-related51,5046.92SS000x
At3g09790.1Polyubiquitin (UBQ8)71,7529.52000x
At3g10410.1Ser carboxypeptidase III, putative57,2845.03SSS021x
At3g14067.1Subtilisin-like Ser protease, putative81,8006.76SSS110xxx
At3g28220.1Expressed protein (meprin and TRAF homology domain-containing protein)42,8698.80111xxx
At3g51730.1Expressed protein, saposin precursor24,0804.74SSS010x
At4g01610.1Cathepsin B-like Cys protease, putative39,4006.09SSS120x
At4g02890.3polyubiquitin (UBQ14)34,1757.82000x
At4g12910.1Ser carboxypeptidase-related54,2116.32SSS111x
At4g16190.1Cys proteinase41,2466.97SSS111x
At4g20850.1Expressed protein (Ser protease domain)152,3515.93MMS000xx
At4g30810.1Serine carboxypeptidase-related53,0386.27SSS110xx
At4g36190.1Expressed protein (Ser carboxypeptidase S28 family)55,4167.17SSS031xx
At4g36195.1Expressed protein (Ser carboxypeptidase S28 family)54,7566.50SSS101xx
At5g03240.2Polyubiquitin (UBQ3) identical to GI:92880934,2627.82000x
At5g23210.2Ser carboxypeptidase-related45,7088.96000x
At5g60360.1Cys proteinase AALP38,9416.70SSS101x
At5g65760.1Hydrolase, α/β fold family; similar to SPP42785 lysosomal pro-X carboxypeptidase precursor58,5555.11SSS111x
Stress Response
At1g02920.1Glutathione transferase, putative23,5806.61M000x
At1g02930.1Glutathione transferase, putative23,4686.18M000x
At1g03860.1Prohibitin 2–related B-cell receptor associated protein31,7939.87SS110x
At1g21250.1Wall-associated kinase 181,1945.43SSS111x
At1g24450.1Ribonuclease III-related20,72410.11SSS221x
At1g25570.1Leu-rich repeat protein-related68,9555.10SSS110x
At1g30360.1ERD4 protein81,9189.61SSS10910x
At1g32400.1Senescence-associated protein family31,5385.10SSS544xx
At1g52040.1Jacalin lectin50,1495.33000x
At1g65820.1Microsomal glutathione S-transferase, putative16,5689.32SSS333x
At1g67360.2Stress-related protein26,4079.41S100xx
At1g71695.1Peroxidase, putative39,5428.39SSS211xx
At1g74020.1Strictosidine synthase35,2755.43SSS000xxx
At1g75040.1Pathogenesis-related protein 5 (PR-5)25,2344.54SSS111x
At2g15970.1Cold acclimation protein21,5879.23M545x
At2g30860.1Glutathione transferase, putative24,1286.64CM010x
At2g30870.1Glutathione transferase, putative24,2125.39MCC110x
At2g33380.1RD20 protein, induced by abscisic acid during dehydration26,5824.98110xx
At2g39330.1Jacalin lectin50,4267.30000x
At2g39780.1S-like ribonuclease RNS229,1356.38SSS100x
At3g05500.1Stress-related protein-related27,1778.56000x
At3g16470.1Jacalin lectin48,4794.91000xx
At3g22060.1Receptor protein kinase-related27,8468.90SSS111x
At3g27280.1Prohibitin-related30,6207.82SS100xx
At3g32980.1Peroxidase, putative38,8296.65CSS000xx
At3g49110.1Peroxidase38,9246.86SSS111x
At3g49120.1Peroxidase, putative38,8147.70SSS110xx
At3g57020.1Strictosidine synthase-related41,4407.01SSS111x
At4g02520.1Glutathione transferase, putative24,1116.32M000xx
At4g08770.1Peroxidase, putative38,1857.72SSS000x
At4g08780.1Peroxidase, putative38,0687.72SSS000x
At4g16500.1Cys proteinase inhibitor-like protein12,5389.72SSS111x
At4g23670.1Major latex protein (MLP)-related17,5006.34000x
At4g25090.1Respiratory burst oxidase (NADPH oxidase), putative96,8469.41554x
At5g01820.1CBL-interacting protein kinase 1450,2808.21110x
At5g18100.1Copper/zinc superoxide dismutase (CSD3)16,9237.73000x
At5g24770.1Vegetative storage protein, Vsp229,8256.28SSS100x
At5g24780.1Vegetative storage protein, Vsp130,2445.39SSS100xx
At5g40770.1Prohibitin (gbAAC49691.1)30,3827.89SS100x
At5g44020.1Vegetative storage protein-related31,0398.03SSS110xx
At5g49760.1Receptor protein kinase-related104,6916.08SSS322xx
At5g58150.1Leu-rich repeat transmembrane protein kinase, putative86,5947.54MSS211x
At5g62740.1Hypersensitive-induced response protein31,4135.07000xx
Membrane Fusion and Remodeling
At1g02130.1Ras-related GTP binding protein ARA-522,6314.77S000x
At1g12360.1KEULE75,0668.08000x
