Table 2.
Identification of CAZymes in fungal secretomes.
| Substrate/enzyme category | Enzyme class | CAZy family | A. terreus | T. reesei | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| T | Ba | Bi | S | C | G | T | Ba | Bi | S | C | G | |||||||||
| Cellulose | Endoglucanases | GH5, 7, 12, 45 | 28/11 | 10 | 7 | 9 | 11 | 2 | 13/5 | 4 | 2 | 5 | 5 | |||||||
| Cellobiohydrolases | GH6, 7 | 6/4 | 4 | 4 | 4 | 4 | 3/3 | 2 | 2 | 3 | 3 | |||||||||
| LPMOs | AA9 | 12/4 | 3 | 2 | 2 | 4 | 3/2 | 2 | 1 | 2 | 2 | |||||||||
| CDHs | AA3_1 | 1/0 | 0/0 | |||||||||||||||||
| Oligosaccharide oxidases | AA7 | 34/2 | 2 | 2 | 22/3 | 3 | ||||||||||||||
| Starch | LPMO | AA13 | 2/1 | 1 | 1 | 0/0 | ||||||||||||||
| Xylan | Xylanases | GH10, 11 | 6/5 | 5 | 5 | 5 | 5 | 4/3 | 2 | 3 | 2 | 2 | ||||||||
| LPMOs | AA14 | 0/0 | 1/0 | |||||||||||||||||
| Arabinan | Endoarabinanases | GH43 | 20/4 | 4 | 2 | 4 | 3 | 3/0 | ||||||||||||
| Exo-arabinanases/arabinofuranosidases | GH51, 62 | 6/2 | 2 | 2 | 2 | 2 | 1/1 | 1 | ||||||||||||
| Mannan | Endomannanases | GH5, 26 | 18/3 | 3 | 2 | 3 | 3 | 8/2 | 2 | 1 | 2 | 2 | ||||||||
| Soluble oligosaccharides | β-glucosidases | GH1 | 3/0 | 2/1 | 1 | 1 | ||||||||||||||
| Mannosidases | GH2 | 10/0 | 7/0 | |||||||||||||||||
| Xylosidases/β-glucosidases | GH3 | 21/3 | 2 | 2 | 2 | 2 | 13/3 | 2 | 3 | 3 | 2 | |||||||||
| Monosugars | PDHs | AA12 | 0/0 | 1/0 | ||||||||||||||||
| Pectin | Polygalacturonases | GH28 | 8/1 | 1 | 1 | 1 | 1 | 4/1 | 1 | |||||||||||
| Rhamnosidases | GH78 | 4/0 | 1/0 | |||||||||||||||||
| Pectin lyases | PL1, 3, 4, 20 | 13/4 | 4 | 4 | 4 | 3 | 3/0 | |||||||||||||
| Pectin methylesterases | CE8 | 1/0 | 0/0 | |||||||||||||||||
| Lignin | Laccases | AA1 | 7/0 | 4/0 | ||||||||||||||||
| Peroxidases | AA2 | 3/0 | 6/0 | |||||||||||||||||
| Oxidoreductases | AA3_2-4 | 15/1 | 1 | 9/0 | ||||||||||||||||
| Vanillyl-alcohol oxidases | AA4 | 3/0 | 4/0 | |||||||||||||||||
| Glyoxal oxidases (GLOX) | AA5_1 | 0/0 | 1/1 | 1 | 1 | |||||||||||||||
| 1,4-benzoquinone reductases | AA6 | 1/0 | 1/0 | |||||||||||||||||
| Noncarbohydrate-active esterases | CE10 | 65/3 | 1 | 3 | 2 | 2 | 30/1 | 1 | ||||||||||||
| Esterases | Feruloyl/p-coumaroyl/acetyl esterases | CE1 | 17/1 | 1 | 1 | 1 | 1 | 12/1 | 1 | 1 | 1 | 1 | ||||||||
| Acetyl esterases | CE2-5, 12, 16 | 28/5 | 5 | 3 | 5 | 4 | 14/1 | 1 | ||||||||||||
| 4-O-methyl-glucoronoyl esterases | CE15 | 1/0 | 1/1 | 1 | 1 | 1 | 1 | |||||||||||||
| Binding modules | CBM only | CBMx | 18/1 | 1 | 13/2 | 2 | 2 | 2 | 2 | |||||||||||
| Substrate/enzyme category | Enzyme class | CAZy family | M. thermophila | N. crassa | P. chrysosporium | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| T | Ba | Bi | S | C | G | T | Ba | Bi | S | C | G | T | Ba | Bi | S | C | G | |||
| Cellulose | Endoglucanases | GH5, 7, 12, 45 | 16/9 | 7 | 6 | 7 | 9 | 14/2 | 1 | 2 | 1 | 28/9 | 9 | 8 | 9 | 5 | ||||
| Cellobiohydrolases | GH6, 7 | 8/6 | 6 | 6 | 6 | 6 | 8/3 | 3 | 3 | 1 | 2 | 8/4 | 4 | 4 | 4 | 3 | 1 | |||
| LPMOs | AA9 | 22/12 | 12 | 12 | 11 | 11 | 14/5 | 1 | 4 | 1 | 16/10 | 9 | 8 | 10 | 3 | |||||
| CDHs | AA3_1 | 2/2 | 2 | 2 | 1 | 2 | 2/0 | 0/0 | ||||||||||||
| Oligosaccharide oxidases | AA7 | 16/4 | 1 | 3 | 1 | 18/0 | 13/0 | |||||||||||||
| Starch | LPMO | AA13 | 1/0 | 1/0 | 0/0 | |||||||||||||||
| Xylan | Xylanases | GH10, 11 | 10 | 8 | 8 | 4 | 4 | 6/3 | 3 | 3 | 7/6 | 6 | 6 | 6 | 1 | |||||
