Table I. Comparative DIGE analysis of the Arabidopsis ftsh4 mitochondrial proteomes

Protein spots with abundances differing between ftsh4 and the wild type were identified by PMF.

Protein Spot No.Accession No. (TAIR)Name of the ProteinStatistical Analysis
2D-DIGE, LD at 30°C2D-DIGE, SD at 22°C
ftsh4-1/Wild TypeaPftsh4-2/Wild TypeaPftsh4-1/Wild TypeaP
Complex I
1ATMG00510.1NADH dehydrogenase subunit 7 (NAD7)[2.03][0.02]1.480.04
2AT5G37510.1NADH-ubiquinone oxidoreductase subunit 75 kD−1.50.03−1.670.01−3.040
3AT1G47260.1γ-Carbonic anhydrase2 (CA2)2.0802.780.041.980.01
4AT5G66510.1γ-Carbonic anhydrase3 (CA3)−1.440.04−1.290.02
ATP synthase
5ATMG01190.1ATP synthase subunit α (ATP1)−1.60−1.490.02−2.010.02
6AT5G08670.1, AT5G08690.1, AT5G08680.1ATP synthase subunit β (ATP2)−1.260.01−1.480.02−3.390
7AT5G08670.1, AT5G08690.1, AT5G08680.1ATP synthase subunit β (ATP2)[−1.27][0.1]−1.930.01
8AT5G08670.1, AT5G08690.1, AT5G08680.1ATP synthase subunit β (ATP2)[−1.5][0]−1.540.03−1.260
9AT5G08670.1, AT5G08690.1, AT5G08680.1ATP synthase subunit β (ATP2)−1.270.11
10AT3G52300.1ATP synthase D subunit (ATPQ)−1.480.04−1.670
11AT2G21870.1ATP synthase subunit Fad (MGP1)−1.60.01[−1.45][0.05][−2.7][0.01]
Tricarboxylic acid cycle
12AT2G44350.1Citrate synthase (ATCS)−1.040.05−1.320.01−1.430
13AT4G26970.1Aconitase2 (ACO2)[−1.65][0.03]−4.850−2.940.02
14AT5G03290.1NAD+-dependent isocitrate dehydrogenase V (IDH-V)−1.430.03
15AT5G65750.12-Oxoglutarate dehydrogenase E1 subunit[−1.45][0.03]−1.650.03
16AT2G20420.1Succinyl-CoA ligase β-subunit−1.340.04−1.460.031.260.01
17AT5G66760.1Succinate dehydrogenase flavoprotein subunit (SDH1-1)1.960.011.370.0414.510.01
18AT2G47510.1Fumarase1 (FUM1)1.590.011.30.051.020.01
19AT3G15020.2Malate dehydrogenase2 (MDH2)−1.130.04−1.30.02
Tricarboxylic acid cycle adjacent
20AT5G18170.1Glu dehydrogenase1 (GDH1)1.870.01−1.080.04
21AT5G07440.1Glu dehydrogenase2 (GDH2)−1.340.01[−1.12][0.01]
22AT3G22200.1γ-Aminobutyrate transaminase (GABA-T)−1.450.04[−1.25][0.85]
Photorespiration and one-carbon metabolism
23AT4G33010.1Gly decarboxylase P-protein1 (GLDP1)[−1.87][0.01][−1.32][0.01]−3.210
24AT2G26080.1Gly decarboxylase P-protein2 (GLDP2)−1.30.05−1.040−2.940.02
25AT1G48030.1Lipoamide dehydrogenase (MTLPD1)1.20.051.430
26AT1G11860.1Aminomethyltransferase (GDC-T)1.360.021.250.06
28AT4G37930.1Ser transhydroxymethyltransferase1 (SHM1)−2.850
29AT4G37930.1Ser transhydroxymethyltransferase1 (SHM1)1.660.031.150.05[−1.32][0.04]
30AT4G37930.1Ser transhydroxymethyltransferase1 (SHM1)1.220.021.130.04
31AT5G14780.1Formate dehydrogenase (FDH)[1.45][0.11]2.140.01
Amino acid metabolism
32AT3G45300.1Isovaleryl-CoA dehydrogenase (IVDH)1.30.041.420.05
33AT5G62530.1Pyrroline-5-carboxylate dehydrogenase (P5CDH)−1.50[−1.26][0]
