Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis

Ooi, Tony Eng Keong; Yeap, Wan Chin; Daim, Leona Daniela Jeffery; Ng, Boon Zean; Lee, Fong Chin; Othman, Ainul Masni; Appleton, David Ross; Chew, Fook Tim; Kulaveerasingam, Harikrishna

doi:10.1186/s12953-015-0085-2

Proteome Science

Table 1 Unique proteins expressed differentially in HY versus LY palms at 12–18 WAP, or exhibiting temporal expression differences in HY palms

From: Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis

Spot #	Protein name^a	NCBI Accession #	Protein MW	Protein PI	Pep.Count	Protein score	Protein Score C. I. %	Total ion score	Total Ion C. I. %	Expression difference HY versus LY (WAP)^b		Temporal expression trend in HY (WAP)^b
										DIGE	Western analysis	DIGE	Western analysis
	Lipid metabolism
63	phospholipase D [Oryza sativa]	gi\|1020415	92151	5.6	11	130	100.0	40	67.4	down (16)	down (16)	down (16)	up (16, 18)
67	biotin carboxylase subunit [Glycine max]	gi\|3219361	58770	7.2	11	302	100.0	222	100.0	-	-	up (16, 18)	up (16, 18)
	Carbohydrate metabolism
26	glyceraldehyde 3-phosphate dehydrogenase [Elaeis guineensis]	gi\|82400215	32136	7.1	7	191	100.0	122	100.0	down (16)	down (12, 16)	-	up (18)
74	fructose-biphosphate aldolase [Elaeis guineensis]	gi\|192910908	38578	6.7	8	174	100.0	119	100.0	up (16)	up (16)	up (16, 18)	up (16, 18)
37	Triosephosphate isomerase, chloroplastic [Secale cereale]	gi\|1174745	31613	6.0	7	103	100.0	56	99.4	down (16)	down (12, 16)	-	up (18)
	Energy metabolism
44	NADPH:quinone reductase family protein [Arabidopsis thaliana]	gi\|30687535	21778	6.1	4	185	100.0	155	100.0	down (12)	nt	up (16)	nt
46	FQR1 (flavodoxin-like quinone reductase 1) [Arabidopsis thaliana]	gi\|15239652	21782	6.0	4	130	100.0	100	100.0	down (12)	nt	up (16)	nt
75	short chain type dehydrogenase [Ricinus communis]	gi\|223550344	33332	9.5	3	104	100.0	88	100.0	-	nt	up (16, 18)	nt
51	mitochondrial peroxiredoxin [Pisum sativum]	gi\|47775654	21463	8.4	3	140	100.0	120	100.0	up (16)	down (16)	up (16, 18)	up (18)
	Amino acid metabolism
21	o-methyltransferase [Ricinus communis]	gi\|223540510	40000	5.3	4	92	100.0	68	99.9	down (16)	down (16)	down (16, 18)	up (18)
5	methionine synthase protein [Sorghum bicolor]	gi\|18483235	83736	5.9	12	211	100.0	166	100.0	down (16)	-	-	up (16, 18)
65	5-methyltetrahydropteroyltri-glutamate-homocysteine methyltransferase [Oryza sativa]	gi\|108862992	84582	5.9	9	84	99.7	39	71.7	-	-	down (16, 18)	up (18)
30	VFB2 (VIER F-BOX PROTEINE 2); ubiquitin-protein ligase [Arabidopsis thaliana]	gi\|18409012	57212	8.7	8	65	80.5	-	-	up (18)	down (18)	-	up (18)
24	proline iminopeptidase, putative [Ricinus communis]	gi\|223538638	44547	6.0	5	94	100.0	71	100.0	up (18)	up (18)	up (16, 18)	up (16, 18)
	Stress related proteins
80	17.6 kDa class I small heat shock protein (HSP17.6C-CI) (AA 1–156) [Arabidopsis thaliana]	gi\|15220832	17593.0	5.4	5	70	94.0	30	-	-	-	up (16. 18)	up (18)
7	OSJNBb0085F13.17 [Oryza sativa]	gi\|38345312	80199.8	5.1	12	102	100.0	28	-	down (16)	nt	-	nt
54	glutathione peroxidase [Triticum monococcum]	gi\|148529480	11668.8	5.7	3	73	97.0	50	97.9	up (16)	down (16)	-	up (18)
41	glutathione S-transferase Phi [Matricaria chamomilla]	gi\|17385642	25264.9	6.0	5	96	100.0	69	100.0	down (16)	-	up (16)	up (16, 18)
