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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