34AT3G61440.1Cys synthase C1 (ATCYSC1)−1.180−1.070.09−1.470
35AT3G59760.3O-Acetyl-Ser(thiol)lyase (OAS-C)−1.820.04[−1.94][0.04]
36AT4G08870.1Arg amidohydrolase2 (ARGAH2)−2.150.01
Chaperones and stress related
37AT3G13860.1Heat shock protein60-3A (HSP60-3A)3.20.01
38AT2G33210.1Heat shock protein60-2 (HSP60-2)1.630.05[1.25][0.02]1.420.01
39AT2G33210.1Heat shock protein60-2 (HSP60-2)1.380.43
40AT4G37910.1Heat shock protein70-1 (mtHSP70-1)1.620.02[1.6][0]
41AT5G09590.1Heat shock protein70-2 (mtHSP70-2)1.120.011.480.021.890
42AT5G40770.1Prohibitin3 (PHB3)1.0901.740.041.720
43AT3G10920.2Manganese superoxide dismutase1 (MSD1)1.030.051.290.011.230.04
Proteases
44AT5G26860.1LON protease1 (LON1)1.560.02
45AT1G51980.1Probable mitochondrial processing peptidase subunit α-1 (α-MPP1)−1.310.02[−1.56][0.01]−1.210.02
46AT3G02090.1Mitochondrial processing peptidase subunit β (MPPBETA)−1.010.04−1.570.02−1.020.05
Transport
47AT5G15090.1Voltage-dependent anion-selective channel3 (VDAC3)3.3501.460.01
48AT5G67500.1Voltage-dependent anion-selective channel2 (VDAC2)[1.53][0]1.420.03
49AT3G01280.1Voltage-dependent anion-selective channel1 (VDAC1)1.570.051.70
Miscellaneous
51AT3G48000.1Aldehyde dehydrogenase (ALDH2B4)−1.520
52AT4G11010.1Nucleoside diphosphate kinase3 (NDPK3)−1.250.01
53AT5G63400.1Adenylate kinase (ADK1)−1.790.01
54AT4G02930.1Elongation factor Tu (EF-Tu)−1.270.03
55AT3G07480.1Electron carrier/iron-sulfur cluster binding, ferredoxin-like1.840.03
Contaminations
56AT3G01500.1Carbonic anhydrase1 (CA1; chloroplast)−3.1401.220.05
57AT2G33150.1Peroxisomal 3-ketoacyl-CoA thiolase3 (PKT3; peroxisome, glyoxisome)−2.080.01−2.940.05
58AT2G13360.1Ala:glyoxylate aminotransferase (AGT; peroxisome)2.940.05
59AT1G20620.1Catalase3 (CAT3; peroxisome)2.2201.790.01
60AT5G14920.1Gibberellin-regulated family protein (extracellular)−2.5501.890.04
61AT1G78850.1Curculin-like (Man-binding) lectin family protein (extracellular)1.570.05
62AT4G32900.1Aminoacyl-tRNA hydrolase (cytosol)−1.330.03
63AT5G45150.1RNase3-like protein (RTL3; nucleus)−1.450.03
64AT2G20630.2Protein phosphatase2C (PP2C; cytosol)−1.650.03
65AT2G26430.1Arg-rich cyclin1 (RCY1; nucleus)−1.270.03
66AT5G60240.1Unknown protein (nucleus)−4.050
67AT1G14060.1GCK domain-containing protein (nucleus)−3.810
68AT3G16420.1PYK10-binding protein1 (PBP1)1.450
69AT1G17290.1Ala aminotransferase (ALAAT1; cytosol)−1.380.04[−1.34][0]−1.640
70AT2G29420.1Glutathione S-transferase U7 (ATGSTU7; cytosol)−1.040.06−1.870.04
  • a Fold change in abundance of ftsh4/wild type with a cutoff of 1.2 and a Student’s t test value of P ≤ 0.05. Values not passing this cutoff are shown in italics, and values in brackets correspond to spots only identified based on their positions on 2D-DIGE gels, due to technical limitations.