At1g16240.1Syntaxin of plants 51 (SYP51)25,8718.22111xx
At1g18070.1EF-1-α-related GTP binding protein, putative59,2254.96100x
At1g18210.2Calcium binding protein, putative18,3323.95000x
At1g22740.1Ras-related GTP binding protein (Rab7)22,9275.09MMM010xx
At1g27480.1Expressed protein similar to lecithin:cholesterol acyltransferase precursor48,2908.78SSS121xxx
At1g28580.1Lipase, putative43,0074.97SSS420x
At1g31550.1Lipase, putative43,0795.54SS300x
At1g32410.2Expressed protein (vacuolar protein sorting 55 family protein)15,0074.19SS424xx
At1g35720.1Ca2+-dependent membrane binding protein annexin36,1865.02000x
At1g43620.1Sterol glucosyltransferase-related68,3275.47320x
At1g45201.1Conserved hypothetical protein contains Pfam profile: PF01764 lipase54,7769.04C021x
At1g52280.1GTP binding protein, putative23,0514.94SSM010x
At1g53590.1C2 domain-containing protein84,8845.81SSS112x
At1g54000.1Myrosinase-associated protein, putative; contains Pfam profile PF00657: GDSL-like lipase/acylhydrolase43,1767.12SSS111x
At1g54010.1Myrosinase-associated protein, putative; contains Pfam profile PF00657: lipase/ acylhydrolase with GDSL-like motif43,1268.19SSS111x
At1g54020.1Myrosinase-associated protein, putative; contains InterPro entry IPR001087 lipolytic enzyme, G-D-S-L family32,4387.84C000xx
At1g54030.1Myrosinase-associated protein- related; contains Pfam profile PF00657: GDSL-like lipase/acylhydrolase46,0656.71C110xxx
At1g64460.1Phosphatidylinositol 3- and 4-kinase33,1585.08000x
At1g65320.1CBS domain containing protein46,5387.27220xx
At1g70490.2ADP-ribosylation factor 1 (ARF1), putative20,5756.96CM100x
At1g74210.1Glycerophosphodiester phosphodiesterase-related45,0047.11SSM000x
At1g79590.1Syntaxin of plants 52 (SYP52)26,0918.70111x
At2g01540.1C2 domain-containing protein20,0676.91000xx
At2g07050.1Cycloartenol synthase [(S)-2,3-epoxysqualene mutase] (CAS1)86,0166.01020x
At2g14720.2Spot 3 protein and vacuolar sorting receptor AtELP2a69,7955.11SSS111x
At2g20990.1C2 domain-containing protein, similar to Ca2+-dependent lipid-binding protein (CLB1)61,7277.67SSS111x
At2g21160.1Signal sequence receptor, α subunit28,1504.84SSS211x
At2g38760.1Annexin-related36,2386.38000x
At2g45200.1cis-Golgi SNARE protein, putative26,4529.64111x
At3g03520.1Phosphoesterase family59,0805.12000x
At3g14210.1Myrosinase-associated protein, putative; contains Pfam profile:PF00657 lipase/ acylhydrolase with GDSL-like motif44,0437.82SSS111xxx
At3g14220.1GDSL-motif lipase/hydrolase protein, similar to myrosinase-associated proteins40,2316.85SSS101x
At3g22845.1Expressed protein (mp24/gp25L/p24 protein-related)24,2646.86111x
At3g46060.1Ras family GTP binding protein23,8178.02S200x
At3g56190.1α-Soluble NSF attachment protein32,7374.98000xx
At3g60340.2Palmitoyl protein thioesterase precursor, putative37,0665.00SSS121xx
At3g62290.1ADP-ribosylation factor20,5906.96MM100x
At4g04910.1Component of vesicle-mediated transport-related, similar to N. tabacum N-ethylmaleimide sensitive fusion protein81,4705.98MC000x
At4g17170.1GTP binding protein (At-RAB2)23,1477.50S000xx
At4g17530.1Ras-related small GTP binding protein RAB1c22,3005.04S000x
At4g20260.2Endomembrane-associated protein24,5664.65000xx
At4g21160.2Zinc finger and C2 domain protein (ZAC)37,1284.90000x
At4g24840.1Brefeldin A-sensitive Golgi protein-like84,6025.49000x
At4g32150.1Synaptobrevin-related protein25,0219.39MSS111x
At4g35790.2Phospholipase D-related97,7627.17010x
At5g13710.124-Sterol C-methyltransferase38,2516.12000xx
At5g39510.1v-SNARE AtVTI1a (ZIG)24,93310.10111xx
At5g46860.1Syntaxin of plants SYP22 (VAM3p)29,4646.37M111x
At5g47710.1C2 domain-containing protein18,3177.30000x
Transporters
At1g11260.1Glucose transporter57,5939.19M121112x
At1g12840.1Vacuolar ATP synthase subunit C-related42,6025.20MM000xxx
At1g15690.1Inorganic pyrophosphatase-related80,8034.89SSS161414xxx
