1
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The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases. Essays Biochem 2023; 67:551-559. [PMID: 36876880 DOI: 10.1042/ebc20220156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
In nature, enzymatic degradation of recalcitrant polysaccharides such as chitin and cellulose takes place by a synergistic interaction between glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The two different families of carbohydrate-active enzymes use two different mechanisms when breaking glycosidic bonds between sugar moieties. GHs employ a hydrolytic activity and LPMOs are oxidative. Consequently, the topologies of the active sites differ dramatically. GHs have tunnels or clefts lined with a sheet of aromatic amino acid residues accommodating single polymer chains being threaded into the active site. LPMOs are adapted to bind to the flat crystalline surfaces of chitin and cellulose. It is believed that the LPMO oxidative mechanism provides new chain ends that the GHs can attach to and degrade, often in a processive manner. Indeed, there are many reports of synergies as well as rate enhancements when LPMOs are applied in concert with GHs. Still, these enhancements vary in magnitude with respect to the nature of the GH and the LPMO. Moreover, impediment of GH catalysis is also observed. In the present review, we discuss central works where the interplay between LPMOs and GHs has been studied and comment on future challenges to be addressed to fully use the potential of this interplay to improve enzymatic polysaccharide degradation.
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2
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Uchiyama T, Uchihashi T, Ishida T, Nakamura A, Vermaas JV, Crowley MF, Samejima M, Beckham GT, Igarashi K. Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface. SCIENCE ADVANCES 2022; 8:eade5155. [PMID: 36563138 PMCID: PMC9788756 DOI: 10.1126/sciadv.ade5155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/21/2022] [Indexed: 05/31/2023]
Abstract
Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.
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Affiliation(s)
- Taku Uchiyama
- 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
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Physics, Structural Biology Center, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8602, Japan
| | - Takuya Ishida
- 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
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Josh V. Vermaas
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - 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
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - 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 Center of Finland Ltd., Tietotie 2, P.O. Box 1000, Espoo, FI-02044 VTT, Finland
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3
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Prabmark K, Boonyapakron K, Bunterngsook B, Arunrattanamook N, Uengwetwanit T, Chitnumsub P, Champreda V. Enhancement of catalytic activity and alkaline stability of cellobiohydrolase by structure-based protein engineering. 3 Biotech 2022; 12:269. [PMID: 36097631 PMCID: PMC9463429 DOI: 10.1007/s13205-022-03339-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Alkaline cellobiohydrolases have the potential for application in various industries, including pulp processing and laundry where operation under high pH conditions is preferred. In this study, variants of CtCel6A cellobiohydrolase from Chaetomium thermophilum were generated by structural-based protein engineering with the rationale of increasing catalytic activity and alkaline stability. The variants included removal of the carbohydrate-binding module (CBM) and substitution of residues 173 and 200. The CBM-deleted enzyme with Y200F mutation predicted to mediate conformational change at the N-terminal loop demonstrated increased alkaline stability at 60 °C, pH 8.0 for 24 h up to 2.25-fold compared with the wild-type enzyme. Another CBM-deleted enzyme with L173E mutation predicted to induce a new hydrogen bond in the substrate-binding cleft showed enhanced hydrolysis yield of pretreated sugarcane trash up to 4.65-fold greater than that of the wild-type enzyme at the pH 8.0. The variant enzymes could thus be developed for applications on cellulose hydrolysis and plant fiber modification operated under alkaline conditions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03339-4.
