Integrating multi-omics analyses of Nonomuraea dietziae to reveal the role of soybean oil in [(4′-OH)MeLeu]4-CsA overproduction

Liu, Huanhuan; Huang, Di; Jin, Lina; Wang, Cheng; Liang, Shaoxiong; Wen, Jianping

doi:10.1186/s12934-017-0739-0

Table 1 Differentially expressed proteins identified by MALDI-TOF/TOF–MS under the soybean oil and the control conditions

From: Integrating multi-omics analyses of Nonomuraea dietziae to reveal the role of soybean oil in [(4′-OH)MeLeu]⁴-CsA overproduction

Spot no.^a	Protein name	Species	NCBI accession no.^b	Protein MW^c	Protein PI	Protein score^d	Protein score C.I. %	MO/MC (48 h)^e	MO/MC (96 h)
1	Glucose-6-phosphate dehydrogenase	Nonomuraea sp. SBT364	gi\|898235202	56.92	5.96	138	100	1.67	0.56
2	Phosphogluconate dehydratase	Nonomuraea sp. SBT364	gi\|898253514	68.06	5.8	67	99.5	Loss	1.64
3	Enolase	Streptosporangium amethystogenes	gi\|664384366	45.33	4.53	72	99.76	1.78	1.89
4	3-phosphoglycerate dehydrogenase	Nonomuraea candida	gi\|759933157	55.53	4.99	135	100	1.96	1.87
5	Dihydrolipoamide dehydrogenase	Nonomuraea candida	gi\|759953882	47.83	5.47	62	98.23	1.93	1.21
6	6-phosphofructokinase	Nonomuraea coxensis	gi\|648522261	36.66	5.53	125	100	2.17	1.74
7	Pyruvate dehydrogenase	Nonomuraea candida	gi\|759929120	102.11	5.83	146	100	2.35	1.85
8	Pyruvate kinase	Nonomuraea candida	gi\|759954395	51.48	5.94	118	100	2.05	1.78
9	Malate dehydrogenase	Nonomuraea sp. SBT364	gi\|898218461	34.1	4.85	65	99.23	1.75	1.64
10	2-oxoglutarate ferredoxin oxidoreductase subunit alpha	Nonomuraea sp. SBT364	gi\|898257150	65.95	5.34	76	99.94	1.68	0.77
11	Citrate synthase	Nonomuraea candida	gi\|759936001	40.74	5.45	67	99.25	3.32	1.71
12	Succinyl-CoA synthetase subunit alpha	Nonomuraea sp. SBT364	gi\|898242487	30.38	6.1	131	100	2.45	1.78
13	Alpha-ketoglutarate decarboxylase	Nonomuraea candida	gi\|759939264	134.27	5.91	103	100	2.19	1.62
14	Cyclopropane-fatty-acyl-phospholipid synthase	Nonomuraea candida	gi\|759945365	46.94	6.07	67	99.35	1.62	0.72
15	Cytochrome P450 hydroxylase sb15	Nonomuraea dietziae	gi\|445067401	51.04	8.82	34	99.11	1.73	1.67
16	2-isopropylmalate synthase	Nonomuraea sp. SBT364	gi\|898222194	63.16	5.04	187	100	1.25	1.84
17	Cytochrome P450 hydroxylase sb8	Nonomuraea dietziae	gi\|445067389	44.43	5.23	25	97.84	1.85	0.82
18	Cytochrome P450 hydroxylase sb17	Nonomuraea dietziae	gi\|445067405	43.62	5.19	25	97.37	2.06	0.71
19	Cytochrome P450 hydroxylase sb2	Nonomuraea dietziae	gi\|445067377	25.04	5.5	33	98.85	1.76	1.22
20	Cytochrome P450 hydroxylase sb20	Nonomuraea dietziae	gi\|445067407	42.77	5.05	34	99.15	1.95	1.65
21	NADH dehydrogenase	Nonomuraea candida	gi\|759944851	49.06	5.22	112	100	3.39	0.97
22	Acyl-CoA thioesterase	Alicyclobacillus acidoterrestris	gi\|916582360	17.26	5.58	89	96.85	0.61	1.68
23	NADP oxidoreductase	Nonomuraea coxensis	gi\|916408869	47.19	6.08	71	99.79	1.87	2.15
24	Flavoprotein disulfide reductase	Streptosporangium amethystogenes	gi\|664385831	48.56	5.37	69	99.55	2.08	1.75
25	NADH dehydrogenase subunit F	Streptosporangium roseum	gi\|502651094	46.67	5.5	115	100	0.68	1.94
26	FAD-linked oxidase	Nonomuraea sp. SBT364	gi\|898280523	55.07	5.87	92	100	1.72	1.98
27	Flavoprotein oxidoreductase	Streptosporangium roseum	gi\|502655712	48.81	5.58	60	99.55	1.79	1.73
28	Transcription termination factor NusA	Nonomuraea coxensis	gi\|522034561	36.32	5.43	87	99.99	2.27	1.17
