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 Class | 2D-PAGE | BN-PAGE | LC-MS | Mr | pl | GRAVY | TP | PT | MP | Accession No. | Protein | At | Ps |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ATP synthase | 11, 12, 64 | 19, 32, 50, 51, 52 | 2 | 55,281 | 5.9 | −0.11 | – | – | – | 2832.m00083, CAA35787 | ATP synthase alpha-subunit | * | * |
| 14 | 18, 31 | 10 | 59,059 | 6.8 | −0.10 | M | M | M | Q01859 | ATP synthase beta-subunit | * | ||
| 17 | 37 | 25,065 | 10.1 | −0.16 | M | M | M | 1903.m00144 | ATP synthase OSCP subunit | * | |||
| 29, 30 | 22 | 3 | 24,359 | 5.0 | −0.71 | – | – | – | TC63644, 3067.m00121 | ATP synthase delta-subunit | * | * | |
| 31 | 38 | 21,213 | 6.0 | 0.15 | M | M | M | 2119.m00096, BAC21366 | ATP synthase delta-subunit | * | * | ||
| 51 | 20, 35 | 4 | 40,955 | 8.5 | −0.10 | – | – | – | 3695.m00193, TC72968 | ATP synthase gamma-subunit | b | ||
| 42, 23 | 6937 | 10.8 | −0.30 | M | M | – | BAB21526 | ATP synthase 6-kD subunit | |||||
| 23 | 7877 | 10.9 | 0.84 | C | C | – | P14863 | ATP synthase subunit 9 | |||||
| 28 | 21 | 2 | 38,217 | 5.0 | −0.44 | M | M | M | 2485.m00122 | ATP synthase FAd subunit | * | * | |
| Complex I | 26 | 2 | 12,492 | 6.7 | −0.99 | – | – | – | AAL67582 | NADH dehydrogenase PDSW subunit | |||
| 76 | 12,033 | 7.6 | −0.22 | M | M | – | 3640.m00126 | NADH dehydrogenase B22 subunit | * | ||||
| 71 | 12 | 23,498 | 4.9 | −0.57 | M | M | – | 3550.m00121 | NADH dehydrogenase (23 kD) | * | |||
| 43 | 57 | 18,518 | 7.1 | −0.90 | M | – | – | 387.m00162 | NADH dehydrogenase B17.2 | ||||
| 4 | 3 | 4 | 81,117 | 6.1 | −0.17 | M | M | M | AAL58200 | NADH dehydrogenase 75-kD subunit | * | ||
| 4, 8, 9 | 1 | 44,309 | 9.6 | −0.08 | M | – | M | 2451.m00084 | NADH dehydrogenase (39 kD) | ||||
| 4, 5 | 56,301 | 8.2 | −0.31 | M | M | M | 2102.m00066 | NADH dehydrogenase (51 kD) | |||||
| 6, 7 | 44,252 | 7.1 | −0.49 | C | – | – | BAC19866 | NADH dehydrogenase subunit 7 | |||||
| 13 | 22,594 | 8.2 | −0.78 | – | – | – | BAA08794 | NADH dehydrogenase subunit 9 | |||||
| 14, 15 | 1 | 21,829 | 4.6 | −0.24 | M | M | M | TC76675, 4381.m00118 | NADH dehydrogenase 13-kD subunit | * | |||
| 16 | 2 | 28,762 | 9.6 | −0.30 | M | M | M | TC79833, 4342.m00113 | NADH dehydrogenase E 16.6-kD subunit | ||||
| Complex III | 24 | – | – | – | – | – | – | TC79968 | Mitochondrial-processing peptidase beta-subunit | * | |||
| 2 | 25 | 53,946 | 7.2 | −0.10 | M | M | – | 2599.m00145, 2709.m00160 | Mitochondrial-processing peptidase alpha-subunit | * | |||
| 27 | 1 | 29,820 | 8.6 | −0.16 | M | M | M | 2341.m00134 | Reiske Fe-S protein | c | |||
| 28 | 16,616 | 9.8 | −0.34 | M | M | M | 2070.m00100, 3403.m00173 | Ubiquinol cytochrome c reductase (14 kD) | * | ||||
