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Okmane L, Sandgren M, Ståhlberg J, Nestor G. 1H, 13C and 15N backbone resonance assignment of Cel45A from Phanerochaete chrysosporium. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10182-6. [PMID: 38888713 DOI: 10.1007/s12104-024-10182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
A glycoside hydrolase family 45 (GH45) enzyme from the white-rot basidiomycete fungus Phanerochaete chrysosporium (PcCel45A) was expressed in Pichia pastoris with 13C and 15N labelling. A nearly complete assignment of 1H, 13C and 15N backbone resonances was obtained, as well as the secondary structure prediction based on the assigned chemical shifts using the TALOS-N software. The predicted secondary structure was almost identical to previously published crystal structures of the same enzyme, except for differences in the termini of the sequence. This is the first NMR study using an isotopically labelled GH45 enzyme.
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Affiliation(s)
- Laura Okmane
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gustav Nestor
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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2
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Okmane L, Fitkin L, Sandgren M, Ståhlberg J. The first crystal structure of a family 45 glycoside hydrolase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A. FEBS Open Bio 2024; 14:505-514. [PMID: 38311343 PMCID: PMC10909974 DOI: 10.1002/2211-5463.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Here we describe the first crystal structure of a beta-1,4-endoglucanase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A, which belongs to subfamily C of glycoside hydrolase family 45 (GH45). GtCel45A is ~ 18 kDa in size and the crystal structure contains 179 amino acids. The structure is refined at 1.30 Å resolution and Rfree 0.18. The enzyme consists of a single catalytic module folded into a six-stranded double-psi beta-barrel domain surrounded by long loops. GtCel45A is very similar in sequence (82% identity) and structure to PcCel45A from the white-rot fungus Phanerochaete chrysosporium. Surprisingly though, initial hydrolysis of barley beta-glucan was almost twice as fast in GtCel45A as compared to PcCel45A.
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Affiliation(s)
- Laura Okmane
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Louise Fitkin
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Mats Sandgren
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Jerry Ståhlberg
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
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3
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Chaudhary N, Grover M. Bioindustrial applications of thermostable Endoglucanase purified from Trichoderma viride towards the conversion of agrowastes to value-added products. Protein Expr Purif 2023; 211:106324. [PMID: 37356677 DOI: 10.1016/j.pep.2023.106324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Importance of biocatalytic reactions and biotransformations mediated by fungal enzymes has increased tremendously in various industries. Endoglucanase obtained from Trichoderma viride has been utilized for bioconversion of agrowastes; wheat straw (WS) and corn stover (CS) as biomass into citric acid and single cell protein (SCP) as value-added products. The enzyme was purified to apparent homogeneity with Mr:44.67 kDa; purification-fold, yield, specific activity to be 19.5-, 29.2%, and 150.4 Units.mg-1, respectively, with thermostability up to 70 °C. The enzyme showed a novel N-terminal peptide and its computational analysis revealed a conserved 'SG' amino acid sequence alike microbial cellulases. The experimental results have shown the potential of endoglucanase for the conversion of agrowastes; wheat straw (WS) and corn stover (CS) into citric acid, maximum yield (KgM-3) found in submerged (WS:50;CS:45) fermentation process. Single-cell protein (SCP) production in WS (68 KgM-3) hydrolysate was superior to both CS hydrolysate (60 KgM-3) and YEPD (standard medium) (58 KgM-3).
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Affiliation(s)
- Nidhee Chaudhary
- Centre of Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Sector-125, Noida, 201313, India.
| | - Monendra Grover
- Centre for Agricultural Bioinformatics, ICAR-IASRI, Library Avenue Pusa, New Delhi, India
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4
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Hwang S, Walker CC, Johnson D, Han Y, Gardner DJ. Spray Drying Enzyme-Treated Cellulose Nanofibrils. Polymers (Basel) 2023; 15:4086. [PMID: 37896330 PMCID: PMC10610161 DOI: 10.3390/polym15204086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Enzyme-treated cellulose nanofibrils (CNFs) were produced via a lab-scale mass colloider using bleached kraft pulp (BKP) to evaluate their processability and power requirements during refining and spray-drying operations. To evaluate the energy efficiency in the CNF refining process, the net energy consumption, degree of polymerization (DP), and viscosity were determined. Less energy was consumed to attain a given fines level by using the endoglucanase enzymes. The DP and viscosity were also decreased using the enzymes. The morphological properties of the enzyme-pretreated spray-dried CNF powders (SDCNFs) were measured. Subsequently, the enzyme-pretreated SDCNFs were added to a PP matrix with MAPP as a coupling agent. The mixture was then compounded through a co-rotating twin-screw extruder to determine whether the enzyme treatment of the CNFs affects the mechanical properties of the composites. Compared to earlier studies on enhancing PMCs with SDCNF powders, this research investigates the use of enzyme-pretreated SDCNF powders. It was confirmed that the strength properties of PP increased by adding SDCNFs, and the strength properties were maintained after adding enzyme-pretreated SDCNFs.
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Affiliation(s)
- Sungjun Hwang
- Advanced Structures and Composites Center, University of Maine, 35 Flagstaff Road, Orono, ME 04469-5793, USA;
- School of Forest Resources, University of Maine, 5755 Nutting Hall, Orono, ME 04469-5755, USA
| | - Colleen C. Walker
- Process Development Center, University of Maine, 5737 Jenness Hall, Orono, ME 04469-5737, USA; (C.C.W.); (D.J.)
| | - Donna Johnson
- Process Development Center, University of Maine, 5737 Jenness Hall, Orono, ME 04469-5737, USA; (C.C.W.); (D.J.)
| | - Yousoo Han
- Advanced Structures and Composites Center, University of Maine, 35 Flagstaff Road, Orono, ME 04469-5793, USA;
- School of Forest Resources, University of Maine, 5755 Nutting Hall, Orono, ME 04469-5755, USA
| | - Douglas J. Gardner
- Advanced Structures and Composites Center, University of Maine, 35 Flagstaff Road, Orono, ME 04469-5793, USA;
- School of Forest Resources, University of Maine, 5755 Nutting Hall, Orono, ME 04469-5755, USA
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5
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Hornung BVH, Terrapon N. An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space. PLoS Comput Biol 2023; 19:e1010881. [PMID: 37585436 PMCID: PMC10461819 DOI: 10.1371/journal.pcbi.1010881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/28/2023] [Accepted: 01/18/2023] [Indexed: 08/18/2023] Open
Abstract
The deluge of genomic data raises various challenges for computational protein annotation. The definition of superfamilies, based on conserved folds, or of families, showing more recent homology signatures, allow a first categorization of the sequence space. However, for precise functional annotation or the identification of the unexplored parts within a family, a division into subfamilies is essential. As curators of an expert database, the Carbohydrate Active Enzymes database (CAZy), we began, more than 15 years ago, to manually define subfamilies based on phylogeny reconstruction. However, facing the increasing amount of sequence and functional data, we required more scalable and reproducible methods. The recently popularized sequence similarity networks (SSNs), allows to cope with very large families and computation of many subfamily schemes. Still, the choice of the optimal SSN subfamily scheme only relies on expert knowledge so far, without any data-driven guidance from within the network. In this study, we therefore decided to investigate several network properties to determine a criterion which can be used by curators to evaluate the quality of subfamily assignments. The performance of the closeness centrality criterion, a network property to indicate the connectedness within the network, shows high similarity to the decisions of expert curators from eight distinct protein families. Closeness centrality also suggests that in some cases multiple levels of subfamilies could be possible, depending on the granularity of the research question, while it indicates when no subfamily emerged in some family evolution. We finally used closeness centrality to create subfamilies in four families of the CAZy database, providing a finer functional annotation and highlighting subfamilies without biochemically characterized members for potential future discoveries.
