1
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Hall K, Mollatt M, Forsberg Z, Golten O, Schwaiger L, Ludwig R, Ayuso-Fernández I, Eijsink VGH, Sørlie M. Impact of the Copper Second Coordination Sphere on Catalytic Performance and Substrate Specificity of a Bacterial Lytic Polysaccharide Monooxygenase. ACS OMEGA 2024; 9:23040-23052. [PMID: 38826537 PMCID: PMC11137697 DOI: 10.1021/acsomega.4c02666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides, such as cellulose and chitin, using a single copper cofactor bound in a conserved histidine brace with a more variable second coordination sphere. Cellulose-active LPMOs in the fungal AA9 family and in a subset of bacterial AA10 enzymes contain a His-Gln-Tyr second sphere motif, whereas other cellulose-active AA10s have an Arg-Glu-Phe motif. To shine a light on the impact of this variation, we generated single, double, and triple mutations changing the His216-Gln219-Tyr221 motif in cellulose- and chitin-oxidizing MaAA10B toward Arg-Glu-Phe. These mutations generally reduced enzyme performance due to rapid inactivation under turnover conditions, showing that catalytic fine-tuning of the histidine brace is complex and that the roles of these second sphere residues are strongly interconnected. Studies of copper reactivity showed remarkable effects, such as an increase in oxidase activity following the Q219E mutation and a strong dependence of this effect on the presence of Tyr at position 221. In reductant-driven reactions, differences in oxidase activity, which lead to different levels of in situ generated H2O2, correlated with differences in polysaccharide-degrading ability. The single Q219E mutant displayed a marked increase in activity on chitin in both reductant-driven reactions and reactions fueled by exogenously added H2O2. Thus, it seems that the evolution of substrate specificity in LPMOs involves both the extended substrate-binding surface and the second coordination sphere.
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Affiliation(s)
- Kelsi
R. Hall
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
- School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Maja Mollatt
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Zarah Forsberg
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Ole Golten
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Lorenz Schwaiger
- Department
of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, BOKU 1190 Vienna, Austria
| | - Roland Ludwig
- Department
of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, BOKU 1190 Vienna, Austria
| | - Iván Ayuso-Fernández
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Morten Sørlie
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
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2
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Ma L, Wang M, Gao Y, Wu Y, Zhu C, An S, Tang S, She Q, Gao J, Meng X. Functional study of a lytic polysaccharide monooxygenase MsLPMO3 from Morchella sextelata in the oxidative degradation of cellulose. Enzyme Microb Technol 2024; 173:110376. [PMID: 38096655 DOI: 10.1016/j.enzmictec.2023.110376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/09/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can improve the effectiveness with which agricultural waste is utilized. This study described the potent AA9 family protein MsLPMO3, derived from Morchella sextelata. It exhibited strong binding to phosphoric acid swollen cellulose (PASC), and had the considerable binding ability to Cu2+ with a Kd value of 2.70 μM by isothermal titration calorimetry (ITC). MsLPMO3 could also act on PASC at the C1 carbon via MALDI-TOF-MS results. Moreover, MsLPMO3 could boost the hydrolysis efficiency of corncob and wheat bran in combination with glycoside hydrolases. MsLPMO3 also exhibited strong oxidizing ability for 2,6-dimethoxyphenol (2,6-DMP), achieving the best Vmax value of 443.36 U·g-1 for pH 7.4 with a H2O2 concentration of 300 µM. The structure of MsLPMO3 was obtained using AlphaFold2, and the molecular docking results elucidated the specific interactions and key residues involved in the recognition process between MsLPMO3 and cellulose. Altogether, this study expands the knowledge of AA9 family proteins in cellulose degradation, providing valuable insights into the mechanisms of synergistic degradation of lignocellulose with cellulases.
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Affiliation(s)
- Lei Ma
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Mengmeng Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, People's Republic of China
| | - Ya Gao
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Yinghong Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Chaoqiang Zhu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Shuyu An
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Siyu Tang
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, Hunan, People's Republic of China
| | - Qiusheng She
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Jianmin Gao
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467000, Henan, People's Republic of China
| | - Xiaohui Meng
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, People's Republic of China.
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3
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Kumar A, Singh A, Sharma VK, Goel A, Kumar A. The upsurge of lytic polysaccharide monooxygenases in biomass deconstruction: characteristic functions and sustainable applications. FEBS J 2024. [PMID: 38291603 DOI: 10.1111/febs.17063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are one of the emerging classes of copper metalloenzymes that have received considerable attention due to their ability to boost the enzymatic conversion of intractable polysaccharides such as plant cell walls and chitin polymers. LPMOs catalyze the oxidative cleavage of β-1,4-glycosidic bonds using molecular O2 or H2 O2 in the presence of an external electron donor. LPMOs have been classified as an auxiliary active (AA) class of enzymes and, further based on substrate specificity, divided into eight families. Until now, multiple LPMOs from AA9 and AA10 families, mostly from microbial sources, have been investigated; the exact mechanism and structure-function are elusive to date, and recently discovered AA families of LPMOs are just scratched. This review highlights the origin and discovery of the enzyme, nomenclature, three-dimensional protein structure, substrate specificity, copper-dependent reaction mechanism, and different techniques used to determine the product formation through analytical and biochemical methods. Moreover, the diverse functions of proteins in various biological activities such as plant-pathogen/pest interactions, cell wall remodeling, antibiotic sensitivity of biofilms, and production of nanocellulose along with certain obstacles in deconstructing the complex polysaccharides have also been summarized, while highlighting the innovative and creative ways to overcome the limitations of LPMOs in hydrolyzing the biomass.
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Affiliation(s)
- Asheesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Aishwarya Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vijay Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Akshita Goel
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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4
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Kipping L, Jehmlich N, Moll J, Noll M, Gossner MM, Van Den Bossche T, Edelmann P, Borken W, Hofrichter M, Kellner H. Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species. THE ISME JOURNAL 2024; 18:wrae050. [PMID: 38519103 PMCID: PMC11022342 DOI: 10.1093/ismejo/wrae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.
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Affiliation(s)
- Lydia Kipping
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ GmbH, 06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, 8092 Zürich, Switzerland
| | - Tim Van Den Bossche
- VIB—UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Pascal Edelmann
- Department of Ecology and Ecosystem Management, Center of School of Life and Food Sciences Weihenstephan, TU München, 85354 Freising, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
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5
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Gao W, Li T, Zhou H, Ju J, Yin H. Carbohydrate-binding modules enhance H 2O 2 tolerance by promoting lytic polysaccharide monooxygenase active site H 2O 2 consumption. J Biol Chem 2024; 300:105573. [PMID: 38122901 PMCID: PMC10825053 DOI: 10.1016/j.jbc.2023.105573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) oxidatively depolymerize recalcitrant polysaccharides, which is important for biomass conversion. The catalytic domains of many LPMOs are linked to carbohydrate-binding modules (CBMs) through flexible linkers, but the function of these CBMs in LPMO catalysis is not well understood. In this study, we utilized MtLPMO9L and MtLPMO9G derived from Myceliophthora thermophila to investigate the impact of CBMs on LPMO activity, with particular emphasis on their influence on H2O2 tolerance. Using truncated forms of MtLPMO9G generated by removing the CBM, we found reduced substrate binding affinity and enzymatic activity. Conversely, when the CBM was fused to the C terminus of the single-domain MtLPMO9L to create MtLPMO9L-CBM, we observed a substantial improvement in substrate binding affinity, enzymatic activity, and notably, H2O2 tolerance. Furthermore, molecular dynamics simulations confirmed that the CBM fusion enhances the proximity of the active site to the substrate, thereby promoting multilocal cleavage and impacting the exposure of the copper active site to H2O2. Importantly, the fusion of CBM resulted in more efficient consumption of H2O2 by LPMO, leading to improved enzymatic activity and reduced auto-oxidative damage of the copper active center.
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Affiliation(s)
- Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tang Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jiu Ju
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese Academy of Sciences, Beijing, China.