| 29, 23 | 13,086 | 10.8 | 0.41 | – | M | M | 3017.m00162, 3017.m00172 | Ubiquinol cytochrome c reductase (8.2 kD) | |||||
| 2 | 33,293 | 6.2 | −0.19 | M | M | M | 2974.m00152 | Cytochrome c1 precursor | c | ||||
| Complex IV | 32 | 18,912 | 4.0 | −1.01 | – | – | – | BAA76393 | Cytochrome c oxidase subunit VIb-1 | ||||
| 33 | 41 | 18,047 | 4.8 | −0.42 | M | M | M | T03033 | Cytochrome c oxidase subunit Vb | * | |||
| 77 | 13,930 | 9.7 | 0.06 | M | M | M | 3550.m00112 | Cytochrome c oxidase subunit Via | |||||
| 44 | 57,767 | 8.6 | 0.69 | – | – | – | P14578 | Cytochrome c oxidase subunit I | |||||
| Pyruvate and | 53 | 47, 48 | 3 | 52,643 | 7.6 | 0.13 | M | M | M | BAB39219, 2726.m00149 | Dihydrolipoamide dehydrogenase (E3) | * | * |
| 2-OG DH | 2 | 55,896 | 7.4 | 0.08 | M | M | M | 3313.m00119 | Dihydrolipoamide dehydrogenase (E3) | * | * | ||
| complexes | 16, 41 | 39,950 | 4.8 | −0.03 | M | – | M | TC57558, 3493.m00141 | Pyruvate dehydrogenase E1 beta-subunit | * | * | ||
| 66 | 59,591 | 8.7 | −0.17 | M | M | M | 3634.m00180 | Dihydrolipoamide acetyltransferase (E2) | a | * | |||
| 52 | 3 | 48,894 | 9.5 | −0.33 | M | M | M | 2307.m00126 | Dihydrolipoamide succinyltransferase (E2) | a | |||
| 2 | 48,283 | 9.1 | −0.30 | – | – | – | CAD40552 | Dihydrolipoamide succinyltransferase (E2) | a | ||||
| 2 | 123,768 | 6.5 | −0.44 | M | M | M | 4591.m00151 | 2-Oxoglurate dehydrogenase E1 | |||||
| Succinyl-CoA | 48, 22 | 34,246 | 8.4 | 0.08 | M | M | M | 2046.m00126 | Succinyl-CoA ligase alpha-subunit | * | |||
| ligase | 15 | 49 | 3 | 45,091 | 6.2 | −0.03 | M | M | M | 2466.m00139 | Succinyl-CoA ligase beta-subunit | * | |
| Isocitrate DH | 40, 49 | 40,629 | 8.1 | −0.06 | M | M | M | 2447.m00175 | NAD-dependent isocitrate dehydrogenase | * | |||
| Malate DH | 20, 21, 47 | 2 | 35,461 | 8.9 | 0.08 | M | M | M | BAB55686, 2720.m00059 | Malate dehydrogenase | * | * | |
| 53 | 4 | 35,436 | 8.3 | 0.14 | M | – | M | 3321.m00193, 2990.m00151 | Putative malate dehydrogenase | * | * | ||
| Citrate synthase | 58 | 2 | 52,121 | 7.2 | −0.07 | M | M | M | AAG28777, 2942.m00114 | Citrate synthase | * | * | |
| Malic enzyme | 30 | 70,721 | 5.9 | −0.19 | M | M | M | 2119.m00105 | NAD-dependent malic enzyme 62-kD subunit | ||||
| 44 | 57,143 | 8.3 | −0.16 | C | – | – | AAG13628 | NAD-dependent malic enzyme 59-kD subunit | |||||
| Complex II | 37 | 59,103 | 6.2 | −0.40 | – | – | – | 2338.m00147 | Succinate dehydrogenase FP alpha-subunit | * | |||
| Aconitase | 36, 63 | 107,452 | 7.3 | −0.18 | C | – | M | TC61943, 4161.m00311 | Aconitate hydratase | * | |||
| 65 | 98,397 | 5.9−0.15 | – | – | – | TC68934, 5178.m00213 | Aconitate hydratase | * | |||||
| GDC | 34 | 4 | 17,367 | 4.7 | −0.23 | M | M | M | AAK39594 | Gly decarboxylase H protein | * | ||