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Affiliation(s)
| | - Nicolas Terrapon
- Aix Marseille Université, CNRS, UMR 7257 AFMB, Marseille, France
- INRAE, USC 1408 AFMB, Marseille, France
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Matsumoto R, Mehjabin JJ, Noguchi H, Miyamoto T, Takasuka TE, Hori C. Genomic and Secretomic Analyses of the Newly Isolated Fungus Perenniporia fraxinea SS3 Identified CAZymes Potentially Related to a Serious Pathogenesis of Hardwood Trees. Appl Environ Microbiol 2023; 89:e0027223. [PMID: 37098943 PMCID: PMC10231188 DOI: 10.1128/aem.00272-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023] Open
Abstract
Perenniporia fraxinea can colonize living trees and cause severe damage to standing hardwoods by secreting a number of carbohydrate-activate enzymes (CAZymes), unlike other well-studied Polyporales. However, significant knowledge gaps exist in understanding the detailed mechanisms for this hardwood-pathogenic fungus. To address this issue, five monokaryotic P. fraxinea strains, SS1 to SS5, were isolated from the tree species Robinia pseudoacacia, and high polysaccharide-degrading activities and the fastest growth were found for P. fraxinea SS3 among the isolates. The whole genome of P. fraxinea SS3 was sequenced, and its unique CAZyme potential for tree pathogenicity was determined in comparison to the genomes of other nonpathogenic Polyporales. These CAZyme features are well conserved in a distantly related tree pathogen, Heterobasidion annosum. Furthermore, the carbon source-dependent CAZyme secretions of P. fraxinea SS3 and a nonpathogenic and strong white-rot Polyporales member, Phanerochaete chrysosporium RP78, were compared by activity measurements and proteomic analyses. As seen in the genome comparisons, P. fraxinea SS3 exhibited higher pectin-degrading activities and higher laccase activities than P. chrysosporium RP78, which were attributed to the secretion of abundant glycoside hydrolase family 28 (GH28) pectinases and auxiliary activity family 1_1 (AA1_1) laccases, respectively. These enzymes are possibly related to fungal invasion into the tree lumens and the detoxification of tree defense substances. Additionally, P. fraxinea SS3 showed secondary cell wall degradation capabilities at the same level as that of P. chrysosporium RP78. Overall, this study suggested mechanisms for how this fungus can attack the cell walls of living trees as a serious pathogen and differs from other nonpathogenic white-rot fungi. IMPORTANCE Many studies have been done to understand the mechanisms underlying the degradation of plant cell walls of dead trees by wood decay fungi. However, little is known about how some of these fungi weaken living trees as pathogens. P. fraxinea belongs to the Polyporales, a group of strong wood decayers, and is known to aggressively attack and fell standing hardwood trees all over the world. Here, we report CAZymes potentially related to plant cell wall degradation and pathogenesis factors in a newly isolated fungus, P. fraxinea SS3, by genome sequencing in conjunction with comparative genomic and secretomic analyses. The present study provides insights into the mechanisms of the degradation of standing hardwood trees by the tree pathogen, which will contribute to the prevention of this serious tree disease.
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Affiliation(s)
- Ruy Matsumoto
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Jakia Jerin Mehjabin
- Research Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | | | - Taichi E. Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- Global Station for Food, Land, and Water Resources, Hokkaido University, Sapporo, Japan
| | - Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
- Research Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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Meng Z, Yang C, Leng J, Zhu W, Cheng Y. Production, purification, characterization and application of two novel endoglucanases from buffalo rumen metagenome. J Anim Sci Biotechnol 2023; 14:16. [PMID: 36740711 PMCID: PMC9900955 DOI: 10.1186/s40104-022-00814-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/02/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lignocellulose biomass is the most abundant and renewable material in nature. The objectives of this study were to characterize two endoglucanases TrepCel3 and TrepCel4, and determine the effect of the combination of them (1.2 mg TrepCel3, 0.8 mg TrepCel4) on in vitro rumen fermentation characteristics. In this study, three nature lignocellulosic substrates (rice straw, RS; wheat straw, WS; leymus chinensis, LC) were evaluated for their in vitro digestibility, gas, NH3-N and volatile fatty acid (VFA) production, and microbial protein (MCP) synthesis by adding enzymatic combination. METHODS Two endoglucanases' genes were successfully expressed in Escherichia coli (E. coli) BL21 (DE3), and enzymatic characteristics were further characterized. The combination of TrepCel3 and TrepCel4 was incubated with lignocellulosic substrates to evaluate its hydrolysis ability. RESULTS The maximum enzymatic activity of TrepCel3 was determined at pH 5.0 and 40 °C, while TrepCel4 was at pH 6.0 and 50 °C. They were stable over the temperature range of 30 to 60 °C, and active within the pH range of 4.0 to 9.0. The TrepCel3 and TrepCel4 had the highest activity in lichenan 436.9 ± 8.30 and 377.6 ± 6.80 U/mg, respectively. The combination of TrepCel3 and TrepCel4 exhibited the highest efficiency at the ratio of 60:40. Compared to maximum hydrolysis of TrepCel3 or TrepCel4 separately, this combination was shown to have a superior ability to maximize the saccharification yield from lignocellulosic substrates up to 188.4% for RS, 236.7% for wheat straw WS, 222.4% for LC and 131.1% for sugar beet pulp (SBP). Supplemental this combination enhanced the dry matter digestion (DMD), gas, NH3-N and VFA production, and MCP synthesis during in vitro rumen fermentation. CONCLUSIONS The TrepCel3 and TrepCel4 exhibited the synergistic relationship (60:40) and significantly increased the saccharification yield of lignocellulosic substrates. The combination of them stimulated in vitro rumen fermentation of lignocellulosic substrates. This combination has the potential to be a feed additive to improve agricultural residues utilization in ruminants. If possible, in the future, experiments in vivo should be carried out to fully evaluate its effect.
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Affiliation(s)
- Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengjian Yang
- Buffalo Research Institute, Chinese Academy of Agricultural, Nanning, 530000, China
| | - Jing Leng
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, 650000, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
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8
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Nagl M, Haske-Cornelius O, Bauer W, Csarman F, Ludwig R, Nyanhongo GS, Guebitz GM. Towards a better understanding of synergistic enzyme effects during refining of cellulose fibers. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2022. [DOI: 10.1016/j.carpta.2022.100223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Gacias-Amengual N, Wohlschlager L, Csarman F, Ludwig R. Fluorescent Imaging of Extracellular Fungal Enzymes Bound onto Plant Cell Walls. Int J Mol Sci 2022; 23:ijms23095216. [PMID: 35563607 PMCID: PMC9105846 DOI: 10.3390/ijms23095216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Lignocelluloytic enzymes are industrially applied as biocatalysts for the deconstruction of recalcitrant plant biomass. To study their biocatalytic and physiological function, the assessment of their binding behavior and spatial distribution on lignocellulosic material is a crucial prerequisite. In this study, selected hydrolases and oxidoreductases from the white rot fungus Phanerochaete chrysosporium were localized on model substrates as well as poplar wood by confocal laser scanning microscopy. Two different detection approaches were investigated: direct tagging of the enzymes and tagging specific antibodies generated against the enzymes. Site-directed mutagenesis was employed to introduce a single surface-exposed cysteine residue for the maleimide site-specific conjugation. Specific polyclonal antibodies were produced against the enzymes and were labeled using N-hydroxysuccinimide (NHS) ester as a cross-linker. Both methods allowed the visualization of cell wall-bound enzymes but showed slightly different fluorescent yields. Using native poplar thin sections, we identified the innermost secondary cell wall layer as the preferential attack point for cellulose-degrading enzymes. Alkali pretreatment resulted in a partial delignification and promoted substrate accessibility and enzyme binding. The methods presented in this study are suitable for the visualization of enzymes during catalytic biomass degradation and can be further exploited for interaction studies of lignocellulolytic enzymes in biorefineries.
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Kojima K, Sunagawa N, Yoshimi Y, Tryfona T, Samejima M, Dupree P, Igarashi K. Acetylated xylan degradation by glycoside hydrolase family 10 and 11 xylanases from the white-rot fungus <i>Phanerochaete chrysosporium</i>. J Appl Glycosci (1999) 2022; 69:35-43. [PMID: 35891899 PMCID: PMC9276525 DOI: 10.5458/jag.jag.jag-2021_0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Endo-type xylanases are key enzymes in microbial xylanolytic systems, and xylanases belonging to glycoside hydrolase (GH) families 10 or 11 are the major enzymes degrading xylan in nature. These enzymes have typically been characterized using xylan prepared by alkaline extraction, which removes acetyl sidechains from the substrate, and thus the effect of acetyl groups on xylan degradation remains unclear. Here, we compare the ability of GH10 and 11 xylanases, PcXyn10A and PcXyn11B, from the white-rot basidiomycete Phanerochaete chrysosporium to degrade acetylated and deacetylated xylan from various plants. Product quantification revealed that PcXyn10A effectively degraded both acetylated xylan extracted from Arabidopsis thaliana and the deacetylated xylan obtained by alkaline treatment, generating xylooligosaccharides. In contrast, PcXyn11B showed limited activity towards acetyl xylan, but showed significantly increased activity after deacetylation of the xylan. Polysaccharide analysis using carbohydrate gel electrophoresis showed that PcXyn11B generated a broad range of products from native acetylated xylans extracted from birch wood and rice straw, including large residual xylooligosaccharides, while non-acetylated xylan from Japanese cedar was readily degraded into xylooligosaccharides. These results suggest that the degradability of native xylan by GH11 xylanases is highly dependent on the extent of acetyl group substitution. Analysis of 31 fungal genomes in the Carbohydrate-Active enZymes database indicated that the presence of GH11 xylanases is correlated to that of carbohydrate esterase (CE) family 1 acetyl xylan esterases (AXEs), while this is not the case for GH10 xylanases. These findings may imply co-evolution of GH11 xylanases and CE1 AXEs.
