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Review

Genomics Review of Holocellulose Deconstruction by Aspergilli

Fernando Segato, André R. L. Damásio, Rosymar C. de Lucas, Fabio M. Squina, Rolf A. Prade
Fernando Segato
aDepartment of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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André R. L. Damásio
aDepartment of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
bLaboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
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Rosymar C. de Lucas
aDepartment of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Fabio M. Squina
bLaboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
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Rolf A. Prade
aDepartment of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
bLaboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
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DOI: 10.1128/MMBR.00019-14
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  • FIG 1
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    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
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    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
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    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
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    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
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    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

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  • TABLE 1

    Polysaccharide composition of energy crops and wood

    Energy crop% Sugars in juice% Biomass in bagasseReference
    CelluloseHemicelluloseLignin
    Sugar cane9.8432422123
    Sweet sorghum11.8452721123
    Hardwood38–5117–3827–32171
    Softwood33–4222–4021–31171
  • TABLE 2

    Complete cellulose degradation gene complementa

    TABLE 2
    • ↵a For complete gene and protein information, refer to Tables S1 to S5 in the supplemental material. Gray-shaded entries are totals.

  • TABLE 3

    Genome-wide distribution of fungal cellobiohydrolases

    FungusCellobiohydrolase(s)
    GH6 (nonreducing end)GH7 (reducing end)
    Without CBMWith CBMWithout CBMWith CBM
    Strains with a complete cellobiohydrolase set
        A. clavatus NRRL-1ACLA_025560ACLA_062560ACLA_088870ACLA_085260
        A. nidulans FGSC A4AN1273AN5282AN5176AN0494
        A. niger CBS 513.88ANI_1_1704074ANI_1_300104ANI_1_2134064ANI_1_1574014
        A. terreus NIH 2624ATEG_00193ATEG_07493ATEG_03727ATEG_05002
    Strains with an incomplete cellobiohydrolase set
        A. fumigatus Af293AFUA_3G01910AFUA_6G07070AFUA_6G11610
        A. flavus NRRL-3357AFLA_069820AFLA_067550, AFLA_021870
        A. oryzae RIB 40AOR_1_734074AOR_1_608164, AOR_1_1654194
    Strains used for reference
        H. jecorina taxid 51453GUX2_HYPJEGUX1_TRIRE
        N. crassa OR 74ANCU03996, NCU07190NCU09680NCU05104NCU07340
  • TABLE 4

    Genome-wide endoglucanase content in aspergillia

    TABLE 4
    • ↵a Among the aspergilli, there were 18, 9, 9, and 6 cellulases in the GH5, GH7, GH12, and GH45 families, respectively, for a total of 37 cellulases. ±, with or without.

  • TABLE 5

    Fungal lytic polysaccharide monooxygenases of the AA9 family

    TABLE 5
  • TABLE 6

    Fungal cellobiose dehydrogenases

    FungusCellobiose dehydrogenase(s)No. of CDH genes per genome
    A. clavatus NRRL1ACLA_076510, ACLA_0944902
    A. flavus NRRL3357AFLA_001890, AFLA_0238202
    A. fumigatus Af293AFUA_2G17620, AFUA_2G011802
    A. nidulans A4AN7230.2, AN39622
    A. niger CBS513.88ANI_1_1681741
    A. oryzae RIB40AOR_1_98134, AOR_1_712114, AOR_1_25661543
    A. terreusATEG_09993, ATEG_081502
    H. jecorina0
    N. crassa OR74ANCU05923, NCU002062
  • TABLE 7

    Fungal β-glucosidases

    TABLE 7
  • TABLE 8

    Fungal hemicellulasesa

    TABLE 8
    • ↵a ±, with or without.

  • TABLE 9

    Fungal accessory enzymes

    TABLE 9
    • a ±, with or without.

  • TABLE 10

    Genome-wide acetyl xylan and feruloyl esterase content in aspergilli

    TABLE 10

Additional Files

  • Figures
  • Tables
  • Supplemental material

    Files in this Data Supplement:

    • Supplemental file 1 -

      Cellobiohydrolase data (Table S1).

      XLS, 55K

    • Supplemental file 2 -

      Endoglucanase data (Table S2).

      XLS, 86K

    • Supplemental file 3 -

      Lytic polysaccharide monooxygenase data (Table S3) and LPMO tree (Fig. S3).

      XLS, 212K

    • Supplemental file 4 -

      Cellobiose dehydrogenase data (Table S4).

      XLS, 53K

    • Supplemental file 5 -

      β-glucosidase data (Table S5).

      XLS, 205K

    • Supplemental file 6 -

      Hemicellulase data (Table S6).

      XLS, 142K

    • Supplemental file 7 -

      Accessory enzyme data (Table S7).

      XLS, 128K

    • Supplemental file 8 -

      Esterase data (Table S8).

      XLS, 101K

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Genomics Review of Holocellulose Deconstruction by Aspergilli
Fernando Segato, André R. L. Damásio, Rosymar C. de Lucas, Fabio M. Squina, Rolf A. Prade
Microbiology and Molecular Biology Reviews Nov 2014, 78 (4) 588-613; DOI: 10.1128/MMBR.00019-14

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Genomics Review of Holocellulose Deconstruction by Aspergilli
Fernando Segato, André R. L. Damásio, Rosymar C. de Lucas, Fabio M. Squina, Rolf A. Prade
Microbiology and Molecular Biology Reviews Nov 2014, 78 (4) 588-613; DOI: 10.1128/MMBR.00019-14
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  • Top
  • Article
    • SUMMARY
    • INTRODUCTION
    • HOLOCELLULOSE ENZYME BREAKDOWN SYSTEMS
    • ENZYME STRUCTURE-FUNCTION AND SUBSTRATE RELATIONSHIPS
    • CONCLUSIONS
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
    • Author Bios
  • Figures & Data
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  • PDF

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