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