Table II.

Identification of proteins from purified rice mitochondria using MS/MS peptide spectra matched to rice ORFs translated by the Institute for Genomic Research (TIGR; XXXX.mXXXXX), TIGR-translated expressed sequence tags (ESTs, TCXXXXX), and rice NCBI entries

Functional Class2D-PAGEBN-PAGELC-MSMrplGRAVYTPPTMPAccession No.ProteinAtPs
ATP synthase11, 12, 6419, 32, 50, 51, 52255,2815.9−0.112832.m00083,CAA35787 ATP synthase alpha-subunit * *
1418, 311059,0596.8−0.10MMM Q01859 ATP synthase beta-subunit *
173725,06510.1−0.16MMM1903.m00144ATP synthase OSCP subunit *
29, 3022324,3595.0−0.71TC63644, 3067.m00121ATP synthase delta-subunit * *
313821,2136.00.15MMM2119.m00096,BAC21366 ATP synthase delta-subunit * *
5120, 35440,9558.5−0.103695.m00193, TC72968ATP synthase gamma-subunit b
42, 23693710.8−0.30MM BAB21526 ATP synthase 6-kD subunit
23787710.90.84CC P14863 ATP synthase subunit 9
2821238,2175.0−0.44MMM2485.m00122ATP synthase FAd subunit * *
Complex I26212,4926.7−0.99 AAL67582 NADH dehydrogenase PDSW subunit
7612,0337.6−0.22MM3640.m00126NADH dehydrogenase B22 subunit *
711223,4984.9−0.57MM3550.m00121NADH dehydrogenase (23 kD) *
435718,5187.1−0.90M387.m00162NADH dehydrogenase B17.2
43481,1176.1−0.17MMM AAL58200 NADH dehydrogenase 75-kD subunit *
4, 8, 9144,3099.6−0.08MM2451.m00084NADH dehydrogenase (39 kD)
4, 556,3018.2−0.31MMM2102.m00066NADH dehydrogenase (51 kD)
6, 744,2527.1−0.49C BAC19866 NADH dehydrogenase subunit 7
1322,5948.2−0.78 BAA08794 NADH dehydrogenase subunit 9
14, 15121,8294.6−0.24MMMTC76675, 4381.m00118NADH dehydrogenase 13-kD subunit *
16228,7629.6−0.30MMMTC79833, 4342.m00113NADH dehydrogenase E 16.6-kD subunit
Complex III24TC79968Mitochondrial-processing peptidase beta-subunit *
22553,9467.2−0.10MM2599.m00145, 2709.m00160Mitochondrial-processing peptidase alpha-subunit *
27129,8208.6−0.16MMM2341.m00134Reiske Fe-S protein c
2816,6169.8−0.34MMM2070.m00100, 3403.m00173Ubiquinol cytochrome c reductase (14 kD) *
29, 2313,08610.80.41MM3017.m00162, 3017.m00172Ubiquinol cytochrome c reductase (8.2 kD)
233,2936.2−0.19MMM2974.m00152Cytochrome c1 precursor c
Complex IV3218,9124.0−1.01BAA76393Cytochrome c oxidase subunit VIb-1
334118,0474.8−0.42MMM T03033 Cytochrome c oxidase subunit Vb *
7713,9309.70.06MMM3550.m00112Cytochrome c oxidase subunit Via
4457,7678.60.69 P14578 Cytochrome c oxidase subunit I
Pyruvate and5347, 48352,6437.60.13MMM BAB39219, 2726.m00149Dihydrolipoamide dehydrogenase (E3) * *
 2-OG DH255,8967.40.08MMM3313.m00119Dihydrolipoamide dehydrogenase (E3) * *
 complexes16, 4139,9504.8−0.03MMTC57558, 3493.m00141Pyruvate dehydrogenase E1 beta-subunit * *
6659,5918.7−0.17MMM3634.m00180Dihydrolipoamide acetyltransferase (E2) a *
52348,8949.5−0.33MMM2307.m00126Dihydrolipoamide succinyltransferase (E2) a
248,2839.1−0.30 CAD40552 Dihydrolipoamide succinyltransferase (E2) a
2123,7686.5−0.44MMM4591.m001512-Oxoglurate dehydrogenase E1
Succinyl-CoA48, 2234,2468.40.08MMM2046.m00126Succinyl-CoA ligase alpha-subunit *
 ligase1549345,0916.2−0.03MMM2466.m00139Succinyl-CoA ligase beta-subunit *
Isocitrate DH40, 4940,6298.1−0.06MMM2447.m00175NAD-dependent isocitrate dehydrogenase *
Malate DH20, 21, 47235,4618.90.08MMM BAB55686, 2720.m00059Malate dehydrogenase * *
53435,4368.30.14MM3321.m00193, 2990.m00151Putative malate dehydrogenase * *
