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	M_r	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 M_r, 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.