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Bioresources and Bioprocessing

Table 3 Expression of genes involved in polypeptides degradation

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)

80863

An14g04710

pepA, peptidase aspartic, active site

2540.17

3.11

3437.07

34,270.0

49.03

10205

9.67

–

9.44

1.74

12707

An01g00370

Peptidase aspartic, active site (AP1) (A. phoenicis, apnS)

1855.35

265.64

549.84

1602.29

42.57

742.46

2.80

1.75

5.23

1.11

5000659

An07g00950

Peptidase aspartic, active site

424.65

7.66

154.19

548.92

17.21

148.96

5.79

1.46

4.99

1.88

61129

An15g06280

peptidase aspartic, active site

210.08

26.26

37.04

605.44

97.34

112.93

3.00

2.50

2.64

2.42

11004

An09g06460

Peptidase, eukaryotic cysteine peptidase active site

388.70

1.60

484.87

200.71

31.84

42.39

7.92

− 1.21

2.65

2.24

2000089

An02g04690

cpdA, Serine carboxypeptidases F (lysosomal cathepsin A)

182.61

5.86

423.40

2358.41

51.97

1327.78

4.96

–

5.50

–

30096

An06g00310

Peptidase S8, serine carboxypeptidases S1 (lysosomal cathepsin A)

96.75

3.44

142.95

161.62

87.04

63.09

4.81

–

–

1.36

90133

An12g05960

Peptidase S28, extracellular serine carboxypeptidase

204.37

27.80

180.01

238.87

20.48

120.63

2.88

–

3.54

 

30678

An08g04490

Peptidase S28, serine peptidase

214.22

40.93

166.05

2417.0

21.60

923.24

2.39

–

6.81

1.39

30666

An08g04640

Peptidase S8 and S53, serine peptidase

107.55

3.15

166.05

349.08

6.92

220.11

5.09

–

5.65

–

1000155

An01g11340

Peptidase M24, methionine aminopeptidase MAP

87.46

3.44

145.30

72.97

3.02

28.31

4.66

–

4.59

1.37

8000249

An14g05960

Arginase family protein (E. coli, speB)

156.44

0

3.61

5.97

0.00001

0.12

∞c

5.43

19.18

5.60

30486

An06g01880

Peptidase M20, beta-ureidopropionase

293.47

4.54

37.29

44.86

38.18

22.38

6.01

2.98

–

1.00

40364

An11g01970

Peptidase C15, pyroglutamyl peptidase I

100.04

15.68

57.07

266.533

77.46

94.93

2.67

–

1.78

1.49

60486

An15g01980

Aminotransferase, class I and II

125.68

15.02

20.95

24.15

14.33

18.70

3.06

2.58

–

–

20000064

An04g08630

Aminotransferase, class IV

68.03

2.52

69.61

265.13

7.80

71.43

4.76

–

5.09

1.89

  1. “–” denotes genes with no differences in transcriptional levels, 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 the 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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