Article Figures & Data
Figures
- FIG 1
Canonical holocellulose structure and deconstructive hydrolytic enzyme interactions. The main polymers integrating biomass are lignin (boxes) and holocellulose, which includes hemicellulose (light-colored, loosely branched chains) and cellulose (black linear bundled chains). Sugars: X, xylose; A, arabinose; Gc, glucuronic acid; M, mannose. Open hexagons, ferulic acid; closed circles, acetyl groups. Biomass is the principal carbon sink on earth and recruits numerous enzymes to deconstruct cellulose and hemicellulose to sway the carbon cycle via the central energy metabolism. Enzymes needed to deconstruct holocellulose include the following: cellulases, i.e., cellobiohydrolases and endoglucanases, with and without CBMs, β-glucosidases, copper-dependent lytic polysaccharide monooxygenases (LPMOs), and cellobiose dehydrogenases; and hemicellulases, i.e., xylanases, mannosidases, xyloglucanases, xylan acetyl esterases, feruloyl esterases, arabinanases, glucuronidases, and arabinofuranosidase xylosidases.
- FIG 2
GH6 (A to C) and GH7 (D to F) cellobiohydrolases. (B and E) Typical tunnel-shaped catalytic cleft found in cellobiohydrolases. (C and F) Cleft depth. Cellobiohydrolases fold into an enclosed catalytic core shaped by a β-sandwich with two large, antiparallel β-sheets packed onto each other, forming a long cellulose-binding tunnel (226). The cellulosic substrate chain has to travel through the tunnel, where β-1,4-glycosyl bonds of cellobiose molecules (dimers) are hydrolyzed off the ends (GH6 or GH7 enzymes). The three-dimensional structures are for Trichoderma reesei GH6 (CBHII; PDB entry 1QK2) (108) and GH7 (CBHI or Cel7A; PDB entry 4C4C) enzymes (227).
- FIG 3
Three-dimensional structures of GH5 (A and B), GH7 (C and D), and GH12 (E and F) endoglucanases. (B, D, and F) Well-defined open clefts in these endoglucanase families. Endoglucanases from the GH5 family show a catalytic module with a typical compact 8-fold β/α barrel architecture, forming an open cleft similar to those of GH7 and GH12 endoglucanases, which share the β-jelly-roll topology with an extended, open substrate-binding groove. Endoglucanases with the open cleft configuration bind randomly to internal portions of a cellulose chain and cleave β-1,4-glycosidic bonds, resulting in shortened fragments. The three-dimensional structures are for the Thermoascus aurantiacus GH5 endoglucanase Cel5A (PDB entry 1GZJ), the Trichoderma reesei GH7 enzyme EGI (PDB entry 1EG1), and the Trichoderma reesei GH12 enzyme EGIII (Egl3 or Cel12A; PDB entry 1H8V) (116, 119, 122).
- FIG 4
Lytic polysaccharide monooxygenases (LPMOs). LPMOs, which are classified in the AA9 family (formerly GH61), are bivalent ion-dependent lytic polysaccharide monooxygenases. These proteins cleave cellulose chains with oxidation of various carbons (C-1, C-4, and C-6). The LPMO three-dimensional structures are for Neurospora crassa (PDB entry 4EIR) (129) (A), Hypocrea jecorina (PDB entry 2VTC) (130) (B), Thielavia terrestris (PDB entry 3EJA) (72) (C), and Phanerochaete chrysosporium (PDB entry 4B5Q) (126) (D).
- FIG 5
GH74 xyloglucanobiohydrolases. (A) The three-dimensional structure consists of two tandem repeats of a seven-blade β-propeller domain which forms a large cleft and a loop where the substrate is bound. (B and C) Two views of the open cleft. The three-dimensional structure of Geotrichum sp. GH74 endoglucanase is from PDB entry 1SQJ (199, 200).
Tables
- TABLE 1
Polysaccharide composition of energy crops and wood
Energy crop % Sugars in juice % Biomass in bagasse Reference Cellulose Hemicellulose Lignin Sugar cane 9.8 43 24 22 123 Sweet sorghum 11.8 45 27 21 123 Hardwood 38–51 17–38 27–32 171 Softwood 33–42 22–40 21–31 171 - TABLE 3
Genome-wide distribution of fungal cellobiohydrolases
Fungus Cellobiohydrolase(s) GH6 (nonreducing end) GH7 (reducing end) Without CBM With CBM Without CBM With CBM Strains with a complete cellobiohydrolase set A. clavatus NRRL-1 ACLA_025560 ACLA_062560 ACLA_088870 ACLA_085260 A. nidulans FGSC A4 AN1273 AN5282 AN5176 AN0494 A. niger CBS 513.88 ANI_1_1704074 ANI_1_300104 ANI_1_2134064 ANI_1_1574014 A. terreus NIH 2624 ATEG_00193 ATEG_07493 ATEG_03727 ATEG_05002 Strains with an incomplete cellobiohydrolase set A. fumigatus Af293 AFUA_3G01910 AFUA_6G07070 AFUA_6G11610 A. flavus NRRL-3357 AFLA_069820 AFLA_067550, AFLA_021870 A. oryzae RIB 40 AOR_1_734074 AOR_1_608164, AOR_1_1654194 Strains used for reference H. jecorina taxid 51453 GUX2_HYPJE GUX1_TRIRE N. crassa OR 74A NCU03996, NCU07190 NCU09680 NCU05104 NCU07340 - TABLE 5
Fungal lytic polysaccharide monooxygenases of the AA9 family
- TABLE 6
Fungal cellobiose dehydrogenases
Fungus Cellobiose dehydrogenase(s) No. of CDH genes per genome A. clavatus NRRL1 ACLA_076510, ACLA_094490 2 A. flavus NRRL3357 AFLA_001890, AFLA_023820 2 A. fumigatus Af293 AFUA_2G17620, AFUA_2G01180 2 A. nidulans A4 AN7230.2, AN3962 2 A. niger CBS513.88 ANI_1_168174 1 A. oryzae RIB40 AOR_1_98134, AOR_1_712114, AOR_1_2566154 3 A. terreus ATEG_09993, ATEG_08150 2 H. jecorina 0 N. crassa OR74A NCU05923, NCU00206 2 - TABLE 7
Fungal β-glucosidases
- TABLE 9
Fungal accessory enzymes
a ±, with or without.
- TABLE 10
Genome-wide acetyl xylan and feruloyl esterase content in aspergilli
Supplemental material
Files in this Data Supplement:
- Supplemental file 1
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Cellobiohydrolase data (Table S1).
XLS, 55K
- Supplemental file 2
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Endoglucanase data (Table S2).
XLS, 86K
- Supplemental file 3
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Lytic polysaccharide monooxygenase data (Table S3) and LPMO tree (Fig. S3).
XLS, 212K
- Supplemental file 4
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Cellobiose dehydrogenase data (Table S4).
XLS, 53K
- Supplemental file 5
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β-glucosidase data (Table S5).
XLS, 205K
- Supplemental file 6
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Hemicellulase data (Table S6).
XLS, 142K
- Supplemental file 7
-
Accessory enzyme data (Table S7).
XLS, 128K
- Supplemental file 8
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Esterase data (Table S8).
XLS, 101K
- Supplemental file 1
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