| 73, 80, 56, 57 | 3 | 29,224 | 6.5 | −0.16 | – | – | – | 2329.m00191 | Aminomethyltransferase precursor (T protein) | * | |||
| 54, 55 | 54,979 | 8.4 | −0.29 | M | M | M | TC52724, 4124.m00171 | Ser hydroxymethyltransferase (SHMT) | * | ||||
| General | 59 | 47,875 | 6.6 | −0.15 | M | M | – | 1207.m00066 | Glutamate dehydrogenase 2 | * | * | ||
| metabolism | 60 | 33 | 40,631 | 6.7 | −0.19 | M | M | M | 2275.m00146 | Glutamate dehydrogenase | * | * | |
| 70 | 2 | 43,762 | 6.8 | −0.18 | M | M | M | 1904.m00155 | NAD-dependent formate dehydrogenase | * | |||
| 50 | 41,243 | 7.4 | −0.21 | M | M | M | BAA77337 | NAD-dependent formate dehydrogenase | * | ||||
| 68 | 1 | 45,255 | 9.6 | −0.21 | – | – | – | 1902.m00219 | Aldehyde dehydrogenase | * | * | ||
| 13 | 59,307 | 6.8 | −0.04 | M | M | M | BAB19052 | Aldehyde dehydrogenase | * | * | |||
| 67 | 2 | 87,073 | 8.4 | −0.10 | M | M | M | 4976.m00233 | Aldehyde dehydrogenase | * | * | ||
| 1 | 56,106 | 5.8 | −0.02 | C | C | – | 4694.m00128 | Aldehyde dehydrogenase | * | * | |||
| 9, 10 | 56,980 | 6.3 | −0.03 | M | M | M | AAC03055 | Methylmalionate semi-aldehyde dehydrogenase | * | * | |||
| 79 | – | – | – | – | – | – | TC59081, TC66764 | Thiosulfate sulfurtransferase | * | ||||
| 38 | 47,495 | 7.8 | −0.25 | M | M | M | JC5125 | Asp transaminase | * | ||||
| 39 | – | – | – | – | – | – | TC54297 | Isovaleryl-CoA dehydrogenase | * | ||||
| 27 | 25,425 | 9.4 | −0.09 | C | C | – | TC62983, 4134.m00168 | Inosine-5′-monophosphate dehydrogenase | * | ||||
| 2 | 252,808 | 6.4 | −0.28 | – | – | – | 4000.m00165 | Acetyl-CoA carboxylase | |||||
| 2 | 36,812 | 8.9 | −0.14 | M | M | M | 2884.m00186 | Formyl transferase | |||||
| 2 | 80,029 | 6.6 | −0.21 | C | – | M | 3385.m00173, 3006.m00143 | Transketolase | |||||
| 2 | 29,775 | 10.6 | −0.32 | – | – | – | 2541.m00142 | Triacylglycerol lipase | |||||
| 46 | 35,327 | 8.2 | −0.09 | – | – | – | 2329.m00193 | (S)-2-hydroxy-acid oxidase | |||||
| Import | 75 | 10,843 | 5.9 | −0.59 | – | – | – | Q9XGX7 | Translocase of inner membrane 9 (TIM9) | ||||
| 57 | 15,677 | 9.0 | 0.12 | – | – | – | 2461.m00155 2506.m00124 | Translocase of inner membrane 17 (TIM17) | |||||
| 34 | 37,956 | 6.8 | −0.13 | – | – | – | 2733.m00140 | Translocase of outer membrane 40 (TOM40) | * | ||||
| 42 | 9665 | 10.2 | −0.01 | M | – | – | 2494.m00117 3845.m00238 | Translocase of outer membrane 9 (TOM9) | |||||
| Transport | 46 | 29,220 | 7.9 | −0.16 | – | M | – | TC48593, CAB82853 | Voltage-dependent anion channel | * | |||
| 45 | – | – | – | – | – | – | TC65294 | Voltage-dependent anion channel | * | ||||
| 18 | 39, 36, 26, 54 | 27,815 | 8.7 | −0.05 | – | C | – | CAC80850, 2981.m00134 | Voltage-dependent anion channel | * | |||
