Table II.
Identification of two-dimensional separated protein spots from purified Arabidopsis mitochondria using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) spectra of trypsinated peptides matched against TrEMBL (TE), Genbank (GB), and the Arabidopsis Information Resource (AT) database (DB) entries
| Sample | DB | Entry | Details of Match | No. MP | Percentage Covered | MM (Da) Match | pl Match | Molecular Mass (Da) Gel | pl Gel | DMA | TargetP | MitoProt | Psort | GRAVY |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Tricarboxylic acid cycle | ||||||||||||||
| 3 | TE | O82661 | Succinyl-CoA-ligase α subunit | 7 | 31 | 36,152 | 8.7 | 36,000 | 7.6 | S | C5 | 0.9709 | Mma (0.898) | 0.000 |
| 100 | TE | O82662 | Succinyl-CoA-ligase β subunit | 9 | 27 | 45,346 | 6.7 | 44,000 | 5.4 | S | M2 | 0.9344 | Mma (0.508) | −0.053 |
| 101, 116, 165 | TE | Q9SIB9 | Aconitate hydratase | 10, 17, 18 | 15, 22, 33 | 98,155 | 6.1 | 93,000–98,000 | 5.9–6.3 | S | 2 | 0.0215 | C (0.450) | −0.184 |
| 21 | TE | Q9SZ36 | Aconitase hydratase | 9 | 15 | 98,953 | 6.2 | 97,000 | 5.8 | S | 2 | 0.0479 | C (0.450) | −0.161 |
| 15, 108 | TE | Q9M5K2 | Lipoamide dehydrogenase | 10, 14 | 36, 43 | 53,986 | 6.6 | 53,000–57,000 | 6.3–6.7 | PM | M1 | 0.9858 | Mma (0.845) | −0.023 |
| 86 | GB | AAF34795 | Lipoamide dehydrogenase | 12 | 34 | 52,872 | 6.5 | 52,000 | 6.7 | N | M3 | 0.9678 | Mma (0.845) | −0.041 |
| 44 | TE | O48685 | Pyruvate dehydrogenase E1 α subunit | 11 | 31 | 43,359 | 8.3 | 42,000 | 7.1 | N | M5 | 0.9982 | Mma (0.810) | −0.317 |
| 132 | TE | Q9SXC2 | Pyruvate dehydrogenase E1 α subunit | 12 | 23 | 43,059 | 7.6 | 41,000 | 6.8 | N | C5 | 0.9995 | Mma (0.903) | −0.330 |
| 18 | SP | ODPB_ARATH | Pyruvate dehydrogenase E1 β subunit | 6 | 21 | 39,188 | 5.8 | 37,000 | 5.2 | S | M1 | 0.9103 | Mma (0.788) | −0.002 |
| 56, 34 | TE | Q9ZP06 | Malate dehydrogenase | 5, 9 | 25, 37 | 35,805 | 8.7 | 35,000–37,000 | 5.7–6.5 | S | M4 | 0.9980 | Mma (0.920) | 0.165 |
| 87 | TE | P93033 | Fumarase | 9 | 34 | 52,830 | 8.2 | 50,000 | 7.5 | S | M4 | 0.6453 | Cls (0.826) | −0.168 |
| 104, 33 | TE | O64869 | Citrate synthase | 15, 13 | 39, 37 | 52,783 | 6.8 | 48,000 | 6.2–6.4 | S | M2 | 0.9710 | Mma (0.883) | −0.211 |
| 112 | TE | O65501 | NAD-isocitrate dehydrogenase subunit 1 | 11 | 28 | 39,627 | 8.5 | 41,000 | 7.2 | N | M2 | 0.9855 | Mma (0.576) | −0.050 |
| Electron transport chain | ||||||||||||||