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Affiliation(s)
- Kanoknart Prabmark
- Enzyme Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Katewadee Boonyapakron
- Enzyme Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Benjarat Bunterngsook
- Enzyme Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Nattapol Arunrattanamook
- Enzyme Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
| | - Verawat Champreda
- Enzyme Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani, 12120 Thailand
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4
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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5
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Schaller KS, Molina GA, Kari J, Schiano-di-Cola C, Sørensen TH, Borch K, Peters GH, Westh P. Virtual Bioprospecting of Interfacial Enzymes: Relating Sequence and Kinetics. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
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6
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Zajki-Zechmeister K, Kaira GS, Eibinger M, Seelich K, Nidetzky B. Processive Enzymes Kept on a Leash: How Cellulase Activity in Multienzyme Complexes Directs Nanoscale Deconstruction of Cellulose. ACS Catal 2021; 11:13530-13542. [PMID: 34777910 PMCID: PMC8576811 DOI: 10.1021/acscatal.1c03465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Indexed: 12/15/2022]
Abstract
Biological deconstruction of polymer materials gains efficiency from the spatiotemporally coordinated action of enzymes with synergetic function in polymer chain depolymerization. To perpetuate enzyme synergy on a solid substrate undergoing deconstruction, the overall attack must alternate between focusing the individual enzymes locally and dissipating them again to other surface sites. Natural cellulases working as multienzyme complexes assembled on a scaffold protein (the cellulosome) maximize the effect of local concentration yet restrain the dispersion of individual enzymes. Here, with evidence from real-time atomic force microscopy to track nanoscale deconstruction of single cellulose fibers, we show that the cellulosome forces the fiber degradation into the transversal direction, to produce smaller fragments from multiple local attacks ("cuts"). Noncomplexed enzymes, as in fungal cellulases or obtained by dissociating the cellulosome, release the confining force so that fiber degradation proceeds laterally, observed as directed ablation of surface fibrils and leading to whole fiber "thinning". Processive cellulases that are enabled to freely disperse evoke the lateral degradation and determine its efficiency. Our results suggest that among natural cellulases, the dispersed enzymes are more generally and globally effective in depolymerization, while the cellulosome represents a specialized, fiber-fragmenting machinery.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Klara Seelich
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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7
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Kari J, Molina GA, Schaller KS, Schiano-di-Cola C, Christensen SJ, Badino SF, Sørensen TH, Røjel NS, Keller MB, Sørensen NR, Kolaczkowski B, Olsen JP, Krogh KBRM, Jensen K, Cavaleiro AM, Peters GHJ, Spodsberg N, Borch K, Westh P. Physical constraints and functional plasticity of cellulases. Nat Commun 2021; 12:3847. [PMID: 34158485 PMCID: PMC8219668 DOI: 10.1038/s41467-021-24075-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gustavo A Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kay S Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stefan J Christensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Silke F Badino
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nanna S Røjel
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Malene B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, Denmark
| | - Nanna Rolsted Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Bartlomiej Kolaczkowski
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | | | | | | | | | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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8
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Bååth JA, Borch K, Jensen K, Brask J, Westh P. Comparative Biochemistry of Four Polyester (PET) Hydrolases*. Chembiochem 2021; 22:1627-1637. [PMID: 33351214 DOI: 10.1002/cbic.202000793] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/22/2020] [Indexed: 11/08/2022]
Abstract
The potential of bioprocessing in a circular plastic economy has strongly stimulated research into the enzymatic degradation of different synthetic polymers. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic-degrading enzymes) acting on the insoluble substrate has not been established. Herein, we propose such a framework, which we have tested against kinetic measurements for four PET hydrolases. The analysis provided values of kcat and KM , as well as an apparent specificity constant in the conventional units of M-1 s-1 . These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. A variant of the PET hydrolase from Ideonella sakaiensis was the most efficient enzyme at ambient conditions; it relied on a high kcat rather than a low KM . Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, whereas the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.
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Affiliation(s)
- Jenny Arnling Bååth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
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9
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A steady-state approach for inhibition of heterogeneous enzyme reactions. Biochem J 2020; 477:1971-1982. [PMID: 32391552 DOI: 10.1042/bcj20200083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
Abstract
The kinetic theory of enzymes that modify insoluble substrates is still underdeveloped, despite the prevalence of this type of reaction both in vivo and industrial applications. Here, we present a steady-state kinetic approach to investigate inhibition occurring at the solid-liquid interface. We propose to conduct experiments under enzyme excess (E0 ≫ S0), i.e. the opposite limit compared with the conventional Michaelis-Menten framework. This inverse condition is practical for insoluble substrates and elucidates how the inhibitor reduces enzyme activity through binding to the substrate. We claim that this type of inhibition is common for interfacial enzyme reactions because substrate accessibility is low, and we show that it can be analyzed by experiments and rate equations that are analogous to the conventional approach, except that the roles of enzyme and substrate have been swapped. To illustrate the approach, we investigated the major cellulases from Trichoderma reesei (Cel6A and Cel7A) acting on insoluble cellulose. As model inhibitors, we used catalytically inactive variants of Cel6A and Cel7A. We made so-called inverse Michaelis-Menten curves at different concentrations of inhibitors and found that a new rate equation accounted well for the data. In most cases, we found a mixed type of surface-site inhibition mechanism, and this probably reflected that the inhibitor both competed with the enzyme for the productive binding-sites (competitive inhibition) and hampered the processive movement on the surface (uncompetitive inhibition). These results give new insights into the complex interplay of Cel7A and Cel6A on cellulose and the approach may be applicable to other heterogeneous enzyme reactions.
