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Cheng C, Haider J, Liu P, Yang J, Tan Z, Huang T, Lin J, Jiang M, Liu H, Zhu L. Engineered LPMO Significantly Boosting Cellulase-Catalyzed Depolymerization of Cellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15257-15266. [PMID: 33290065 DOI: 10.1021/acs.jafc.0c05979] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play a crucial role in the enzymatic depolymerization of cellulose through oxidative cleavage of the glycosidic bond in the highly recalcitrant crystalline cellulose region. Improving the activity of LPMOs is of considerable importance for second-generation biorefinery. In this study, we identified a beneficial amino acid substitution (N526S) located in the cellulose binding module (CBM) of HcLPMO10 (LPMO of Hahella chejuensis) using directed evolution. The improved variant HcLPMO10 M1 (N526S) exhibits 2.1-fold higher activity for the H2O2 production, 2.7-fold higher oxidation activity, and 1.9-fold higher binding capacity toward cellulose compared with those of the wild type (WT). Furthermore, M1 shows 2.1-fold higher activity for degradation of crystalline cellulose in synergy with cellulase, compared to the WT. Structural analysis through molecular modeling and molecular dynamics (MD) simulation revealed that the substitution N526S located in the CBM likely stabilizes the cellulose binding surface and enhances the binding capacity of HcLPMO10 to cellulose, thereby enhancing enzyme activity. These findings demonstrate the important role of the CBM in the catalytic function of LPMO.
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Affiliation(s)
- Chao Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Zijian Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Tianchen Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Department of Biological Engineering, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, P. R. China
| | - Jianping Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Haifeng Liu
- Institute of Chemistry, NAWI Graz, BioTechMed Graz, University of Graz, Heinrichstrasse 28, Graz 8010, Austria
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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52
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Lienemann M. Molecular mechanisms of electron transfer employed by native proteins and biological-inorganic hybrid systems. Comput Struct Biotechnol J 2020; 19:206-213. [PMID: 33425252 PMCID: PMC7772364 DOI: 10.1016/j.csbj.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 11/19/2022] Open
Abstract
Recent advances in enzymatic electrosynthesis of desired chemicals in biological-inorganic hybrid systems has generated interest because it can use renewable energy inputs and employs highly specific catalysts that are active at ambient conditions. However, the development of such innovative processes is currently limited by a deficient understanding of the molecular mechanisms involved in electrode-based electron transfer and biocatalysis. Mechanistic studies of non-electrosynthetic electron transferring proteins have provided a fundamental understanding of the processes that take place during enzymatic electrosynthesis. Thus, they may help explain how redox proteins stringently control the reduction potential of the transferred electron and efficiently transfer it to a specific electron acceptor. The redox sites at which electron donor oxidation and electron acceptor reduction take place are typically located in distant regions of the redox protein complex and are electrically connected by an array of closely spaced cofactors. These groups function as electron relay centers and are shielded from the surrounding environment by the electrically insulating apoporotein. In this matrix, electrons travel via electron tunneling, i.e. hopping between neighboring cofactors, over impressive distances of upto several nanometers and, as in the case of the Shewanella oneidensis Mtr electron conduit, traverse the bacterial cell wall to extracellular electron acceptors such as solid ferrihydrite. Here, the biochemical strategies of protein-based electron transfer are presented in order to provide a basis for future studies on the basis of which a more comprehensive understanding of the structural biology of enzymatic electrosynthesis may be attained.
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53
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2020; 60:2385-2392. [DOI: 10.1002/anie.202011408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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54
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Gaber Y, Rashad B, Hussein R, Abdelgawad M, Ali NS, Dishisha T, Várnai A. Heterologous expression of lytic polysaccharide monooxygenases (LPMOs). Biotechnol Adv 2020; 43:107583. [DOI: 10.1016/j.biotechadv.2020.107583] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/20/2022]
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55
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Wang B, Wang Z, Davies GJ, Walton PH, Rovira C. Activation of O2 and H2O2 by Lytic Polysaccharide Monooxygenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02914] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martı́ i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08020 Barcelona, Spain
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56
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Gangwar R, Rasool S, Mishra S. Purified cellobiose dehydrogenase of Termitomyces sp. OE147 fuels cellulose degradation resulting in the release of reducing sugars. Prep Biochem Biotechnol 2020; 51:488-496. [PMID: 33063604 DOI: 10.1080/10826068.2020.1833343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Termitomyces sp. OE 147 is one of the active cellulose degraders in the ecosphere and produces large amount of cellobiose dehydrogenase (CDH) and β-glucosidases when cultivated on cellulose. In order to investigate its effect on cellulose, a highly purified preparation of CDH was obtained from the culture supernatant of the fungus cultivated on cellulose. A combination of ultrafiltration, ion-exchange and gel-filtration chromatography was used to purify CDH by ∼172-fold to a high specific activity of ∼324 U/mg protein on lactose which was used for routine measurement of enzyme activity. The enzyme displayed a pH optimum of 5.0 and stability between pH 5.0 and 8.0 with maximum catalytic efficiency (kcat/Km) of 397 mM-1 s-1 on cellobiose. Incubation of microcrystalline cellulose with the purified CDH led to production of reducing sugars which was accelerated by the addition of FeCl3 during the early stages of incubation. A mass spectrometric analysis revealed fragmentation products of cellulose which were concluded to be cellodextrins, sugars, and corresponding aldonic acids suggesting that CDH can release reducing sugars in the absence of externally added lytic polysaccharide monooxygenases. Polymerized products of glucose were also detected at low intensity.
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Affiliation(s)
- Rishabh Gangwar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.,School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Shafaq Rasool
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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57
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Guo X, Sang J, Chai C, An Y, Wei Z, Zhang H, Ma L, Dai Y, Lu F, Liu F. A lytic polysaccharide monooxygenase from Myceliophthora thermophila C1 and its characterization in cleavage of glycosidic chain of cellulose. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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58
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Herzog PL, Borghi E, Traxlmayr MW, Obinger C, Sikes HD, Peterbauer CK. Developing a cell-bound detection system for the screening of oxidase activity using the fluorescent peroxide sensor roGFP2-Orp1. Protein Eng Des Sel 2020; 33:gzaa019. [PMID: 32930800 PMCID: PMC7720637 DOI: 10.1093/protein/gzaa019] [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: 02/19/2020] [Revised: 06/02/2020] [Accepted: 07/08/2020] [Indexed: 11/14/2022] Open
Abstract
Accurate yet efficient high-throughput screenings have emerged as essential technology for enzyme engineering via directed evolution. Modern high-throughput screening platforms for oxidoreductases are commonly assisted by technologies such as surface display and rely on emulsification techniques to facilitate single-cell analysis via fluorescence-activated cell sorting. Empowered by the dramatically increased throughput, the screening of significantly larger sequence spaces in acceptable time frames is achieved but usually comes at the cost of restricted applicability. In this work, we tackle this problem by utilizing roGFP2-Orp1 as a fluorescent one-component detection system for enzymatic H2O2 formation. We determined the kinetic parameters of the roGFP2-Orp1 reaction with H2O2 and established an efficient immobilization technique for the sensor on Saccharomyces cerevisiae cells employing the lectin Concanavalin A. This allowed to realize a peroxide-sensing shell on enzyme-displaying cells, a system that was successfully employed to screen for H2O2 formation of enzyme variants in a whole-cell setting.
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Affiliation(s)
- P L Herzog
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - E Borghi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 287, 41124 Modena, Italy
| | - M W Traxlmayr
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - C Obinger
- Institute of Biochemistry, Department of Chemistry, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - H D Sikes
- Department of Chemical Engineering, MIT – Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge 02139, MA, USA
| | - C K Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
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59
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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: 64] [Impact Index Per Article: 16.0] [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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60
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Abstract
Enzymatic methods for the oxidation of alcohols are critically reviewed. Dehydrogenases and oxidases are the most prominent biocatalysts, enabling the selective oxidation of primary alcohols into aldehydes or acids. In the case of secondary alcohols, region and/or enantioselective oxidation is possible. In this contribution, we outline the current state-of-the-art and discuss current limitations and promising solutions.