| 46 | TE | O82663 | Succinate dehydrogenase α subunit | 15 | 32 | 69,657 | 6.2 | 69,000 | 5.5 | PM | M2 | 0.9416 | Mma (0.810) | −0.355 |
| 72 | SP | NUIM_ARATH | NADH-ubiquinone reductase 23-kDa subunit | 9 | 31 | 25,503 | 5.4 | 29,000 | 4.3 | N | M1 | 0.9680 | Mma (0.920) | −0.559 |
| 80 | SP | NUHM_ARATH | NADH-ubiquinone reductase 24-kDa subunit | 6 | 29 | 27,182 | 8 | 31,000 | 6 | N | M2 | 0.8675 | Mma (0.717) | −0.381 |
| 20 | GB | BAB10432 | NADH-ubiquinone reductase 13-kDa subunit | 6 | 35 | 19,179 | 4.7 | 22,000 | 4.3 | N | M2 | 0.8923 | Mma (0.470) | −0.478 |
| 22 | GB | BAB10668 | NADH-ubiquinone reductase 75-kDa subunit | 5 | 16 | 81,183 | 6.2 | 80,000 | 5.8 | PM | M3 | 0.9890 | Mma (0.648) | −0.129 |
| 91 | GB | AAG51074 | NADH-ubiquinone reductase B14 subunit | 7 | 58 | 15,082 | 9.1 | 16,000 | 9.5 | N | M5 | 0.2240 | C (0.450) | −0.238 |
| 4 | SP | ATPO_ARATH | ATP synthase Δ chain | 9 | 54 | 26,207 | 9.7 | 26,000 | 7.5 | PM | M4 | 0.8111 | Mma (0.683) | −0.106 |
| 24 | SP | ATP0_ARATH | ATP synthase α chain | 13 | 36 | 54,971 | 6.5 | 56,000 | 6.4 | PM | 4 | 0.2910 | Mma (0.479) | −0.070 |
| 23 | TE | O24345 | ATP synthase, β subunit | 10 | 36 | 49,135 | 5.3 | 57,000 | 5.4 | PM | – | – | – | – |
| 164 | TE | Q9SJ12 | ATP synthase Fad subunit | 8 | 38 | 27,597 | 6.6 | 31,000 | 5.3 | PM | M1 | 0.9000 | N (0.760) | −0.656 |
| 1 | GB | T46100 | ATP synthase D subunit | 8 | 48 | 19,586 | 5.1 | 23,000 | 4.8 | PM | 3 | 0.5303 | C (0.450) | −0.896 |
| 170 | TE | Q9SUU5 | Ubiquinol-cytochrome c reductase | 7 | 40 | 14,527 | 9.9 | 15,000 | 9.9 | N | M4 | 0.8264 | C (0.450) | −0.633 |
| 151 | TE | Q9SSB8 | Cytochrome c oxidase VB subunit | 6 | 29 | 18,583 | 5.7 | 15,000 | 4 | N | C4 | 0.9175 | Mma (0.759) | −0.321 |
| 82 | TE | Q9SRR8 | Adrenodoxin/mitochondrial ferridoxin | 5 | 30 | 17,602 | 8.3 | 17,000 | 5.7 | N | C5 | 0.9430 | Cls (0.623) | −0.275 |
| 10 | TE | Q9SRK3 | MN superoxide dismutase | 8 | 55 | 25,444 | 8.7 | 26,000 | 6.5 | S | M2 | 0.9609 | Mma (0.699) | −0.338 |
| 79 | GB | BAA96953 | UQ biosynthesis methyltransferase | 5 | 25 | 32,290 | 6.7 | 31,000 | 5.9 | N | M2 | 0.9970 | Mma (0.920) | −0.166 |
| Membrane carriers | ||||||||||||||
| 57, 96 | TE | Q9SRH5 | V-DEP anion-selective channel protein | 8, 8 | 45, 47 | 29,425 | 9 | 30,000–31,000 | 9.3–9.5 | IM | 2 | 0.1328 | N (0.760) | −0.114 |