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Affiliation(s)
- Keisuke Kojima
- Department of Biomaterial Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, The University of Tokyo
| | | | | | | | - Paul Dupree
- Department of Biochemistry, University of Cambridge
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11
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Okmane L, Nestor G, Jakobsson E, Xu B, Igarashi K, Sandgren M, Kleywegt GJ, Ståhlberg J. Glucomannan and beta-glucan degradation by Mytilus edulis Cel45A: Crystal structure and activity comparison with GH45 subfamily A, B and C. Carbohydr Polym 2022; 277:118771. [PMID: 34893216 DOI: 10.1016/j.carbpol.2021.118771] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022]
Abstract
The enzymatic hydrolysis of barley beta-glucan, konjac glucomannan and carboxymethyl cellulose by a β-1,4-D-endoglucanase MeCel45A from blue mussel, Mytilus edulis, which belongs to subfamily B of glycoside hydrolase family 45 (GH45), was compared with GH45 members of subfamilies A (Humicola insolens HiCel45A), B (Trichoderma reesei TrCel45A) and C (Phanerochaete chrysosporium PcCel45A). Furthermore, the crystal structure of MeCel45A is reported. Initial rates and hydrolysis yields were determined by reducing sugar assays and product formation was characterized using NMR spectroscopy. The subfamily B and C enzymes exhibited mannanase activity, whereas the subfamily A member was uniquely able to produce monomeric glucose. All enzymes were confirmed to be inverting glycoside hydrolases. MeCel45A appears to be cold adapted by evolution, as it maintained 70% activity on cellohexaose at 4 °C relative to 30 °C, compared to 35% for TrCel45A. Both enzymes produced cellobiose and cellotetraose from cellohexaose, but TrCel45A additionally produced cellotriose.
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Affiliation(s)
- Laura Okmane
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gustav Nestor
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emma Jakobsson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Bingze Xu
- Center for Surface Biotechnology, Uppsala University, Uppsala, Sweden
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gerard J Kleywegt
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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12
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Kojima K, Sunagawa N, Mikkelsen NE, Hansson H, Karkehabadi S, Samejima M, Sandgren M, Igarashi K. Comparison of Glycoside Hydrolase family 3 β-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J Biol Chem 2022; 298:101670. [PMID: 35120929 PMCID: PMC8913315 DOI: 10.1016/j.jbc.2022.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems, which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) β-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the KM values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X2), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.
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Affiliation(s)
- Keisuke Kojima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano 380-8533, Japan
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo FI-02044 VTT, Finland.
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13
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Amengual NG, Csarman F, Wohlschlager L, Ludwig R. Expression and characterization of a family 45 glycosyl hydrolase from Fomitopsis pinicola and comparison to Phanerochaete chrysosporium Cel45A. Enzyme Microb Technol 2022; 156:110000. [PMID: 35123123 PMCID: PMC7613719 DOI: 10.1016/j.enzmictec.2022.110000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
To efficiently decompose biomass, fungi have developed various enzymatic and non-enzymatic strategies and are a source of versatile biocatalysts. The endoglucanases in glycosyl hydrolase CAZy family 45 (GH45) are known for their small size, a high thermostability and a broad substrate specificity that has been employed in textile and detergent industries. Here we report the heterologous expression and characterisation of an GH45 endoglucanase from the brown rot Fomitopsis pinicola and its direct comparison to an already characterised GH45 from the white rot Phanerochaete chrysosporium. Both enzymes were recombinantly expressed in Pichia pastoris and purified by two chromatographic steps. The biochemical characterisation highlighted the acidophilic character, with an optimal pH of 4, and a preference for amorphous substrates as carboxymethyl cellulose (CMC) and substrates containing β-1,4-glucans rather than the previously reported β-1,3/1,4-glucans lichenan and β-glucan. The dominating products from β-1,4-glucans were C3-C6 oligosaccharides, whereas from β-1,3/1,4-glucans glucose was the main reaction product. From the characterisation no differences between the brown rot and the white rot GH45 was evident.
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Affiliation(s)
- Neus Gacias Amengual
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Florian Csarman
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Lena Wohlschlager
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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14
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Tanaka D, Ohnishi KI, Watanabe S, Suzuki S. Isolation of cellulase-producing Microbulbifer sp. from marine teleost blackfish (Girella melanichthys) intestine and the enzyme characterization. J GEN APPL MICROBIOL 2021; 67:47-53. [PMID: 33250506 DOI: 10.2323/jgam.2020.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Most animals cannot digest cellulose but have symbiotic microbes that degrade the matrix polysaccharides of plant matter. Herbivorous and omnivorous marine fish are similarly expected to rely on symbiotic microbes, but reports to date on cellulase-producing bacteria in fish intestines are limited. Here, we report the isolation of new cellulase-producing bacteria from the marine omnivorous teleost, blackfish (Girella melanichthys), and the characterization of cellulase activity. Three strains of cellulase-producing bacteria sp. were isolated from the hindgut of wild G. melanichthys. The strains of cellulase-producing bacteria grew in medium with artificial seawater but not in NaCl alone. Growth was optimum at 20-35°C, but there was no growth at 40°C, suggesting adaptation in a marine environment at a low temperature. Isolates were identified to Microbulbifer sp., among which GL-2 strain produced a high enzyme activity. The GL-2 strain was further used for enzyme characterization with carboxymethyl cellulose (CMC) as the substrate. Maximum activity of the cellulase was observed at 60°C, and activity was more than 30% at 20°C, while commercial cellulase Enthiron showed an optimum activity at 50°C and 17% activity at 20°C. Hydrolytic products by GL-2 cellulase were cellobiose but not glucose, suggesting a deficiency of β-glucosidase activity. Active gel electrophoresis containing CMC showed five bands, suggesting several cellulolytic enzymes. The GL-2 strain and its enzyme are potential probiotics for aquaculture fish and the industrial production of cellobiose.
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Affiliation(s)
- Daiki Tanaka
- Center for Marine Environmental Studies, Ehime University.,Graduate School of Agriculture, Ehime University
| | | | - Seiya Watanabe
- Center for Marine Environmental Studies, Ehime University.,Graduate School of Agriculture, Ehime University
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University.,Graduate School of Agriculture, Ehime University.,Food and Health Sciences Research Center, Ehime University
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15
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Purification and characterization of novel, thermostable and non-processive GH5 family endoglucanase from Fomitopsis meliae CFA 2. Int J Biol Macromol 2021; 182:1161-1169. [PMID: 33892036 DOI: 10.1016/j.ijbiomac.2021.04.110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/18/2021] [Indexed: 11/23/2022]
Abstract
Endoglucanases from glycoside hydrolase family 5 (GH5) are the key enzymes in degradation of diverse plant polysaccharides. Present study reports purification, characterization and partial sequencing of novel thermostable GH5 family endoglucanase from a newly isolated brown rot fungi Fomitopsis meliae CFA 2. Endoglucanase was purified 34.18 fold with a specific activity of 302.90 U/mg. The molecular weight of the endoglucanase was 37.87 kDa as determined by SDS PAGE. LC MS/MS analysis identified the protein to be a member of GH5_5 family. The temperature and pH optima for endoglucanase activity were 70 °C and 4.8, respectively. The enzyme catalyzed the hydrolysis of carboxymethyl-cellulose with a Km of 12.0 mg/ml, Vmax of 556.58 μmol/min/mg and Kcat of 129.41/sec. The enzyme was stimulated by Zn+2 and K+ metal ions and DTT. Half-life (t1/2) for endoglucanase was found to be 11.36 h with decimal reduction time (D) of 37.75 h at 70 °C. The activation energy for endoglucanase was found to be 30.76 kJ/mol (50 °C-70 °C). Looking at the results, the endoglucanase from Fomitopsis meliae CFA 2 seems to be a promising thermostable enzyme which may be applicable in applications like biomass hydrolysis.