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61
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Li X, Han C, Li W, Chen G, Wang L. Insights into the cellulose degradation mechanism of the thermophilic fungus Chaetomium thermophilum based on integrated functional omics. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:143. [PMID: 32817759 PMCID: PMC7425565 DOI: 10.1186/s13068-020-01783-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant and renewable biomass resource on the planet. Lignocellulose can be converted into biofuels and high-value compounds; however, its recalcitrance makes its breakdown a challenge. Lytic polysaccharide monooxygenases (LPMOs) offer tremendous promise for the degradation of recalcitrant polysaccharides. Chaetomium thermophilum, having many LPMO-coding genes, is a dominant thermophilic fungus in cellulose-rich and self-heating habitats. This study explores the genome, secretomes and transcript levels of specific genes of C. thermophilum. RESULTS The genome of C. thermophilum encoded a comprehensive set of cellulose- and xylan-degrading enzymes, especially 18 AA9 LPMOs that belonged to different subfamilies. Extracellular secretomes showed that arabinose and microcrystalline cellulose (MCC) could specifically induce the secretion of carbohydrate-active enzymes (CAZymes), especially AA9 LPMOs, by C. thermophilum under different carbon sources. Temporal analyses of secretomes and transcripts revealed that arabinose induced the secretion of xylanases by C. thermophilum, which was obviously different from other common filamentous fungi. MCC could efficiently induce the specific secretion of LPMO2s, possibly because the insert in loop3 on the substrate-binding surface of LPMO2s strengthened its binding capacity to cellulose. LPMO2s, cellobio hydrolases (CBHs) and cellobiose dehydrogenases (CDHs) were cosecreted, forming an efficient cellulose degradation system of oxidases and hydrolases under thermophilic conditions. CONCLUSIONS The specific expression of LPMO2s and cosecretion of hydrolases and oxidases by the thermophilic fungus C. thermophilum play an important role in cellulose degradation. This insight increases our understanding of the cellulose degradation under thermophilic conditions and may inspire the design of the optimal enzyme cocktails for more efficient exploration of biomass resources in industrial applications.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Chao Han
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Weiguang Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
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Yanase T, Okuda-Shimazaki J, Mori K, Kojima K, Tsugawa W, Sode K. Creation of a novel DET type FAD glucose dehydrogenase harboring Escherichia coli derived cytochrome b 562 as an electron transfer domain. Biochem Biophys Res Commun 2020; 530:82-86. [PMID: 32828319 DOI: 10.1016/j.bbrc.2020.06.132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]
Abstract
Fungi-derived flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenases (FADGDHs) are the most popular and advanced enzymes for SMBG sensors because of their high substrate specificity toward glucose and oxygen insensitivity. However, this type of FADGDH hardly shows direct electron transfer (DET) ability. In this study, we developed a new DET-type FADGDH by harboring Cytochrome b562 (cyt b562) derived from Escherichia coli as the electron transfer domain. The structural genes encoding fusion enzymes composed of cyt b562 at either the N- or C-terminus of fungal FADGDH, (cyt b562-GDH or GDH-cyt b562), were constructed, recombinantly expressed, and characteristics of the fusion proteins were investigated. Both constructed fusion enzymes were successfully expressed in E. coli, as the soluble and GDH active proteins, showing cyt b562 specific redox properties. Thusconstructed fusion proteins showed internal electron transfer between FAD in FADGDH and fused cyt b562. Consequently, both cyt b562-GDH and GDH-cyt b562 showed DET abilities toward electrode. Interestingly, cyt b562-GDH showed much rapid internal electron transfer and higher DET ability than GDH-cyt b562. Thus, we demonstrated the construction and production of a new DET-type FADGDH using E.coli as the host cells, which is advantageous for future industrial application and further engineering.
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Affiliation(s)
- Takumi Yanase
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Junko Okuda-Shimazaki
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599, USA
| | - Kazushige Mori
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Katsuhiro Kojima
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Wakako Tsugawa
- Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599, USA.
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63
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Alfaro M, Majcherczyk A, Kües U, Ramírez L, Pisabarro AG. Glucose counteracts wood-dependent induction of lignocellulolytic enzyme secretion in monokaryon and dikaryon submerged cultures of the white-rot basidiomycete Pleurotus ostreatus. Sci Rep 2020; 10:12421. [PMID: 32709970 PMCID: PMC7381666 DOI: 10.1038/s41598-020-68969-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The secretome complexity and lignocellulose degrading capacity of Pleurotus ostreatus monokaryons mkPC9 and mkPC15 and mated dikaryon dkN001 were studied in submerged liquid cultures containing wood, glucose, and wood plus glucose as carbon sources. The study revealed that this white-rot basidiomycete attacks all the components of the plant cell wall. P. ostreatus secretes a variety of glycoside hydrolases, carbohydrate esterases, and polysaccharide lyases, especially when wood is the only carbon source. The presence of wood increased the secretome complexity, whereas glucose diminished the secretion of enzymes involved in cellulose, hemicellulose and pectin degradation. In contrast, the presence of glucose did not influence the secretion of redox enzymes or proteases, which shows the specificity of glucose on the secretion of cellulolytic enzymes. The comparison of the secretomes of monokaryons and dikaryons reveals that secretome complexity is unrelated to the nuclear composition of the strain.
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Affiliation(s)
- Manuel Alfaro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Andrzej Majcherczyk
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain.
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64
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Troiano D, Orsat V, Dumont MJ. Status of Biocatalysis in the Production of 2,5-Furandicarboxylic Acid. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02378] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Derek Troiano
- Bioresource Engineering Department, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Valérie Orsat
- Bioresource Engineering Department, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Marie-Josée Dumont
- Bioresource Engineering Department, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
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65
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Breslmayr E, Laurent CVFP, Scheiblbrandner S, Jerkovic A, Heyes DJ, Oostenbrink C, Ludwig R, Hedison TM, Scrutton NS, Kracher D. Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase. ACS Catal 2020; 10:4842-4853. [PMID: 32382450 PMCID: PMC7199207 DOI: 10.1021/acscatal.0c00754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Indexed: 12/30/2022]
Abstract
Large-scale protein domain dynamics and electron transfer are often associated. However, as protein motions span a broad range of time and length scales, it is often challenging to identify and thus link functionally relevant dynamic changes to electron transfer in proteins. It is hypothesized that large-scale domain motions direct electrons through a FAD and a heme b cofactor of the fungal cellobiose dehydrogenase (CDH) enzymes to the type-II copper center (T2Cu) of the polysaccharide-degrading lytic polysaccharide monooxygenases (LPMOs). However, as of yet, domain motions in CDH have not been linked formally to enzyme-catalyzed electron transfer reactions. The detailed structural features of CDH, which govern the functional conformational landscapes of the enzyme, have only been partially resolved. Here, we use a combination of pressure, viscosity, ionic strength, and temperature perturbation stopped-flow studies to probe the conformational landscape associated with the electron transfer reactions of CDH. Through the use of molecular dynamics simulations, potentiometry, and stopped-flow spectroscopy, we investigated how a conserved Tyr99 residue plays a key role in shaping the conformational landscapes for both the interdomain electron transfer reactions of CDH (from FAD to heme) and the delivery of electrons from the reduced heme cofactor to the LPMO T2Cu. Our studies show how motions gate the electron transfer within CDH and from CDH to LPMO and illustrate the conformational landscape for interdomain and interprotein electron transfer in this extracellular fungal electron transfer chain.
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Affiliation(s)
- Erik Breslmayr
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Christophe V. F. P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Anita Jerkovic
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Tobias M. Hedison
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Daniel Kracher
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Barbosa FC, Silvello MA, Goldbeck R. Cellulase and oxidative enzymes: new approaches, challenges and perspectives on cellulose degradation for bioethanol production. Biotechnol Lett 2020; 42:875-884. [DOI: 10.1007/s10529-020-02875-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 01/04/2023]
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Zhou X, Zhu H. Current understanding of substrate specificity and regioselectivity of LPMOs. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0300-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractRenewable biomass such as cellulose and chitin are the most abundant sustainable sources of energy and materials. However, due to the low degradation efficiency of these recalcitrant substrates by conventional hydrolases, these biomass resources cannot be utilized efficiently. In 2010, the discovery of lytic polysaccharide monooxygenases (LPMOs) led to a major breakthrough. Currently, LPMOs are distributed in 7 families in CAZy database, including AA9–11 and AA13–16, with different species origins, substrate specificity and oxidative regioselectivity. Effective application of LPMOs in the biotransformation of biomass resources needs the elucidation of the molecular basis of their function. Since the discovery of LPMOs, great advances have been made in the study of their substrate specificity and regioselectivity, as well as their structural basis, which will be reviewed below.