| 14, 128 | TE | Q9SMX3 | V-DEP anion-selective channel protein | 7, 8 | 43, 51 | 29,211 | 8.4 | 30,000 | 8.1–9.2 | IM | 3 | 0.1576 | P (0.560) | −0.183 |
| RNA metabolism and translational apparatus | ||||||||||||||
| 47, 94, 168 | TE | Q9ZT91 | Mitochondrial elongation factor TU | 12, 12, 22 | 41, 39, 52 | 49,410 | 6.6 | 43,000 | 5.4–6.2 | N | C5 | 0.8743 | Cls (0.570) | −0.117 |
| 102, 103 | TE | Q9SHD6 | Mitochondrial elongation factor G | 9, 20 | 16, 31 | 83,112 | 6.3 | 86,000 | 6.7–6.8 | S | M4 | 0.8737 | ERm (0.600) | −0.259 |
| 145 | TE | O82505 | Translation elongation factor TS | 10 | 27 | 43,566 | 6 | 40,000 | 5.3 | N | M4 | 0.9538 | Mma (0.704) | −0.129 |
| 2 | TE | Q39105 | Gly-rich RNA-binding protein | 4 | 41 | 15,702 | 6.7 | 15,000 | 5.1 | S | M4 | 0.7432 | P (0.640) | −0.294 |
| 163 | GB | BAB01770 | Dead-box RNA helicase | 17 | 32 | 65,359 | 9.5 | 61,000 | 9.3 | N | M3 | 0.9822 | Mma (0.867) | −0.315 |
| Heat shock protein, chaperonin, and protein processing | ||||||||||||||
| 97 | GB | 116229 | Chaperonin 60 | 4 | 11 | 61,351 | 5.7 | 66,000 | 5.2 | S | M3 | 0.9898 | Mma (0.685) | −0.069 |
| 45 | TE | O49314 | Chaperonin 60 | 11 | 35 | 55,254 | 5.3 | 66,000 | 5.3 | S | 1 | 0.0495 | C (0.450) | −0.023 |
| 32, 99 | TE | Q9SZJ3 | Heat shock protein 70 | 10 | 18, 22 | 71,174 | 5.3 | 67,000, 74,000 | 4.8, 5.1 | S | C5 | 0.8846 | Cls (0.520) | −0.298 |
| 28 | GB | T49939 | Heat shock protein 70 | 13 | 35 | 72,991 | 5.6 | 74,000 | 5.3 | S | M4 | 0.9879 | Mma (0.907) | −0.306 |
| 30 | TE | Q9S7E7 | Putative heat shock protein 90 | 18 | 33 | 90,956 | 5.3 | 94,000 | 4.8 | IM | M4 | 0.9919 | Mma (0.793) | −0.600 |
| 31 | TE | Q9SIF2 | Putative heat shock protein 90 | 9 | 16 | 88,663 | 5 | 90,000 | 4.5 | N | C3 | 0.7324 | N (0.600) | −0.552 |
| 65 | GB | BAB09831 | ATP-DEP protease (clpP-like) | 8 | 30 | 26,283 | 6.7 | 27,000 | 6.4 | S | M3 | 0.7529 | P (0.640) | 0.031 |
| 25, 167 | TE | Q9SGA7 | Processing peptidase β subunit | 12, 18 | 34, 39 | 59,160 | 6.7 | 56,000, 61,000 | 5.6, 6.2 | IM | M2 | 0.9910 | Mma (0.920) | −0.342 |
| 17 | TE | Q9ZU25 | Processing peptidase α subunit | 12 | 32 | 54,402 | 6.2 | 54,000 | 5.3 | IM | M3 | 0.9556 | Mma (0.898) | −0.126 |
| 13 | TE | O04331 | Prohibitin | 9 | 51 | 30,400 | 7.7 | 31,000 | 7.5 | IM | S2 | 0.5098 | C (0.450) | −0.013 |
| 58 | TE | O49460 | Prohibitin | 6 | 33 | 31,707 | 9.5 | 32,000 | 9.7 | IM | 3 | 0.5580 | ERm (0.550) | −0.128 |