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6
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Adnan M, Ma X, Xie Y, Waheed A, Liu G. Heterologously Expressed Cellobiose Dehydrogenase Acts as Efficient Electron-Donor of Lytic Polysaccharide Monooxygenase for Cellulose Degradation in Trichoderma reesei. Int J Mol Sci 2023; 24:17202. [PMID: 38139031 PMCID: PMC10743782 DOI: 10.3390/ijms242417202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The conversion of lignocellulosic biomass to second-generation biofuels through enzymes is achieved at a high cost. Filamentous fungi through a combination of oxidative enzymes can easily disintegrate the glycosidic bonds of cellulose. The combination of cellobiose dehydrogenase (CDH) with lytic polysaccharide monooxygenases (LPMOs) enhances cellulose degradation in many folds. CDH increases cellulose deconstruction via coupling the oxidation of cellobiose to the reductive activation of LPMOs by catalyzing the addition of oxygen to C-H bonds of the glycosidic linkages. Fungal LPMOs show different regio-selectivity (C1 or C4) and result in oxidized products through modifications at reducing as well as nonreducing ends of the respective glucan chain. T. reesei LPMOs have shown great potential for oxidative cleavage of cellobiose at C1 and C4 glucan bonds, therefore, the incorporation of heterologous CDH further increases its potential for biofuel production for industrial purposes at a reduced cost. We introduced CDH of Phanerochaete chrysosporium (PcCDH) in Trichoderma reesei (which originally lacked CDH). We purified CDH through affinity chromatography and analyzed its enzymatic activity, electron-donating ability to LPMO, and the synergistic effect of LPMO and CDH on cellulose deconstruction. The optimum temperature of the recombinant PcCDH was found to be 45 °C and the optimum pH of PcCDH was observed as 4.5. PcCDH has high cello-oligosaccharide kcat, Km, and kcat/Km values. The synergistic effect of LPMO and cellulase significantly improved the degradation efficiency of phosphoric acid swollen cellulose (PASC) when CDH was used as the electron donor. We also found that LPMO undergoes auto-oxidative inactivation, and when PcCDH is used an electron donor has the function of a C1-type LPMO electron donor without additional substrate increments. This work provides novel insights into finding stable electron donors for LPMOs and paves the way forward in discovering efficient CDHs for enhanced cellulose degradation.
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Affiliation(s)
| | | | | | | | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (M.A.); (X.M.); (Y.X.)
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7
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Ma L, Li G, Liu Y, Li Z, Miao Y, Wan Q, Liu D, Zhang R. Investigating the effect of substrate binding on the catalytic activity of xylanase. Appl Microbiol Biotechnol 2023; 107:6873-6886. [PMID: 37715802 DOI: 10.1007/s00253-023-12774-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/28/2023] [Accepted: 09/03/2023] [Indexed: 09/18/2023]
Abstract
XynAF1 from Aspergillus fumigatus Z5 is an efficient thermophilic xylanase belonging to glycoside hydrolase family 10 (GH10). The non-catalytic amino acids N179 and R246 in its catalytic center formed one and three intermolecular H-bonds with the substrate in the aglycone region, respectively. Here we purified XynAF1-N179S and XynAF1-R246K, and obtained the protein-product complex structures by X-ray diffraction. The snapshots indicated that mutations at N179 and R246 had decreased the substrate-binding ability in the aglycone region. XynAF1-N179S, XynAF1-R246K, and XynAF1-N179S-R246K lost one, three, and four H-bonds with the substrate in comparison with the wild-type XynAF1, respectively, but this had little influence on the protein structure. As expected, N179S, R246K, and N179S-R246K led to a gradual decrease of substrate affinity of XynAF1. Interestingly, the enzyme assay showed that N179S increased catalytic efficiency, while both R246K and N179S-R246K had decreased catalytic efficiency. KEY POINTS: • The non-catalytic amino acids of XynAF1 could form H-bonds with the substrate. • The protein-product complex structures were obtained by X-ray diffraction. • The enzyme-substrate-binding capacity could affect enzyme catalytic efficiency.
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Affiliation(s)
- Lei Ma
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467000, Henan, People's Republic of China
| | - Guangqi Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhihong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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8
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Østby H, Christensen IA, Hennum K, Várnai A, Buchinger E, Grandal S, Courtade G, Hegnar OA, Aachmann FL, Eijsink VGH. Functional characterization of a lytic polysaccharide monooxygenase from Schizophyllum commune that degrades non-crystalline substrates. Sci Rep 2023; 13:17373. [PMID: 37833388 PMCID: PMC10575960 DOI: 10.1038/s41598-023-44278-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that use O2 or H2O2 to oxidatively cleave glycosidic bonds. LPMOs are prevalent in nature, and the functional variation among these enzymes is a topic of great interest. We present the functional characterization of one of the 22 putative AA9-type LPMOs from the fungus Schizophyllum commune, ScLPMO9A. The enzyme, expressed in Escherichia coli, showed C4-oxidative cleavage of amorphous cellulose and soluble cello-oligosaccharides. Activity on xyloglucan, mixed-linkage β-glucan, and glucomannan was also observed, and product profiles differed compared to the well-studied C4-oxidizing NcLPMO9C from Neurospora crassa. While NcLPMO9C is also active on more crystalline forms of cellulose, ScLPMO9A is not. Differences between the two enzymes were also revealed by nuclear magnetic resonance (NMR) titration studies showing that, in contrast to NcLPMO9C, ScLPMO9A has higher affinity for linear substrates compared to branched substrates. Studies of H2O2-fueled degradation of amorphous cellulose showed that ScLPMO9A catalyzes a fast and specific peroxygenase reaction that is at least two orders of magnitude faster than the apparent monooxygenase reaction. Together, these results show that ScLPMO9A is an efficient LPMO with a broad substrate range, which, rather than acting on cellulose, has evolved to act on amorphous and soluble glucans.
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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, Ås, Norway
| | - Idd A Christensen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands Vei 6/8, 7491, Trondheim, Norway
| | - Karen Hennum
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Edith Buchinger
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands Vei 6/8, 7491, Trondheim, Norway
| | - Siri Grandal
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands Vei 6/8, 7491, Trondheim, Norway
| | - Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands Vei 6/8, 7491, Trondheim, Norway
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands Vei 6/8, 7491, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Ås, Norway.
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9
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Grace Barrios-Gutiérrez S, Inés Vélez-Mercado M, Rodrigues Ortega J, da Silva Lima A, Luiza da Rocha Fortes Saraiva A, Leila Berto G, Segato F. Oxidative Machinery of basidiomycetes as potential enhancers in lignocellulosic biorefineries: A lytic polysaccharide monooxygenases approach. BIORESOURCE TECHNOLOGY 2023; 386:129481. [PMID: 37437815 DOI: 10.1016/j.biortech.2023.129481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Basidiomycetes are renowned as highly effective decomposers of plant materials, due to their extensive array of oxidative enzymes, which enable them to efficiently break down complex lignocellulosic biomass structures. Among the oxidative machinery of industrially relevant basidiomycetes, the role of lytic polysaccharide monooxygenases (LPMO) in lignocellulosic biomass deconstruction is highlighted. So far, only a limited number of basidiomycetes LPMOs have been identified and heterologously expressed. These LPMOs have presented activity on cellulose and hemicellulose, as well as participation in the deconstruction of lignin. Expanding on this, the current review proposes both enzymatic and non-enzymatic mechanisms of LPMOs for biomass conversion, considering the significance of the Carbohydrate-Binding Modules and other C-terminal regions domains associated with their structure, which is involved in the deconstruction of lignocellulosic biomass.
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Affiliation(s)
- Solange Grace Barrios-Gutiérrez
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Martha Inés Vélez-Mercado
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Júlia Rodrigues Ortega
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Awana da Silva Lima
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Ana Luiza da Rocha Fortes Saraiva
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Gabriela Leila Berto
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil
| | - Fernando Segato
- Synthetic and Molecular Biology Laboratory (SyMB), Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, São Paulo, Brazil.
