. 2016 Sep 21;7:1394. doi: 10.3389/fpls.2016.01394

Table 1.

The proteins changing in abundance and identified by MALDI-TOF-TOF MS in embryos during aging of Yliangyou 2 hybrid rice seeds.

Biological process	Spot ID	Identified protein	Accession No.	Mascot score	Sequence coverage (%)	No. of sequenced/matched peptides	Theo. protein mass (kDa)/pI	Exp. protein mass (kDa)/pI
METABOLISM (6)
Amino acid	10	5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 1^a	Q2QLY5	479	20	7/13	84.874/5.93	70/6.4
	11	5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 1^a	Q2QLY5	374	24	6/16	84.874/5.93	69/6.5
	34	Wheat adenosylhomocysteinase-like protein	AAO72664	1080	54	14/25	53.860/5.62	55/6.2
	40	Hypothetical protein OsI_06236 (fumarylacetoacetase)^*	EEC72678	299	53	4/18	47.659/5.62	51/6.1
Sugar and polysaccharide	52	Glucose and ribitol dehydrogenase homolog	Q75KH3	252	28	6/9	32.475/5.76	38/5.9
Lipid	22	2-Hydroxyacyl-CoA lyase^a	Q0JMH0	413	31	7/13	61.187/5.95	62/6.6
ENERGY (21)
Glycolysis	13	Os03g0712700 (phosphoglucomutase)^a	NP_001051066	239	31	3/16	63.138/5.40	65/5.9
	24	Os11g0148500 (pyruvate kinase 1, cytosolic)	NP_001065749	111	13	3/7	57.740/6.30	60/7.1
	32	Enolase	Q42971	645	46	8/17	48.285/5.41	56/5.7
	41	Phosphoglycerate kinase	ABI74567	491	56	5/19	42.224/5.64	50/6.1
	47	Glyceraldehyde-3-phosphate dehydrogenase 3, cytosolic^a	Q6K5G8	421	32	4/7	36.716/7.68	42/6.6
	49	Glyceraldehyde-3-phosphate dehydrogenase 3, cytosolic^a	Q6K5G8	1070	55	10/19	36.716/7.68	42/7.6
	65	Hypothetical protein OsI_04384 (triosephosphate isomerase)	EAY76450	471	46	7/11	27.415/5.39	31/5.7
	66	Triosephosphate isomerase, cytosolic	P48494	485	73	6/15	27.274/5.38	30/5.6
TCA cycle	14	Hypothetical protein OsJ_03416 (malic enzyme, NAD⁺-linked)^a	EAZ13499	758	27	10/16	63.556/6.50	65/7.4
Respiration	35	ATP synthase subunit beta, mitochondrial^a	Q01859	390	46	8/19	59.012/5.95	55/5.5
	36	ATP synthase subunit alpha, mitochondrial	P0C520	198	12	3/5	55.624/5.85	55/5.9
Fermentation	16	Pyruvate decarboxylase 2^a	Q10MW3	393	38	5/18	65.761/5.53	63/6.1
	17	Pyruvate decarboxylase 2^a	Q10MW3	389	33	4/17	65.761/5.53	63/6.0
	18	Pyruvate decarboxylase 2^a	Q10MW3	443	15	5/6	65.761/5.53	63/5.9
	20	Pyruvate decarboxylase 2^a	Q10MW3	142	7	3/3	65.761/5.53	63/5.7
	42	Alcohol dehydrogenase 1	Q75ZX4	458	48	6/17	41.699/6.20	48/6.8
Glyoxylate cycle	4	Putative aconitate hydratase, cytoplasmic	Q6YZX6	875	38	10/34	98.591/5.67	76/6.1
	5	Putative aconitate hydratase, cytoplasmic	Q6YZX6	615	35	9/30	98.591/5.67	75/6.3
	48	Malate dehydrogenase (cytoplasmic, NAD⁺-linked)^a	Q7XDC8	248	35	5/9	35.888/5.75	42/6.0
Photosynthesis	8	Pyruvate, phosphate dikinase 2	Q75KR1	902	40	12/38	97.232/5.42	73/6.0
	33	Ribulose bisphosphate carboxylase large chain	P0C510	718	47	14/23	53.418/6.22	56/6.7
CELL GROWTH AND DIVISION (1)
	79	Os08g0127900 (putative early embryogenesis protein)	NP_001060907	345	15	4/10	58.352/8.72	21/5.6
TRANSCRIPTION (3)
	46	Hypothetical protein OsI_22334 (methyltransferase)^*	EAZ00317	237	32	3/7	40.445/5.27	41/5.5
	63	Os01g0728700 (histone acetyltransferase)^*	NP_001044131	366	62	6/14	27.724/5.98	34/6.5
	81	Hypothetical protein OsI_27689 (glycine-rich 2)^*	EAZ05473	800	84	8/12	18.782/6.28	19/6.7
PROTEIN SYNTHESIS AND DESTINATION (7)
Protein synthesis	6	Os04g0118400 (elongation factor)^a	NP_001052057	236	17	4/14	94.939/5.85	75/6.4
	7	Os04g0118400 (elongation factor)^a	NP_001052057	648	40	11/30	94.939/5.85	74/6.5
	19	Hypothetical protein OsI_08509 (aspartyl-tRNA synthetase)^*	EEC73805	191	26	4/16	61.437/5.99	63/6.4
	39	Elongation factor 1-gamma 3	Q5Z627	253	16	3/7	47.702/6.10	54/6.8