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10
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Qu M, Watanabe-Nakayama T, Sun S, Umeda K, Guo X, Liu Y, Ando T, Yang Q. High-Speed Atomic Force Microscopy Reveals Factors Affecting the Processivity of Chitinases during Interfacial Enzymatic Hydrolysis of Crystalline Chitin. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02751] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingbo Qu
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
| | | | - Shaopeng Sun
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Xiaoxi Guo
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Yuansheng Liu
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7 Pengfei Road, Shenzhen 518120, China
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11
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Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
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Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
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12
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Keller MB, Sørensen TH, Krogh KBRM, Wogulis M, Borch K, Westh P. Activity of fungal β-glucosidases on cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:121. [PMID: 32670408 PMCID: PMC7350674 DOI: 10.1186/s13068-020-01762-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Fungal beta-glucosidases (BGs) from glucoside hydrolase family 3 (GH3) are industrially important enzymes, which convert cellooligosaccharides into glucose; the end product of the cellulolytic process. They are highly active against the β-1,4 glycosidic bond in soluble substrates but typically reported to be inactive against insoluble cellulose. RESULTS We studied the activity of four fungal GH3 BGs on cellulose and found significant activity. At low temperatures (10 ℃), we derived the approximate kinetic parameters k cat = 0.3 ± 0.1 s-1 and K M = 80 ± 30 g/l for a BG from Aspergillus fumigatus (AfBG) acting on Avicel. Interestingly, this maximal turnover is higher than reported values for typical cellobiohydrolases (CBH) at this temperature and comparable to those of endoglucanases (EG). The specificity constant of AfGB on Avicel was only moderately lowered compared to values for EGs and CBHs. CONCLUSIONS Overall these observations suggest a significant promiscuous side activity of the investigated GH3 BGs on insoluble cellulose. This challenges the traditional definition of a BG and supports suggestions that functional classes of cellulolytic enzymes may represent a continuum of overlapping modes of action.
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Affiliation(s)
- Malene B. Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 23 Rolighedsvej, 1958 Frederiksberg, Denmark
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Trine H. Sørensen
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
- Novozymes A/S, 2 Biologiens Vej, 2800 Kgs. Lyngby, Denmark
| | | | - Mark Wogulis
- Novozymes Ltd, 1445 Drew Ave, Davis, CA 95618 USA
| | - Kim Borch
- Novozymes A/S, 2 Biologiens Vej, 2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 221 Søltofts Plads, 2800 Kgs. Lyngby, Denmark
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Christensen SJ, Badino SF, Cavaleiro AM, Borch K, Westh P. Functional analysis of chimeric TrCel6A enzymes with different carbohydrate binding modules. Protein Eng Des Sel 2020; 32:401-409. [PMID: 32100026 DOI: 10.1093/protein/gzaa003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 11/14/2022] Open
Abstract
The glycoside hydrolase (GH) family 6 is an important group of enzymes that constitute an essential part of industrial enzyme cocktails used to convert lignocellulose into fermentable sugars. In nature, enzymes from this family often have a carbohydrate binding module (CBM) from the CBM family 1. These modules are known to promote adsorption to the cellulose surface and influence enzymatic activity. Here, we have investigated the functional diversity of CBMs found within the GH6 family. This was done by constructing five chimeric enzymes based on the model enzyme, TrCel6A, from the soft-rot fungus Trichoderma reesei. The natural CBM of this enzyme was exchanged with CBMs from other GH6 enzymes originating from different cellulose degrading fungi. The chimeric enzymes were expressed in the same host and investigated in adsorption and quasi-steady-state kinetic experiments. Our results quantified functional differences of these phylogenetically distant binding modules. Thus, the partitioning coefficient for substrate binding varied 4-fold, while the maximal turnover (kcat) showed a 2-fold difference. The wild-type enzyme showed the highest cellulose affinity on all tested substrates and the highest catalytic turnover. The CBM from Serendipita indica strongly promoted the enzyme's ability to form productive complexes with sites on the substrate surface but showed lower turnover of the complex. We conclude that the CBM plays an important role for the functional differences between GH6 wild-type enzymes.