43	glutathione-S-transferase theta, gst, putative [Ricinus communis]	gi\|223528475	24482.6	5.8	1	82	99.6	77	100.0	up (18)	nt	up (16, 18)	nt
78	abscisic stress ripening protein [Musa acuminata]	gi\|219963178	16735.8	5.6	3	76	98.5	51	97.8	-	nt	down (16, 18)	nt
53	temperature-induced lipocalin [Elaeis guineensis]	gi\|192911934	21614.8	5.7	5	93	100.0	51	98.8	up (16)	-	up (16)	up (18)
	Structure related proteins
22	actin [Populus trichocarpa]	gi\|224117708	40592.4	5.1	15	375	100.0	258	100.0	down (16)	-	-	up (18)
23	caffeic acid O-methyltransferase [Vanilla planifolia]	gi\|45444737	40632.5	5.7	4	92	100.0	72	100.0	down (12, 16)	down (12, 16)	down (16, 18)	-
73	fibrillin-like protein [Elaeis guineensis]	gi\|32250939	18991.0	5.0	7	109	100.0	37	46.0	up (12)	nt	down (16)	nt
68	Os12g0163700 (actine gamma 2) [Oryza sativa]	gi\|115487492	39837.0	5.3	10	137	100.0	62	99.9	-	-	up (16, 18)	up (18)
	Other Proteins
13	V-type proton ATPase catalytic subunit A [Daucus carota]	gi\|137460	68792	5.3	17	250	100.0	107	100.0	down (16)	down (16)	down (16)	up (18)
9	catalase 2 [Elaeis guineensis]	gi\|192910916	56922.4	6.5	11	100	100.0	25	-	up (18)	up (18)	-	up (18)
56	large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase [Chlorogonium elongatum]	gi\|74267421	41910.0	7.0	5	71	95.3	40	73.0	up (18)	up (18)	up (16, 18)	up (18)
32	Ran GTPase binding protein [Ricinus communis]	gi\|223434074	119713.4	9.0	12	67	87.9	-	-	up (12)	-	up (16, 18)	up (18)
72	ribosomal protein L10 [Elaeis guineensis]	gi\|192910684	34609.4	5.4	6	251	100.0	198	100.0	down (12)	down (12)	up (16, 18)	up (16, 18)
49	ABC1 family protein [Arabidopsis thaliana]	gi\|79325958	73790.7	5.6	13	73	96.7	-	-	down (18)	-	down (18)	up (16, 18)
48	Lea1P [Daucus carota]	gi\|10945667	16361.9	7.8	7	66	84.5	-	-	up (16)	-	up (16)	up (18)
33	nascent polypeptide associated complex alpha [Vitis vinifera]	gi\|225470846	22013.8	4.3	5	305	100.0	262	100.0	up (12)	down (12)	down (16, 18)	up (16, 18)
58	Os02g0753300 [Oryza sativa]	gi\|115448731	19972.8	6.2	2	87	99.9	71	100.0	up (16)	nt	-	nt
66	Os05g0482700 [Oryza sativa]	gi\|115464537	60774.8	5.3	10	256	100.0	183	100.0	-	nt	down (16)	nt
84	regulator of ribonuclease activity A [Zea mays]	gi\|195638112	18105.2	5.8	5	80	99.4	34	-	-	nt	up (16, 18)	nt
36	retroelement pol polyprotein-like [Arabidopsis thaliana]	gi\|9759493	126284.1	9.0	15	66	85.2	-	-	down (12)	nt	up (16)	nt
59	conserved hypothetical protein [Ricinus communis]	gi\|223539131	16333.4	6.6	1	55	-	49	97.5	up (16)	nt	up (16, 18)	nt
34	predicted protein [Ostreococcus lucimarinus CCE9901]	gi\|145345862	14575.0	4.6	3	66	85.2	46	92.4	up (16)	nt	up (16)	nt
79	predicted protein [Physcomitrella patens]	gi\|168027637	23578.3	6.9	2	70	93.8	58	99.7	-	nt	up (16)	nt
55	hypothetical protein isoform 1 [Vitis vinifera]	gi\|225434277	22608.8	8.7	5	88	99.9	54	99.0	up (12)	nt	down (18)	nt

^aIdentification of proteins was carried out using MASCOT against the NCBI non-redundant database
^bWestern dot blot immunoassay was conducted for validation. up = up regulated, down = down regulated, − = no differential, nt not tested

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