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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