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Filandr F, Kavan D, Kracher D, Laurent CV, Ludwig R, Man P, Halada P. Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis. Biomolecules 2020; 10:E242. [PMID: 32033404 PMCID: PMC7072406 DOI: 10.3390/biom10020242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are industrially important oxidoreductases employed in lignocellulose saccharification. Using advanced time-resolved mass spectrometric techniques, we elucidated the structural determinants for substrate-mediated stabilization of the fungal LPMO9C from Neurosporacrassa during catalysis. LPMOs require a reduction in the active-site copper for catalytic activity. We show that copper reduction in NcLPMO9C leads to structural rearrangements and compaction around the active site. However, longer exposure to the reducing agent ascorbic acid also initiated an uncoupling reaction of the bound oxygen species, leading to oxidative damage, partial unfolding, and even fragmentation of NcLPMO9C. Interestingly, no changes in the hydrogen/deuterium exchange rate were detected upon incubation of oxidized or reduced LPMO with crystalline cellulose, indicating that the LPMO-substrate interactions are mainly side-chain mediated and neither affect intraprotein hydrogen bonding nor induce significant shielding of the protein surface. On the other hand, we observed a protective effect of the substrate, which slowed down the autooxidative damage induced by the uncoupling reaction. These observations further complement the picture of structural changes during LPMO catalysis.
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Affiliation(s)
- Frantisek Filandr
- Institute of Microbiology of the CAS, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic; (F.F.); (D.K.)
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague 2, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the CAS, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic; (F.F.); (D.K.)
| | - Daniel Kracher
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (D.K.); (R.L.)
| | - Christophe V.F.P. Laurent
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (D.K.); (R.L.)
| | - Roland Ludwig
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; (D.K.); (R.L.)
| | - Petr Man
- Institute of Microbiology of the CAS, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic; (F.F.); (D.K.)
| | - Petr Halada
- Institute of Microbiology of the CAS, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic; (F.F.); (D.K.)
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Tuoriniemi J, Gorton L, Ludwig R, Safina G. Determination of the Distance Between the Cytochrome and Dehydrogenase Domains of Immobilized Cellobiose Dehydrogenase by Using Surface Plasmon Resonance with a Center of Mass Based Model. Anal Chem 2020; 92:2620-2627. [PMID: 31916434 PMCID: PMC7003987 DOI: 10.1021/acs.analchem.9b04490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Changes
in the tertiary conformation of adsorbed biomolecules can
induce detectable shifts (Δθr) in the surface plasmon resonance (SPR) angle. Here it is shown
how to calculate the corresponding shifts in the adsorbate’s
center of mass (Δzavg) along the
sensing surface normal from the measured Δθr. The novel developed model was used for determining
the mean distance between the cytochrome (CYT) and flavodehydrogenase
(DH) domains of the enzyme cellobiose dehydrogenase (CDH) isolated
from the fungi Neurospora crassa, Corynascus thermophilus, and Myriococcum
thermophilum as a function of pH, [Ca2+], and substrate concentration. SPR confirmed the results from earlier
electrochemical and SAXS studies stating that the closed conformation,
where the two domains are in close vicinity, is stabilized by a lower
pH and an increased [Ca2+]. Interestingly, an increasing
substrate concentration in the absence of any electron acceptors stabilizes
the open conformation as the electrostatic repulsion due to the reaped
electrons pushes the DH and CYT domains apart. The accuracy of distance
determination was limited mostly by the random fluctuations between
replicate measurements, and it was possible to detect movements <1
nm of the domains with respect to each other. The results agreed with
calculations using already established models treating conformational
changes as contraction or expansion of the thickness of the adsorbate
layer (tprotein). Although the models
yielded equivalent results, in this case, the Δzavg-based method also works in situations, where the adsorbate’s
mass is not evenly distributed within the layer.
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Affiliation(s)
- Jani Tuoriniemi
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemigården 4 , 412 96 Gothenburg , Sweden
| | - Lo Gorton
- Department of Biochemistry and Structural Biology , Lund University , P.O. Box 124, 221 00 Lund , Sweden
| | - Roland Ludwig
- Department of Food Science and Technology , BOKU - University of Natural Resources and Life Sciences , Vienna, Muthgasse 18 , 1190 Vienna , Austria
| | - Gulnara Safina
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemigården 4 , 412 96 Gothenburg , Sweden.,Division of Biological Physics, Department of Physics , Chalmers University of Technology , Kemigården 1 , 412 96 Gothenburg , Sweden
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Cellobiose dehydrogenase. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:457-489. [DOI: 10.1016/bs.enz.2020.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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71
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Filandr F, Man P, Halada P, Chang H, Ludwig R, Kracher D. The H 2O 2-dependent activity of a fungal lytic polysaccharide monooxygenase investigated with a turbidimetric assay. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:37. [PMID: 32158501 PMCID: PMC7057652 DOI: 10.1186/s13068-020-01673-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/01/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent redox enzymes that cleave recalcitrant biopolymers such as cellulose, chitin, starch and hemicelluloses. Although LPMOs receive ample interest in industry and academia, their reaction mechanism is not yet fully understood. Recent studies showed that H2O2 is a more efficient cosubstrate for the enzyme than O2, which could greatly affect the utilization of LPMOs in industrial settings. RESULTS We probe the reactivity of LPMO9C from the cellulose-degrading fungus Neurospora crassa with a turbidimetric assay using phosphoric acid-swollen cellulose (PASC) as substrate and H2O2 as a cosubstrate. The measurements were also followed by continuous electrochemical H2O2 detection and LPMO reaction products were analysed by mass spectrometry. Different systems for the in situ generation of H2O2 and for the reduction of LPMO's active-site copper were employed, including glucose oxidase, cellobiose dehydrogenase, and the routinely used reductant ascorbate. CONCLUSIONS We found for all systems that the supply of H2O2 limited LPMO's cellulose depolymerization activity, which supports the function of H2O2 as the relevant cosubstrate. The turbidimetric assay allowed rapid determination of LPMO activity on a cellulosic substrate without the need for time-consuming and instrumentally elaborate analysis methods.
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Affiliation(s)
- Frantisek Filandr
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague 2, Czech Republic
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Petr Man
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Petr Halada
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Hucheng Chang
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Kracher
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- The University of Manchester, Manchester Institute of Biotechnology, Manchester, M1 7DN UK
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Laurent CV, Sun P, Scheiblbrandner S, Csarman F, Cannazza P, Frommhagen M, van Berkel WJ, Oostenbrink C, Kabel MA, Ludwig R. Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity. Int J Mol Sci 2019; 20:E6219. [PMID: 31835532 PMCID: PMC6940765 DOI: 10.3390/ijms20246219] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 12/07/2019] [Indexed: 12/29/2022] Open
Abstract
In past years, new lytic polysaccharide monooxygenases (LPMOs) have been discovered as distinct in their substrate specificity. Their unconventional, surface-exposed catalytic sites determine their enzymatic activities, while binding sites govern substrate recognition and regioselectivity. An additional factor influencing activity is the presence or absence of a family 1 carbohydrate binding module (CBM1) connected via a linker to the C-terminus of the LPMO. This study investigates the changes in activity induced by shortening the second active site segment (Seg2) or removing the CBM1 from Neurospora crassa LPMO9C. NcLPMO9C and generated variants have been tested on regenerated amorphous cellulose (RAC), carboxymethyl cellulose (CMC) and xyloglucan (XG) using activity assays, conversion experiments and surface plasmon resonance spectroscopy. The absence of CBM1 reduced the binding affinity and activity of NcLPMO9C, but did not affect its regioselectivity. The linker was found important for the thermal stability of NcLPMO9C and the CBM1 is necessary for efficient binding to RAC. Wild-type NcLPMO9C exhibited the highest activity and strongest substrate binding. Shortening of Seg2 greatly reduced the activity on RAC and CMC and completely abolished the activity on XG. This demonstrates that Seg2 is indispensable for substrate recognition and the formation of productive enzyme-substrate complexes.