Citrate synthase58252,1217.2−0.07MMM AAG28777, 2942.m00114Citrate synthase * *
Malic enzyme3070,7215.9−0.19MMM2119.m00105NAD-dependent malic enzyme 62-kD subunit
4457,1438.3−0.16C AAG13628 NAD-dependent malic enzyme 59-kD subunit
Complex II3759,1036.2−0.402338.m00147Succinate dehydrogenase FP alpha-subunit *
Aconitase36, 63107,4527.3−0.18CMTC61943, 4161.m00311Aconitate hydratase *
6598,3975.9−0.15TC68934, 5178.m00213Aconitate hydratase *
GDC34417,3674.7−0.23MMM AAK39594 Gly decarboxylase H protein *
73, 80, 56, 57329,2246.5−0.162329.m00191Aminomethyltransferase precursor (T protein) *
54, 5554,9798.4−0.29MMMTC52724, 4124.m00171Ser hydroxymethyltransferase (SHMT) *
General5947,8756.6−0.15MM1207.m00066Glutamate dehydrogenase 2 * *
 metabolism603340,6316.7−0.19MMM2275.m00146Glutamate dehydrogenase * *
70243,7626.8−0.18MMM1904.m00155NAD-dependent formate dehydrogenase *
5041,2437.4−0.21MMM BAA77337 NAD-dependent formate dehydrogenase *
68145,2559.6−0.211902.m00219Aldehyde dehydrogenase * *
1359,3076.8−0.04MMM BAB19052 Aldehyde dehydrogenase * *
67287,0738.4−0.10MMM4976.m00233Aldehyde dehydrogenase * *
156,1065.8−0.02CC4694.m00128Aldehyde dehydrogenase * *
9, 1056,9806.3−0.03MMM AAC03055 Methylmalionate semi-aldehyde dehydrogenase * *
79TC59081, TC66764Thiosulfate sulfurtransferase *
3847,4957.8−0.25MMMJC5125Asp transaminase *
39TC54297Isovaleryl-CoA dehydrogenase *
2725,4259.4−0.09CCTC62983, 4134.m00168Inosine-5′-monophosphate dehydrogenase *
2252,8086.4−0.284000.m00165Acetyl-CoA carboxylase
236,8128.9−0.14MMM2884.m00186Formyl transferase
280,0296.6−0.21CM3385.m00173, 3006.m00143Transketolase
229,77510.6−0.322541.m00142Triacylglycerol lipase
4635,3278.2−0.092329.m00193(S)-2-hydroxy-acid oxidase
Import7510,8435.9−0.59Q9XGX7Translocase of inner membrane 9 (TIM9)
5715,6779.00.122461.m00155 2506.m00124Translocase of inner membrane 17 (TIM17)
3437,9566.8−0.132733.m00140Translocase of outer membrane 40 (TOM40) *
42966510.2−0.01M2494.m00117 3845.m00238Translocase of outer membrane 9 (TOM9)
Transport4629,2207.9−0.16MTC48593, CAB82853Voltage-dependent anion channel *
45TC65294Voltage-dependent anion channel *
1839, 36, 26, 5427,8158.7−0.05CCAC80850, 2981.m00134Voltage-dependent anion channel *
45224,5347.70.01CCM5186.m00209Voltage-dependent anion channel *
233,6639.8−0.123497.m00176Voltage-dependent anion channel *
36341,51010.3−0.10C2506.m00136 2986.m00110Adenine nucleotide translocator ANT b
233,0219.40.14C3698.m00164, 3631.m00202Phosphate transporter b
332,80210.10.103317.m000752-Oxoglutarate/malate translocator b
Ox stress155324,9477.0−0.10SMMAAA57130,Q43008 Manganese superoxide dismutase * *
2420,8748.20.01MMM BAA90363 Peroxiredoxin *
5717,1467.5−0.03MMM3606.m00327, 3602.m00254Adrenodoxin precursor *
Chaperones5283,3808.1−0.42MMMTC51015, 4256.m00159Heat shock protein 70 * *
6, 7560,8505.6−0.08MMM1379.m00089, 5187.m00183Chaperonin 60 * *
365,2764.8−0.104781.m00152Chaperonin 60 *
78, 25310,6439.0−0.09MCM3664.m00136,T03585 Chaperonin 10 *
213,99610.2−0.39MMM5140.m00090Chaperonin 10 *
191130,6437.10.03S2952.m00055Prohibitin *
1, 231,41310.1−0.24S4127.m00167,BAC07170 Prohibitin *
Transcription/848,4236.4−0.06MMMAAL5626tTranslational elongation factor T0 * *
 translation3515,5478.9−0.59CM CAA05729 Gly-rich RNA-binding protein *