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10
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Samaniego LVB, Higasi PMR, de Mello Capetti CC, Cortez AA, Pratavieira S, de Oliveira Arnoldi Pellegrini V, Dabul ANG, Segato F, Polikarpov I. Staphylococcus aureus microbial biofilms degradation using cellobiose dehydrogenase from Thermothelomyces thermophilus M77. Int J Biol Macromol 2023; 247:125822. [PMID: 37451383 DOI: 10.1016/j.ijbiomac.2023.125822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
This work reports biochemical characterization of Thermothelomyces thermophilus cellobiose dehydrogenase (TthCDHIIa) and its application as an antimicrobial and antibiofilm agent. We demonstrate that TthCDHIIa is thermostable in different ionic solutions and is capable of oxidizing multiple mono and oligosaccharide substrates and to continuously produce H2O2. Kinetics measurements depict the enzyme catalytic characteristics consistent with an Ascomycota class II CDH. Our structural analyses show that TthCDHIIa substrate binding pocket is spacious enough to accommodate larger cello and xylooligosaccharides. We also reveal that TthCDHIIa supplemented with cellobiose reduces the viability of S. aureus ATCC 25923 up to 32 % in a planktonic growth model and also inhibits its biofilm growth on 62.5 %. Furthermore, TthCDHIIa eradicates preformed S. aureus biofilms via H2O2 oxidative degradation of the biofilm matrix, making these bacteria considerably more susceptible to gentamicin and tetracycline.
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Affiliation(s)
| | - Paula Miwa Rabelo Higasi
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Caio Cesar de Mello Capetti
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Anelyse Abreu Cortez
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Sebastião Pratavieira
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | | | - Andrei Nicoli Gebieluca Dabul
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil
| | - Fernando Segato
- Lorena School of Engineering, University of Sao Paulo, Estrada Municipal do Campinho, 12602-810 Lorena, SP, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, 1100 João Dagnone Avenue, 13563-120 São Carlos, SP, Brazil.
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11
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Hall K, Joseph C, Ayuso-Fernández I, Tamhankar A, Rieder L, Skaali R, Golten O, Neese F, Røhr ÅK, Jannuzzi SAV, DeBeer S, Eijsink VGH, Sørlie M. A Conserved Second Sphere Residue Tunes Copper Site Reactivity in Lytic Polysaccharide Monooxygenases. J Am Chem Soc 2023; 145:18888-18903. [PMID: 37584157 PMCID: PMC10472438 DOI: 10.1021/jacs.3c05342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 08/17/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful monocopper enzymes that can activate strong C-H bonds through a mechanism that remains largely unknown. Herein, we investigated the role of a conserved glutamine/glutamate in the second coordination sphere. Mutation of the Gln in NcAA9C to Glu, Asp, or Asn showed that the nature and distance of the headgroup to the copper fine-tune LPMO functionality and copper reactivity. The presence of Glu or Asp close to the copper lowered the reduction potential and decreased the ratio between the reduction and reoxidation rates by up to 500-fold. All mutants showed increased enzyme inactivation, likely due to changes in the confinement of radical intermediates, and displayed changes in a protective hole-hopping pathway. Electron paramagnetic resonance (EPR) and X-ray absorption spectroscopic (XAS) studies gave virtually identical results for all NcAA9C variants, showing that the mutations do not directly perturb the Cu(II) ligand field. DFT calculations indicated that the higher experimental reoxidation rate observed for the Glu mutant could be reconciled if this residue is protonated. Further, for the glutamic acid form, we identified a Cu(III)-hydroxide species formed in a single step on the H2O2 splitting path. This is in contrast to the Cu(II)-hydroxide and hydroxyl intermediates, which are predicted for the WT and the unprotonated glutamate variant. These results show that this second sphere residue is a crucial determinant of the catalytic functioning of the copper-binding histidine brace and provide insights that may help in understanding LPMOs and LPMO-inspired synthetic catalysts.
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Affiliation(s)
- Kelsi
R. Hall
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Chris Joseph
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Iván Ayuso-Fernández
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ashish Tamhankar
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Rieder
- Institute
for Molecular Biotechnology, Graz University
of Technology, 8010, Graz, Austria
| | - Rannei Skaali
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ole Golten
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Åsmund K. Røhr
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Sergio A. V. Jannuzzi
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
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12
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Yu X, Zhao Y, Yu J, Wang L. Recent advances in the efficient degradation of lignocellulosic metabolic networks by lytic polysaccharide monooxygenase. Acta Biochim Biophys Sin (Shanghai) 2023; 55:529-539. [PMID: 37036250 DOI: 10.3724/abbs.2023059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Along with long-term evolution, the plant cell wall generates lignocellulose and other anti-degradation barriers to confront hydrolysis by fungi. Lytic polysaccharide monooxygenase (LPMO) is a newly defined oxidase in lignocellulosic degradation systems that significantly fuels hydrolysis. LPMO accepts electrons from wide sources, such as cellobiose dehydrogenase (CDH), glucose-methanol-choline (GMC) oxidoreductases, and small phenols. In addition, the extracellular cometabolic network formed by cosubstrates improves the degradation efficiency, forming a stable and efficient lignocellulose degradation system. In recent years, using structural proteomics to explore the internal structure and the complex redox system of LPMOs has become a research hotspot. In this review, the diversity of LPMOs, catalytic domains, carbohydrate binding modules, direct electron transfer with CDH, cosubstrates, and degradation networks of LPMOs are explored, which can provide a systematic reference for the application of lignocellulosic degradation systems in industrial approaches.
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Affiliation(s)
- Xinran Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266035, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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13
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Martinez-D’Alto A, Yan X, Detomasi TC, Sayler RI, Thomas WC, Talbot NJ, Marletta MA. Characterization of a unique polysaccharide monooxygenase from the plant pathogen Magnaporthe oryzae. Proc Natl Acad Sci U S A 2023; 120:e2215426120. [PMID: 36791100 PMCID: PMC9974505 DOI: 10.1073/pnas.2215426120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023] Open
Abstract
Blast disease in cereal plants is caused by the fungus Magnaporthe oryzae and accounts for a significant loss in food crops. At the outset of infection, expression of a putative polysaccharide monooxygenase (MoPMO9A) is increased. MoPMO9A contains a catalytic domain predicted to act on cellulose and a carbohydrate-binding domain that binds chitin. A sequence similarity network of the MoPMO9A family AA9 showed that 220 of the 223 sequences in the MoPMO9A-containing cluster of sequences have a conserved unannotated region with no assigned function. Expression and purification of the full length and two MoPMO9A truncations, one containing the catalytic domain and the domain of unknown function (DUF) and one with only the catalytic domain, were carried out. In contrast to other AA9 polysaccharide monooxygenases (PMOs), MoPMO9A is not active on cellulose but showed activity on cereal-derived mixed (1→3, 1→4)-β-D-glucans (MBG). Moreover, the DUF is required for activity. MoPMO9A exhibits activity consistent with C4 oxidation of the polysaccharide and can utilize either oxygen or hydrogen peroxide as a cosubstrate. It contains a predicted 3-dimensional fold characteristic of other PMOs. The DUF is predicted to form a coiled-coil with six absolutely conserved cysteines acting as a zipper between the two α-helices. MoPMO9A substrate specificity and domain architecture are different from previously characterized AA9 PMOs. The results, including a gene ontology analysis, support a role for MoPMO9A in MBG degradation during plant infection. Consistent with this analysis, deletion of MoPMO9A results in reduced pathogenicity.
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Affiliation(s)
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NorwichNR4 7UH, UK
| | - Tyler C. Detomasi
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Richard I. Sayler
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - William C. Thomas
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NorwichNR4 7UH, UK
| | - Michael A. Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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14
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Revisiting the role of electron donors in lytic polysaccharide monooxygenase biochemistry. Essays Biochem 2023; 67:585-595. [PMID: 36748351 PMCID: PMC10154616 DOI: 10.1042/ebc20220164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The plant cell wall is rich in carbohydrates and many fungi and bacteria have evolved to take advantage of this carbon source. These carbohydrates are largely locked away in polysaccharides and so these organisms deploy a range of enzymes that can liberate individual sugars from these challenging substrates. Glycoside hydrolases (GHs) are the enzymes that are largely responsible for bringing about this sugar release; however, 12 years ago, a family of enzymes known as lytic polysaccharide monooxygenases (LPMOs) were also shown to be of key importance in this process. LPMOs are copper-dependent oxidative enzymes that can introduce chain breaks within polysaccharide chains. Initial work demonstrated that they could activate O2 to attack the substrate through a reaction that most likely required multiple electrons to be delivered to the enzyme. More recently, it has emerged that LPMO kinetics are significantly improved if H2O2 is supplied to the enzyme as a cosubstrate instead of O2. Only a single electron is required to activate an LPMO and H2O2 cosubstrate and the enzyme has been shown to catalyse multiple turnovers following the initial one-electron reduction of the copper, which is not possible if O2 is used. This has led to further studies of the roles of the electron donor in LPMO biochemistry, and this review aims to highlight recent findings in this area and consider how ongoing research could impact our understanding of the interplay between redox processes in nature.