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16
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Zhang H, Wang Y, Brunecky R, Yao B, Xie X, Zheng F, Luo H. A Swollenin From Talaromyces leycettanus JCM12802 Enhances Cellulase Hydrolysis Toward Various Substrates. Front Microbiol 2021; 12:658096. [PMID: 33854492 PMCID: PMC8039133 DOI: 10.3389/fmicb.2021.658096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/10/2021] [Indexed: 12/02/2022] Open
Abstract
Swollenins exist within some fungal species and are candidate accessory proteins for the biodegradation of cellulosic substrates. Here, we describe the identification of a swollenin gene, Tlswo, in Talaromyces leycettanus JCM12802. Tlswo was successfully expressed in both Trichoderma reesei and Pichia pastoris. Assay results indicate that TlSWO is capable of releasing reducing sugars from lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin. The specific activity of TlSWO toward lichenan, barley β-glucan, carboxymethyl cellulose sodium (CMC-Na) and laminarin is 9.0 ± 0.100, 8.9 ± 0.100, 2.3 ± 0.002 and 0.79 ± 0.002 U/mg, respectively. Additionally, TlSWO had disruptive activity on Avicel and a synergistic effect with cellobiohydrolases, increasing the activity on pretreated corn stover by up to 72.2%. The functional diversity of TlSWO broadens its applicability in experimental settings, and indicating that it may be a promising candidate for future industrial applications.
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Affiliation(s)
- Honghai Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangming Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fei Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Pereira CS, Silveira RL, Skaf MS. QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase. J Chem Inf Model 2021; 61:1902-1912. [PMID: 33760586 PMCID: PMC8154253 DOI: 10.1021/acs.jcim.0c01380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Glycoside hydrolases
(GH) cleave carbohydrate glycosidic bonds
and play pivotal roles in living organisms and in many industrial
processes. Unlike acid-catalyzed hydrolysis of carbohydrates in solution,
which can occur either via cyclic or acyclic oxocarbenium-like transition
states, it is widely accepted that GH-catalyzed hydrolysis proceeds
via a general acid mechanism involving a cyclic oxocarbenium-like
transition state with protonation of the glycosidic oxygen. The GH45
subfamily C inverting endoglucanase from Phanerochaete chrysosporium (PcCel45A) defies the classical inverting mechanism as its crystal
structure conspicuously lacks a general Asp or Glu base residue. Instead,
PcCel45A has an Asn residue, a notoriously weak base in solution,
as one of its catalytic residues at position 92. Moreover, unlike
other inverting GHs, the relative position of the catalytic residues
in PcCel45A impairs the proton abstraction from the nucleophilic water
that attacks the anomeric carbon, a key step in the classical mechanism.
Here, we investigate the viability of an endocyclic mechanism for
PcCel45A using hybrid quantum mechanics/molecular mechanics (QM/MM)
simulations, with the QM region treated with the self-consistent-charge
density-functional tight-binding level of theory. In this mechanism,
an acyclic oxocarbenium-like transition state is stabilized leading
to the opening of the glucopyranose ring and formation of an unstable
acyclic hemiacetal that can be readily decomposed into hydrolysis
product. In silico characterization of the Michaelis
complex shows that PcCel45A significantly restrains the sugar ring
to the 4C1 chair conformation at the −1
subsite of the substrate binding cleft, in contrast to the classical
exocyclic mechanism in which ring puckering is critical. We also show
that PcCel45A provides an environment where the catalytic Asn92 residue
in its standard amide form participates in a cooperative hydrogen
bond network resulting in its increased nucleophilicity due to an
increased negative charge on the oxygen atom. Our results for PcCel45A
suggest that carbohydrate hydrolysis catalyzed by GHs may take an
alternative route from the classical mechanism.
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Affiliation(s)
- Caroline S Pereira
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil.,Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Rio de Janeiro, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas-Unicamp, Campinas 13084-862, Sao Paulo, Brazil
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18
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Nakamura A, Kanazawa T, Furuta T, Sakurai M, Saloheimo M, Samejima M, Koivula A, Igarashi K. Role of Tryptophan 38 in Loading Substrate Chain into the Active-site Tunnel of Cellobiohydrolase I from Trichoderma reesei. J Appl Glycosci (1999) 2021; 68:19-29. [PMID: 34354542 PMCID: PMC8116176 DOI: 10.5458/jag.jag.jag-2020_0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/27/2021] [Indexed: 11/18/2022] Open
Abstract
Cellobiohydrolase I from Trichoderma reesei ( Tr Cel7A) is one of the best-studied cellulases, exhibiting high activity towards crystalline cellulose. Tryptophan residues at subsites -7 and -4 (Trp40 and Trp38 respectively) are located at the entrance and middle of the tunnel-like active site of Tr Cel7A, and are conserved among the GH family 7 cellobiohydrolases. Trp40 of Tr Cel7A is important for the recruitment of cellulose chain ends on the substrate surface, but the role of Trp38 is less clear. Comparison of the effects of W38A and W40A mutations on the binding energies of sugar units at the two subsites indicated that the contribution of Trp38 to the binding was greater than that of Trp40. In addition, the smooth gradient of binding energy was broken in W38A mutant. To clarify the importance of Trp38, the activities of Tr Cel7A WT and W38A towards crystalline cellulose and amorphous cellulose were compared. W38A was more active than WT towards amorphous cellulose, whereas its activity towards crystalline cellulose was only one-tenth of that of WT. To quantify the effect of mutation at subsite -4, we measured kinetic parameters of Tr Cel7A WT, W40A and W38A towards cello-oligosaccharides. All combinations of enzymes and substrates showed substrate inhibition, and comparison of the inhibition constants showed that the Trp38 residue increases the velocity of substrate intake ( kon for forming productive complex) from the minus side of the subsites. These results indicate a key role of Trp38 residue in processively loading the reducing-end of cellulose chain into the catalytic tunnel.
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Affiliation(s)
- Akihiko Nakamura
- 1 Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University
| | - Takashi Kanazawa
- 2 School of Life Science and Technology, Tokyo Institute of Technology
| | - Tadaomi Furuta
- 2 School of Life Science and Technology, Tokyo Institute of Technology
| | - Minoru Sakurai
- 2 School of Life Science and Technology, Tokyo Institute of Technology
| | | | - Masahiro Samejima
- 4 Faculty of Engineering, Shinshu University.,5 Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo
| | - Anu Koivula
- 3 VTT Technical Research Centre of Finland Ltd
| | - Kiyohiko Igarashi
- 3 VTT Technical Research Centre of Finland Ltd.,5 Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo
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19
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Joshi N, Kaushal G, Singh SP. Biochemical characterization of a novel thermo-halo-tolerant GH5 endoglucanase from a thermal spring metagenome. Biotechnol Bioeng 2021; 118:1531-1544. [PMID: 33410140 DOI: 10.1002/bit.27668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/31/2022]
Abstract
A novel endoglucanase gene, celM , was cloned from a thermal spring metagenome. The gene was expressed in Escherichia coli, and the protein was extracted and purified. The protein catalyzed the hydrolysis of amorphous cellulose in a wide range of temperatures, 30-95°C, with optimal activity at 80°C. It was able to tolerate high temperature (80°C) with a half-life of 8 h. Its activity was eminent in a wide pH range of 3.0-11.0, with the highest activity at pH 6.0. The enzyme was tested for halostability. Any significant loss was not recorded in the activity of CelM after the exposure to salinity (3 M NaCl) for 30 days. Furthermore, CelM displayed a substantial resistance toward metal ions, denaturant, reducing agent, organic solvent, and non-ionic surfactants. The amorphous cellulose, treated with CelM , was randomly cleaved, generating cello-oligosaccharides of 2-5 degree of polymerization. Furthermore, CelM was demonstrated to catalyze the hydrolysis of cellulose fraction in the delignified biomass samples, for example, sweet sorghum bagasse, rice straw, and corncob, into cello-oligosaccharides. Given that CelM is a thermo-halo-tolerant GH5 endoglucanase, with resistance to detergents and organic solvent, the biocatalyst could be of potential usefulness for a variety of industrial applications.
