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Table 2 Transcriptional levels of all CAZyme families when grown on glucose and lignocellulosic biomass substrates

From: Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

Family Number of transcripts Normalized (FPKM) when grown ona Fold change in expression compared to glucoseb Putative substrate
Glucose Alfalfa Energy cane Corn stover Sorghum Alfalfa Energy cane Corn stover Sorghum
Glycosyl hydrolase families
GH1 9 1771.34 3969.55 2979.04 3698.85 3909.06 1.16 0.75 1.06 1.14 Cellulose
GH2 1 5.92 8.56 1.30 1.05 4.12 0.53 2.19 2.50 −0.52 Xylan accessory
GH3 17 714.37 673.63 1050.78 3505.03 1394.83 −0.08 0.56 2.29 0.97 Cellulose
GH4 3 24.53 6.31 12.16 17.96 11.59 1.96 1.01 −0.45 1.08 Other: catabolism
GH5 36 875.19 785.76 950.37 1080.05 844.70 −0.16 0.12 0.30 −0.05 Cellulose
GH6 18 1799.30 3264.96 3861.61 6956.76 4372.47 0.86 1.10 1.95 1.28 Cellulose
GH8 2 117.56 32.19 32.93 13.32 111.82 1.87 1.84 3.14 −0.07 Cellulose, hemicellulose
GH9 21 607.91 887.25 1416.88 2192.44 2208.01 0.55 1.22 1.85 1.86 Cellulose
GH10 28 2347.94 2686.49 1930.29 2488.99 3482.82 0.19 −0.28 0.08 0.57 Xylan
GH11 24 1488.52 1007.52 1918.48 1979.64 6240.67 −0.56 0.37 0.41 2.07 Xylan
GH13 17 2427.14 337.37 2709.48 2410.50 2781.37 2.85 0.16 −0.01 0.20 Starch
GH16 10 3323.52 1589.54 1295.78 1372.04 1217.24 −1.06 −1.36 −1.28 −1.45 Mixed glucan
GH17 1 0.00 0.00 0.68 1.18 0.69 0.00 19.38 20.17 19.40 Unknown
GH18 12 214.01 319.16 561.21 530.93 330.65 0.58 1.39 1.31 0.63 Chitin
GH20 1 2.89 2.07 4.41 5.20 3.29 −0.48 0.61 0.85 0.19 Other: N-acetyl-β-d-hexosamines
GH25 3 9.17 86.84 52.25 9.90 19.69 3.24 2.51 0.11 1.10 Peptidoglycan
GH26 7 136.35 167.23 73.65 94.95 46.23 0.29 0.89 −0.52 1.56 Mannan
GH28 5 107.74 67.83 65.97 65.68 85.86 0.67 0.71 0.71 −0.33 Pectin
GH30 3 41.17 31.90 9.74 19.92 20.84 −0.37 2.08 1.05 0.98 Xylan accessory
GH31 17 1730.49 371.79 621.35 1815.81 646.34 2.22 1.48 0.07 1.42 Xylan accessory
GH32 2 26.28 10.46 27.34 14.64 17.18 1.33 0.06 −0.84 −0.61 Other: fructan
GH36 1 3.41 1.85 6.92 8.23 4.80 −0.88 1.02 1.27 0.49 Other: fructan
GH37 1 12.40 6.41 9.35 8.58 4.14 −0.95 −0.41 −0.53 −1.58 Other: trehalose
GH38 1 3.26 1.06 7.18 4.16 3.38 1.62 1.14 0.35 0.05 Other: anabolic
GH39 9 115.54 90.68 93.64 155.76 129.98 −0.35 −0.30 0.43 0.17 Xylan
GH43 32 711.65 822.50 465.65 494.55 747.27 0.21 −0.61 −0.53 0.07 Xylan
GH45 16 2974.32 2653.90 1981.70 1653.87 2315.32 −0.16 −0.59 0.85 −0.36 Cellulose
GH47 3 12.98 5.33 32.56 19.49 14.89 1.28 1.33 0.59 0.20 Other: anabolic
GH48 17 3609.25 1928.40 2587.13 3989.36 2077.62 0.90 −0.48 0.14 0.80 Cellulose
GH53 2 24.78 31.13 17.52 27.93 17.37 0.33 −0.50 0.17 −0.51 Pectin
GH55 1 6.91 17.95 10.63 9.13 15.71 1.38 0.62 0.40 1.18 β-1,3, Glucan (laminarin)
GH57 7 156.86 540.18 751.41 414.40 377.49 1.78 2.26 1.40 1.27 Starch