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15
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Hagemann MM, Hedegård ED. Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations. Chemistry 2023; 29:e202202379. [PMID: 36207279 PMCID: PMC10107554 DOI: 10.1002/chem.202202379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.
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Affiliation(s)
- Marlisa M Hagemann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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16
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Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chem Sci 2022; 13:13303-13320. [PMID: 36507176 PMCID: PMC9683017 DOI: 10.1039/d2sc05031e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Simon P. Webb
- VeraChem LLC12850 Middlebrook Rd. Ste 205GermantownMD 20874-5244USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterOK 74078USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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17
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Yu W, Yu J, Li D. Analysis of lytic polysaccharide monooxygenase activity in thermophilic fungi by high-performance liquid chromatography–refractive index detector. Front Microbiol 2022; 13:1063025. [DOI: 10.3389/fmicb.2022.1063025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
IntroductionMost current methods for analysing the activity of LPMO are based on the quantification of H2O2, a side product of LPMO; however, these methods cannot assay the LPMO activity of thermophilic fungi because of the low thermostability of H2O2. Therefore, we present a high-performance liquid chromatography–refractive index detector (HPLC-RID) method to assay the LPMO activity of the thermophilic fungus Thermoascus aurantiacus.ResultsAccording to the established method, the specific activities of nTaAA9A C1 and C4 oxidation were successfully analysed and were 0.646 and 0.574 U/mg, respectively. By using these methods, we analyzed the C1 and C4 oxidation activities of the recombinant TaAA9A (rTaAA9A) and mutated rTaAA9A (Y24A, F43A, and Y212A) expressed in Pichia pastoris. The specific activities of rTaAA9A C1 and C4 oxidation were 0.155 and 0.153 U/mg, respectively. The specific activities of Y24A, F43A, and Y212A C1 and C4 oxidation were 0.128 and 0.125 U/mg, 0.194 and 0.192 U/mg, and 0.097 and 0.146 U/mg, respectively.DiscussionIn conclusion, the method can assay the LPMO activity of thermophilic fungi and directly target C1 and C4 oxidation, which provides an effective activity assay method for LPMOs of thermophilic fungi.
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18
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Tandrup T, Muderspach SJ, Banerjee S, Santoni G, Ipsen JØ, Hernández-Rollán C, Nørholm MHH, Johansen KS, Meilleur F, Lo Leggio L. Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. IUCRJ 2022; 9:666-681. [PMID: 36071795 PMCID: PMC9438499 DOI: 10.1107/s2052252522007175] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes capable of degrading polysaccharide substrates oxidatively. The generally accepted first step in the LPMO reaction is the reduction of the active-site metal ion from Cu2+ to Cu+. Here we have used a systematic diffraction data collection method to monitor structural changes in two AA9 LPMOs, one from Lentinus similis (LsAA9_A) and one from Thermoascus auranti-acus (TaAA9_A), as the active-site Cu is photoreduced in the X-ray beam. For LsAA9_A, the protein produced in two different recombinant systems was crystallized to probe the effect of post-translational modifications and different crystallization conditions on the active site and metal photoreduction. We can recommend that crystallographic studies of AA9 LPMOs wishing to address the Cu2+ form use a total X-ray dose below 3 × 104 Gy, while the Cu+ form can be attained using 1 × 106 Gy. In all cases, we observe the transition from a hexa-coordinated Cu site with two solvent-facing ligands to a T-shaped geometry with no exogenous ligands, and a clear increase of the θ2 parameter and a decrease of the θ3 parameter by averages of 9.2° and 8.4°, respectively, but also a slight increase in θT. Thus, the θ2 and θ3 parameters are helpful diagnostics for the oxidation state of the metal in a His-brace protein. On binding of cello-oligosaccharides to LsAA9_A, regardless of the production source, the θT parameter increases, making the Cu site less planar, while the active-site Tyr-Cu distance decreases reproducibly for the Cu2+ form. Thus, the θT increase found on copper reduction may bring LsAA9_A closer to an oligosaccharide-bound state and contribute to the observed higher affinity of reduced LsAA9_A for cellulosic substrates.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sebastian J. Muderspach
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sanchari Banerjee
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Gianluca Santoni
- ESRF, Structural Biology Group, 71 avenue des Martyrs, 38027 Grenoble cedex, France
| | - Johan Ø. Ipsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Katja S. Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
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19
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Long L, Hu Y, Sun F, Gao W, Hao Z, Yin H. Advances in lytic polysaccharide monooxygenases with the cellulose-degrading auxiliary activity family 9 to facilitate cellulose degradation for biorefinery. Int J Biol Macromol 2022; 219:68-83. [PMID: 35931294 DOI: 10.1016/j.ijbiomac.2022.07.240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/18/2022]
Abstract
One crucial step in processing the recalcitrant lignocellulosic biomass is the fast hydrolysis of natural cellulose to fermentable sugars that can be subsequently converted to biofuels and bio-based chemicals. Recent studies have shown that lytic polysaccharide monooxygenase (LPMOs) with auxiliary activity family 9 (AA9) are capable of efficiently depolymerizing the crystalline cellulose via regioselective oxidation reaction. Intriguingly, the catalysis by AA9 LPMOs requires reductant to provide electrons, and lignin and its phenolic derivatives can be oxidized, releasing reductant to activate the reaction. The activity of AA9 LPMOs can be enhanced by in-situ generation of H2O2 in the presence of O2. Although scientific understanding of these enzymes remains somewhat unknown or controversial, structure modifications on AA9 LPMOs through protein engineering have emerged in recent years, which are prerequisite for their extensive applications in the development of cellulase-mediated lignocellulosic biorefinery processes. In this review, we critically comment on advances in studies for AA9 LPMOs, i.e., characteristic of AA9 LPMOs catalysis, external electron donors to AA9 LPMOs, especially the role of the oxidization of lignin and its derivatives, and AA9 LPMOs protein engineering as well as their extensive applications in the bioprocessing of lignocellulosic biomass. Perspectives are also highlighted for addressing the challenges.
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Affiliation(s)
- Lingfeng Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
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20
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Dade CM, Douzi B, Cambillau C, Ball G, Voulhoux R, Forest KT. The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases. Acta Crystallogr D Struct Biol 2022; 78:1064-1078. [PMID: 35916229 PMCID: PMC9344471 DOI: 10.1107/s2059798322007033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas aeruginosa secretes diverse proteins via its type 2 secretion system, including a 39 kDa chitin-binding protein, CbpD. CbpD has recently been shown to be a lytic polysaccharide monooxygenase active on chitin and to contribute substantially to virulence. To date, no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the CBM73 domain of Cellvibrio japonicus CjLPMO10A. Here, the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement is reported, which required ab initio models of each CbpD domain generated by the artificial intelligence deep-learning structure-prediction algorithm RoseTTAFold. The structure of CbpD confirms some previously reported substrate-specificity motifs among LPMOAA10s, while challenging the predictive power of others. Additionally, the structure of CbpD shows that post-translational modifications occur on the chitin-binding surface. Moreover, the structure raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure-prediction algorithms in making challenging structural targets tractable.
