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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