GH64 2 5.43 17.40 6.22 3.17 2.99 1.68 0.20 0.78 0.86 β-1,3, Glucan (laminarin)
GH67 1 0.99 6.39 1.61 2.11 2.92 2.69 0.71 1.10 1.57 Xyloglucan
GH74 4 50.30 94.58 65.58 64.75 31.52 0.91 0.38 0.36 −0.67 Xyloglucan
GH78 1 15.39 18.06 4.18 2.60 3.97 0.23 1.88 2.56 1.96 Pectin
GH95 1 35.79 39.09 21.54 16.34 37.22 0.13 0.73 1.13 0.06 Xyloglucan
GH97 2 7.13 1.86 4.94 1.01 5.06 1.94 −0.53 2.82 −0.49 Xyloglucan
GH105 1 31.80 47.57 22.45 14.56 30.55 0.58 −0.50 1.13 −0.06 Pectin
GH109 3 6.74 10.53 23.54 19.34 14.64 0.64 1.80 1.52 1.12 Polygalactosamine
GH114 16 70.57 355.00 213.95 121.41 123.15 2.33 1.60 0.78 0.80 Other (polygalactosamine)
GH115 4 89.40 27.51 7.26 2.56 6.07 −1.70 3.62 5.12 3.88 Xylan accessory
GH119 20 3049.91 946.89 966.78 820.70 519.50 1.69 1.66 1.89 2.55 Starch
GH124 3 70.07 89.06 117.98 178.06 103.34 0.35 0.75 1.35 0.56 Cellulose
Polysaccharide lyase families
PL1 21 154.13 343.14 236.82 140.09 116.49 1.15 0.62 −0.14 −0.40 Pectate/pectin lyase
PL2 1 2.24 0.64 4.08 3.90 2.58 1.80 0.87 0.80 0.21 Pectate lyase, exo-polygalacturonate lyase
PL3 9 46.40 177.00 46.85 75.80 29.12 1.93 0.01 0.71 0.67 Pectate lyase
PL4 4 54.08 56.23 77.28 88.88 137.43 0.06 0.52 0.72 1.35 Rhamnogalacturonan lyase
PL9 1 9.09 28.83 6.25 3.16 7.53 1.67 −0.54 1.52 −0.27 Pectate lyase, exo-polygalacturonate lyase
PL10 1 8.71 15.27 19.57 21.08 11.62 0.81 1.17 1.27 0.42 Pectate lyase
PL11 1 0.96 0.34 1.61 1.59 1.31 1.51 0.74 0.73 0.45 Rhamnogalacturonan lyase
PL22 5 73.10 42.63 32.88 17.93 29.22 0.78 1.15 2.03 1.32 Oligogalacturonate lyase
Carboxyl esterase families
CE1 67 1064.51 1482.74 1331.78 824.56 2043.05 0.48 0.32 −0.37 0.94  
CE2 4 18.08 59.94 61.97 84.97 41.02 1.73 1.78 2.23 1.18  
CE3 9 190.73 200.04 258.23 170.58 311.61 0.07 0.44 −0.16 0.71  
CE4 66 5195.95 3586.97 4918.19 5519.76 4410.55 −0.53 −0.08 0.09 −0.24  
CE6 10 950.25 208.31 165.10 142.38 367.79 2.19 2.52 2.74 1.37  
CE7 4 428.18 226.89 367.54 378.99 358.44 0.92 −0.22 −0.18 −0.26  
CE8 5 25.32 48.98 84.27 53.33 44.48 0.95 1.73 1.07 0.81  
CE9 3 0.74 4.64 3.44 1.35 1.33 2.64 2.21 0.86 0.84  
CE10 58 559.63 576.67 758.11 433.52 332.26 0.04 0.44 −0.37 0.75  
CE12 4 133.25 137.86 137.67 201.83 175.85 0.05 0.05 0.60 0.40  
CE14 1 1.17 1.91 5.03 2.62 2.64 0.71 2.10 1.16 1.18  
CE15 2 259.98 238.38 105.97 41.58 240.61 −0.13 1.29 2.64 −0.11  
CE16 12 125.10 160.06 118.64 47.91 156.38 0.36 −0.08 1.38 0.32  
CEX 7 906.91 381.49 426.72 481.87 779.19 1.25 1.09 0.91 −0.22  
  1. aCorrected FPKM values normalized by the library size, as calculated using the estimateDispersions function in the R package DESeq [44]
  2. bFold change is shown as Log2 expression levels compared to glucose. Italics represents significantly over-expressed (a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq), bold italics represents significantly under-expressed (a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq [44]