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Affiliation(s)
- Christopher M. Dade
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Badreddine Douzi
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
- Aix-Marseille University, CNRS, AFMB, Marseille, France
| | | | - Genevieve Ball
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Romé Voulhoux
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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21
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Selective xyloglucan oligosaccharide hydrolysis by a GH31 α-xylosidase from Escherichia coli. Carbohydr Polym 2022; 284:119150. [DOI: 10.1016/j.carbpol.2022.119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022]
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22
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Wang Y, Li L, Xia Y, Zhang T. Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data. FRONTIERS IN BIOINFORMATICS 2022; 2:813771. [PMID: 36304268 PMCID: PMC9580877 DOI: 10.3389/fbinf.2022.813771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
In the era of high-throughput sequencing, genetic information that is inherently whispering hints of the microbes’ functional niches is becoming easily accessible; however, properly identifying and characterizing these genetic hints to infer the microbes’ functional niches remains a challenge. Regarding genome-centric interpretation on the specific functional niche of cellulose hydrolysis for anaerobes, often encountered in practice is a lack of confidence in predicting the anaerobes’ real cellulolytic competency based solely on abundances of the varying carbohydrate-active enzyme modules annotated or on their taxonomy affiliation. Recognition of the synergy machineries that include but not limited to the cellulosome gene clusters is equally important as the annotation of individual carbohydrate-active modules or genes. In the interpretation of complete genomes of 2,768 microbe strains whose phenotypes have been well documented, with the incorporation of an automatic recognition of synergy among the carbohydrate active elements annotated, an explicit genotype–phenotype correlation was evidenced to be feasible for cellulolytic anaerobes, and a bioinformatic pipeline was developed accordingly. This genome-centric pipeline would categorize putative cellulolytic anaerobes into six genotype groups based on differential cellulose-hydrolyzing capacity and varying synergy mechanisms. Suggested in this genotype–phenotype correlation analysis was a finer categorization of the cellulosome gene clusters: although cellulosome complexes, by their nature, could enable the assembly of a number of carbohydrate-active units, they do not certainly guarantee the formation of the cellulose–enzyme–microbe complex or the cellulose-hydrolyzing activity of the corresponding anaerobe strains, for example, the well-known Clostridium acetobutylicum strains. Also, recognized in this genotype-phenotype correlation analysis was the genetic foundation of a previously unrecognized machinery that may mediate the microbe–cellulose adhesion, to be specific, enzymes encoded by genes harboring both the surface layer homology and cellulose-binding CBM modules. Applicability of this pipeline on scalable annotation of large genome datasets was further tested with the annotation of 7,902 reference genomes downloaded from NCBI, from which 14 genomes of putative paradigm cellulose-hydrolyzing anaerobes were identified. We believe the pipeline developed in this study would be a good add as a bioinformatic tool for genome-centric interpretation of uncultivated anaerobes, specifically on their functional niche of cellulose hydrolysis.
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Affiliation(s)
- Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Yu Xia
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- *Correspondence: Tong Zhang,
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23
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Vandhana TM, Reyre JL, Sushmaa D, Berrin JG, Bissaro B, Madhuprakash J. On the expansion of biological functions of lytic polysaccharide monooxygenases. THE NEW PHYTOLOGIST 2022; 233:2380-2396. [PMID: 34918344 DOI: 10.1111/nph.17921] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 05/21/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) constitute an enigmatic class of enzymes, the discovery of which has opened up a new arena of riveting research. LPMOs can oxidatively cleave the glycosidic bonds found in carbohydrate polymers enabling the depolymerisation of recalcitrant biomasses, such as cellulose or chitin. While most studies have so far mainly explored the role of LPMOs in a (plant) biomass conversion context, alternative roles and paradigms begin to emerge. In the present review, we propose a historical perspective of LPMO research providing a succinct overview of the major achievements of LPMO research over the past decade. This journey through LPMOs landscape leads us to dive into the emerging biological functions of LPMOs and LPMO-like proteins. We notably highlight roles in fungal and oomycete plant pathogenesis (e.g. potato late blight), but also in mutualistic/commensalism symbiosis (e.g. ectomycorrhizae). We further present the potential importance of LPMOs in other microbial pathogenesis including diseases caused by bacteria (e.g. pneumonia), fungi (e.g. human meningitis), oomycetes and viruses (e.g. entomopox), as well as in (micro)organism development (including several plant pests). Our assessment of the literature leads to the formulation of outstanding questions, promising for the coming years exciting research and discoveries on these moonlighting proteins.
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Affiliation(s)
- Theruvothu Madathil Vandhana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Lou Reyre
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Dangudubiyyam Sushmaa
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Guy Berrin
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Bastien Bissaro
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
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24
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Wang Z, Fang W, Peng W, Wu P, Wang B. Recent Computational Insights into the Oxygen Activation by Copper-Dependent Metalloenzymes. Top Catal 2022. [DOI: 10.1007/s11244-021-01444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Guo X, An Y, Jiang L, Zhang J, Lu F, Liu F. The discovery and enzymatic characterization of a novel AA10 LPMO from Bacillus amyloliquefaciens with dual substrate specificity. Int J Biol Macromol 2022; 203:457-465. [PMID: 35065137 DOI: 10.1016/j.ijbiomac.2022.01.110] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/24/2021] [Accepted: 01/17/2022] [Indexed: 01/06/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes, which can catalyze the oxidative cleavage of polysaccharide β-1,4 glycosidic bonds to improve the hydrolysis efficiency of the substrate by other glycoside hydrolases. To improve the conversion efficiency of cellulose and chitin, a strain was screened from the soil of Yuelu Mountain in Hunan province, China. The gene sequence of a novel AA10 LPMO (BaLPMO10) was successfully cloned from the genome of the strain and heterologously expressed in E. coli BL21 (DE3). The optimal enzyme activity of BaLPMO10 was observed at pH 6.0 and 70 °C using 2,6-dimethoxyphenol as substrate, and its maximum specific activity was 91.4 U/g. When BaLPMO10 synergized with glycoside hydrolase to degrade microcrystalline cellulose and colloidal chitin, the reducing sugar content increased by 7% and 23%, respectively, compared to glycoside hydrolase alone. Moreover, the results of molecular docking and molecular dynamics simulation showed that the distance between BaLPMO10 and cellohexaose were further than that of BaLPMO10 and chitohexaose, and the number of hydrogen bonds between BaLPMO10 and cellohexaose were lower than that of BaLPMO10 and chitohexaose. Finally, the hot spot residues of BaLPMO10 interacting with chitohexaose/cellohexaose were identified.
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Affiliation(s)
- Xiao Guo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Jiayu Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China.
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China.
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26
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Quantifying Oxidation of Cellulose-Associated Glucuronoxylan by Two Lytic Polysaccharide Monooxygenases from Neurospora crassa. Appl Environ Microbiol 2021; 87:e0165221. [PMID: 34613755 PMCID: PMC8612270 DOI: 10.1128/aem.01652-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Family AA9 lytic polysaccharide monooxygenases (LPMOs) are abundant in fungi, where they catalyze oxidative depolymerization of recalcitrant plant biomass. These AA9 LPMOs cleave cellulose and some also act on hemicelluloses, primarily other (substituted) β-(1→4)-glucans. Oxidative cleavage of xylan has been shown for only a few AA9 LPMOs, and it remains unclear whether this activity is a minor side reaction or primary function. Here, we show that Neurospora crassa LPMO9F (NcLPMO9F) and the phylogenetically related, hitherto uncharacterized NcLPMO9L from N. crassa are active on both cellulose and cellulose-associated glucuronoxylan but not on glucuronoxylan alone. A newly developed method for simultaneous quantification of xylan-derived and cellulose-derived oxidized products showed that NcLPMO9F preferentially cleaves xylan when acting on a cellulose–beechwood glucuronoxylan mixture, yielding about three times more xylan-derived than cellulose-derived oxidized products. Interestingly, under similar conditions, NcLPMO9L and the previously characterized McLPMO9H, from Malbranchea cinnamomea, showed different xylan-to-cellulose preferences, giving oxidized product ratios of about 0.5:1 and 1:1, respectively, indicative of functional variation among xylan-active LPMOs. Phylogenetic and structural analysis of xylan-active AA9 LPMOs led to the identification of characteristic structural features, including unique features that do not occur in phylogenetically remote AA9 LPMOs, such as four AA9 LPMOs whose lack of activity toward glucuronoxylan was demonstrated in the present study. Taken together, the results provide a path toward discovery of additional xylan-active LPMOs and show that the huge family of AA9 LPMOs has members that preferentially act on xylan. These findings shed new light on the biological role and industrial potential of these fascinating enzymes. IMPORTANCE Plant cell wall polysaccharides are highly resilient to depolymerization by hydrolytic enzymes, partly due to cellulose chains being tightly packed in microfibrils that are covered by hemicelluloses. Lytic polysaccharide monooxygenases (LPMOs) seem well suited to attack these resilient copolymeric structures, but the occurrence and importance of hemicellulolytic activity among LPMOs remain unclear. Here, we show that certain AA9 LPMOs preferentially cleave xylan when acting on a cellulose–glucuronoxylan mixture, and that this ability is the result of protein evolution that has resulted in a clade of AA9 LPMOs with specific structural features. Our findings strengthen the notion that the vast arsenal of AA9 LPMOs in certain fungal species provides functional versatility and that AA9 LPMOs may have evolved to promote oxidative depolymerization of a wide variety of recalcitrant, copolymeric plant polysaccharide structures. These findings have implications for understanding the biological roles and industrial potential of LPMOs.