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Affiliation(s)
- Namrata Joshi
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
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20
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Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S. Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium. J Biol Chem 2020; 295:18539-18552. [PMID: 33093171 PMCID: PMC7939473 DOI: 10.1074/jbc.ra120.016149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Naomi Kishine
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Toshihisa Kotake
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Yoichi Tsumuraya
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; Faculty of Engineering, Shinshu University, Nagano, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Satoshi Kaneko
- Department of Subtropical Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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21
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Fujii T, Igarashi K, Samejima M. Single Amino Acid Mutation of Pyranose 2-Oxidase Results in Increased Specificity for Diabetes Biomarker 1,5-Anhydro-D-Glucitol. J Appl Glycosci (1999) 2020; 67:73-78. [PMID: 34354532 PMCID: PMC8135088 DOI: 10.5458/jag.jag.jag-2020_0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/14/2020] [Indexed: 10/25/2022] Open
Abstract
Pyranose 2-oxidases catalyze the oxidation of various pyranose sugars at the C2 position. However, their potential application for detecting sugars other than glucose in blood is hindered by relatively high activity towards glucose. In this study, in order to find a mutant enzyme with enhanced specificity for 1,5-anhydro-D-glucitol (1,5-AG), which is a biomarker for diabetes mellitus, we conducted site-directed mutagenesis of pyranose 2-oxidase from the basidiomycete Phanerochaete chrysosporium ( Pc POX). Considering the three-dimensional structure of the substrate-binding site of Pc POX and the structural difference between glucose and 1,5-AG, we selected alanine 551 of Pc POX as a target residue for mutation. Kinetic studies of the 19 mutants of Pc POX expressed as recombinant proteins in E. coli revealed that the ratio of k cat / K m for 1,5-AG to k cat / K m for glucose was three times higher for the A551L mutant than for wild-type Pc POX. Although the A551L mutant has lower specific activity towards each substrate than the wild-type enzyme, its increased specificity for 1,5-AG makes it a promising lead for the development of POX-based 1,5-AG detection systems.
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Affiliation(s)
- Takahiro Fujii
- 1 Ikeda Food Research Co., Ltd.,2 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- 2 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,3 VTT Technical Research Centre of Finland
| | - Masahiro Samejima
- 2 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,4 Faculty of Engineering, Shinshu University
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22
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A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH. Int J Biol Macromol 2020; 154:349-360. [DOI: 10.1016/j.ijbiomac.2020.03.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/22/2022]
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23
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Pitsch J, Weghuber J. Hydrophilic Interaction Chromatography Coupled with Charged Aerosol Detection for Simultaneous Quantitation of Carbohydrates, Polyols and Ions in Food and Beverages. Molecules 2019; 24:molecules24234333. [PMID: 31783530 PMCID: PMC6930467 DOI: 10.3390/molecules24234333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Here, we report an accurate and versatile method for the simultaneous determination of 17 sugars (arabinose, erythrose, fructose, galactose, glucose, isomaltulose, lactose, lyxose, maltose, maltotriose, mannose, raffinose, rhamnose, ribose, sucrose, sorbose and xylose), seven polyols (erythritol, inositol, lactitol, maltitol, mannitol, sorbitol and xylitol), five ions (K+, Br−, Cl−, NO3− and SO42−) and the pseudosaccharide acarbose. For compound separation, hydrophilic interaction chromatography (HILIC) coupled to a corona charged aerosol detector (CAD) was used. The method was validated for linearity, precision, reproducibility, retention factor and optimal injection volume. Standards were measured in the range of 1–1000 mg L−1 and showed good intraday and interday repeatability, as well as precision (relative standard deviation (RSD) < 5%). The LODs and LOQs for the 30 analytes were in the range of 0.032–2.675 mg L−1 and 0.107–8.918 mg L−1, respectively. This method exhibited correlation coefficients of at least R2 > 0.97 for all analytes. The method was tested in 24 food and beverage samples to validate the separation efficiency and sensitivity in natural food matrices and to show the practicability of its use for routine food analysis.
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Affiliation(s)
- Johannes Pitsch
- FFoQSI-Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office, FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria;
- Center of Excellence—Food Technology and Nutrition, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Julian Weghuber
- FFoQSI-Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office, FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria;
- Center of Excellence—Food Technology and Nutrition, University of Applied Sciences Upper Austria, 4600 Wels, Austria
- Correspondence: ; Tel.: +43-50804-44403
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24
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Molecular simulation of PcCel45A protein expressed from Aspergillus nidulans to understand its structure, dynamics, and thermostability. J Mol Model 2019; 25:317. [PMID: 31598788 DOI: 10.1007/s00894-019-4175-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/19/2019] [Indexed: 10/25/2022]
Abstract
PACS and mathematical subject classification numbers as needed. Molecular dynamic simulation is a very usable tool to understand various factors, including structure temperature dependence, dynamics, and stability for protein structure. The three main components, namely endoglucanase, exoglucanase, and β-glucosidase, effectively convert lignocellulosic biomass into fermentable sugar. Cellulose is the major component of plant cell walls and is the most abundant organic compound on the earth. Somewhat organisms can use cellulose as a food source, possessing cellulases (cellobiohydrolases and endoglucanases) that can catalyze the hydrolysis of the β-(1,4) glycosidic bonds. In this work, we investigated conformational and structural properties of PcCel45A protein by changing at temperatures with 300 K, 333 K, and 352 K. We found that the ASN92 residue was the major contributor to the stability of structure; some other residues correlated significantly with thermal stability. We also compared the theoretical results of the current study with the experimental ones published in previous studies.
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25
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Kadowaki MAS, Polikarpov I. Structural insights into the hydrolysis pattern and molecular dynamics simulations of GH45 subfamily a endoglucanase from Neurospora crassa OR74A. Biochimie 2019; 165:275-284. [PMID: 31472178 DOI: 10.1016/j.biochi.2019.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolase (GH) family 45 is one of the smallest and poorly studied endoglucanase family with a broad biotechnological application ranging from treatment of textiles to conversion of complex cell wall polysaccharides into simple oligo- and monosaccharides. In a present study, GH45 cellulase from Neurospora crassa OR74A (NcCel45A) was characterized both biochemically and structurally. HPLC analysis of the hydrolytic products confirmed the endo-β(1,4) mode of action of the enzyme. Moreover, such pattern revealed that NcCel45A cannot hydrolyze efficiently oligosaccharides with a degree of polymerization smaller than six. The crystal structure of NcCel45A catalytic domain in the apo-form was determined at 1.9 Å resolution and the structure of the enzyme bound to cellobiose was solved and refined to 1.8 Å resolution. Comparative structural analyses and molecular dynamics simulations show that the enzyme dynamics is affected by substrate binding. Taken together, MD simulations and statistical coupling analysis revealed previously unknown correlation of a loop 6 with the breakdown of cellulose substrates by GH45.
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Affiliation(s)
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil.
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Nomura T, Iwase H, Saka N, Takahashi N, Mikami B, Mizutani K. High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:426-436. [PMID: 30988259 DOI: 10.1107/s2059798319003000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/27/2019] [Indexed: 11/10/2022]
Abstract
Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1.00 Å resolution; this is the highest resolution structure of an animal endoglucanase. The results showed that EG27II has a double-ψ six-stranded β-barrel and that the structure of EG27II more closely resembles those of subfamily C enzymes than those of subfamily A enzymes. The structure of EG27II complexed with cellobiose was also determined under cryoconditions and at room temperature at three pH values, pH 4.0, 5.5 and 8.0, and no structural changes were found to be associated with the change in pH. The structural comparison and catalytic activity measurements showed that Asp137 and Asn112 function as the catalytic acid and base, respectively, and that Asp27 is also an important residue for catalysis. These high-resolution structures of EG27II provide a large amount of information for structure-based enzyme modification and cell-surface engineering, which will advance biofuel production using animal-derived cellulases.