At1g20260.1Vacuolar H+-ATPase subunit B-related36,3414.56000x
At1g20840.1Transporter-related79,4685.06MS111010x
At1g30400.1Glutathione S-conjugate ABC transporter (AtMRP1)181,9116.08151414x
At1g64200.1H+-transporting ATPase protein-related27,0676.11000x
At1g76030.1Vacuolar ATP synthase subunit B54,0904.73000xxx
At1g78900.1ATPase 70-kD subunit-related68,7954.86000xxx
At1g80310.1Sulfate transporter-related49,5348.56C1089x
At2g02040.1His transport protein (PTR2-B)64,4045.34111010x
At2g18960.1ATPase 1, plasma membrane-type (proton pump 1)104,2076.6710910x
At2g21410.1Vacuolar proton-ATPase subunit-related93,0895.24676xxx
At2g26975.1Copper transport protein-related15,7888.50C223x
At2g28900.1Membrane channel protein-related15,4649.59C400xx
At2g38170.1Calcium exchanger (CAX1)50,1596.16C1098xxx
At2g41560.1Potential calcium-transporting ATPase 4112,7335.941098xxx
At2g43330.1Sugar transporter family54,7954.94C12912x
At2g47800.1Glutathione-conjugate transporter AtMRP4169,0647.70CC171415x
At2g48020.2Sugar transporter, putative49,6828.96121012xx
At3g01280.1Porin-related29,4089.23M000x
At3g01390.2Vacuolar membrane ATPase subunit G (AVMA10)12,3795.82000xx
At3g03720.1Cationic amino acid transporter-related63,6216.09141314x
At3g16240.1δ Tonoplast integral protein (δ-TIP)25,0095.43S766xxx
At3g26520.1Tonoplast intrinsic protein, putative25,8314.72667xxx
At3g26590.1MATE efflux protein54,3045.73121111x
At3g28710.1Adenosine triphosphatase-related, similar to vacuolar adenosine triphosphatase subunit D40,7744.82010xxx
At3g28715.1Expressed protein, similar to vacuolar adenosine triphosphatase subunit D40,7704.75010xxx
At3g30390.1Amino acid transporter49,5006.50111011x
At3g42050.1Vacuolar ATP synthase subunit H-related50,2677.04010xxx
At3g57330.1Potential calcium-transporting ATPase 11111,9286.27C10910xxx
At3g58730.1V-ATPase subunit D (vATPD)29,04110.17SM000xx
At3g62700.1Glutathione-conjugate transporter, putative172,1218.72M171416xx
At4g02620.1V-ATPase-related14,2426.53210xx
At4g03560.1Two-pore calcium channel (TPC1)84,8564.62121411xxx
At4g11150.1H+-transporting ATPase chain E, vacuolar26,0426.31000xxx
At4g23710.1V-ATPase subunit G (vag2 gene)11,7245.28000x
At4g35300.1Transporter-related, low similarity to hexose transporter79,7095.35SS111011x
At4g38510.1Probable H+-transporting ATPase54,2884.78000xxx
At4g38920.1H+-pumping ATPase 16- kD proteolipid, vacuolar (ava-p1)16,5548.68SS444xx
At4g39080.1Proton pump-related vacuolar proton ATPase 100-kD subunit92,8175.77676xxx
At5g14120.1Nodulin-related protein63,1327.54MMS131112x
At5g15090.1Voltage-dependent anion-selective channel protein hsr229,1938.68M000x
At5g39040.1ABC transporter family protein69,0868.28M654xx
At5g64870.1Nodulin-related52,8167.29M000x
At5g67330.1NRAMP metal ion transporter 4 (NRAMP4)56,3684.72121112x
Cytoskeleton
At1g49240.1Actin 841,8455.29000x
At1g52410.1Myosin-related protein84,0014.29SSS110xx
At1g59610.1Dynamin-related protein100,2119.59000x
At1g64330.1Expressed protein, myosin heavy chain-related64,4774.82000xx
At3g58160.1Myosin heavy chain MYA3141,3975.95100x
At3g60190.1Dynamin-related protein 4 (ADL4)69,7877.59C000xx
At3g60840.1Microtubule associated protein (MAP65/ASE1)73,4307.60000x
At5g41790.1Myosin heavy chain-related protein149,9454.55000xx
At5g42080.1Dynamin-related protein68,1558.51000x
At5g55400.1Fimbrin79,7714.88MCC000x
  • Locus numbers and descriptions are based on TAIR annotations. Subcellular localization predictions are listed in order by iPSORT, PREDOTAR, and TargetP (–, no signal; S, signal peptide; C, chloroplast transit peptide; M, mitochondrial transit peptide). Transmembrane domain (TMD) predictions are listed in order by HMMTOP, THUMBUP, and TMHMM. The fraction/method in which each protein was identified is also indicated. MW, predicted molecular weight.