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Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass. J Fungi (Basel) 2021; 7:jof7100835. [PMID: 34682256 PMCID: PMC8541250 DOI: 10.3390/jof7100835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 10/03/2021] [Indexed: 01/03/2023] Open
Abstract
Cerrena unicolor is an ecologically and biotechnologically important wood-degrading basidiomycete with high lignocellulose degrading ability. Biological and genetic investigations are limited in the Cerrena genus and, thus, hinder genetic modification and commercial use. The aim of the present study was to provide a global understanding through genomic and experimental research about lignocellulosic biomass utilization by Cerrena unicolor. In this study, we reported the genome sequence of C. unicolor SP02 by using the Illumina and PacBio 20 platforms to obtain trustworthy assembly and annotation. This is the combinational 2nd and 3rd genome sequencing and assembly of C. unicolor species. The generated genome was 42.79 Mb in size with an N50 contig size of 2.48 Mb, a G + C content of 47.43%, and encoding of 12,277 predicted genes. The genes encoding various lignocellulolytic enzymes including laccase, lignin peroxidase, manganese peroxidase, cytochromes P450, cellulase, xylanase, α-amylase, and pectinase involved in the degradation of lignin, cellulose, xylan, starch, pectin, and chitin that showed the C. unicolor SP02 potentially have a wide range of applications in lignocellulosic biomass conversion. Genome-scale metabolic analysis opened up a valuable resource for a better understanding of carbohydrate-active enzymes (CAZymes) and oxidoreductases that provide insights into the genetic basis and molecular mechanisms for lignocellulosic degradation. The C. unicolor SP02 model can be used for the development of efficient microbial cell factories in lignocellulosic industries. The understanding of the genetic material of C. unicolor SP02 coding for the lignocellulolytic enzymes will significantly benefit us in genetic manipulation, site-directed mutagenesis, and industrial biotechnology.
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28
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C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases. Biochem J 2021; 478:2927-2944. [PMID: 34240737 PMCID: PMC8981238 DOI: 10.1042/bcj20210376] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
The release of glucose from lignocellulosic waste for subsequent fermentation into biofuels holds promise for securing humankind's future energy needs. The discovery of a set of copper-dependent enzymes known as lytic polysaccharide monooxygenases (LPMOs) has galvanised new research in this area. LPMOs act by oxidatively introducing chain breaks into cellulose and other polysaccharides, boosting the ability of cellulases to act on the substrate. Although several proteins have been implicated as electron sources in fungal LPMO biochemistry, no equivalent bacterial LPMO electron donors have been previously identified, although the proteins Cbp2D and E from Cellvibrio japonicus have been implicated as potential candidates. Here we analyse a small c-type cytochrome (CjX183) present in Cellvibrio japonicus Cbp2D, and show that it can initiate bacterial CuII/I LPMO reduction and also activate LPMO-catalyzed cellulose-degradation. In the absence of cellulose, CjX183-driven reduction of the LPMO results in less H2O2 production from O2, and correspondingly less oxidative damage to the enzyme than when ascorbate is used as the reducing agent. Significantly, using CjX183 as the activator maintained similar cellulase boosting levels relative to the use of an equivalent amount of ascorbate. Our results therefore add further evidence to the impact that the choice of electron source can have on LPMO action. Furthermore, the study of Cbp2D and other similar proteins may yet reveal new insight into the redox processes governing polysaccharide degradation in bacteria.
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29
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Manavalan T, Stepnov AA, Hegnar OA, Eijsink VGH. Sugar oxidoreductases and LPMOs - two sides of the same polysaccharide degradation story? Carbohydr Res 2021; 505:108350. [PMID: 34049079 DOI: 10.1016/j.carres.2021.108350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides such as chitin and cellulose and their discovery has revolutionized our understanding of enzymatic biomass conversion. The discovery of LPMOs raises interesting new questions regarding the roles of other oxidoreductases and abiotic redox processes in biomass conversion. LPMOs need reducing power and an oxygen co-substrate and biomass degrading ecosystems contain a multitude of redox enzymes that affect the availability of both. For example, biomass degrading fungi produce multiple sugar oxidoreductases whose biological functions so far have remained somewhat enigmatic. It is now conceivable that these redox enzymes, in particular H2O2-producing sugar oxidases, could play a role in fueling and controlling LPMO reactions. Here, we shortly review contemporary issues in the LPMO field, paying particular attention to the possible roles of sugar oxidoreductases.
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Affiliation(s)
- Tamilvendan Manavalan
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway.
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30
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Tõlgo M, Hüttner S, Rugbjerg P, Thuy NT, Thanh VN, Larsbrink J, Olsson L. Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:131. [PMID: 34082802 PMCID: PMC8176577 DOI: 10.1186/s13068-021-01975-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail. RESULTS We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy. CONCLUSIONS Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.
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Affiliation(s)
- Monika Tõlgo
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Silvia Hüttner
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Peter Rugbjerg
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Nguyen Thanh Thuy
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Vu Nguyen Thanh
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Johan Larsbrink
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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31
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Ma L, Liu Z, Kong Z, Wang M, Li T, Zhu H, Wan Q, Liu D, Shen Q. Functional characterization of a novel copper-dependent lytic polysaccharide monooxygenase TgAA11 from Trichoderma guizhouense NJAU 4742 in the oxidative degradation of chitin. Carbohydr Polym 2021; 258:117708. [DOI: 10.1016/j.carbpol.2021.117708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/14/2020] [Accepted: 01/22/2021] [Indexed: 01/05/2023]
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32
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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 2021. [DOI: 10.1002/ange.202011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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33
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Hedison TM, Breslmayr E, Shanmugam M, Karnpakdee K, Heyes DJ, Green AP, Ludwig R, Scrutton NS, Kracher D. Insights into the H 2 O 2 -driven catalytic mechanism of fungal lytic polysaccharide monooxygenases. FEBS J 2021; 288:4115-4128. [PMID: 33411405 PMCID: PMC8359147 DOI: 10.1111/febs.15704] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Fungal lytic polysaccharide monooxygenases (LPMOs) depolymerise crystalline cellulose and hemicellulose, supporting the utilisation of lignocellulosic biomass as a feedstock for biorefinery and biomanufacturing processes. Recent investigations have shown that H2O2 is the most efficient cosubstrate for LPMOs. Understanding the reaction mechanism of LPMOs with H2O2 is therefore of importance for their use in biotechnological settings. Here, we have employed a variety of spectroscopic and biochemical approaches to probe the reaction of the fungal LPMO9C from N. crassa using H2O2 as a cosubstrate and xyloglucan as a polysaccharide substrate. We show that a single ‘priming’ electron transfer reaction from the cellobiose dehydrogenase partner protein supports up to 20 H2O2‐driven catalytic cycles of a fungal LPMO. Using rapid mixing stopped‐flow spectroscopy, alongside electron paramagnetic resonance and UV‐Vis spectroscopy, we reveal how H2O2 and xyloglucan interact with the enzyme and investigate transient species that form uncoupled pathways of NcLPMO9C. Our study shows how the H2O2 cosubstrate supports fungal LPMO catalysis and leaves the enzyme in the reduced Cu+ state following a single enzyme turnover, thus preventing the need for external protons and electrons from reducing agents or cellobiose dehydrogenase and supporting the binding of H2O2 for further catalytic steps. We observe that the presence of the substrate xyloglucan stabilises the Cu+ state of LPMOs, which may prevent the formation of uncoupled side reactions.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Erik Breslmayr
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Photon Science Institute, The University of Manchester, UK
| | - Kwankao Karnpakdee
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Derren J Heyes
- Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, The University of Manchester, UK
| | - Daniel Kracher
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