| 45 | 2 | 24,534 | 7.7 | 0.01 | C | C | M | 5186.m00209 | Voltage-dependent anion channel | * | |||
| 2 | 33,663 | 9.8 | −0.12 | – | – | – | 3497.m00176 | Voltage-dependent anion channel | * | ||||
| 36 | 3 | 41,510 | 10.3 | −0.10 | C | – | – | 2506.m00136 2986.m00110 | Adenine nucleotide translocator ANT | b | |||
| 2 | 33,021 | 9.4 | 0.14 | C | – | – | 3698.m00164, 3631.m00202 | Phosphate transporter | b | ||||
| 3 | 32,802 | 10.1 | 0.10 | – | – | – | 3317.m00075 | 2-Oxoglutarate/malate translocator | b | ||||
| Ox stress | 1 | 55 | 3 | 24,947 | 7.0 | −0.10 | S | M | M | AAA57130, Q43008 | Manganese superoxide dismutase | * | * |
| 24 | 20,874 | 8.2 | 0.01 | M | M | M | BAA90363 | Peroxiredoxin | * | ||||
| 57 | 17,146 | 7.5 | −0.03 | M | M | M | 3606.m00327, 3602.m00254 | Adrenodoxin precursor | * | ||||
| Chaperones | 5 | 2 | 83,380 | 8.1 | −0.42 | M | M | M | TC51015, 4256.m00159 | Heat shock protein 70 | * | * | |
| 6, 7 | 5 | 60,850 | 5.6 | −0.08 | M | M | M | 1379.m00089, 5187.m00183 | Chaperonin 60 | * | * | ||
| 3 | 65,276 | 4.8 | −0.10 | – | – | – | 4781.m00152 | Chaperonin 60 | * | ||||
| 78, 25 | 3 | 10,643 | 9.0 | −0.09 | M | C | M | 3664.m00136, T03585 | Chaperonin 10 | * | |||
| 2 | 13,996 | 10.2 | −0.39 | M | M | M | 5140.m00090 | Chaperonin 10 | * | ||||
| 19 | 11 | 30,643 | 7.1 | 0.03 | S | – | – | 2952.m00055 | Prohibitin | * | |||
| 1, 2 | 31,413 | 10.1 | −0.24 | S | – | – | 4127.m00167, BAC07170 | Prohibitin | * | ||||
| Transcription/ | 8 | 48,423 | 6.4 | −0.06 | M | M | M | AAL5626t | Translational elongation factor T0 | * | * | ||
| translation | 35 | 15,547 | 8.9 | −0.59 | C | – | M | CAA05729 | Gly-rich RNA-binding protein | * | |||
| 2 | 97,919 | 10.8 | −0.89 | – | – | – | 3373.m00119 | DEAD box RNA helicase | * | ||||
| 3 | 127,634 | 6.3 | −0.53 | C | – | M | 3952.m00081 | DEAD box RNA helicase | * | ||||
| 2 | 172,773 | 9.1 | −0.58 | – | M | – | AAK54292 | Putative helicase | * | ||||
| 2 | 31,230 | 9.2 | −0.46 | C | – | – | 5028.m00163 | C2H2-type zinc finger protein | |||||
| 2 | 62,012 | 8.8 | 0.04 | M | M | M | AAL59047 | PPR protein | |||||
| 2 | 79,219 | 8.5 | −0.06 | M | M | – | BAB64813 | PPR protein | |||||
| 2 | 184,237 | 8.1 | −0.70 | – | – | – | 2474.m00123, 5076.m00090 | CREB-binding protein | |||||
| Miscellaneous | 69 | 29,437 | 4.2 | −0.53 | M | – | M | 2772.m00163 | Mitochondrial glycoprotein | ||||
| function | 23 | 27,499 | 7.9 | 0.12 | M | M | M | TC65865, 4358.m00206 | Ferripyochelin-binding protein | * | |||
| 44 | 11 | 26,455 | 6.4 | −0.02 | M | M | M | 2030.m00175 | Ferripyochelin-binding protein | * | |||
| 61 | 10 | 23,214 | 6.4 | −0.19 | M | – | – | TC48467, 2868.m00167 | Ferripyochelin-binding protein | * | |||