| 156 | TE | Q9ZNT7 | Prohibitin 2 | 10 | 50 | 31,811 | 9.6 | 31,000 | 9.8 | IM | S2 | 0.5916 | C (0.650) | −0.155 |
| 166 | TE | Q9SIL6 | Prohibitin | 12 | 58 | 31,637 | 9.9 | 31,000 | 9.8 | IM | 4 | 0.3587 | ERm (0.550) | −0.140 |
| 169 | GB | BAB02123 | Prohibitin | 10 | 44 | 30,638 | 6.9 | 31,000 | 6.7 | IM | S1 | 0.3396 | Cls (0.471) | −0.083 |
| 89 | GB | BAB03165 | TOM40 protein receptor | 11 | 39 | 32,316 | 5.9 | 37,000 | 6.8 | IM | 2 | 0.0737 | P (0.397) | −0.224 |
| Carbon metabolism | ||||||||||||||
| 16 | TE | Q9SU63 | NAD+ aldehyde dehydrogenase | 12 | 35 | 58,589 | 7.6 | 56,000 | 6 | S | M3 | 0.9988 | Mma (0.920) | −0.072 |
| 158 | GB | BAB11503 | Proline/aldehyde dehydrogenase | 7 | 20 | 61,742 | 6.3 | 62,000 | 6.5 | N | M3 | 0.9841 | Mma (0.808) | −0.159 |
| 40, 43 | TE | Q43314 | Glutamate dehydrogenase 1 | 5, 8 | 15, 25 | 44,524 | 6.8 | 43,000 | 7–7.4 | S | M4 | 0.6226 | Mma (0.665) | −0.174 |
| 41 | TE | Q38946 | Glutamate dehydrogenase 2 | 10 | 34 | 44,699 | 6.4 | 44,000 | 6.5 | PM | M3 | 0.7886 | Mma (0.659) | −0.148 |
| 26 | TE | Q9SEK4 | Succinic semialdehyde dehydrogenase | 17 | 48 | 56,559 | 6.9 | 57,000 | 5.6 | PM | M3 | 0.9856 | Mma (0.601) | 0.036 |
| 54 | SP | CYSM_ARATH | Cys synthase | 8 | 26 | 45,149 | 8.8 | 39,000 | 5.5 | N | C4 | 0.9698 | Mma (0.741) | −0.086 |
| 76 | TE | O64530 | 3-Mercapopyruvate sulphurtransferase | 9 | 28 | 41,893 | 6.3 | 37,000 | 5 | N | C4 | 0.9860 | Mma (0.814) | −0.292 |
| 107 | TE | Q9SWG0 | Isovaleryl-CoA-dehydrogenase | 7 | 18 | 44,772 | 7.9 | 43,000 | 5.9 | N | M3 | 0.9893 | Mma (0.884) | −0.181 |
| 27 | TE | Q9SI43 | Methylmalonate semi-aldehyde DH | 6 | 11 | 65,927 | 9 | 59,000 | 5.7 | PM | M4 | 0.7168 | P (0.300) | −0.176 |
| 111 | GB | U15026 | Asp aminotransferase | 12 | 32 | 47,758 | 8.5 | 41,000 | 7.8 | N | M4 | 0.9264 | Mma (0.674) | −0.303 |
| 154 | GB | AAF827821 | Ala aminotransferase | 8 | 15 | 59,807 | 5.9 | 60,000 | 5.2 | N | M5 | 0.8319 | Mma (0.609) | −0.254 |
| 141 | TE | Q9SZ48 | Enoyl-CoA hydratase-like protein | 6 | 24 | 46,063 | 5.1 | 48,000 | 4.6 | N | M1 | 0.8055 | Mma (0.647) | −0.171 |
| 130 | TE | Q9SMN1 | Acetyltransferase-like protein | 4 | 26 | 27,956 | 9 | 28,000 | 7.9 | N | M5 | 0.9958 | Mma (0.908) | 0.041 |
| 11 | GB | AAG52641 | Acetyltransferase-like protein | 12 | 59 | 30,065 | 6.7 | 32,000 | 7.3 | IM | M2 | 0.7411 | C (0.650) | −0.157 |
