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Bioresources and Bioprocessing

Table 4 Expression of genes involved in central metabolism processes

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)

Glycolysis

 15000076

An13g00950

alcB, alcohol dehydrogenase, class V

52.65

11.95

14.25

22.79

8.00

12.23

2.13

1.88

1.51

–

 50661

No

Aldehyde dehydrogenase

406.67

10.58

34.53

101.40

23.60

25.76

5.26

3.55

2.10

1.97

 160032

An10g00850

Aldehyde dehydrogenase (NAD+)

154.32

1.60

6.90

7.62

3.29

8.48

6.58

4.48

1.21

–

 9.735.1

No

Glyceraldehyde 3-phosphate dehydrogenase

673.82

0.32

1455.29

404.21

0.00001

421.74

11.05

− 1.11

25.26

–

 90161

An12g08610

glkA, Glucokinase

228.90

99.06

151.49

158.72

89.83

119.21

1.21

–

–

–

 70571

An16g02990

Phosphoglycerate mutase

182.92

426.80

143.55

48.55

204.61

119.11

− 1.22

–

− 2.08

− 1.29

 100101

An18g01670

pfkA, 6-phosphofructokinase

141.71

396.31

126.75

18.73

117.42

83.83

− 1.48

–

− 2.65

− 2.16

 50068

An07g08990

 pkiA, pyruvate kinase

1339.84

713.44

791.51

111.70

301.28

309.77

–

–

− 1.43

− 1.47

TCA cycle

 3.2152.1

An08g10920

citB, citrate synthase

79.42

0.07

349.09

0.34

0.16

1.10

10.06

− 2.13

1.06

–

 6000119

An15g01920

mscA, methylcitrate synthase

286.25

20.60

47.61

43.11

34.60

49.59

3.79

2.58

–

–

 130482

An04g02090

pycA, Pyruvate carboxylase

176.18

242.37

174.54

42.81

49.14

33.15

1

1.44

–

–

 20251

An02g12770

Succinate dehydrogenase SDH1

499.46

384.63

166.11

53.31

297.99

201.71

–

1.58

− 2.48

− 1.91

 40489

An11g02550

Phosphoenolpyruvate carboxykinase (A. nidulans, acuF)

71.15

98.07

18.84

71.19

313.94

113.38

–

1.91

− 2.14

–

 30306

An06g00990

Fumarate reductase FRDS

199.86

270.39

99.20

38.69

307.69

145.62

–

1.01

− 2.99

− 1.9

 50562

An07g02160

mdh1, malate dehydrogenase

1452.29

1178.52

1336.53

1725.86

810.04

764.45

–

–

1.09

1.17

 101221

An18g06760

Isocitrate dehydrogenase, gamma subunit

1198.24

711.97

1113.35

2581.7

700.18

808.43

–

–

2.03

1.82

 110571

An09g03870

Aconitase

202.23

332.86

80.18

8.67

33.42

41.12

–

–

− 1.94

− 2.24

 40119

An11g00510

aclB, ATP-citrate lyase

950.20

459.53

554.44

46.72

181.23

63.03

1.05

–

− 1.96

–

 40123

An11g00530

aclA, ATP-citrate lyase

980.48

473.78

682.24

110.4

211.46

81.49

1.05

–

–

–

Fatty acid metabolism

 7000050

An16g04830

Acyl-CoA synthetase

90.11

4.06

43.06

33.90

2.32

11.33

4.47

1.06

3.86

–

 170132

An04g05720

3-ketoacyl-CoA thiolase

95.82

62.70

40.55

684.04

62.88

149.85

–

1.24

3.44

2.19

 13000035

An04g04330

afeA, acyl-CoA synthetase

196.82

0.31

113.28

10.26

1.27

2.41

9.31

–

3.01

2.81

Glyoxylic acid metabolism

 11071

An01g09270

acuB, isocitrate lyase

29.32

9.50

1.90

133.18

63.90

116.37

1.62

3.94

1.05

–

 160030

An10g00820

oahA, isocitrate lyase/oxaloacetate acetylhydrolase

623.51

0.26

65.54

5.66

10.70

6.91

9.97

3.25

–

–

 6000115

An15g01860

acuE, malate synthase

26.01

175.50

11.42

95.47

127.09

85.78

− 2.75

1.18

–

–

  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
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