	84	Eukaryotic translation initiation factor 5A-2^a	ABF98987	419	51	4/11	17.930/5.87	19/6.3
Protein folding	25	Putative t-complex protein 1 theta chain	BAD45605	785	33	10/17	60.683/6.16	60/6.8
Proteolysis	67	Os05g0187000 (proteasome subunit beta type)	NP_001054834	348	20	3/5	29.264/6.45	30/6.7
STORAGE PROTEIN (13)
	29	Putative globulin (with alternative splicing)^a	AAS07324	1040	46	12/21	63.845/8.35	57/7.9
	30	Putative globulin (with alternative splicing)^a	AAS07324	816	46	10/21	63.845/8.35	56/7.1
	38	Hypothetical protein OsI_13867 (globulin-like protein)^*	EEC76319	706	48	9/23	52.370/6.99	54/6.8
	51	Hypothetical protein OsI_13867 (globulin-like protein)^*	EEC76319	932	34	10/17	52.370/6.99	40/6.3
	53	Hypothetical protein OsI_13867 (globulin-like protein)^*	EEC76319	301	18	3/6	52.370/6.99	38/6.3
	56	Putative globulin (with alternative splicing)	AAS07324	330	27	5/10	63.845/8.35	36/6.1
	57	Os03g0663800 (putative globulin, with alternative splicing)^*	NP_001173574	248	15	3/6	45.512/6.07	35/5.7
	58	Os03g0663800 (putative globulin, with alternative splicing)^*	NP_001173574	222	22	4/7	45.512/6.07	36/5.4
	61	Putative globulin (with alternative splicing)^a	AAS07324	439	29	6/11	63.845/8.35	34/6.1
	62	Cupin family protein, expressed	ABF95817	195	20	4/9	61.742/7.18	34/5.9
	64	Hypothetical protein OsI_13867 (globulin-like protein)^*	EEC76319	466	28	4/16	52.370/6.99	31/6.0
	71	Globulin-like protein^a	AAM33459	294	25	3/13	52.376/6.78	27/5.8
	75	Globulin-like protein^a	AAM33459	761	23	7/13	52.376/6.78	23/5.9
CELL DEFENSE AND RESCUE (20)
Defense-related	69	Cysteine proteinase inhibitor 12	Q0JNR2	239	50	3/13	27.252/6.07	29/6.4
	83	Bowman-Birk type bran trypsin inhibitor	A2WK50	65	12	3/4	29.219/5.38	19/6.4
Detoxifacation	31	Aldehyde dehydrogenase	AAF73828	927	32	10/19	59.626/6.33	56/6.3
	54	Hypothetical protein OsI_08976 (annexin)	EAY87564	548	64	9/23	35.689/7.13	37/7.4
	55	Lactoylglutathione lyase	Q948T6	716	39	9/13	32.875/5.51	36/5.5
	60	Lactoylglutathione lyase	Q948T6	103	10	2/4	32.875/5.51	35/6.5
	68	1-Cys peroxiredoxin A	P0C5C9	237	56	4/11	24.198/5.97	29/6.3
	70	1-Cys peroxiredoxin A	P0C5C9	255	58	4/12	24.198/5.97	28/6.7
	82	Superoxide dismutase	A2XGP6	190	20	2/3	15.356/5.71	19/6.5
	85	Superoxide dismutase	P28757	255	48	2/5	15.185/5.92	17/6.7
Stress response	1	Chaperone protein ClpB1	Q6F2Y7	580	30	10/25	101.062/5.90	76/6.4
	2	Chaperone protein ClpB1	Q6F2Y7	1040	43	13/36	101.062/5.90	76/6.5
	12	Heat shock cognate 70 kDa protein, putative, expressed^a	ABF95267	237	24	4/13	71.932/5.30	67/5.6
	27	Hypothetical protein OsI_06577 (putative late embryogenesis abundant protein)^*	EEC72841	299	19	4/7	45.019/6.50	58/6.9
	28	Hypothetical protein OsI_06577 (putative late embryogenesis abundant protein)^*	EEC72841	456	40	6/17	45.019/6.50	58/7.0
	43	Late embryogenesis abundant protein 1	A2XG55	412	55	4/18	35.869/6.01	46/6.3
	44	Late embryogenesis abundant protein 1	A2XG55	227	34	3/9	35.869/6.01	46/6.1
	74	Late embryogenesis abundant protein, group 3^a	A2Y720	325	28	4/5	20.455/6.45	24/7.8
	76	Os02g0707900 (ethylene-responsive protein-like)	NP_001047879	76	20	2/4	20.204/5.96	23/6.5
	86	Glycine-rich RNA binding protein	ACA50486	229	67	3/11	16.089/6.32	15/6.0

Only protein spots that changed in volume at least 2-fold in all three replicates for a given treatment are included. Some fold changes are between −2 and +2, because there is a change of at least 2-fold in one of the treatments (see Supplementary Table S3 for spot volume and P-value). The positions of the spots are shown in Figure 3A. No, number; Theo, theoretical; Exp, experimental.

Blast result.

This protein also changed significantly in the endosperm.