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Affiliation(s)
- Christophe V.F.P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Florian Csarman
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Pietro Cannazza
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
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Trichoderma reesei Dehydrogenase, a Pyrroloquinoline Quinone-Dependent Member of Auxiliary Activity Family 12 of the Carbohydrate-Active Enzymes Database: Functional and Structural Characterization. Appl Environ Microbiol 2019; 85:AEM.00964-19. [PMID: 31604773 PMCID: PMC6881810 DOI: 10.1128/aem.00964-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/10/2019] [Indexed: 01/08/2023] Open
Abstract
Pyrroloquinoline quinone (PQQ) is an ortho-quinone cofactor of several prokaryotic oxidases. Widely available in the diet and necessary for the correct growth of mice, PQQ has been suspected to be a vitamin for eukaryotes. However, no PQQ-dependent eukaryotic enzyme had been identified to use the PQQ until 2014, when a basidiomycete enzyme catalyzing saccharide dehydrogenation using PQQ as a cofactor was characterized and served to define auxiliary activity family 12 (AA12). Here we report the biochemical characterization of the AA12 enzyme encoded by the genome of the ascomycete Trichoderma reesei (TrAA12). Surprisingly, only weak activity against uncommon carbohydrates like l-fucose or d-arabinose was measured. The three-dimensional structure of TrAA12 reveals important similarities with bacterial soluble glucose dehydrogenases (sGDH). The enzymatic characterization and the structure solved in the presence of calcium confirm the importance of this ion in catalysis, as observed for sGDH. The structural characterization of TrAA12 was completed by modeling PQQ and l-fucose in the enzyme active site. Based on these results, the AA12 family of enzymes is likely to have a catalytic mechanism close to that of bacterial sGDH.IMPORTANCE Pyrroloquinoline quinone (PQQ) is an important cofactor synthesized by prokaryotes and involved in enzymatic alcohol and sugar oxidation. In eukaryotes, the benefit of PQQ as a vitamin has been suggested but never proved. Recently, the first eukaryotic enzyme using PQQ was characterized in the basidiomycete Coprinopsis cinerea, demonstrating that fungi are able to use PQQ as an enzyme cofactor. This discovery led to the classification of the fungal PQQ-dependent enzymes in auxiliary activity family 12 (AA12) of the Carbohydrate-Active Enzymes (CAZy) database (www.cazy.org) classification. In the present paper, we report on the characterization of the ascomycete AA12 enzyme from Trichoderma reesei (TrAA12). Our enzymatic and phylogenetic results show divergence with the only other member of the family characterized, that from the basidiomycete Coprinopsis cinerea The crystallographic structure of TrAA12 shows similarities to the global active-site architecture of bacterial glucose dehydrogenases, suggesting a common evolution between the two families.
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Crystal Structure of the Catalytic and Cytochrome b Domains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase. Appl Environ Microbiol 2019; 85:AEM.01692-19. [PMID: 31604769 PMCID: PMC6881789 DOI: 10.1128/aem.01692-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/10/2019] [Indexed: 01/14/2023] Open
Abstract
Pyrroloquinoline quinone (PQQ) is known as the “third coenzyme” following nicotinamide and flavin. PQQ-dependent enzymes have previously been found only in prokaryotes, and the existence of a eukaryotic PQQ-dependent enzyme was in doubt. In 2014, we found an enzyme in mushrooms that catalyzes the oxidation of various sugars in a PQQ-dependent manner and that was a PQQ-dependent enzyme found in eukaryotes. This paper presents the X-ray crystal structures of this eukaryotic PQQ-dependent quinohemoprotein, which show the active site, and identifies the amino acid residues involved in the binding of the cofactor PQQ. The presented X-ray structures reveal that the AA12 domain is in a binary complex with the coenzyme, clearly proving that PQQ-dependent enzymes exist in eukaryotes as well as prokaryotes. Because no biosynthetic system for PQQ has been reported in eukaryotes, future research on the symbiotic systems is expected. Pyrroloquinoline quinone (PQQ) was discovered as a redox cofactor of prokaryotic glucose dehydrogenases in the 1960s, and subsequent studies have demonstrated its importance not only in bacterial systems but also in higher organisms. We have previously reported a novel eukaryotic quinohemoprotein that exhibited PQQ-dependent catalytic activity in a eukaryote. The enzyme, pyranose dehydrogenase (PDH), from the filamentous fungus Coprinopsis cinerea (CcPDH) of the Basidiomycete division, is composed of a catalytic PQQ-dependent domain classified as a member of the novel auxiliary activity family 12 (AA12), an AA8 cytochrome b domain, and a family 1 carbohydrate-binding module (CBM1), as defined by the Carbohydrate-Active Enzymes (CAZy) database. Here, we present the crystal structures of the AA12 domain in its apo- and holo-forms and the AA8 domain of this enzyme. The crystal structures of the holo-AA12 domain bound to PQQ provide direct evidence that eukaryotes have PQQ-dependent enzymes. The AA12 domain exhibits a six-blade β-propeller fold that is also present in other known PQQ-dependent glucose dehydrogenases in bacteria. A loop structure around the active site and a calcium ion binding site are unique among the known structures of bacterial quinoproteins. The AA8 cytochrome domain has a positively charged area on its molecular surface, which is partly due to the propionate group of the heme interacting with Arg181; this feature differs from the characteristics of cytochrome b in the AA8 domain of the fungal cellobiose dehydrogenase and suggests that this difference may affect the pH dependence of electron transfer. IMPORTANCE Pyrroloquinoline quinone (PQQ) is known as the “third coenzyme” following nicotinamide and flavin. PQQ-dependent enzymes have previously been found only in prokaryotes, and the existence of a eukaryotic PQQ-dependent enzyme was in doubt. In 2014, we found an enzyme in mushrooms that catalyzes the oxidation of various sugars in a PQQ-dependent manner and that was a PQQ-dependent enzyme found in eukaryotes. This paper presents the X-ray crystal structures of this eukaryotic PQQ-dependent quinohemoprotein, which show the active site, and identifies the amino acid residues involved in the binding of the cofactor PQQ. The presented X-ray structures reveal that the AA12 domain is in a binary complex with the coenzyme, clearly proving that PQQ-dependent enzymes exist in eukaryotes as well as prokaryotes. Because no biosynthetic system for PQQ has been reported in eukaryotes, future research on the symbiotic systems is expected.
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Okuda-Shimazaki J, Yoshida H, Sode K. FAD dependent glucose dehydrogenases - Discovery and engineering of representative glucose sensing enzymes. Bioelectrochemistry 2019; 132:107414. [PMID: 31838457 DOI: 10.1016/j.bioelechem.2019.107414] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/24/2019] [Accepted: 11/10/2019] [Indexed: 11/17/2022]
Abstract
The history of the development of glucose sensors goes hand-in-hand with the history of the discovery and the engineering of glucose-sensing enzymes. Glucose oxidase (GOx) has been used for glucose sensing since the development of the first electrochemical glucose sensor. The principle utilizing oxygen as the electron acceptor is designated as the first-generation electrochemical enzyme sensors. With increasing demand for hand-held and cost-effective devices for the "self-monitoring of blood glucose (SMBG)", second-generation electrochemical sensor strips employing electron mediators have become the most popular platform. To overcome the inherent drawback of GOx, namely, the use of oxygen as the electron acceptor, various glucose dehydrogenases (GDHs) have been utilized in second-generation principle-based sensors. Among the various enzymes employed in glucose sensors, GDHs harboring FAD as the redox cofactor, FADGDHs, especially those derived from fungi, fFADGDHs, are currently the most popular enzymes in the sensor strips of second-generation SMBG sensors. In addition, the third-generation principle, employing direct electron transfer (DET), is considered the most elegant approach and is ideal for use in electrochemical enzyme sensors. However, glucose oxidoreductases capable of DET are limited. One of the most prominent GDHs capable of DET is a bacteria-derived FADGDH complex (bFADGDH). bFADGDH has three distinct subunits; the FAD harboring the catalytic subunit, the small subunit, and the electron-transfer subunit, which makes bFADGDH capable of DET. In this review, we focused on the two representative glucose sensing enzymes, fFADGDHs and bFADGDHs, by presenting their discovery, sources, and protein and enzyme properties, and the current engineering strategies to improve their potential in sensor applications.
