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Bioresources and Bioprocessing

Table 6 Expression of genes involved in energy metabolism, transcription factor regulation, and resistance mechanism

From: Transcriptomic analysis of Aspergillus niger strains reveals the mechanism underlying high citric acid productivity

Gene ID (1015)

Gene ID (513.88)

Predicted function (homolog and organism)a

FPKM-10 h

FPKM-40 h

Fold changeb

S1

S3

S2

S1

S3

S2

S1/S3 (10 h)

S1/S2 (10 h)

S1/S3 (40 h)

S1/S2 (40 h)

Energy metabolism

 9.1179.1

An05g00300

Cytochrome b5 (Musca domestica, cytb5)

43.10

208.68

41.02

1503.85

162.33

333.18

− 2.27

–

3.21

2.17

 40169

An11g04370

Cytochrome b5

1411.35

658.03

895.69

5202.49

565.65

883.43

1.10

–

3.20

2.55

 21.34.1

An12g09940

Cytochrome b5

69.63

3.12

4.94

1.49

0.33

 

4.47

3.81

2.17

–

 3.1942.1

An08g06550

Ubiquinol cytochrome c reductase, subunit QCR8

944.78

1718.06

1690.58

6710.39

755.36

1955.17

–

–

3.15

1.77

 4.1469.1

No

Cytochrome c heme-binding site

34.15

9.48

30.55

185.57

28.69

80.69

1.84

–

2.69

1.20

 2000458

An02g06550

Ferric reductase, NADH/NADPH oxidase and related proteins

109.62

6.85

5.55

4.73

4.43

2.40

3.99

4.30

–

–

 6000073

An15g00690

NADH:ubiquinone oxidoreductase, NDUFA6/B14 subunit

336.69

335.46

351.26

1782.8

206.93

367.27

–

–

3.10

2.27

 2.1052.1

An02g09730

NADH:ubiquinone oxidoreductase, NDUFB7/B18 subunit

588.21

870.88

791.99

3764.33

578.95

671.06

–

–

2.70

2.49

Transcription factor

 1.2786.1

An01g13950

Upstream transcription factor 2/L-myc-2 protein

92.02

0

21.14

543.05

39.25

183.80

∞c

2.12

3.79

1.56

 80804

An14g04200

rghB, transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins, rhamnogalacturonase B

101.42

3.72

19.40

46.80

6.79

2.75

4.76

2.38

2.78

 

 5.1343.1

An07g07370

Transcription factor, Myb superfamily

46.57

4.25

31.47

134.79

71.56

1.04

3.45

–

–

–

 8.1025.1

An14g00780

Putative translation initiation inhibitor UK114/IBM1

98.99

26.99

80.59

1084.41

129.09

105.30

1.87

–

3.07

3.36

 800003

An18g04840

Translation elongation factor EF-1 alpha/Tu

630.05

1919.49

2031.67

1059.85

0.00001

0.00001

-1.60

-1.68

26.65

26.65

 12000021

An12g00240

Putative translation initiation inhibitor UK114/IBM1

664.05

638.32

624.75

2105.6

187.81

208.68

–

–

3.48

2.04

 1000929

An01g02900

Translation initiation factor 5A (S. cerevisiae, anbA)

1299.2

2868.77

1426.52

3715.03

808.85

1219.28

–

–

2.19

1.61

 2000159

An02g07890

pacC, pH-response transcription factor

91.52

55.30

39.50

29.38

89.03

32.46

–

1.21

− 1.60

–

Resistance mechanism

 20494

An02g02750

Catalase

59.61

35.89

8.12

68.79

9.45

19.16

–

2.87

2.86

1.84

 10568

An01g01550

Catalase (A. fumigates, cat1)

257.06

106.96

4.78

0.33

56.87

5.29

1.26

5.74

− 7.42

− 3.99

 1.973.1

An01g12530

Manganese superoxide dismutase

1308.37

30.85

3758.22

116.36

9.46

1.82

5.40

− 1.52

3.62

5.97

 10.1058.1

An18g00260

Cytochrome P450 CYP3/CYP5/CYP6/CYP9 subfamilies (A. parasiticus, avnA)

69.73

2.98

75.30

126.19

9.63

20.70

4.54

–

3.71

2.60

 11000284

An09g03210

Cytochrome P450 CYP2 subfamily

92.33

21.67

17.98

175.49

3.08

22.36

2.09

2.36

5.83

2.97

 130837

An04g00480

Basic-leucine zipper (bZIP) transcription factor

119.36

42.05

114.03

223.53

644.36

74.15

1.50

–

− 1.53

1.59

 4000214

An11g05340

FAD-dependent oxidoreductase

534.85

43.75

408.23

37.98

20.96

39.89

3.61

–

–

–

 160248

An17g00010

Copper amine oxidase (H. polymorpha AMO)

2319.99

1.33

4.91

4.92

2.37

2.71

10.77

8.88

1.05

–

 150032

An13g00710

Copper amine oxidase AO-1

944.56

7.30

16.52

133.7

37.95

78.39

7.30

5.83

1.81

–

 110401

An09g01550

ao-1, copper amine oxidase

713.37

0.95

9.10

222.50

23.89

22.92

9.55

6.29

3.21

3.27

 19000158

An03g00730

Hypothetical copper amine oxidase with signal peptide motif

255.57

13.09

25.24

116.39

32.08

36.72

4.28

3.34

1.85

1.66

 50349

An07g08720

Glycosyl transferase, family 20, trehalose-6-phosphate synthase

115.01

19.63

14.41

11.60

69.86

71.36

2.55

2.99

− 2.58

− 2.62

 80430

An14g02180

tpsB, trehalose-6-phosphate synthase component TPS1 and related subunits

41.24

23.10

6.07

7.16

24.02

19.63

–

2.76

− 1.74

− 1.45

  1. “–” denotes genes with no differences at transcriptional level, fold change ≤ 1. Some of the genes have small differences, but have a decisive impact on CA production. We also used fold change as an indicator
  2. “No” denotes that sequence was not mapped to the genome sequence assembly of A. niger strain CBS 513.88
  3. a Description of gene or closest homolog (BLASTP)
  4. b Fold change of differentially expressed (FDR < 0.05, FPKM ≥ 50 in A. niger YX-1217 at time 10 or time 40) genes based on a comparison of transcription levels at YX-1217/ATCC 1015 (designated as S1/S3) (10 h), YX-1217/YX-1217G (designated as S1/S2) (10 h), YX-1217/ATCC 1015 (designated as S1/S3) (40 h), and YX-1217/YX-1217G (designated as S1/S2) (40 h), respectively
  5. c The FPKM of ATCC 1015 is zero
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