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Felice AKG, Schuster C, Kadek A, Filandr F, Laurent CVFP, Scheiblbrandner S, Schwaiger L, Schachinger F, Kracher D, Sygmund C, Man P, Halada P, Oostenbrink C, Ludwig R. Chimeric Cellobiose Dehydrogenases Reveal the Function of Cytochrome Domain Mobility for the Electron Transfer to Lytic Polysaccharide Monooxygenase. ACS Catal 2021; 11:517-532. [PMID: 33489432 PMCID: PMC7818652 DOI: 10.1021/acscatal.0c05294] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/11/2020] [Indexed: 12/11/2022]
Abstract
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The natural function of cellobiose
dehydrogenase (CDH) to donate
electrons from its catalytic flavodehydrogenase (DH) domain via its
cytochrome (CYT) domain to lytic polysaccharide monooxygenase (LPMO)
is an example of a highly efficient extracellular electron transfer
chain. To investigate the function of the CYT domain movement in the
two occurring electron transfer steps, two CDHs from the ascomycete Neurospora crassa (NcCDHIIA and NcCDHIIB) and five chimeric CDH enzymes created by domain
swapping were studied in combination with the fungus’ own LPMOs
(NcLPMO9C and NcLPMO9F). Kinetic
and electrochemical methods and hydrogen/deuterium exchange mass spectrometry
were used to study the domain movement, interaction, and electron
transfer kinetics. Molecular docking provided insights into the protein–protein
interface, the orientation of domains, and binding energies. We find
that the first, interdomain electron transfer step from the catalytic
site in the DH domain to the CYT domain depends on steric and electrostatic
interface complementarity and the length of the protein linker between
both domains but not on the redox potential difference between the
FAD and heme b cofactors. After CYT reduction, a
conformational change of CDH from its closed state to an open state
allows the second, interprotein electron transfer (IPET) step from
CYT to LPMO to occur by direct interaction of the b-type heme and the type-2 copper center. Chimeric CDH enzymes favor
the open state and achieve higher IPET rates by exposing the heme b cofactor to LPMO. The IPET, which is influenced by interface
complementarity and the heme b redox potential, is
very efficient with bimolecular rates between 2.9 × 105 and 1.1 × 106 M–1 s–1.
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Affiliation(s)
- Alfons K. G. Felice
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Schuster
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alan Kadek
- BIOCEV−Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Frantisek Filandr
- BIOCEV−Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - 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
- Department of Material Sciences and Process Engineering, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Lorenz Schwaiger
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Franziska Schachinger
- 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
| | - Christoph Sygmund
- 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
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague, Czech Republic
| | - Petr Halada
- BIOCEV−Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, 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
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35
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Lytic polysaccharide monooxygenases and other histidine-brace copper proteins: structure, oxygen activation and biotechnological applications. Biochem Soc Trans 2021; 49:531-540. [PMID: 33449071 PMCID: PMC7924993 DOI: 10.1042/bst20201031] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mononuclear copper enzymes that catalyse the oxidative cleavage of glycosidic bonds. They are characterised by two histidine residues that coordinate copper in a configuration termed the Cu-histidine brace. Although first identified in bacteria and fungi, LPMOs have since been found in all biological kingdoms. LPMOs are now included in commercial enzyme cocktails used in industrial biorefineries. This has led to increased process yield due to the synergistic action of LPMOs with glycoside hydrolases. However, the introduction of LPMOs makes control of the enzymatic step in industrial stirred-tank reactors more challenging, and the operational stability of the enzymes is reduced. It is clear that much is still to be learned about the interaction between LPMOs and their complex natural and industrial environments, and fundamental scientific studies are required towards this end. Several atomic-resolution structures have been solved providing detailed information on the Cu-coordination sphere and the interaction with the polysaccharide substrate. However, the molecular mechanisms of LPMOs are still the subject of intense investigation; the key question being how the proteinaceous environment controls the copper cofactor towards the activation of the O-O bond in O2 and cleavage of the glycosidic bonds in polysaccharides. The need for biochemical characterisation of each putative LPMO is discussed based on recent reports showing that not all proteins with a Cu-histidine brace are enzymes.
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36
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Bernardi AV, Gerolamo LE, de Gouvêa PF, Yonamine DK, Pereira LMS, de Oliveira AHC, Uyemura SA, Dinamarco TM. LPMO AfAA9_B and Cellobiohydrolase AfCel6A from A. fumigatus Boost Enzymatic Saccharification Activity of Cellulase Cocktail. Int J Mol Sci 2020; 22:E276. [PMID: 33383972 PMCID: PMC7795096 DOI: 10.3390/ijms22010276] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulose is the most abundant polysaccharide in lignocellulosic biomass, where it is interlinked with lignin and hemicellulose. Bioethanol can be produced from biomass. Since breaking down biomass is difficult, cellulose-active enzymes secreted by filamentous fungi play an important role in degrading recalcitrant lignocellulosic biomass. We characterized a cellobiohydrolase (AfCel6A) and lytic polysaccharide monooxygenase LPMO (AfAA9_B) from Aspergillus fumigatus after they were expressed in Pichia pastoris and purified. The biochemical parameters suggested that the enzymes were stable; the optimal temperature was ~60 °C. Further characterization revealed high turnover numbers (kcat of 147.9 s-1 and 0.64 s-1, respectively). Surprisingly, when combined, AfCel6A and AfAA9_B did not act synergistically. AfCel6A and AfAA9_B association inhibited AfCel6A activity, an outcome that needs to be further investigated. However, AfCel6A or AfAA9_B addition boosted the enzymatic saccharification activity of a cellulase cocktail and the activity of cellulase Af-EGL7. Enzymatic cocktail supplementation with AfCel6A or AfAA9_B boosted the yield of fermentable sugars from complex substrates, especially sugarcane exploded bagasse, by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass.
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Affiliation(s)
- Aline Vianna Bernardi
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Luis Eduardo Gerolamo
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Paula Fagundes de Gouvêa
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Deborah Kimie Yonamine
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Lucas Matheus Soares Pereira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Arthur Henrique Cavalcante de Oliveira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Sérgio Akira Uyemura
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil;
| | - Taisa Magnani Dinamarco
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
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37
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Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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38
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Guo X, An Y, Chai C, Sang J, Jiang L, Lu F, Dai Y, Liu F. Construction of the R17L mutant of MtC1LPMO for improved lignocellulosic biomass conversion by rational point mutation and investigation of the mechanism by molecular dynamics simulations. BIORESOURCE TECHNOLOGY 2020; 317:124024. [PMID: 32836036 DOI: 10.1016/j.biortech.2020.124024] [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] [Received: 07/17/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
To enhance the biomass conversion efficiency, the R17L mutant of the lytic polysaccharide monooxygenase (LPMO) MtC1LPMO with improved catalytic efficiency was constructed via rational point mutation based on the HotSpot Wizard 3.0 and dezyme web servers. Compared with the wild-type (WT) MtC1LPMO, R17L exhibited a 1.8-fold increase of specific activity and 1.92-fold increase of catalytic efficiency (kcat/Km). The degree of increase of the reducing sugar yield from microcrystalline cellulose and three plant biomass materials during synergistic hydrolysis using cellulase in combination with R17L was about 2 times higher than with the WT. Molecular dynamics simulations revealed that the R17L mutation reduced the stability of the region R18-I36, which then weakened the direct interactions between region N24-V31 and the substrate cellohexaose. Consequently, the deflection time of the cellohexaose conformation in R17L was prolonged compared to the WT, which enhanced its catalytic efficiency.
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Affiliation(s)
- Xiao Guo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Chengcheng Chai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Jingcheng Sang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yujie Dai
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin 300457, PR China; Tianjin Key Laboratory of Industrial Microbiology, Tianjin 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China.