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Affiliation(s)
- Junko Okuda-Shimazaki
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA.
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Kracher D, Forsberg Z, Bissaro B, Gangl S, Preims M, Sygmund C, Eijsink VGH, Ludwig R. Polysaccharide oxidation by lytic polysaccharide monooxygenase is enhanced by engineered cellobiose dehydrogenase. FEBS J 2019; 287:897-908. [PMID: 31532909 PMCID: PMC7078924 DOI: 10.1111/febs.15067] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/13/2019] [Accepted: 09/16/2019] [Indexed: 11/30/2022]
Abstract
The catalytic function of lytic polysaccharide monooxygenases (LPMOs) to cleave and decrystallize recalcitrant polysaccharides put these enzymes in the spotlight of fundamental and applied research. Here we demonstrate that the demand of LPMO for an electron donor and an oxygen species as cosubstrate can be fulfilled by a single auxiliary enzyme: an engineered fungal cellobiose dehydrogenase (CDH) with increased oxidase activity. The engineered CDH was about 30 times more efficient in driving the LPMO reaction due to its 27 time increased production of H2O2 acting as a cosubstrate for LPMO. Transient kinetic measurements confirmed that intra‐ and intermolecular electron transfer rates of the engineered CDH were similar to the wild‐type CDH, meaning that the mutations had not compromised CDH’s role as an electron donor. These results support the notion of H2O2‐driven LPMO activity and shed new light on the role of CDH in activating LPMOs. Importantly, the results also demonstrate that the use of the engineered CDH results in fast and steady LPMO reactions with CDH‐generated H2O2 as a cosubstrate, which may provide new opportunities to employ LPMOs in biomass hydrolysis to generate fuels and chemicals.
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Affiliation(s)
- Daniel Kracher
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sonja Gangl
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marita Preims
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Roland Ludwig
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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Zhou X, Qi X, Huang H, Zhu H. Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity. Int J Mol Sci 2019; 20:ijms20184594. [PMID: 31533304 PMCID: PMC6771041 DOI: 10.3390/ijms20184594] [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: 08/13/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xiaohua Qi
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Hongxia Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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78
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Yoshida H, Kojima K, Shiota M, Yoshimatsu K, Yamazaki T, Ferri S, Tsugawa W, Kamitori S, Sode K. X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein. Acta Crystallogr D Struct Biol 2019; 75:841-851. [PMID: 31478907 PMCID: PMC6719666 DOI: 10.1107/s2059798319010878] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Katsuhiro Kojima
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaki Shiota
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Keiichi Yoshimatsu
- Department of Chemistry, Missouri State University, Springfield, MO 65897, USA
| | - Tomohiko Yamazaki
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Stefano Ferri
- Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
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79
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Scheiblbrandner S, Ludwig R. Cellobiose dehydrogenase: Bioelectrochemical insights and applications. Bioelectrochemistry 2019; 131:107345. [PMID: 31494387 DOI: 10.1016/j.bioelechem.2019.107345] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 12/17/2022]
Abstract
Cellobiose dehydrogenase (CDH) is a flavocytochrome with a history of bioelectrochemical research dating back to 1992. During the years, it has been shown to be capable of mediated electron transfer (MET) and direct electron transfer (DET) to a variety of electrodes. This versatility of CDH originates from the separation of the catalytic flavodehydrogenase domain and the electron transferring cytochrome domain. This uncoupling of the catalytic reaction from the electron transfer process allows the application of CDH on many different electrode materials and surfaces, where it shows robust DET. Recent X-ray diffraction and small angle scattering studies provided insights into the structure of CDH and its domain mobility, which can change between a closed-state and an open-state conformation. This structural information verifies the electron transfer mechanism of CDH that was initially established by bioelectrochemical methods. A combination of DET and MET experiments has been used to investigate the catalytic mechanism and the electron transfer process of CDH and to deduce a protein structure comprising of mobile domains. Even more, electrochemical methods have been used to study the redox potentials of the FAD and the haem b cofactors of CDH or the electron transfer rates. These electrochemical experiments, their results and the application of the characterised CDHs in biosensors, biofuel cells and biosupercapacitors are combined with biochemical and structural data to provide a thorough overview on CDH as versatile bioelectrocatalyst.
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Affiliation(s)
- Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
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80
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Kundu S. Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases. J Mol Model 2019; 25:240. [PMID: 31338614 PMCID: PMC7385011 DOI: 10.1007/s00894-019-4133-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/11/2019] [Indexed: 02/03/2023]
Abstract
Biofuels such as γ-valerolactone, bioethanol, and biodiesel are derived from potentially fermentable cellulose and vegetable oils. Plant class C GH9 endoglucanases are CBM49-encompassing hydrolases that cleave the β (1 → 4) glycosidic linkage of contiguous D-glucopyranose residues of crystalline cellulose. Here, I analyse 3D-homology models of characterised and putative class C enzymes to glean insights into the contribution of the GH9, linker, and CBM49 to the mechanism(s) of crystalline cellulose digestion. Crystalline cellulose may be accommodated in a surface groove which is imperfectly bounded by the GH9_CBM49, GH9_linker, and linker_CBM49 surfaces and thence digested in a solvent accessible subsurface cavity. The physical dimensions and distortions thereof, of the groove, are mediated in part by the bulky side chains of aromatic amino acids that comprise it and may also result in a strained geometry of the bound cellulose polymer. These data along with an almost complete absence of measurable cavities, along with poorly conserved, hydrophobic, and heterogeneous amino acid composition, increased atomic motion of the CBM49_linker junction, and docking experiements with ligands of lower degrees of polymerization suggests a modulatory rather than direct role for CBM49 in catalysis. Crystalline cellulose is the de facto substrate for CBM-containing plant and non-plant GH9 enzymes, a finding supported by exceptional sequence- and structural-homology. However, despite the implied similarity in general acid-base catalysis of crystalline cellulose, this study also highlights qualitative differences in substrate binding and glycosidic bond cleavage amongst class C members. Results presented may aid the development of novel plant-based GH9 endoglucanases that could extract and utilise potential fermentable carbohydrates from biomass. Crystalline cellulose digestion by plant class C GH9 endoglucanases - an in silico assessment of function. ![]()
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Brar Square, Delhi Cantt., New Delhi, 110010, India.