| 3 | 43 | 67,681 | 5.0 | −0.60 | M | M | M | 2249.m00144 | Mitofilin motor protein | ||||
| 47 | 60,729 | 4.4 | −0.74 | S | – | – | 2296.m00078 | Calnexin-like protein | |||||
| 1 | 72,778 | 4.8 | −0.46 | C | – | – | 2673.m00127 | ADP-ribosylation factor binding protein | |||||
| 2 | 53,280 | 6.5 | −0.30 | – | – | – | 2500.m00126 | Actin | |||||
| 2 | 39,196 | 6.1 | −0.27 | S | – | – | AAM01174 | Wall-associated kinase 2-like protein | |||||
| 2 | 28,078 | 8.3 | −0.37 | – | – | – | BAB92895 | sec14-Like protein | |||||
| 3 | 98,221 | 6.6 | −0.28 | – | – | – | 2251.m00196 | Disease resistance protein | |||||
| 2 | 94,632 | 7.6 | −0.27 | S | – | – | 4193.m00176 | Disease resistance protein | |||||
| Unknown | 42, 23 | 10,945 | 9.4 | −0.40 | – | M | – | 2419.m00150 | Unknown protein | ||||
| function | 56 | 12,914 | 7.3 | −0.21 | C | C | – | 4127.m00174 | Unknown protein | * | |||
| protein | 17 | 7466 | 10.7 | −0.55 | M | M | – | 2468.m00122, 2520.m00121 | Unknown protein | ||||
| 72 | 27,479 | 9.2 | −0.03 | M | M | M | 2284.m00104 | Unknown protein | * | ||||
| 74 | 13,273 | 8.7 | −0.13 | M | C | M | 32.m00149 | Unknown protein | |||||
| 42 | – | – | – | – | – | – | TC48363 | Unknown protein | |||||
| Unknown function | 1 | 134,187 | 5.6 | −0.20 | – | – | – | 3273.m00129 | Unknown protein | ||||
| protein | 1 | 8786 | 9.2 | −0.17 | S | – | – | 3018.m00158 | Unknown protein | ||||
| (continued) | 1 | 8101 | 9.8 | −0.50 | C | – | – | 1987.m00120 | Unknown protein | ||||
| 1 | 19,438 | 5.9 | −0.33 | – | – | – | 4958.m00111 | Unknown protein | |||||
| 3 | 126,829 | 6.7 | −0.21 | – | – | – | 4983.m00113 | Unknown protein | |||||
| 2 | 100,723 | 9.2 | −0.41 | M | M | – | 4638.m00135 | Unknown protein | |||||
| 2 | 78,515 | 10.7 | −0.72 | M | M | M | BAA84788 | Unknown protein | |||||
| 2 | 12,966 | 12.1 | −0.30 | – | C | – | AAL58157 | Unknown protein | |||||
| 3 | 75,587 | 5.8 | 0.01 | – | – | – | AAN06831 | Unknown protein | |||||
| 2 | 57,805 | 5.7 | −0.46 | M | C | – | 2366.m00159, 2275.m00133 | Unknown protein | |||||
| 2 | 48,104 | 8.7 | −0.07 | – | – | – | 2284.m00111 | Unknown protein | |||||
| 2 | 171,963 | 7.4 | −0.63 | – | M | – | 4183.m00149, 3872.m00127 | Unknown protein | |||||
| 2 | 69,967 | 8.7 | −0.37 | C | – | – | 2475.m00089 | Unknown protein | |||||
| 2 | 48,779 | 8.7 | −0.21 | M | M | M | 2631.m00097 | Unknown protein | |||||
| 2 | 129,607 | 8.7 | −0.87 | M | – | – | BAC20757 | Unknown protein | |||||
| 3 | 84,126 | 5.0 | −0.65 | M | – | – | 5113.m00174 | Unknown protein | |||||
| 3 | 21,831 | 12.5 | −1.27 | M | – | – | 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; Kruft et 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.