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39
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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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40
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Shi Y, Chen K, Long L, Ding S. A highly xyloglucan active lytic polysaccharide monooxygenase EpLPMO9A from Eupenicillium parvum 4-14 shows boosting effect on hydrolysis of complex lignocellulosic substrates. Int J Biol Macromol 2020; 167:202-213. [PMID: 33271180 DOI: 10.1016/j.ijbiomac.2020.11.177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The recently identified lytic polysaccharide monooxygenases (LPMOs) are important auxiliary proteins which contribute to lignocellulose biodegradation by oxidatively cleaving the glycosidic bonds in cellulose and other polysaccharides. The vast differences in terms of substrate specificity and regioselectivity within LPMOs provide us new possibilities to find promising candidates for the use in enzyme cocktails in biorefinery applications. In this study, a highly xyloglucan active family AA9 lytic polysaccharide monooxygenase EpLPMO9A was identified from Eupenicillium parvum 4-14. EpLPMO9A exhibited a mixed C1/C4 oxidative cleavage activity on cellulose and xyloglucan with a broad range of pH stability and good thermal stability at 40 °C. It showed a higher boosting effect on the enzymatic saccharification of complex lignocellulosic substrates associated with xyloglucan than on the lignocellulosic substrates without xyloglucan particularly in low commercial cellulase dosage cases. The oxidative cleavage of xyloglucan by EpLPMO9A may facilitate to open up the sterical hindrance of cellulose by xyloglucan and thereby increase accessibility for cellulase to lignocellulosic substrates. The discovery of more and more hemicellulose-active LPMOs and their contribution to breaking down the barriers by oxidatively acting on hemicellulose may expand our knowledge for their functions of LPMOs in lignocellulose biodegradation.
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Affiliation(s)
- Yuexin Shi
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Kaixiang Chen
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Liangkun Long
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Shaojun Ding
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
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41
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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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42
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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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43
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Forsberg Z, Stepnov AA, Nærdal GK, Klinkenberg G, Eijsink VGH. Engineering lytic polysaccharide monooxygenases (LPMOs). Methods Enzymol 2020; 644:1-34. [PMID: 32943141 DOI: 10.1016/bs.mie.2020.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze the hydroxylation of glycosidic bonds found in the most abundant and recalcitrant polysaccharides on Earth. Since their discovery in 2010, these enzymes have received extensive attention in both fundamental and applied research due to their remarkable oxidative power and synergistic interplay with hydrolytic enzymes. The harsh and unnatural conditions used in industrial enzymatic saccharification processes and the sensitivity of LPMOs for damage induced by reactive oxygen species call for enzyme engineering to develop LPMOs to become robust industrial biocatalysts. Other engineering targets include improved catalytic activity, adjusted substrate specificity and the introduction of completely new activities. Reaching these targets not only requires appropriate methods for measuring enzyme activity, but also requires in-depth knowledge of the active site and the reaction mechanism, which is yet to be achieved in the LPMO field. Here we describe what has been done in the LPMO engineering field so far. Furthermore, we address the difficulties involved in properly assessing LPMO functionality, which are due to common side reactions taking place in LPMO reactions and which complicate screening methods.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Guro Kruge Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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44
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Tandrup T, Tryfona T, Frandsen KEH, Johansen KS, Dupree P, Lo Leggio L. Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases. Biochemistry 2020; 59:3347-3358. [PMID: 32818374 DOI: 10.1021/acs.biochem.0c00312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that cleave polysaccharide substrates oxidatively. First discovered because of their action on recalcitrant crystalline substrates (chitin and cellulose), a number of LPMOs are now reported to act on soluble substrates, including oligosaccharides. However, crystallographic complexes with oligosaccharides have been reported for only a single LPMO so far, an enzyme from the basidiomycete fungus Lentinus similis (LsAA9_A). Here we present a more detailed comparative study of LsAA9_A and an LPMO from the ascomycete fungus Collariella virescens (CvAA9_A) with which it shares 41.5% sequence identity. LsAA9_A is considerably more thermostable than CvAA9_A, and the structural basis for the difference has been investigated. We have compared the patterns of oligosaccharide cleavage and the patterns of binding in several new crystal structures explaining the basis for the product preferences of the two enzymes. Obtaining structural information about complexes of LPMOs with carbohydrates has proven to be very difficult in general judging from the structures reported in the literature thus far, and this can be attributed only partly to the low affinity for small substrates. We have thus evaluated the use of differential scanning fluorimetry as a guide to obtaining complex structures. Furthermore, an analysis of crystal packing of LPMOs and glycoside hydrolases corroborates the hypothesis that active site occlusion is a very significant problem for LPMO-substrate interaction analysis by crystallography, due to their relatively flat and extended substrate binding sites.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK Copenhagen, Denmark
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K
| | - Kristian Erik Høpfner Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK Copenhagen, Denmark.,INRAE, Aix-Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), 13288 Marseille, France
| | - Katja Salomon Johansen
- Department for Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK Frederiksberg, Denmark
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK Copenhagen, Denmark
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45
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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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46
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Monclaro AV, Petrović DM, Alves GSC, Costa MMC, Midorikawa GEO, Miller RNG, Filho EXF, Eijsink VGH, Várnai A. Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity. PLoS One 2020; 15:e0235642. [PMID: 32640001 PMCID: PMC7343150 DOI: 10.1371/journal.pone.0235642] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Aspergillus tamarii grows abundantly in naturally composting waste fibers of the textile industry and has a great potential in biomass decomposition. Amongst the key (hemi)cellulose-active enzymes in the secretomes of biomass-degrading fungi are the lytic polysaccharide monooxygenases (LPMOs). By catalyzing oxidative cleavage of glycoside bonds, LPMOs promote the activity of other lignocellulose-degrading enzymes. Here, we analyzed the catalytic potential of two of the seven AA9-type LPMOs that were detected in recently published transcriptome data for A. tamarii, namely AtAA9A and AtAA9B. Analysis of products generated from cellulose revealed that AtAA9A is a C4-oxidizing enzyme, whereas AtAA9B yielded a mixture of C1- and C4-oxidized products. AtAA9A was also active on cellopentaose and cellohexaose. Both enzymes also cleaved the β-(1→4)-glucan backbone of tamarind xyloglucan, but with different cleavage patterns. AtAA9A cleaved the xyloglucan backbone only next to unsubstituted glucosyl units, whereas AtAA9B yielded product profiles indicating that it can cleave the xyloglucan backbone irrespective of substitutions. Building on these new results and on the expanding catalog of xyloglucan- and oligosaccharide-active AA9 LPMOs, we discuss possible structural properties that could underlie the observed functional differences. The results corroborate evidence that filamentous fungi have evolved AA9 LPMOs with distinct substrate specificities and regioselectivities, which likely have complementary functions during biomass degradation.
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Affiliation(s)
- Antonielle V. Monclaro
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Dejan M. Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriel S. C. Alves
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Marcos M. C. Costa
- Brazilian Agricultural Research Corporation, Embrapa CENARGEN, Brasília, Brazil
| | - Glaucia E. O. Midorikawa
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Robert N. G. Miller
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Edivaldo X. F. Filho
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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47
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Zhou H, Zhang Y, Li T, Tan H, Li G, Yin H. Distinct Interaction of Lytic Polysaccharide Monooxygenase with Cellulose Revealed by Computational and Biochemical Studies. J Phys Chem Lett 2020; 11:3987-3992. [PMID: 32352790 DOI: 10.1021/acs.jpclett.0c00918] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A distinct interaction pattern of lytic polysaccharide monooxygenases (LPMOs) with their insoluble substrate, cellulose, was revealed through the combination of computational and biochemical approaches. The results indicated that the enzymes can stably bind on the flat hydrophobic surface of cellulose via the interactions of the key residues located in the axis across the conserved distal tyrosine residue and copper ion with two adjacent cellulose chains. Further studies on the correlation of substrate binding and H2O2 accumulation suggested that LPMOs involved in the productive binding on the insoluble polysaccharides not only fail to accumulate H2O2 but also consume the H2O2 produced by the unbound molecules under the lab condition. This was further substantiated by quantum-mechanical calculations. These findings broadened our knowledge of the interaction between enzymes and insoluble substrates and deepened our understanding of the role that H2O2 plays in LPMO activity.
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Affiliation(s)
- Haichuan Zhou
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haidong Tan
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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48
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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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49
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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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50
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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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