29	MFS transporter	Streptosporangium amethystogenes	gi\|664381342	79.76	6.34	57	97.78	1.64	1.32
30	Thiosulfate sulfurtransferase	Nonomuraea coxensis	gi\|522033492	31.21	4.81	62	98.19	1.74	1.94
31	Sulfonate ABC transporter ATP-binding protein	Nonomuraea candida	gi\|759950693	25.17	7	55	97.5	1.80	1.68
32	ATP-binding protein	Nonomuraea coxensis	gi\|648523005	48.21	5.74	150	100	1.67	0.88
33	S-adenosylmethionine synthetase	Streptosporangium amethystogenes	gi\|664383325	42.57	4.98	120	100	2.04	1.17
34	S-adenosyl-l-homocysteine hydrolase	Nonomuraea coxensis	gi\|522030148	52.1	5.33	91	100	1.66	4.28
35	Glutamate synthase	Nonomuraea coxensis	gi\|703367593	160.46	5.48	79	99.96	2.47	0.62
36	Phenylalanine–tRNA ligase subunit alpha	Nonomuraea coxensis	gi\|522035904	38.25	5.4	93	100	1.74	1.32
37	Aspartyl/glutamyl-tRNA amidotransferase subunit B	Streptosporangium roseum	gi\|502658302	54.44	5.13	117	100	1.88	2.38
38	Proline–tRNA ligase	Nonomuraea candida	gi\|759956543	63.49	5.24	107	100	11.29	2.46
39	Tryptophanyl-tRNA synthetase	Nonomuraea sp. SBT364	gi\|898218468	37.51	6.21	100	100	0.45	1.46
40	Cysteine synthase	Nonomuraea coxensis	gi\|522035423	34.18	5.47	70	99.75	2.45	1.45
41	ATPase AAA	Lachnoanaerobaculum sp. ICM7	gi\|497349325	83.91	5.1	186	100	1.82	1.63
42	Urocanate hydratase	Nonomuraea coxensis	gi\|703370540	59.91	5.54	75	99.9	1.71	2.08
43	Histidine ammonia-lyase	Nonomuraea sp. SBT364	gi\|898282330	53.36	5.34	67	99.4	1.74	0.97
44	Inosine-5-monophosphate dehydrogenase	Nonomuraea sp. SBT364	gi\|759938464	39.48	5.74	150	100	2.02	1.76
45	Polynucleotide phosphorylase	Nonomuraea coxensis	gi\|522034552	84.03	5.11	158	100	0.76	1.62
46	Elongation factor Ts	Streptosporangium roseum	gi\|502652347	30.18	5.27	121	100	9.17	0.89
47	DNA-directed RNA polymerase subunit alpha	Alkalibacillus haloalkaliphilus	gi\|515752615	35.17	4.8	282	96.64	1.61	0.69
48	DNA polymerase III subunit beta	Nonomuraea sp. SBT364	gi\|898216335	40.14	4.79	215	100	1.67	0.73
49	30S ribosomal protein S2	Nonomuraea sp. SBT364	gi\|898235817	34.47	5.02	161	100	1.78	1.62
50	Transcription termination factor Rho	Nonomuraea sp. SBT364	gi\|898215154	73.6	8.73	140	100	1.62	0.49
51	Dihydrolipoyl dehydrogenase	Nonomuraea sp. SBT364	gi\|898266057	49.7	5.51	126	100	1.74	1.85
52	Peptide chain release factor 2	Nonomuraea candida	gi\|759935368	41.51	4.69	109	100	0.65	1.94
53	Molecular chaperone GroEL	Nonomuraea candida	gi\|759948935	57.13	4.84	166	100	0.42	1.32
54	Histidine kinase	Nonomuraea coxensis	gi\|703366436	148.43	4.97	267	100	1.74	1.36
55	Elongation factor P	Nonomuraea coxensis	gi\|522034280	19.93	5.00	130	100	0.45	0.90
56	ATP-dependent Clp protease proteolytic subunit	Nonomuraea candida	gi\|759955675	23.2	5.03	108	100	0.70	1.67
57	Two-component system sensor histidine kinase	Nonomuraea candida	gi\|759950142	37.01	9.94	59	96.39	1.68	1.51
58	Proteasome subunit alpha	Nonomuraea coxensis	gi\|916409057	30.52	4.99	91	100	1.71	0.76
59	ATPase AAA	Nonomuraea sp. SBT364	gi\|898282349	65.47	5.04	186	100	1.07	1.75
60	Carbamoyl phosphate synthase large subunit	Nonomuraea sp. SBT364	gi\|898274197	117.27	4.79	139	100	1.64	0.96
61	LysR family transcriptional regulator	Streptosporangium roseum	gi\|759969058	33.7	6.28	62	98.03	0.93	1.05
62	DNA-binding response regulator	Nonomuraea coxensis	gi\|522033451	25.6	5.17	69	99.64	1.69	0.90
63	Hypothetical protein	Kiloniella laminariae	gi\|759750848	27.62	10.15	115	100	2.69	0.81
