Table 4.
Glycosyl hydrolase (GH) transcripts in C1A cellulosome under different growth conditions
| CAZyme family | Grown on | Number of genes | Total expression level (corrected FKPM)a | Cellulosomal expression as the percentage of overall expression | ||
|---|---|---|---|---|---|---|
| Cellulosomal transcripts | Non-cellulosomal transcripts | Cellulosomal transcripts | Non-cellulosomal transcripts | |||
| GH2 | Glucose | 1 | 1 | 5.92 | 0 | 100 |
| Alfalfa | 1 | 1 | 8.56 | 0 | 100 | |
| Energy cane | 1 | 1 | 1.3 | 0 | 100 | |
| Corn stover | 1 | 1 | 1.05 | 0 | 100 | |
| Sorghum | 1 | 1 | 4.12 | 0 | 100 | |
| GH3 | Glucose | 2 | 17 | 314.9 | 399.47 | 44.08 |
| Alfalfa | 2 | 17 | 242.54 | 431.09 | 36.01 | |
| Energy cane | 2 | 17 | 351.98 | 698.8 | 33.5 | |
| Corn stover | 2 | 16 | 652.1 | 2852.93 | 18.6 | |
| Sorghum | 2 | 17 | 446.42 | 948.41 | 32.01 | |
| GH5 | Glucose | 17 | 30 | 726.01 | 149.18 | 82.95 |
| Alfalfa | 16 | 34 | 483.4 | 302.36 | 61.52 | |
| Energy cane | 15 | 34 | 607.37 | 343 | 63.91 | |
| Corn stover | 16 | 34 | 804.65 | 275.4 | 74.5 | |
| Sorghum | 19 | 34 | 556.98 | 287.72 | 65.94 | |
| GH6 | Glucose | 5 | 17 | 238.21 | 1561.09 | 13.24 |
| Alfalfa | 6 | 18 | 281.87 | 2983.09 | 8.63 | |
| Energy cane | 6 | 18 | 495.5 | 3366.11 | 12.83 | |
| Corn stover | 6 | 18 | 615.54 | 6341.22 | 8.85 | |
| Sorghum | 6 | 18 | 473.62 | 3898.85 | 10.83 | |
| GH8 | Glucose | 1 | 2 | 113.21 | 4.35 | 96.3 |
| Alfalfa | 1 | 2 | 30.34 | 1.85 | 94.25 | |
| Energy cane | 1 | 2 | 30.81 | 2.12 | 93.56 | |
| Corn stover | 1 | 2 | 13 | 0.32 | 97.6 | |
| Sorghum | 1 | 99.22 | 12.6 | 88.73 | ||
| GH9 | Glucose | 9 | 21 | 340.63 | 267.28 | 56.03 |
| Alfalfa | 9 | 21 | 529.3 | 357.95 | 59.66 | |
| Energy cane | 9 | 20 | 686.42 | 730.46 | 48.45 | |
| Corn stover | 9 | 20 | 1124.22 | 1068.22 | 51.28 | |
| Sorghum | 9 | 20 | 931.39 | 1276.62 | 42.18 | |
| GH10 | Glucose | 9 | 28 | 1339.11 | 1008.83 | 57.03 |
| Alfalfa | 9 | 28 | 1121.04 | 1565.45 | 41.73 | |
| Energy cane | 9 | 28 | 927.74 | 1002.55 | 48.06 | |
| Corn stover | 9 | 28 | 1300.71 | 1188.28 | 52.26 | |
| Sorghum | 9 | 28 | 1167.53 | 2315.29 | 33.52 | |
| GH11 | Glucose | 5 | 23 | 194.91 | 1293.61 | 13.09 |
| Alfalfa | 5 | 23 | 96.62 | 910.9 | 9.59 | |
| Energy cane | 5 | 24 | 110.25 | 1808.23 | 5.75 | |
| Corn stover | 5 | 23 | 171.18 | 1808.46 | 8.65 | |
| Sorghum | 5 | 24 | 175.12 | 6065.55 | 2.81 | |
| GH26 | Glucose | 5 | 6 | 136 | 0.35 | 99.74 |
| Alfalfa | 4 | 7 | 127.33 | 39.9 | 76.14 | |
| Energy cane | 4 | 7 | 56.67 | 16.98 | 76.94 | |
| Corn stover | 4 | 7 | 88 | 6.95 | 92.68 | |
| Sorghum | 4 | 7 | 35.69 | 10.54 | 77.19 | |
| GH43 | Glucose | 4 | 31 | 318.72 | 392.93 | 44.79 |
| Alfalfa | 4 | 31 | 433.95 | 388.55 | 52.76 | |
| Energy cane | 4 | 32 | 251.13 | 214.52 | 53.93 | |
| Corn stover | 4 | 31 | 285.36 | 209.19 | 57.7 | |
| Sorghum | 4 | 32 | 298.46 | 448.81 | 39.94 | |
| GH45 | Glucose | 6 | 16 | 602.8 | 2371.52 | 20.27 |
| Alfalfa | 6 | 16 | 377.34 | 2276.56 | 14.22 | |
| Energy cane | 6 | 16 | 322.7 | 1659 | 16.28 | |
| Corn stover | 6 | 16 | 420.71 | 1233.16 | 25.44 | |
| Sorghum | 8 | 16 | 343.55 | 1971.77 | 14.84 | |
| GH48 | Glucose | 15 | 17 | 3094.01 | 515.24 | 85.72 |
| Alfalfa | 14 | 16 | 1715.18 | 213.22 | 88.94 | |
| Energy cane | 14 | 16 | 2345.99 | 241.14 | 90.68 | |
| Corn stover | 14 | 16 | 3980 | 9.36 | 99.77 | |
| Sorghum | 16 | 16 | 1622.43 | 455.19 | 78.09 | |
| GH74 | Glucose | 3 | 4 | 50 | 0.3 | 99.4 |
| Alfalfa | 3 | 4 | 87.66 | 6.92 | 92.68 | |
| Energy cane | 3 | 4 | 53.55 | 12.03 | 81.66 | |
| Corn stover | 3 | 4 | 59.07 | 5.68 | 91.23 | |
| Sorghum | 3 | 4 | 23.3 | 8.22 | 73.92 | |
| GH95 | Glucose | 1 | 1 | 35.79 | 0 | 100 |
| Alfalfa | 1 | 1 | 39.09 | 0 | 100 | |
| Energy cane | 1 | 1 | 21.54 | 0 | 100 | |
| Corn stover | 1 | 1 | 16.34 | 0 | 100 | |
| Sorghum | 1 | 1 | 37.22 | 0 | 100 | |
| GH115 | Glucose | 1 | 4 | 89 | 0.4 | 99.55 |
| Alfalfa | 1 | 4 | 21.09 | 6.42 | 76.66 | |
| Energy cane | 1 | 4 | 6.09 | 1.17 | 83.83 | |
| Corn stover | 1 | 4 | 2.55 | 0.01 | 99.72 | |
| Sorghum | 1 | 4 | 4.41 | 1.66 | 72.7 | |
| GH124 | Glucose | 1 | 3 | 35.19 | 34.88 | 50.22 |
| Alfalfa | 1 | 3 | 41.2 | 47.86 | 46.26 | |
| Energy cane | 1 | 3 | 56.3 | 61.68 | 47.72 | |
| Corn stover | 1 | 3 | 98.51 | 79.55 | 55.33 | |
| Sorghum | 1 | 3 | 43.06 | 60.28 | 41.67 | |
aCorrected FPKM values normalized by the library size, as calculated using the estimateDispersions function in the R package DESeq [44]