| LPMOs | AA14 | 0/0 | 0/0 | 2/0 | ||||||||||||||||
| Arabinan | Endoarabinanases | GH43 | 13/9 | 9 | 7 | 5 | 2 | 7/0 | 4/2 | 1 | 2 | 2 | ||||||||
| Exo-arabinanases/arabinofuranosidases | GH51, 62 | 4/3 | 3 | 1 | 2 | 1 | 1/1 | 1 | 1 | 1 | 2/1 | 1 | 1 | 1 | 1 | 1 | ||||
| Mannan | Endomannanases | GH5, 26 | 10/4 | 3 | 2 | 3 | 4 | 7/1 | 1 | 19/5 | 5 | 4 | 5 | 2 | ||||||
| Soluble oligosaccharides | β-glucosidases | GH1 | 1/1 | 1 | 1 | 1/0 | 2/0 | |||||||||||||
| Mannosidases | GH2 | 7/2 | 1 | 1 | 1 | 1 | 6/0 | 2/1 | 1 | 1 | ||||||||||
| Xylosidases/β-glucosidases | GH3 | 10/2 | 2 | 2 | 2 | 2 | 10/1 | 1 | 10/3 | 3 | 2 | 3 | ||||||||
| Monosugars | PDHs | AA12 | 3/1 | 1 | 3/0 | 1/1 | 1 | |||||||||||||
| Pectin | Polygalacturonases | GH28 | 2/0 | 2/0 | 5/4 | 3 | 2 | 4 | 1 | 1 | ||||||||||
| Rhamnosidases | GH78 | 1/0 | 1/0 | 1/1 | 1 | |||||||||||||||
| Pectin lyases | PL1, 3, 4, 20 | 8/5 | 3 | 4 | 5 | 2 | 4/1 | 1 | 0/0 | |||||||||||
| Pectin methylesterases | CE8 | 2/1 | 1 | 1 | 1 | 1/0 | 2/2 | 1 | 1 | 2 | ||||||||||
| Lignin | Laccases | AA1 | 5/0 | 10/0 | 2/0 | |||||||||||||||
| Peroxidases | AA2 | 4/1 | 1 | 1 | 1 | 4/0 | 17/6 | 5 | 5 | 5 | 1 | |||||||||
| Oxidoreductases | AA3_2-4 | 5/3 | 3 | 2 | 2 | 1 | 2/0 | 30/1 | 1 | 1 | ||||||||||
| Vanillyl-alcohol oxidases | AA4 | 2/0 | 3/0 | 1/0 | ||||||||||||||||
| Glyoxal oxidases (GLOX) | AA5_1 | 1/1 | 1 | 1 | 1 | 1 | 1 | 1/0 | 7/2 | 2 | 1 | 2 | ||||||||
| 1,4-benzoquinone reductases | AA6 | 1/0 | 1/0 | 4/0 | ||||||||||||||||
| Noncarbohydrate-active esterases | CE10 | 24/3 | 2 | 2 | 1 | 1 | 26/0 | 35/5 | 4 | 4 | 5 | |||||||||
| Esterases | Feruloyl/p-coumaroyl/acetyl esterases | CE1 | 15/4 | 4 | 1 | 2 | 1 | 16/0 | 17/2 | 2 | 1 | 2 | 1 | 1 | ||||||
| Acetyl esterases | CE2-5, 12, 16 | 21/8 | 7 | 6 | 3 | 2 | 17/0 | 18/3 | 2 | 1 | 3 | |||||||||
| 4-O-methyl-glucoronoyl esterases | CE15 | 2/1 | 1 | 1 | 1 | 1/0 | 2/2 | 2 | 2 | 2 | ||||||||||
| Binding modules | CBM only | CBMx | 14/2 | 1 | 1 | 1 | 1 | 1 | 13/0 | 32/2 | 2 | 2 | 2 | 2 | ||||||
The table shows a subset of CAZymes most relevant for lignocellulose deconstruction and how these are expressed in each fungus, categorized by enzyme class and (expected) substrate of action. In the column ‘T’, the first number shows the total number of predicted CAZymes found in the whole genome using dbCAN while the second number shows the total number of proteins detected in the secretomes across all substrates. The columns labeled Ba: sugarcane bagasse, Bi: birch, S: spruce, C: cellulose, G: glucose, show the number of proteins detected in the secretome during growth on these respective substrates, including if the protein was identified in a single biological replicate, given that it was found in at least two replicates on another carbon source. In two cases (AA3 and AA5), CAZy subfamilies are included for class differentiation. For quantitative expression values, see the heat maps (Figures S1–S5). Note that enzymes listed as active on arabinan may also be active on xylan and pectin due to the presence of arabinosyl groups in these polymers. ‘CBM only’ refers to proteins with no predicted CAZyme function but still containing a carbohydrate-binding module. Note that CAZy enzyme classes may, in some cases, act on more than one substrate. In such cases enzymes are counted as both, e.g. for GH5 which is counted as both endoglucanase and endomannanase.