64	Gamma-aminobutyraldehyde dehydrogenase	Nonomuraea candida	gi\|759930674	49.16	5.26	107	100	1.68	1.74
65	Monooxygenase	Nonomuraea candida	gi\|759940588	49.69	6.00	62	98.31	2.14	1.76
66	GntR family transcriptional regulator	Bacillus cereus	gi\|872654957	54.7	9.01	86	96.79	0.90	1.62
67	Molecular chaperone	Nonomuraea candida	gi\|759944965	67.07	4.81	318	100	0.42	1.32
68	Cyclophilin	Nonomuraea candida	gi\|759934622	19.5	5.96	55	96.73	1.61	0.74
69	Bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase	Nonomuraea coxensis	gi\|648522670	29.34	5.4	86	99.99	1.65	1.35
70	Alanine dehydrogenase	Nonomuraea candida	gi\|759942142	38.78	5.78	80	99.97	1.94	0.47
71	Hydrolase	Nonomuraea candida	gi\|759945898	46.66	4.64	77	99.93	0.49	1.64
72	RNase J family beta-CASP ribonuclease	Streptosporangium amethystogenes	gi\|664377501	60.89	5.68	138	99	1.25	1.68
73	Methylmalonyl-CoA mutase	Streptosporangium roseum	gi\|502654007	116.92	5.5	67	99.3	1.32	1.86
74	Phage-shock protein	Nonomuraea candida	gi\|759953906	29.75	5.4	107	99.78	0.45	0.97
75	Citrate synthase 2	Nonomuraea sp. SBT364	gi\|898229311	39.82	5.97	159	100	1.71	1.05
76	Adenylosuccinate synthetase	Streptosporangium amethystogenes	gi\|664389689	46.43	5.85	134	100	1.84	0.85
77	NDP-hexose 4-ketoreductase	Streptosporangium roseum	gi\|665581403	92.72	5.73	252	100	1.63	0.31
78	Vitamin B12-dependent ribonucleotide reductase	Nonomuraea candida	gi\|759929294	103.74	5.64	99	100	2.20	1.69
79	DNA-binding response regulator	Nonomuraea sp. SBT364	gi\|898242523	22.86	5.87	157	100	3.99	0.89
80	Acetyltransferase	Nonomuraea candida	gi\|759934501	20.5	8.7	56	98.61	0.43	1.85
81	Peptidase M48	Nonomuraea sp. SBT364	gi\|898280126	38.21	5.89	204	99.91	0.43	1.31
82	Argininosuccinate lyase	Streptosporangium roseum	gi\|759973125	53.3	5.43	59	96.67	2.44	1.32
83	GlmZ(sRNA)-inactivating NTPase	Streptosporangium roseum	gi\|665597475	31.53	5.55	110	100	0.16	0.73
84	Adenylosuccinate lyase	Nonomuraea candida	gi\|759952039	51.67	6.18	141	100	0.78	1.69
85	Sulfate adenylyltransferase	Nonomuraea coxensis	gi\|522034000	46.94	5.6	194	100	1.64	0.83
86	Serine hydroxymethyltransferase	Nonomuraea coxensis	gi\|522029537	44.16	6.01	162	100	1.74	1.64
87	Glycosyl transferase	Streptosporangium amethystogenes	gi\|664380822	33.06	9.09	56	96.21	1.07	1.82
88	Hypothetical protein	Nonomuraea coxensis	gi\|918028067	34.38	5.27	61	97.09	1.25	0.48
89	Hypothetical protein	Ruminococcaceae bacterium AE2021	gi\|522080859	26.13	9.69	103	100	2.06	0.73
90	Hypothetical protein	Borrelia afzelii	gi\|522034300	51.1	4.66	61	97.35	0.74	1.75
91	Hypothetical protein	Streptosporangium roseum	gi\|648523244	38.07	5.88	119	100	1.51	0.42
92	Hypothetical protein	Streptosporangium roseum	gi\|502657796	77.87	6.54	66	99.1	1.94	1.04
93	Hypothetical protein	Streptomyces fradiae	gi\|921240484	26.09	5.42	103	100	1.65	0.77
94	Hypothetical protein	Nonomuraea sp. SBT364	gi\|759929790	14.37	4.86	62	98.15	1.88	0.64
95	Hypothetical protein	Sunxiuqinia dokdonensis	gi\|501669599	85.44	8.09	97	98	1.82	0.78

^aSpot number of the differentially protein in Fig. 2
^bAccession numbers in the NCBInr database
^cTheoretical molecular weight (kDa) and isoelectric point (pI)
^dMascot score from the NCBInr
^eMean fold change is the ratio of protein abundance between medium MO and MC at 48 and 96 h, respectively

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