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Affiliation(s)
- Taisuke Nomura
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisamu Iwase
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoki Saka
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuyuki Takahashi
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kimihiko Mizutani
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Berto GL, Velasco J, Tasso Cabos Ribeiro C, Zanphorlin LM, Noronha Domingues M, Tyago Murakami M, Polikarpov I, de Oliveira LC, Ferraz A, Segato F. Functional characterization and comparative analysis of two heterologous endoglucanases from diverging subfamilies of glycosyl hydrolase family 45. Enzyme Microb Technol 2019; 120:23-35. [DOI: 10.1016/j.enzmictec.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/26/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022]
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Biochemical and functional characterization of a novel thermoacidophilic, heat and halo-ionic liquids tolerant endo-β-1,4-glucanase from saline-alkaline lake soil microbial metagenomic DNA. Int J Biol Macromol 2018; 118:1035-1044. [DOI: 10.1016/j.ijbiomac.2018.06.141] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022]
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Impact of disulfide bonds on the folding and refolding capability of a novel thermostable GH45 cellulase. Appl Microbiol Biotechnol 2018; 102:9183-9192. [DOI: 10.1007/s00253-018-9256-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/08/2018] [Accepted: 07/13/2018] [Indexed: 12/22/2022]
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Cha JH, Yoon JJ, Cha CJ. Functional characterization of a thermostable endoglucanase belonging to glycoside hydrolase family 45 from Fomitopsis palustris. Appl Microbiol Biotechnol 2018; 102:6515-6523. [DOI: 10.1007/s00253-018-9075-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/03/2018] [Accepted: 05/06/2018] [Indexed: 11/25/2022]
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Godoy AS, Pereira CS, Ramia MP, Silveira RL, Camilo CM, Kadowaki MA, Lange L, Busk PK, Nascimento AS, Skaf MS, Polikarpov I. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. Sci Rep 2018; 8:3678. [PMID: 29487297 PMCID: PMC5829257 DOI: 10.1038/s41598-018-21798-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/23/2018] [Indexed: 11/09/2022] Open
Abstract
The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.
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Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Caroline S Pereira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Marina Paglione Ramia
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Cesar M Camilo
- Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo, Brazil
| | - Marco A Kadowaki
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Lene Lange
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Peter K Busk
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark
| | - Alessandro S Nascimento
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.
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de Eugenio LI, Méndez-Líter JA, de los Ríos V, Prieto A, Martínez MJ. β-1,4-endoglucanases from Talaromyces amestolkiae: Production of glucooligosaccharides from different β-glucans. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2017.1306741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - V. de los Ríos
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - A. Prieto
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - M. J. Martínez
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
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Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis. Appl Environ Microbiol 2017; 83:AEM.01251-17. [PMID: 28802264 DOI: 10.1128/aem.01251-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/03/2017] [Indexed: 11/20/2022] Open
Abstract
Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from Aspergillus luchuensis (AlAXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family. AlAXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from Aspergillus niger indicated that AlAXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of AlAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan.IMPORTANCE Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of thermoplastic polymers.
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Shinohara N, Sunagawa N, Tamura S, Yokoyama R, Ueda M, Igarashi K, Nishitani K. The plant cell-wall enzyme AtXTH3 catalyses covalent cross-linking between cellulose and cello-oligosaccharide. Sci Rep 2017; 7:46099. [PMID: 28443615 PMCID: PMC5405413 DOI: 10.1038/srep46099] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/02/2017] [Indexed: 11/09/2022] Open
Abstract
Cellulose is an economically important material, but routes of its industrial processing have not been fully explored. The plant cell wall - the major source of cellulose - harbours enzymes of the xyloglucan endotransglucosylase/hydrolase (XTH) family. This class of enzymes is unique in that it is capable of elongating polysaccharide chains without the requirement for activated nucleotide sugars (e.g., UDP-glucose) and in seamlessly splitting and reconnecting chains of xyloglucan, a naturally occurring soluble analogue of cellulose. Here, we show that a recombinant version of AtXTH3, a thus far uncharacterized member of the Arabidopsis XTH family, catalysed the transglycosylation between cellulose and cello-oligosaccharide, between cellulose and xyloglucan-oligosaccharide, and between xyloglucan and xyloglucan-oligosaccharide, with the highest reaction rate observed for the latter reaction. In addition, this enzyme formed cellulose-like insoluble material from a soluble cello-oligosaccharide in the absence of additional substrates. This newly found activity (designated "cellulose endotransglucosylase," or CET) can potentially be involved in the formation of covalent linkages between cellulose microfibrils in the plant cell wall. It can also comprise a new route of industrial cellulose functionalization.
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Affiliation(s)
- Naoki Shinohara
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Satoru Tamura
- Laboratory of Organic Chemistry, Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-Ku, Sendai 980-8578, Japan
| | - Ryusuke Yokoyama
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
| | - Minoru Ueda
- Laboratory of Organic Chemistry, Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-Ku, Sendai 980-8578, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan.,VTT Technical Research Centre of Finland, P.O. Box 1000, Tietotie 2, Espoo FI-02044, Finland
| | - Kazuhiko Nishitani
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
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The use of neutron scattering to determine the functional structure of glycoside hydrolase. Curr Opin Struct Biol 2016; 40:54-61. [PMID: 27494120 DOI: 10.1016/j.sbi.2016.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 11/21/2022]
Abstract
Neutron diffraction provides different information from X-ray diffraction, because neutrons are scattered by atomic nuclei, whereas X-rays are scattered by electrons. One of the key advantages of neutron crystallography is the ability to visualize hydrogen and deuterium atoms, making it possible to observe the protonation state of amino acid residues, hydrogen bonds, networks of water molecules and proton relay pathways in enzymes. But, because of technical difficulties, less than 100 enzyme structures have been evaluated by neutron crystallography to date. In this review, we discuss the advantages and disadvantages of neutron crystallography as a tool to investigate the functional structure of glycoside hydrolases, with some examples.
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Valadares F, Gonçalves TA, Gonçalves DSPO, Segato F, Romanel E, Milagres AMF, Squina FM, Ferraz A. Exploring glycoside hydrolases and accessory proteins from wood decay fungi to enhance sugarcane bagasse saccharification. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:110. [PMID: 27222665 PMCID: PMC4877993 DOI: 10.1186/s13068-016-0525-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/10/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) and accessory proteins are key components for efficient and cost-effective enzymatic hydrolysis of polysaccharides in modern, biochemically based biorefineries. Currently, commercialized GHs and accessory proteins are produced by ascomycetes. However, the role of wood decay basidiomycetes proteins in biomass saccharification has not been extensively pursued. Wood decay fungi degrade polysaccharides in highly lignified tissues in natural environments, and are a promising enzyme source for improving enzymatic cocktails that are designed for in vitro lignocellulose conversion. RESULTS GHs and accessory proteins were produced by representative brown- and white-rot fungi, Laetiporus sulphureus and Pleurotus ostreatus, respectively. Concentrated protein extracts were then used to amend commercial enzymatic cocktails for saccharification of alkaline-sulfite pretreated sugarcane bagasse. The main enzymatic activities found in the wood decay fungal protein extracts were attributed to endoglucanases, xylanases and β-glucosidases. Cellobiohydrolase (CBH) activities in the L. sulphureus and P. ostreatus extracts were low and nonexistent, respectively. The initial glucan conversion rates were boosted when the wood decay fungal proteins were used to replace half of the enzymes from the commercial cocktails. L. sulphureus proteins increased the glucan conversion levels, with values above those observed for the full load of commercial enzymes. Wood decay fungal proteins also enhanced the xylan conversion efficiency due to their high xylanase activities. Proteomic studies revealed 104 and 45 different proteins in the P. ostreatus and L. sulphureus extracts, respectively. The enhancement of the saccharification of alkaline-pretreated substrates by the modified enzymatic cocktails was attributed to the following protein families: GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases. CONCLUSIONS The extracellular proteins produced by wood decay fungi provide useful tools to improve commercial enzyme cocktails that are currently used for the saccharification of alkaline-pretreated lignocellulosic substrates. The relevant proteins encompass multiple glycoside hydrolase families, including the GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases.
