Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment

Cheng, Pengfei; Zhou, Chengxu; Wang, Yan; Xu, Zhihui; Xu, Jilin; Zhou, Dongqing; Zhang, Yinghui; Wu, Haizhen; Zhang, Xuezhi; Liu, Tianzhong; Tang, Ming; Yang, Qiyong; Yan, Xiaojun; Fan, Jianhua

doi:10.1186/s13068-018-1331-5

Biotechnology for Biofuels and Bioproducts

Table 3 List of annotated enzymes that potentially involved in botryococcene or squalene biosynthesis

From: Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment

EC #	Enzyme description	Unigene number	LogFC (2 days)^a	LogFC (4 days)	LogFC (8 days)
IPP and DMAPP biosynthesis
2.3.1.9	Acetyl-CoA C-acetyltransferase	28	0.46	0.40	− 1.28
2.3.3.10	Hydroxymethylglutaryl-CoA synthase	12	0.48	0.50	− 0.98
1.1.1.34	Hydroxymethylglutaryl-CoA reductase (NADPH)	15	0.55	0.31	− 1.15
2.7.1.36	Mevalonate kinase	5	3.44	-0.21	− 3.20
4.1.1.33	Diphosphomevalonate decarboxylase	7	2.16	0.23	− 2.48
2.7.2.3	Phosphoglycerate kinase	27	0.03	− 0.01	− 0.33
1.2.1.12	Glyceraldehyde 3-phosphate dehydrogenase	40	0.04	− 0.29	− 0.46
1.2.1.9	Glyceraldehyde-3-phosphate dehydrogenase (NADP+)	2	0.35	0.94	− 0.99
5.4.2.12	2,3-Bisphosphoglycerate-independent phosphoglycerate mutase	9	− 0.32	− 0.34	− 0.51
5.4.2.11	2,3-Bisphosphoglycerate-dependent phosphoglycerate mutase	10	1.41	0.28	− 1.90
4.2.1.11	Enolase	32	− 0.18	− 0.49	− 0.80
2.7.1.40	Pyruvate kinase	55	0.47	− 0.14	− 0.96
2.2.1.7	1-Deoxy-d-xylulose-5-phosphate synthase	6	0.00	− 0.25	− 0.35
1.1.1.267	1-Deoxy-d-xylulose-5-phosphate reductoisomerase	5	0.25	0.21	− 0.39
2.7.7.60	2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase	3	− 0.59	0.09	− 0.62
2.7.1.148	4-Diphosphocytidyl-2-C-methyl-d-erythritol kinase	4	− 0.05	− 0.22	− 1.35
4.6.1.12	2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase	5	− 0.37	0.41	− 0.49
1.17.1.2	4-Hydroxy-3-methylbut-2-enyl diphosphate reductase	5	− 0.07	− 0.41	− 0.30
1.17.7.3	(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase	9	0.03	− 0.07	− 0.39
5.3.3.2	Isopentenyl-diphosphate delta-isomerase	7	0.48	0.01	− 1.07
5.1.3.1	Ribulose-phosphate 3-epimerase	17	− 0.08	0.02	− 0.53
2.2.1.1	Transketolase	27	0.42	− 0.05	− 0.43
4.1.2.22	Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase	3	0.52	N.D.^b	N.D.
Polyprenyl diphosphate synthases
2.5.1.1	Geranyl diphosphate synthase	1	0.68	− 0.38	− 0.09
2.5.1.10	Farnesyl diphosphate synthase	14	0.43	− 0.35	− 1.08
2.5.1.29	Geranylgeranyl diphosphate synthase, type III	10	1.44	0.75	− 1.64
2.5.1.29	Geranylgeranyl diphosphate synthase, type II	5	0.37	0.09	− 0.75
2.5.1.91	Decaprenyl-diphosphate synthase subunit 1	7	0.68	0.80	− 1.09
Triterpenoid hydrocarbon biosynthesis
2.5.1.21	Squalene synthase/farnesyl-diphosphate farnesyltransferase	12	− 0.19	− 0.48	− 0.68
2.1.1.41	Sterol 24-C-methyltransferase	32	0.28	− 0.45	− 1.26
2.1.1.143	24-Methylenesterol C-methyltransferase	3	0.44	0.00	0.50
1.14.14.17	Squalene monooxygenase	8	0.47	0.05	− 0.22
Triterpenoid sterol biosynthesis