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81
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Ma S, Laurent CVFP, Meneghello M, Tuoriniemi J, Oostenbrink C, Gorton L, Bartlett PN, Ludwig R. Direct Electron-Transfer Anisotropy of a Site-Specifically Immobilized Cellobiose Dehydrogenase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02014] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Marta Meneghello
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, U.K
| | - Jani Tuoriniemi
- Department of Analytical Chemistry/Biochemistry and Structural Biology, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | | | - Lo Gorton
- Department of Analytical Chemistry/Biochemistry and Structural Biology, Lund University, P.O. Box 124, Lund SE-221 00, Sweden
| | - Philip N. Bartlett
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, U.K
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82
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Wang B, Walton PH, Rovira C. Molecular Mechanisms of Oxygen Activation and Hydrogen Peroxide Formation in Lytic Polysaccharide Monooxygenases. ACS Catal 2019; 9:4958-4969. [PMID: 32051771 PMCID: PMC7007194 DOI: 10.1021/acscatal.9b00778] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/17/2019] [Indexed: 12/26/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes for the degradation of recalcitrant polysaccharides such as chitin and cellulose. Unlike classical hydrolytic enzymes (cellulases), LPMOs catalyze the cleavage of the glycosidic bond via an oxidative mechanism using oxygen and a reductant. The full enzymatic molecular mechanisms, starting from the initial electron transfer from a reductant to oxygen activation and hydrogen peroxide formation, are not yet understood. Using quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, we have uncovered the oxygen activation mechanisms by LPMO in the presence of ascorbic acid, one of the most-used reductants in LPMOs assays. Our simulations capture the sequential formation of Cu(II)-O2 - and Cu(II)-OOH- intermediates via facile H atom abstraction from ascorbate. By investigating all the possible reaction pathways from the Cu(II)-OOH- intermediate, we ruled out Cu(II)-O• - formation via direct O-O cleavage of Cu(II)-OOH-. Meanwhile, we identified a possible pathway in which the proximal O atom of Cu(II)-OOH- abstracts a hydrogen atom from ascorbate, leading to Cu(I) and H2O2. The in-situ-generated H2O2 either converts to LPMO-Cu(II)-O• - via a homolytic reaction, or diffuses into the bulk water in an uncoupled pathway. The competition of these two pathways is strongly dependent on the binding of the carbohydrate substrate, which plays a role in barricading the in-situ-generated H2O2 molecule, preventing its diffusion from the active site into the bulk water. Based on the present results, we propose a catalytic cycle of LPMOs that is consistent with the experimental information available. In particular, it explains the enigmatic substrate dependence of the reactivity of the LPMO with H2O2.
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Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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83
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Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. Comput Biol Chem 2019; 82:65-73. [PMID: 31272063 DOI: 10.1016/j.compbiolchem.2019.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/18/2019] [Accepted: 05/28/2019] [Indexed: 02/03/2023]
Abstract
Filamentous fungi secrete various oxidative enzymes to degrade the glycosidic bonds of polysaccharides. Cellobiose dehydrogenase (CDH) (E.C.1.1.99.18) is one of the important lignocellulose degrading enzymes produced by various filamentous fungi. It contains two stereo specific ligand binding domains, cytochrome and dehydrogenase - one for heme and the other for flavin adenine dinucleotide (FAD) respectively. The enzyme is of commercial importance for its use in amperometric biosensor, biofuel production, lactose determination in food, bioremediation etc. Termitomyces clypeatus, an edible fungus belonging to the basidiomycetes group, is a good producer of CDH. In this paper we have analyzed the structural properties of this enzyme from T. clypeatus and identified a distinct carbohydrate binding module (CBM) which is not present in most fungi belonging to the basidiomycetes group. In addition, the dehydrogenase domain of T. clypeatus CDH exhibited the absence of cellulose binding residues which is in contrast to the dehydrogenase domains of CDH of other basidiomycetes. Sequence analysis of cytochrome domain showed that the important residues of this domain were conserved like in other fungal CDHs. Phylogenetic tree, constructed using basidiomycetes and ascomycetes CDH sequences, has shown that very surprisingly the CDH from T. clypeatus, which is classified as a basidiomycetes fungus, is clustered with the ascomycetes group. A homology model of this protein has been constructed using the CDH enzyme of ascomycetes fungus Myricoccum thermophilum as a template since it has been found to be the best match sequence with T. clypeatus CDH. We also have modelled the protein with its substrate, cellobiose, which has helped us to identify the substrate interacting residues (L354, P606, T629, R631, Y649, N732, H733 and N781) localized within its dehydrogenase domain. Our computational investigation revealed for the first time the presence of all three domains - cytochrome, dehydrogenase and CBM - in the CDH of T. clypeatus, a basidiomycetes fungus. In addition to discovering the unique structural attributes of this enzyme from T. clypeatus, our study also discusses the possible phylogenetic status of this fungus.
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84
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Zhang W, Corwin JA, Copeland DH, Feusier J, Eshbaugh R, Cook DE, Atwell S, Kliebenstein DJ. Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. eLife 2019; 8:e44279. [PMID: 31081752 PMCID: PMC6557632 DOI: 10.7554/elife.44279] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/08/2019] [Indexed: 12/27/2022] Open
Abstract
A central goal of studying host-pathogen interaction is to understand how host and pathogen manipulate each other to promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection and provide a systematic map of the cross-kingdom communication between two species. Here we used the Arabidopsis-B. cinerea pathosystem to test how plant host and fungal pathogen interact at the transcriptomic level. We assessed the impact of genetic diversity in pathogen and host by utilization of a collection of 96 isolates infection on Arabidopsis wild-type and two mutants with jasmonate or salicylic acid compromised immunities. We identified ten B. cinereagene co-expression networks (GCNs) that encode known or novel virulence mechanisms. Construction of a dual interaction network by combining four host- and ten pathogen-GCNs revealed potential connections between the fungal and plant GCNs. These co-transcriptome data shed lights on the potential mechanisms underlying host-pathogen interaction.
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Affiliation(s)
- Wei Zhang
- Department of Plant PathologyKansas State UniversityManhattanUnited States
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Jason A Corwin
- Department of Ecology and Evolution BiologyUniversity of ColoradoBoulderUnited States
| | | | - Julie Feusier
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Robert Eshbaugh
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - David E Cook
- Department of Plant PathologyKansas State UniversityManhattanUnited States
| | - Suzi Atwell
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Daniel J Kliebenstein
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
- DynaMo Center of ExcellenceUniversity of CopenhagenFrederiksbergDenmark
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85
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Sützl L, Foley G, Gillam EMJ, Bodén M, Haltrich D. The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:118. [PMID: 31168323 PMCID: PMC6509819 DOI: 10.1186/s13068-019-1457-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/02/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The glucose-methanol-choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alcohol oxidase, cellobiose dehydrogenase, glucose oxidase, glucose dehydrogenase, pyranose dehydrogenase, and pyranose oxidase, which together form family AA3 of the auxiliary activities in the CAZy database of carbohydrate-active enzymes. Overall, little is known about the extant sequence space of these GMC oxidoreductases and their phylogenetic relations. Although some individual forms are well characterised, it is still unclear how they compare in respect of the complete enzyme class and, therefore, also how generalizable are their characteristics. RESULTS To improve the understanding of the GMC superfamily as a whole, we used sequence similarity networks to cluster large numbers of fungal GMC sequences and annotate them according to functionality. Subsequently, different members of the GMC superfamily were analysed in detail with regard to their sequences and phylogeny. This allowed us to define the currently characterised sequence space and show that complete clades of some enzymes have not been studied in any detail to date. Finally, we interpret our results from an evolutionary perspective, where we could show, for example, that pyranose dehydrogenase evolved from aryl-alcohol oxidoreductase after a change in substrate specificity and that the cytochrome domain of cellobiose dehydrogenase was regularly lost during evolution. CONCLUSIONS This study offers new insights into the sequence variation and phylogenetic relationships of fungal GMC/AA3 sequences. Certain clades of these GMC enzymes identified in our phylogenetic analyses are completely uncharacterised to date, and might include enzyme activities of varying specificities and/or activities that are hitherto unstudied.
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Affiliation(s)
- Leander Sützl
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Vienna, Austria
- Doctoral Programme BioToP-Biomolecular Technology of Proteins, BOKU-University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gabriel Foley
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Vienna, Austria
- Doctoral Programme BioToP-Biomolecular Technology of Proteins, BOKU-University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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86
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Hangasky JA, Detomasi TC, Marletta MA. Glycosidic Bond Hydroxylation by Polysaccharide Monooxygenases. TRENDS IN CHEMISTRY 2019. [DOI: 10.1016/j.trechm.2019.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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87
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Chylenski P, Bissaro B, Sørlie M, Røhr ÅK, Várnai A, Horn SJ, Eijsink VG. Lytic Polysaccharide Monooxygenases in Enzymatic Processing of Lignocellulosic Biomass. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00246] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr Chylenski
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Svein J. Horn
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
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88
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Laurent CFP, Breslmayr E, Tunega D, Ludwig R, Oostenbrink C. Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase. Biochemistry 2019; 58:1226-1235. [PMID: 30715860 PMCID: PMC6404106 DOI: 10.1021/acs.biochem.8b01178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/24/2019] [Indexed: 01/10/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are ubiquitous oxidoreductases, facilitating the degradation of polymeric carbohydrates in biomass. Cellobiose dehydrogenase (CDH) is a biologically relevant electron donor in this process, with the electrons resulting from cellobiose oxidation being shuttled from the CDH dehydrogenase domain to its cytochrome domain and then to the LPMO catalytic site. In this work, we investigate the interaction of four Neurospora crassa LPMOs and five CDH cytochrome domains from different species using computational methods. We used HADDOCK to perform protein-protein docking experiments on all 20 combinations and subsequently to select four complexes for extensive molecular dynamics simulations. The potential of mean force is computed for a rotation of the cytochrome domain relative to LPMO. We find that the LPMO loops are largely responsible for the preferred orientations of the cytochrome domains. This leads us to postulate a hybrid version of NcLPMO9F, with exchanged loops and predicted altered cytochrome binding preferences for this variant. Our work provides insight into the possible mechanisms of electron transfer between the two protein systems, in agreement with and complementary to previously published experimental data.