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Affiliation(s)
- Fernanda Valadares
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Thiago A. Gonçalves
- />Laboratório Nacional de Ciência & Tecnolologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970 Brazil
- />Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862 Brazil
| | - Dayelle S. P. O. Gonçalves
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Fernando Segato
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Elisson Romanel
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Adriane M. F. Milagres
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Fabio M. Squina
- />Laboratório Nacional de Ciência & Tecnolologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970 Brazil
| | - André Ferraz
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
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Nakamura A, Ishida T, Kusaka K, Yamada T, Fushinobu S, Tanaka I, Kaneko S, Ohta K, Tanaka H, Inaka K, Higuchi Y, Niimura N, Samejima M, Igarashi K. "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. SCIENCE ADVANCES 2015; 1:e1500263. [PMID: 26601228 PMCID: PMC4643802 DOI: 10.1126/sciadv.1500263] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takuya Ishida
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kazunori Ohta
- Japanese Experiment Module (JEM) Utilization Center, Japan Aerospace Exploration Agency, Ibaraki 305-8505, Japan
| | | | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Nara 639-1123, Japan
| | - Yoshiki Higuchi
- Department of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Masahiro Samejima
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Corresponding author. E-mail:
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Huy ND, Nguyen CL, Park HS, Loc NH, Choi MS, Kim DH, Seo JW, Park SM. Characterization of a novel manganese dependent endoglucanase belongs in GH family 5 from Phanerochaete chrysosporium. J Biosci Bioeng 2015; 121:154-9. [PMID: 26173955 DOI: 10.1016/j.jbiosc.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/31/2015] [Accepted: 06/18/2015] [Indexed: 01/22/2023]
Abstract
The cDNA encoding a putative glycoside hydrolase family 5, which has been predicted to be an endoglucanase (PcEg5A), was cloned from Phanerochaete chrysosporium and expressed in Pichia pastoris. PcEg5A contains a carbohydrate-binding domain and two important amino acids, E209 and E319, playing as proton donor and nucleophile in substrate catalytic domain. SDS-PAGE analysis indicated that the recombinant endoglucanase 5A (rPcEg5A) has a molecular size of 43 kDa which corresponds with the theoretical calculation. Optimum pH and temperature were found to be 4.5-6.0, and 50°C-60°C, respectively. Moreover, rPcEg5A exhibited maximal activity in the pH range of 3.0-8.0, whereas over 50% of activity still remained at 20°C and 80°C. rPcEg5A was stable at 60°C for 12 h incubation, indicating that rPcEg5A is a thermostable enzyme. Manganese ion enhanced the enzyme activity by 77%, indicating that rPcEg5A is a metal dependent enzyme. The addition of rPcEg5A to cellobiase (cellobiohydrolase and β-glucosidase) resulted in a 53% increasing saccharification of NaOH-pretreated barley straw, whereas the glucose release was 47% higher than that cellobiase treatment alone. Our study suggested that rPcEg5A is an enzyme with great potential for biomass saccharification.
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Affiliation(s)
- Nguyen Duc Huy
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea; Institute of Biotechnology, Hue University, Hue 530000, Viet Nam
| | - Cu Le Nguyen
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea
| | - Han-Sung Park
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea
| | | | - Myoung-Suk Choi
- Institute of Molecular Biology and Genetics, College of Natural Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Dae-Hyuk Kim
- Institute of Molecular Biology and Genetics, College of Natural Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Jeong-Woo Seo
- Applied Microbiology Research Center, Bio-Materials Research Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 580-185, Republic of Korea
| | - Seung-Moon Park
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea.
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Kadowaki MAS, Camilo CM, Muniz AB, Polikarpov I. Functional Characterization and Low-Resolution Structure of an Endoglucanase Cel45A from the Filamentous Fungus Neurospora crassa OR74A: Thermostable Enzyme with High Activity Toward Lichenan and β-Glucan. Mol Biotechnol 2015; 57:574-88. [DOI: 10.1007/s12033-015-9851-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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41
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Characterization of Lignocellulolytic Enzymes from White-Rot Fungi. Curr Microbiol 2014; 70:485-98. [DOI: 10.1007/s00284-014-0743-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/27/2014] [Indexed: 12/26/2022]
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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43
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Tang B, Zhang Y, Yang Y, Song Z, Li X. Expression and functional analysis of a glycoside hydrolase family 45 endoglucanase from Rhizopus stolonifer. World J Microbiol Biotechnol 2014; 30:2943-52. [PMID: 25164957 DOI: 10.1007/s11274-014-1722-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
A novel endoglucanase gene was cloned from Rhizopus stolonifer and expressed in Escherichia coli, the gene product EG II (45 kDa) was assigned to Glycoside Hydrolase Family 45 (GH45), and its specific activity on phosphoric acid-swollen cellulose (PASC) was 48 IU/mg. To solve the problem of substrate accumulation in the cellulose hydrolysis and enhance the catalytic efficiency of endoglucanase, the eg2 gene was modified by site directed mutagenesis. Mutations generated by overlapping PCR have been proven to increase its catalytic activity on carboxymenthyl cellulose, microcrystalline cellulose (Avicel) and PASC, among which the mutant EG II-E containing all 6 mutations (N39S, V136D, T251G, D255G, P256S and E260D) peaked 121 IU/mg on PASC. The bioinformatic analysis showed that 2 key catalytic residues (D136 and D260) moved closer with the opening of a loop after mutagenesis, and a tunnel was formed by structural transformation. This structure was conducive for the substrate to access the active centre, and D136 played an indispensable role in the substrate recognition.
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Affiliation(s)
- Bin Tang
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China,
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44
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Suzuki K, Hori A, Kawamoto K, Thangudu RR, Ishida T, Igarashi K, Samejima M, Yamada C, Arakawa T, Wakagi T, Koseki T, Fushinobu S. Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad. Proteins 2014; 82:2857-67. [PMID: 25066066 DOI: 10.1002/prot.24649] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/27/2014] [Accepted: 07/15/2014] [Indexed: 11/12/2022]
Abstract
Feruloyl esterase (FAE) catalyzes the hydrolysis of the ferulic and diferulic acids present in plant cell wall polysaccharides, and tannase catalyzes the hydrolysis of tannins to release gallic acid. The fungal tannase family in the ESTHER database contains various enzymes, including FAEs and tannases. Despite the importance of FAEs and tannases in bioindustrial applications, three-dimensional structures of the fungal tannase family members have been unknown. Here, we determined the crystal structure of FAE B from Aspergillus oryzae (AoFaeB), which belongs to the fungal tannase family, at 1.5 Å resolution. AoFaeB consists of a catalytic α/β-hydrolase fold domain and a large lid domain, and the latter has a novel fold. To estimate probable binding models of substrates in AoFaeB, an automated docking analysis was performed. In the active site pocket of AoFaeB, residues responsible for the substrate specificity of the FAE activity were identified. The catalytic triad of AoFaeB comprises Ser203, Asp417, and His457, and the serine and histidine residues are directly connected by a disulfide bond of the neighboring cysteine residues, Cys202 and Cys458. This structural feature, the "CS-D-HC motif," is unprecedented in serine hydrolases. A mutational analysis indicated that the novel structural motif plays essential roles in the function of the active site.
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Affiliation(s)
- Kentaro Suzuki
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
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45
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Sequence diversity and gene expression analyses of expansin-related proteins in the white-rot basidiomycete, Phanerochaete carnosa. Fungal Genet Biol 2014; 72:115-123. [PMID: 24880035 DOI: 10.1016/j.fgb.2014.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/07/2014] [Accepted: 05/19/2014] [Indexed: 11/21/2022]
Abstract
Expansin and expansin-related proteins loosen plant cell wall architectures and are widely distributed in several types of organisms, including plants, fungi and bacteria. Here we describe sequence diversity and unique gene expression profiles of multiple expansin-related proteins identified in the basidiomycete, Phanerochaete carnosa. The protein sequences were homologous to loosenin, an expansin-related protein reported in the basidiomycete, Bjerkandera adusta. We identified homologous sequences of each of those P. carnosa proteins in many basidiomycete species. Twelve P. carnosa loosenin-like proteins (LOOLs) were classified into two subgroups according to sequence homology. Conservation of polysaccharide-binding amino acid residues was stricter in subgroup A. Subgroup A sequences included a conserved 8-9 amino acid insertion in a polysaccharide-binding groove whereas subgroup B contained a 12-18 amino acid insertion next to the binding groove. The P. carnosa genome also encodes the expansin-related protein, DREX1, which adopts a loosenin-like structure but has lower sequence homology to other LOOLs. The gene expression analysis of those proteins showed distinct patterns that were not significantly related to subgroupings. The variation in the protein sequences and gene expression patterns, and wide distribution among the basidiomycota, suggest that the diverse cell wall loosening proteins contribute to effective plant cell wall association and utilization by basidiomycetes.