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Affiliation(s)
- Stefan Jarl Christensen
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark
| | - Silke Flindt Badino
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark
| | - Ana Mafalda Cavaleiro
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark.,Novozymes A/S, Department of Enzyme Discovery, Rævehøjvej 32A, DK-2800 Kgs. Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Department of Enzyme Discovery, Rævehøjvej 32A, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, building 224, DK-2800, Kgs. Lyngby, Denmark
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Tokin R, Ipsen JØ, Westh P, Johansen KS. The synergy between LPMOs and cellulases in enzymatic saccharification of cellulose is both enzyme- and substrate-dependent. Biotechnol Lett 2020; 42:1975-1984. [DOI: 10.1007/s10529-020-02922-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
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15
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Kołaczkowski BM, Schaller KS, Sørensen TH, Peters GHJ, Jensen K, Krogh KBRM, Westh P. Removal of N-linked glycans in cellobiohydrolase Cel7A from Trichoderma reesei reveals higher activity and binding affinity on crystalline cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:136. [PMID: 32782472 PMCID: PMC7412794 DOI: 10.1186/s13068-020-01779-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/29/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cellobiohydrolase from glycoside hydrolase family 7 is a major component of commercial enzymatic mixtures for lignocellulosic biomass degradation. For many years, Trichoderma reesei Cel7A (TrCel7A) has served as a model to understand structure-function relationships of processive cellobiohydrolases. The architecture of TrCel7A includes an N-glycosylated catalytic domain, which is connected to a carbohydrate-binding module through a flexible, O-glycosylated linker. Depending on the fungal expression host, glycosylation can vary not only in glycoforms, but also in site occupancy, leading to a complex pattern of glycans, which can affect the enzyme's stability and kinetics. RESULTS Two expression hosts, Aspergillus oryzae and Trichoderma reesei, were utilized to successfully express wild-types TrCel7A (WT Ao and WT Tr ) and the triple N-glycosylation site deficient mutants TrCel7A N45Q, N270Q, N384Q (ΔN-glyc Ao and ΔN-glyc Tr ). Also, we expressed single N-glycosylation site deficient mutants TrCel7A (N45Q Ao , N270Q Ao , N384Q Ao ). The TrCel7A enzymes were studied by steady-state kinetics under both substrate- and enzyme-saturating conditions using different cellulosic substrates. The Michaelis constant (K M ) was consistently found to be lowered for the variants with reduced N-glycosylation content, and for the triple deficient mutants, it was less than half of the WTs' value on some substrates. The ability of the enzyme to combine productively with sites on the cellulose surface followed a similar pattern on all tested substrates. Thus, site density (number of sites per gram cellulose) was 30-60% higher for the single deficient variants compared to the WT, and about twofold larger for the triple deficient enzyme. Molecular dynamic simulation of the N-glycan mutants TrCel7A revealed higher number of contacts between CD and cellulose crystal upon removal of glycans at position N45 and N384. CONCLUSIONS The kinetic changes of TrCel7A imposed by removal of N-linked glycans reflected modifications of substrate accessibility. The presence of N-glycans with extended structures increased K M and decreased attack site density of TrCel7A likely due to steric hindrance effect and distance between the enzyme and the cellulose surface, preventing the enzyme from achieving optimal conformation. This knowledge could be applied to modify enzyme glycosylation to engineer enzyme with higher activity on the insoluble substrates.
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Affiliation(s)
| | - Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | | | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kgs. Lyngby, Denmark
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17
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Kari J, Christensen SJ, Andersen M, Baiget SS, Borch K, Westh P. A practical approach to steady-state kinetic analysis of cellulases acting on their natural insoluble substrate. Anal Biochem 2019; 586:113411. [PMID: 31520594 DOI: 10.1016/j.ab.2019.113411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
Measurement of steady-state rates (vSS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of vss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental vSS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Stefan Jarl Christensen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | - Morten Andersen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | | | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark.
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18
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A biochemical comparison of fungal GH6 cellobiohydrolases. Biochem J 2019; 476:2157-2172. [DOI: 10.1042/bcj20190185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 02/02/2023]
Abstract
AbstractCellobiohydrolases (CBHs) from glycoside hydrolase family 6 (GH6) make up an important part of the secretome in many cellulolytic fungi. They are also of technical interest, particularly because they are part of the enzyme cocktails that are used for the industrial breakdown of lignocellulosic biomass. Nevertheless, functional studies of GH6 CBHs are scarce and focused on a few model enzymes. To elucidate functional breadth among GH6 CBHs, we conducted a comparative biochemical study of seven GH6 CBHs originating from fungi living in different habitats, in addition to one enzyme variant. The enzyme sequences were investigated by phylogenetic analyses to ensure that they were not closely related phylogenetically. The selected enzymes were all heterologously expressed in Aspergillus oryzae, purified and thoroughly characterized biochemically. This approach allowed direct comparisons of functional data, and the results revealed substantial variability. For example, the adsorption capacity on cellulose spanned two orders of magnitude and kinetic parameters, derived from two independent steady-state methods also varied significantly. While the different functional parameters covered wide ranges, they were not independent since they changed in parallel between two poles. One pole was characterized by strong substrate interactions, high adsorption capacity and low turnover number while the other showed weak substrate interactions, poor adsorption and high turnover. The investigated enzymes essentially defined a continuum between these two opposites, and this scaling of functional parameters raises interesting questions regarding functional plasticity and evolution of GH6 CBHs.
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19
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Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J Biol Chem 2019; 294:13233-13247. [PMID: 31324716 DOI: 10.1074/jbc.ra119.009861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, 13007 Marseille, France; INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 13007 Marseille, France
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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