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Affiliation(s)
- Christophe
V. F. P. Laurent
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Erik Breslmayr
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Daniel Tunega
- Institute
of Soil Research, BOKU-University of Natural
Resources and Life Sciences, 1190 Vienna, Austria
| | - Roland Ludwig
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
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89
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Chen J, Guo X, Zhu M, Chen C, Li D. Polysaccharide monooxygenase-catalyzed oxidation of cellulose to glucuronic acid-containing cello-oligosaccharides. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:42. [PMID: 30858879 PMCID: PMC6391835 DOI: 10.1186/s13068-019-1384-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polysaccharide monooxygenases (PMOs) play an important role in the enzymatic degradation of cellulose. They have been demonstrated to able to C6-oxidize cellulose to produce C6-hexodialdoses. However, the biological function of C6 oxidation of PMOs remains unknown. In particular, it is unclear whether C6-hexodialdoses can be further oxidized to uronic acid (glucuronic acid-containing oligosaccharides). RESULTS A PMO gene, Hipmo1, was isolated from Humicola insolens and expressed in Pichia pastoris. This PMO (HiPMO1), belonging to the auxiliary activity 9 (AA9) family, was shown to able to cleave cellulose to yield non-oxidized and oxidized cello-oligosaccharides. The enzyme oxidizes C6 positions in cellulose to form glucuronic acid-containing cello-oligosaccharides, followed by hydrolysis with beta-glucosidase and beta-glucuronidase to yield glucose, glucuronic acid, and saccharic acid. This indicates that HiPMO1 can catalyze C6 oxidation of hydroxyl groups of cellulose to carboxylic groups. CONCLUSIONS HiPMO1 oxidizes C6 of cellulose to form glucuronic acid-containing cello-oligosaccharides followed by hydrolysis with beta-glucosidase and beta-glucuronidase to yield glucose, glucuronic acid, and saccharic acid, and even possibly by beta-eliminative cleavage to produce unsaturated cello-oligosaccharides. This study provides a new mechanism for cellulose cleavage by C6 oxidation of HiPMO1.
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Affiliation(s)
- Jinyin Chen
- Department of Mycology, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Xiuna Guo
- Department of Mycology, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Min Zhu
- Department of Mycology, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Chen Chen
- Department of Mycology, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Duochuan Li
- Department of Mycology, Shandong Agricultural University, Taian, 271018 Shandong China
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90
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Ma S, Ludwig R. Direct Electron Transfer of Enzymes Facilitated by Cytochromes. ChemElectroChem 2019; 6:958-975. [PMID: 31008015 PMCID: PMC6472588 DOI: 10.1002/celc.201801256] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/12/2018] [Indexed: 01/03/2023]
Abstract
The direct electron transfer (DET) of enzymes has been utilized to develop biosensors and enzymatic biofuel cells on micro- and nanostructured electrodes. Whereas some enzymes exhibit direct electron transfer between their active-site cofactor and an electrode, other oxidoreductases depend on acquired cytochrome domains or cytochrome subunits as built-in redox mediators. The physiological function of these cytochromes is to transfer electrons between the active-site cofactor and a redox partner protein. The exchange of the natural electron acceptor/donor by an electrode has been demonstrated for several cytochrome carrying oxidoreductases. These multi-cofactor enzymes have been applied in third generation biosensors to detect glucose, lactate, and other analytes. This review investigates and classifies oxidoreductases with a cytochrome domain, enzyme complexes with a cytochrome subunit, and covers designed cytochrome fusion enzymes. The structurally and electrochemically best characterized proponents from each enzyme class carrying a cytochrome, that is, flavoenzymes, quinoenzymes, molybdenum-cofactor enzymes, iron-sulfur cluster enzymes, and multi-haem enzymes, are featured, and their biochemical, kinetic, and electrochemical properties are compared. The cytochromes molecular and functional properties as well as their contribution to the interdomain electron transfer (IET, between active-site and cytochrome) and DET (between cytochrome and electrode) with regard to the achieved current density is discussed. Protein design strategies for cytochrome-fused enzymes are reviewed and the limiting factors as well as strategies to overcome them are outlined.
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Affiliation(s)
- Su Ma
- Biocatalysis and Biosensing Laboratory Department of Food Science and TechnologyBOKU – University of Natural Resources and Life SciencesMuthgasse 181190ViennaAustria
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory Department of Food Science and TechnologyBOKU – University of Natural Resources and Life SciencesMuthgasse 181190ViennaAustria
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91
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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92
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Grippo V, Ma S, Ludwig R, Gorton L, Bilewicz R. Cellobiose dehydrogenase hosted in lipidic cubic phase to improve catalytic activity and stability. Bioelectrochemistry 2019; 125:134-141. [DOI: 10.1016/j.bioelechem.2017.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/15/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022]
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93
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Meneghello M, Al-Lolage FA, Ma S, Ludwig R, Bartlett PN. Studying direct electron transfer by site-directed immobilization of cellobiose dehydrogenase. ChemElectroChem 2019; 6:700-713. [PMID: 31700765 PMCID: PMC6837870 DOI: 10.1002/celc.201801503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/10/2022]
Abstract
Covalent coupling between a surface exposed cysteine residue and maleimide groups was used to immobilize variants of Myriococcum thermophilum cellobiose dehydrogenase (MtCDH) at multiwall carbon nanotube electrodes. By introducing individual cysteine residues at particular places on the surface of the flavodehydrogenase domain of the flavocytochrome we are able to immobilize the different variants in different orientations. Our results show that direct electron transfer (DET) occurs exclusively through the haem b cofactor and that the redox potential of the haem is unaffected by the orientation of the enzyme. Electron transfer between the haem and the electrode is fast in all cases and at high glucose concentrations the catalytic currents are limited by the rate of inter-domain electron transfer (IET) between the FAD and the haem. Using ferrocene carboxylic acid as a mediator we find that the total amount of immobilized enzyme is 4 to 5 times greater than the amount of enzyme that participates in DET. The role of IET in the overall DET catalysed oxidation was also demonstrated by the effects of changing Ca2+ concentration and by proteolytic cleavage of the cytochrome domain on the DET and MET currents.
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Affiliation(s)
- Marta Meneghello
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Firas A. Al-Lolage
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
- Department of Chemistry, College of Science, University of Mosul, Mosul, Iraq
| | - Su Ma
- Department of Food Science and Technology, BOKU − University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Roland Ludwig
- Department of Food Science and Technology, BOKU − University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Philip N. Bartlett
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
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94
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Eijsink VGH, Petrovic D, Forsberg Z, Mekasha S, Røhr ÅK, Várnai A, Bissaro B, Vaaje-Kolstad G. On the functional characterization of lytic polysaccharide monooxygenases (LPMOs). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:58. [PMID: 30923566 PMCID: PMC6423801 DOI: 10.1186/s13068-019-1392-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are abundant in nature and best known for their role in the enzymatic conversion of recalcitrant polysaccharides such as chitin and cellulose. LPMO activity requires an oxygen co-substrate, which was originally thought to be O2, but which may also be H2O2. Functional characterization of LPMOs is not straightforward because typical reaction mixtures will promote side reactions, including auto-catalytic inactivation of the enzyme. For example, despite some recent progress, there is still limited insight into the kinetics of the LPMO reaction. Recent discoveries concerning the role of H2O2 in LPMO catalysis further complicate the picture. Here, we review commonly used methods for characterizing LPMOs, with focus on benefits and potential pitfalls, rather than on technical details. We conclude by pointing at a few key problems and potential misconceptions that should be taken into account when interpreting existing data and planning future experiments.