297,91910.8−0.893373.m00119DEAD box RNA helicase *
3127,6346.3−0.53CM3952.m00081DEAD box RNA helicase *
2172,7739.1−0.58M AAK54292 Putative helicase *
231,2309.2−0.46C5028.m00163C2H2-type zinc finger protein
262,0128.80.04MMM AAL59047 PPR protein
279,2198.5−0.06MM BAB64813 PPR protein
2184,2378.1−0.702474.m00123, 5076.m00090CREB-binding protein
Miscellaneous6929,4374.2−0.53MM2772.m00163Mitochondrial glycoprotein
 function2327,4997.90.12MMMTC65865, 4358.m00206Ferripyochelin-binding protein *
441126,4556.4−0.02MMM2030.m00175Ferripyochelin-binding protein *
611023,2146.4−0.19MTC48467, 2868.m00167Ferripyochelin-binding protein *
34367,6815.0−0.60MMM2249.m00144Mitofilin motor protein
4760,7294.4−0.74S2296.m00078Calnexin-like protein
172,7784.8−0.46C2673.m00127ADP-ribosylation factor binding protein
253,2806.5−0.302500.m00126Actin
239,1966.1−0.27S AAM01174 Wall-associated kinase 2-like protein
228,0788.3−0.37 BAB92895 sec14-Like protein
398,2216.6−0.282251.m00196Disease resistance protein
294,6327.6−0.27S4193.m00176Disease resistance protein
Unknown42, 2310,9459.4−0.40M2419.m00150Unknown protein
 function5612,9147.3−0.21CC4127.m00174Unknown protein *
 protein17746610.7−0.55MM2468.m00122, 2520.m00121Unknown protein
7227,4799.2−0.03MMM2284.m00104Unknown protein *
7413,2738.7−0.13MCM32.m00149Unknown protein
42TC48363Unknown protein
Unknown function1134,1875.6−0.203273.m00129Unknown protein
 protein187869.2−0.17S3018.m00158Unknown protein
 (continued)181019.8−0.50C1987.m00120Unknown protein
119,4385.9−0.334958.m00111Unknown protein
3126,8296.7−0.214983.m00113Unknown protein
2100,7239.2−0.41MM4638.m00135Unknown protein
278,51510.7−0.72MMM BAA84788 Unknown protein
212,96612.1−0.30C AAL58157 Unknown protein
375,5875.80.01AAN06831Unknown protein
257,8055.7−0.46MC2366.m00159, 2275.m00133Unknown protein
248,1048.7−0.072284.m00111Unknown protein
2171,9637.4−0.63M4183.m00149, 3872.m00127Unknown protein
269,9678.7−0.37C2475.m00089Unknown protein
248,7798.7−0.21MMM2631.m00097Unknown protein
2129,6078.7−0.87M BAC20757 Unknown protein
384,1265.0−0.65M5113.m00174Unknown protein
321,83112.5−1.27M AAM22746 Unknown protein

Proteins were identified either from gel spots derived from IEF/SDS-PAGE (2-D PAGE), BN SDS-PAGE (BN-PAGE), or HPLC separation of total digested mitochondrial samples (LC-MS). Numerals in 2D-PAGE and BN-PAGE columns are spot nos. for reference to Figures 1 and 2. Numerals in the LC-MS column are the no. of peptides matches to each predicted protein sequence. The Mr, pI, and hydropathicity (GRAVY) for each predicted protein sequence are shown along with prediction of targeting by TargetP (TP), Predotar (PT), and MitoProtII (MP). Asterisks in final columns indicate the presence of orthologs in the IEF/SDS-PAGE proteome reports from Arabidopsis (At; Kruftet al., 2001; Millar et al., 2001) and pea (Ps; Bardel et al., 2002). Several other Arabidopsis proteins identified elsewhere by a variety of different electrophoresis techniques have also been included for comparison: a, Sweetlove et al.(2002); b, Millar and Heazlewood (2003); and c,Werhahn and Braun (2002). Spot 62 from IEF/SDS-PAGE was identified as bovine serum albumin, used in the preparation of mitochondria, and has not been included in the table.