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46
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Zhao XH, Wei DZ, Wang W. Cloning, Expression, Sequence Analysis, and Partial Characterization of Two Alkaline β-1, 4-endoglucanases of Phaeosphaeria sp. LH21 from Deep-Sea Mud. Appl Biochem Biotechnol 2014; 173:1295-302. [DOI: 10.1007/s12010-014-0924-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/16/2014] [Indexed: 11/30/2022]
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47
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Nakamura A, Ishida T, Fushinobu S, Kusaka K, Tanaka I, Inaka K, Higuchi Y, Masaki M, Ohta K, Kaneko S, Niimura N, Igarashi K, Samajima M. Phase-diagram-guided method for growth of a large crystal of glycoside hydrolase family 45 inverting cellulase suitable for neutron structural analysis. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:859-63. [PMID: 24121328 PMCID: PMC3795544 DOI: 10.1107/s0909049513020943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/27/2013] [Indexed: 05/07/2023]
Abstract
Neutron protein crystallography (NPC) is a powerful tool for determining the hydrogen position and water orientation in proteins, but a much larger protein crystal is needed for NPC than for X-ray crystallography, and thus crystal preparation is a bottleneck. To obtain large protein crystals, it is necessary to know the properties of the target protein in the crystallization solution. Here, a crystal preparation method of fungal cellulase PcCel45A is reported, guided by the phase diagram. Nucleation and precipitation conditions were determined by sitting-drop vapor diffusion. Saturation and unsaturation conditions were evaluated by monitoring crystal dissolution, and a crystallization phase diagram was obtained. To obtain a large crystal, crystallization solution was prepared on a sitting bridge (diameter = 5 mm). Initial crystallization conditions were 40 µl of crystallization solution (40 mg ml(-1) protein with 30.5% 3-methyl-1,5-pentanediol in 50 mM tris-HCl pH 8.0) with a 1,000 µl reservoir (61% 3-methyl-1,5,-pentanediol in 50 mM tris-HCl pH 8.0) at 293 K. After the first crystal appeared, the concentration of precipitant in the reservoir solution was reduced to 60% to prevent formation of further crystals. Finally, we obtained a crystal of 6 mm(3) volume (3 mm × 2 mm × 1 mm), which was suitable for neutron diffraction.
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Affiliation(s)
- Akihiko Nakamura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Ishida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 164-1 Shirakita, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 164-1 Shirakita, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences, 170-1 Tsutsui, Yamatokouriyama, Nara 639-1123, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Mika Masaki
- Japan Aerospace Exploration Agency, Tsukuba Space Center, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Kazunori Ohta
- Japan Aerospace Exploration Agency, Tsukuba Space Center, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Satoshi Kaneko
- National Food Research Institute, 1-2-12 Kannondai, Tsukuba, Ibaraki 304-8642, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 164-1 Shirakita, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan
| | - Kiyohiko Igarashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence e-mail:
| | - Masahiro Samajima
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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48
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Hori C, Gaskell J, Igarashi K, Samejima M, Hibbett D, Henrissat B, Cullen D. Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay. Mycologia 2013; 105:1412-27. [PMID: 23935027 DOI: 10.3852/13-072] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To degrade the polysaccharides, wood-decay fungi secrete a variety of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) classified into various sequence-based families of carbohydrate-active enzymes (CAZys) and their appended carbohydrate-binding modules (CBM). Oxidative enzymes, such as cellobiose dehydrogenase (CDH) and lytic polysaccharide monooxygenase (LPMO, formerly GH61), also have been implicated in cellulose degradation. To examine polysaccharide-degrading potential between white- and brown-rot fungi, we performed genomewide analysis of CAZys and these oxidative enzymes in 11 Polyporales, including recently sequenced monokaryotic strains of Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora. Furthermore, we conducted comparative secretome analysis of seven Polyporales grown on wood culture. As a result, it was found that genes encoding cellulases belonging to families GH6, GH7, GH9 and carbohydrate-binding module family CBM1 are lacking in genomes of brown-rot polyporales. In addition, the presence of CDH and the expansion of LPMO were observed only in white-rot genomes. Indeed, GH6, GH7, CDH and LPMO peptides were identified only in white-rot polypores. Genes encoding aldose 1-epimerase (ALE), previously detected with CDH and cellulases in the culture filtrates, also were identified in white-rot genomes, suggesting a physiological connection between ALE, CDH, cellulase and possibly LPMO. For hemicellulose degradation, genes and peptides corresponding to GH74 xyloglucanase, GH10 endo-xylanase, GH79 β-glucuronidase, CE1 acetyl xylan esterase and CE15 glucuronoyl methylesterase were significantly increased in white-rot genomes compared to brown-rot genomes. Overall, relative to brown-rot Polyporales, white-rot Polyporales maintain greater enzymatic diversity supporting lignocellulose attack.
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Affiliation(s)
- Chiaki Hori
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, l-l-l, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan, and Institute for Microbial and Biochemical Technology, Forest Products Laboratory, 1 Gifford Pinchot Drive, Madison, Wisconsin 53726
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49
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Wu M, Beckham GT, Larsson AM, Ishida T, Kim S, Payne CM, Himmel ME, Crowley MF, Horn SJ, Westereng B, Igarashi K, Samejima M, Ståhlberg J, Eijsink VGH, Sandgren M. Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the Basidiomycota fungus Phanerochaete chrysosporium. J Biol Chem 2013; 288:12828-39. [PMID: 23525113 PMCID: PMC3642327 DOI: 10.1074/jbc.m113.459396] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/15/2013] [Indexed: 01/11/2023] Open
Abstract
Carbohydrate structures are modified and degraded in the biosphere by a myriad of mostly hydrolytic enzymes. Recently, lytic polysaccharide mono-oxygenases (LPMOs) were discovered as a new class of enzymes for cleavage of recalcitrant polysaccharides that instead employ an oxidative mechanism. LPMOs employ copper as the catalytic metal and are dependent on oxygen and reducing agents for activity. LPMOs are found in many fungi and bacteria, but to date no basidiomycete LPMO has been structurally characterized. Here we present the three-dimensional crystal structure of the basidiomycete Phanerochaete chrysosporium GH61D LPMO, and, for the first time, measure the product distribution of LPMO action on a lignocellulosic substrate. The structure reveals a copper-bound active site common to LPMOs, a collection of aromatic and polar residues near the binding surface that may be responsible for regio-selectivity, and substantial differences in loop structures near the binding face compared with other LPMO structures. The activity assays indicate that this LPMO primarily produces aldonic acids. Last, molecular simulations reveal conformational changes, including the binding of several regions to the cellulose surface, leading to alignment of three tyrosine residues on the binding face of the enzyme with individual cellulose chains, similar to what has been observed for family 1 carbohydrate-binding modules. A calculated potential energy surface for surface translation indicates that P. chrysosporium GH61D exhibits energy wells whose spacing seems adapted to the spacing of cellobiose units along a cellulose chain.
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Affiliation(s)
- Miao Wu
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
| | - Gregg T. Beckham
- the National Bioenergy Center and
- the Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401
| | - Anna M. Larsson
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
| | - Takuya Ishida
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | - Christina M. Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, and
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Svein J. Horn
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Bjørge Westereng
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Kiyohiko Igarashi
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masahiro Samejima
- the Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jerry Ståhlberg
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
| | - Vincent G. H. Eijsink
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
| | - Mats Sandgren
- From the Department of Molecular Biology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
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50
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Zhao J, Shi P, Li Z, Yang P, Luo H, Bai Y, Wang Y, Yao B. Two neutral thermostable cellulases from Phialophora sp. G5 act synergistically in the hydrolysis of filter paper. BIORESOURCE TECHNOLOGY 2012; 121:404-410. [PMID: 22868008 DOI: 10.1016/j.biortech.2012.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 06/01/2023]
Abstract
Two novel cellulase genes, cbh6A and egGH45, were cloned from Phialophora sp. G5 and successfully expressed in Pichia pastoris. The putative polypeptide of CBH6A consists of a family 1 CBM and a catalytic domain of glycosyl hydrolase family 6 cellobiohydrolases, while deduced EgGH45 only contains a catalytic domain of family 45 endoglucanases. CBH6A and EgGH45 were optimally active at pH 7.0 and 65°C, and pH 6.0 and 60°C, respectively. Both enzymes exhibited high activities and stabilities over a wide pH range and had good thermostability at 70°C. CBH6A and EgGH45 had significant resistance to SDS (10mM), remaining 35% and 54% activities, respectively. These enzymes had synergic effect on the hydrolysis of filter paper, showing the highest efficiency in the ratio of CBH6A to EgGH45 at 80:20. The properties make this enzyme combination potential for application in textile and detergents industries.
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Affiliation(s)
- Junqi Zhao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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