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Affiliation(s)
- Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Dejan Petrovic
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Sophanit Mekasha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
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Courtade G, Aachmann FL. Chitin-Active Lytic Polysaccharide Monooxygenases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:115-129. [PMID: 31102244 DOI: 10.1007/978-981-13-7318-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the cleavage of 1,4-glycosidic bonds various plant cell wall polysaccharides and chitin. In contrast to glycoside hydrolases, LPMOs are active on the crystalline regions of polysaccharides and thus synergize with hydrolytic enzymes. This synergism leads to an overall increase in the biomass-degradation activity of enzyme mixtures. Chitin-active LPMOs were discovered in 2010 and are currently classified in families AA10, AA11, and AA15 of the Carbohydrate-Active enZYmes database, which include LPMOs from bacteria, fungi, insects, and viruses. LPMOs have become important enzymes both industrially and scientifically and, in this chapter, we provide a brief introduction to chitin-active LPMOs including a summary of the 20+ chitin-active LPMOs that have been characterized so far. Then, we describe their structural features, catalytic mechanism, and appended carbohydrate modules. Finally, we show how chitin-active LPMOs can be used to perform chemo-enzymatic modification of chitin substrates.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
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96
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Fowler CA, Sabbadin F, Ciano L, Hemsworth GR, Elias L, Bruce N, McQueen-Mason S, Davies GJ, Walton PH. Discovery, activity and characterisation of an AA10 lytic polysaccharide oxygenase from the shipworm symbiont Teredinibacter turnerae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:232. [PMID: 31583018 PMCID: PMC6767633 DOI: 10.1186/s13068-019-1573-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/21/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND The quest for novel enzymes for cellulosic biomass-degradation has recently been focussed on lytic polysaccharide monooxygenases (LPMOs/PMOs), Cu-containing proteins that catalyse the oxidative degradation of otherwise recalcitrant polysaccharides using O2 or H2O2 as a co-substrate. RESULTS Although classical saprotrophic fungi and bacteria have been a rich source of lytic polysaccharide monooxygenases (LPMOs), we were interested to see if LPMOs from less evident bio-environments could be discovered and assessed for their cellulolytic activity in a biofuel context. In this regard, the marine shipworm Lyrodus pedicellatus represents an interesting source of new enzymes, since it must digest wood particles ingested during its natural tunnel boring behaviour and plays host to a symbiotic bacterium, Teredinibacter turnerae, the genome of which has revealed a multitude of enzymes dedicated to biomass deconstruction. Here, we show that T. turnerae encodes a cellulose-active AA10 LPMO. The 3D structure, at 1.4 Å resolution, along with its EPR spectrum is distinct from other AA10 polysaccharide monooxygenases insofar as it displays a "histidine-brace" catalytic apparatus with changes to the surrounding coordination sphere of the copper. Furthermore, TtAA10A possesses a second, surface accessible, Cu site 14 Å from the classical catalytic centre. Activity measurements show that the LPMO oxidises cellulose and thereby significantly augments the rate of degradation of cellulosic biomass by classical glycoside hydrolases. CONCLUSION Shipworms are wood-boring marine molluscs that can live on a diet of lignocellulose. Bacterial symbionts of shipworms provide many of the enzymes needed for wood digestion. The shipworm symbiont T. turnerae produces one of the few LPMOs yet described from the marine environment, notably adding to the capability of shipworms to digest recalcitrant polysaccharides.
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Affiliation(s)
| | - Federico Sabbadin
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Luisa Ciano
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: School of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Glyn R. Hemsworth
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Luisa Elias
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Neil Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Simon McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | | | - Paul H. Walton
- Department of Chemistry, University of York, York, YO10 5DD UK
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Takeda K, Umezawa K, Várnai A, Eijsink VG, Igarashi K, Yoshida M, Nakamura N. Fungal PQQ-dependent dehydrogenases and their potential in biocatalysis. Curr Opin Chem Biol 2018; 49:113-121. [PMID: 30580186 DOI: 10.1016/j.cbpa.2018.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/16/2018] [Accepted: 12/04/2018] [Indexed: 10/27/2022]
Abstract
In 2014, the first fungal pyrroloquinoline-quinone (PQQ)-dependent enzyme was discovered as a pyranose dehydrogenase from the basidiomycete Coprinopsis cinerea (CcPDH). This discovery laid the foundation for a new Auxiliary Activities (AA) family, AA12, in the Carbohydrate-Active enZymes (CAZy) database and revealed a novel enzymatic activity potentially involved in biomass conversion. This review summarizes recent progress made in research on this fungal oxidoreductase and related enzymes. CcPDH consists of the catalytic PQQ-binding AA12 domain, an N-terminal cytochrome b AA8 domain, and a C-terminal family 1 carbohydrate-binding module (CBM1). CcPDH oxidizes 2-keto-d-glucose (d-glucosone), l-fucose, and rare sugars such as d-arabinose and l-galactose, and can activate lytic polysaccharide monooxygenases (LPMOs). Bioinformatic studies suggest a widespread occurrence of quinoproteins in eukaryotes as well as prokaryotes.
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Affiliation(s)
- Kouta Takeda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kiwamu Umezawa
- Department of Applied Biological Chemistry, Kindai University, Nara 631-8505, Japan
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Vincent Gh Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Yoshida
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
| | - Nobuhumi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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98
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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100
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Ito K, Okuda-Shimazaki J, Mori K, Kojima K, Tsugawa W, Ikebukuro K, Lin CE, La Belle J, Yoshida H, Sode K. Designer fungus FAD glucose dehydrogenase capable of direct electron transfer. Biosens Bioelectron 2018; 123:114-123. [PMID: 30057265 DOI: 10.1016/j.bios.2018.07.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 01/16/2023]
Abstract
Fungi-derived flavin adenine dinucleotide glucose dehydrogenases (FADGDHs) are currently the most popular and advanced enzymes for self-monitoring of blood glucose sensors; however, the achievement of direct electron transfer (DET) with FADGDHs is difficult. In this study, a designer FADGDH was constructed by fusing Aspergillus flavus derived FADGDH (AfGDH) and a Phanerochaete chrisosporium CDH (PcCDH)-derived heme b-binding cytochrome domain to develop a novel FADGDH that is capable of direct electron transfer with an electrode. A structural prediction suggested that the heme in the CDH may exist in proximity to the FAD of AfGDH if the heme b-binding cytochrome domain is fused to the AfGDH N-terminal region. Spectroscopic observations of recombinantly produced designer FADGDH confirmed the intramolecular electron transfer between FAD and the heme. A decrease in pH and the presence of a divalent cation improved the intramolecular electron transfer. An enzyme electrode with the immobilized designer FADGDH showed an increase in current immediately after the addition of glucose in a glucose concentration-dependent manner, whereas those with wild-type AfGDH did not show an increase in current. Therefore, the designer FADGDH was confirmed to be a novel GDH that possesses electrode DET ability. The difference in the surface electrostatic potentials of AfGDH and the catalytic domain of PcCDH might be why their intramolecular electron transfer ability is inferior to that of CDH. These relevant and consistent findings provide us with a novel strategic approach for the improvement of the DET properties of designer FADGDH. (241 words).
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Affiliation(s)
- Kohei Ito
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | - Kazushige Mori
- Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan
| | - Katsuhiro Kojima
- Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Chi-En Lin
- School of Biological and Health System Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, P.O. Box 879709, Tempe, AZ 85287-9719, USA
| | - Jeffrey La Belle
- School of Biological and Health System Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, P.O. Box 879709, Tempe, AZ 85287-9719, USA
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan; Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA.
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