5.4.99.8	Cycloartenol synthase	4	− 0.10	− 0.20	0.55
1.14.13.72	Methylsterol monooxygenase	17	0.52	0.68	− 1.37
5.5.1.9	Cycloeucalenol cycloisomerase	7	0.85	0.20	− 1.06
1.14.13.70	Sterol 14-demethylase	14	0.33	− 0.03	− 0.45
1.3.1.70	Delta14-sterol reductase	10	− 0.34	− 0.25	− 0.55
5.3.3.5	Cholestenol Delta-isomerase	5	0.51	0.05	0.13
1.3.1.21	Cholesterol 7-dehydrogenase	13	2.10	0.75	0.41
1.3.1.21	7-Dehydrocholesterol reductase	9	1.37	1.45	− 1.67
1.1.1.170	Sterol-4alpha-carboxylate 3-dehydrogenase (decarboxylating)	12	− 0.76	− 0.54	− 0.24
1.14.13.159	Vitamin D 25-hydroxylase	1	− 0.86	− 4.87	N.D.
3.1.1.13	Bile salt-stimulated lipase	2	− 1.03	− 4.22	N.D.
3.1.1.13	Lysosomal acid lipase/cholesteryl ester hydrolase	37	0.88	0.31	− 0.98
Tetraterpenoid biosynthesis
2.5.1.32	Phytoene synthase	5	0.06	0.15	− 1.18
1.3.5.5	15-cis-phytoene desaturase	6	0.42	0.31	− 0.18
1.3.5.6	Zeta-carotene desaturase	5	0.42	0.59	− 0.03
5.2.1.13	Prolycopene isomerase	4	0.30	0.08	− 0.19
5.5.1.18	Lycopene epsilon-cyclase	3	− 0.22	0.15	− 0.67
5.5.1.19	Lycopene beta-cyclase	5	0.34	0.24	0.10
1.14.13.129	Beta-carotene 3-hydroxylase	2	− 0.09	− 0.45	− 0.45
1.14.99.45	Carotene epsilon-monooxygenase	4	0.64	0.29	0.14
1.14.13.90	Zeaxanthin epoxidase	10	0.00	− 0.36	− 0.24
1.23.5.1	Violaxanthin de-epoxidase	4	− 0.17	0.00	− 0.59
Meroterpenoid quinone biosynthesis
1.3.1.83	Geranylgeranyl reductase	7	0.30	0.37	− 0.62
2.5.1.62	Chlorophyll synthase	5	0.15	0.52	− 0.34
2.5.1.116	Homogentisate phytyltransferase/homogentisate geranylgeranyltransferase	5	0.86	0.53	− 0.24
5.5.1.24	Tocopherol cyclase	3	0.20	− 0.96	0.34
2.1.1.95	Tocopherol O-methyltransferase	9	− 0.03	− 0.67	0.14
2.5.1.117	Homogentisate solanesyltransferase	3	0.52	0.12	− 0.83
2.5.1.74	1,4-Dihydroxy-2-naphthoate octaprenyltransferase	3	0.39	0.64	− 1.29
2.5.1.39	4-Hydroxybenzoate polyprenyltransferase	4	0.40	0.24	0.08
2.1.1.64	Polyprenyldihydroxybenzoate methyltransferase	7	− 0.73	1.00	− 0.40
1.14.13.-	Ubiquinone biosynthesis monooxygenase Coq7	2	− 0.17	− 3.14	− 3.75
1.14.13.-	Ubiquinone biosynthesis monooxygenase Coq6	6	0.97	0.07	− 0.05
2.1.1.201	2-Methoxy-6-polyprenyl-1,4-benzoquinol methylase Coq5	14	− 0.22	0.00	− 0.14
Biosynthesis of gibberellic acid diterpenes
1.14.11.12	Gibberellin 20-oxidase	1	− 1.78	− 0.37	− 1.18
S-adenosylmethionine regeneration
3.3.1.1	Adenosylhomocysteinase	27	0.14	− 0.32	0.19
2.1.1.10	Homocysteine S-methyltransferase	4	− 0.08	− 0.44	− 0.52
2.1.1.13	5-Methyltetrahydrofolate–homocysteine methyltransferase	24	0.23	0.07	− 0.71
2.1.1.14	5-Methyltetrahydropteroyltriglutamate–homocysteine methyltransferase	8	− 0.86	0.87	− 0.27
2.5.1.6	S-Adenosylmethionine synthetase	26	0.28	0.07	− 0.24

^a Summation of all FPKM values of unigenes that associated with the same enzyme were used for logFC calculation
^b N.D. means could not detect
^c More than twofold increase or decrease were marked as italic type

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