| 131 | GB | BAB10927 | Ferripyrochelin-binding protein-like | 6 | 50 | 22,601 | 5.6 | 33,000 | 7.5 | IM | 2 | 0.0480 | C (0.650) | −0.223 |
| 50 | TE | O82514 | Adenylate kinase | 7 | 41 | 26,934 | 8.5 | 32,000 | 7 | PM | 2 | 0.0150 | C (0.450) | −0.400 |
| 53 | TE | O23443 | Isomerase like protein | 5 | 33 | 24,154 | 7.6 | 27,000 | 6.9 | S | M5 | 0.9880 | Mma (0.464) | −0.023 |
| Unknown function | ||||||||||||||
| 19 | TE | Q9SX77 | Unknown function | 6 | 36 | 28,106 | 6.6 | 20,000 | 4.2 | N | M2 | 0.3842 | C (0.650) | −0.323 |
| 105 | TE | Q9SZT3 | Unknown function | 13 | 30 | 54,217 | 7.9 | 48,000 | 6 | N | M3 | 0.0709 | Mma (0.681) | −0.363 |
| 106, 148 | TE | Q9T082 | Stomatin like protein | 11, 11 | 23, 24 | 55,923 | 5.2 | 47,000, 49,000 | 5.8, 5.9 | IM | M3 | 0.9912 | Mma (0.497) | −0.375 |
| 48 | GB | T50795 | Bacterial inosine-5′-MP dehydrogenase-like | 8 | 38 | 22,729 | 9.1 | 19,000 | 7.8 | N | M5 | 0.8549 | C (0.650) | −0.224 |
| 125 | GB | AAF75065 | Unknown function | 5 | 23 | 21,410 | 5.5 | 22,000 | 5.6 | PM | C2 | 0.0148 | Cls (0.871) | −0.339 |
| 143 | TE | Q9SHJ6 | Unknown function | 7 | 27 | 36,119 | 4.8 | 42,000 | 4.3 | N | 1 | 0.0048 | PM (0.700) | −0.844 |
| 144 | AT | AT2G28000 | Unknown function | 12 | 25 | 62,072 | 5.1 | 65,000 | 4.5 | N | C2 | 0.9984 | Cls (0.927) | 0.002 |
| 78 | TE | Q9ZVC3 | Unknown function | 9 | 42 | 30,558 | 5.4 | 34,000 | 5.3 | PM | 5 | 0.1412 | P (0.559) | −0.409 |
| 124 | TE | O25390 | Bacterial oxidoreductase-like | 5 | 28 | 32,941 | 6 | 35,000 | 5.8 | N | 4 | 0.2212 | P (0.640) | −0.159 |
No. MP, No. of peptides matching ± 50 ppm to predicted protein sequence; percentage covered, percentage of predicted protein sequence covered by matched peptides; predicted molecular mass and pI of matched sequence and observed MM and pI of the sample is from the gel in Figure 3. TargetP, Predicted localization of sequence by TargetP; M1–5, mitochondrial; C1–5, chloroplast; S1–5, secretory pathway; 1–5, other (1, high probability; 5, low probability); MitoProt, probability of mitochondrial targeting (P = 0–1); Psort, predicted localization; Mma, mitochondrial matrix; Cls, chloroplast; C, cytosol; N, nucleus; ER, endoplasmic reticulum; PM, plasma membrane; P, peroxisome (P = 0–1). DMA, Degree of membrane association as determined from Figure 2; GRAVY, grand average of hydropathicity index calculated using the matched protein sequence.