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Forsberg Z, Tuveng TR, Eijsink VGH. A modular enzyme with combined hemicellulose-removing and LPMO activity increases cellulose accessibility in softwood. FEBS J 2024. [PMID: 39190632 DOI: 10.1111/febs.17250] [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: 04/12/2024] [Revised: 07/05/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
Because of the association with other complex polysaccharides, extracting and utilizing cellulose from lignocellulosic materials requires the combined action of a broad range of carbohydrate-active enzymes, including multiple glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The interplay between these enzymes and the way in which Nature orchestrates their co-existence and combined action are topics of great scientific and industrial interest. To gain more insight into these issues, we have studied the lignocellulose-degrading abilities of an enzyme from Caldibacillus cellulovorans (CcLPMO10-Man5), comprising an LPMO domain, a GH5 mannanase domain and two family 3 carbohydrate-binding modules (CBM3). Using a natural softwood substrate, we show that this enzyme promotes cellulase activity, i.e., saccharification of cellulose, both by removing mannan covering the cellulose and by oxidatively breaking up the cellulose structure. Synergy with CcLPMO10-Man5 was most pronounced for two tested cellobiohydrolases, whereas effects were smaller for a tested endoglucanase, which is in line with the notion that cellobiohydrolases and LPMOs attack the same crystalline regions of the cellulose, whereas endoglucanases attack semi-crystalline and amorphous regions. Importantly, the LPMO domain of CcLPMO10-Man5 is incapable of accessing the softwood cellulose in absence of the mannanase domain. Considering that LPMOs not bound to a substrate are sensitive to autocatalytic inactivation, this intramolecular synergy provides a perfect rationale for the evolution of modular enzymes such as CcLPMO10-Man5. The intramolecular coupling of the LPMO with a mannanase and two CBMs ensures that the LPMO is directed to areas where mannans are removed and cellulose thus becomes available.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Tina R Tuveng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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2
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Truong NH, Le TTH, Nguyen HD, Nguyen HT, Dao TK, Tran TMN, Tran HL, Nguyen DT, Nguyen TQ, Phan THT, Do TH, Phan NH, Ngo TCN, Vu VV. Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam. PeerJ 2024; 12:e17553. [PMID: 38938609 PMCID: PMC11210479 DOI: 10.7717/peerj.17553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
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Affiliation(s)
- Nam-Hai Truong
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Thu-Hong Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hong-Duong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Trong-Khoa Dao
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Minh-Nguyet Tran
- The Key Laboratory of Enzyme and Protein Technology (KLEPT), VNU University of Science, Hanoi, Vietnam
| | - Huyen-Linh Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Dinh-Trong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Quy Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Hong-Thao Phan
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Huyen Do
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Ngoc-Han Phan
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Thi-Cam-Nhung Ngo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Van-Van Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
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3
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Munzone A, Pujol M, Tamhankar A, Joseph C, Mazurenko I, Réglier M, Jannuzzi SAV, Royant A, Sicoli G, DeBeer S, Orio M, Simaan AJ, Decroos C. Integrated Experimental and Theoretical Investigation of Copper Active Site Properties of a Lytic Polysaccharide Monooxygenase from Serratia marcescens. Inorg Chem 2024; 63:11063-11078. [PMID: 38814816 DOI: 10.1021/acs.inorgchem.4c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens (SmAA10). The structure of the holo-enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca. 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of SmAA10 but also establishes a robust framework for future studies of similar enzymatic systems.
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Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Manon Pujol
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Ashish Tamhankar
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Chris Joseph
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Sergio A V Jannuzzi
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
- European Synchrotron Radiation Facility, Grenoble 38043, France
| | - Giuseppe Sicoli
- LASIRE UMR CNRS 8516, Université de Lille, Villeneuve-d'Arcy 59655, France
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Christophe Decroos
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
- Department of Integrative Structural Biology, Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch 67400, France
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4
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Ayuso-Fernández I, Emrich-Mills TZ, Haak J, Golten O, Hall KR, Schwaiger L, Moe TS, Stepnov AA, Ludwig R, Cutsail Iii GE, Sørlie M, Kjendseth Røhr Å, Eijsink VGH. Mutational dissection of a hole hopping route in a lytic polysaccharide monooxygenase (LPMO). Nat Commun 2024; 15:3975. [PMID: 38729930 PMCID: PMC11087555 DOI: 10.1038/s41467-024-48245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Oxidoreductases have evolved tyrosine/tryptophan pathways that channel highly oxidizing holes away from the active site to avoid damage. Here we dissect such a pathway in a bacterial LPMO, member of a widespread family of C-H bond activating enzymes with outstanding industrial potential. We show that a strictly conserved tryptophan is critical for radical formation and hole transference and that holes traverse the protein to reach a tyrosine-histidine pair in the protein's surface. Real-time monitoring of radical formation reveals a clear correlation between the efficiency of hole transference and enzyme performance under oxidative stress. Residues involved in this pathway vary considerably between natural LPMOs, which could reflect adaptation to different ecological niches. Importantly, we show that enzyme activity is increased in a variant with slower radical transference, providing experimental evidence for a previously postulated trade-off between activity and redox robustness.
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Affiliation(s)
- Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway.
| | - Tom Z Emrich-Mills
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Julia Haak
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Ole Golten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Kelsi R Hall
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Lorenz Schwaiger
- Biocatalysis and Biosensing Laboratory, Department of Food Sciences and Technology, Institute of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18/2, Vienna, 1190, Austria
| | - Trond S Moe
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Sciences and Technology, Institute of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18/2, Vienna, 1190, Austria
| | - George E Cutsail Iii
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Åsmund Kjendseth Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway.
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5
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Isaksen I, Jana S, Payne CM, Bissaro B, Røhr ÅK. The rotamer of the second-sphere histidine in AA9 lytic polysaccharide monooxygenase is pH dependent. Biophys J 2024; 123:1139-1151. [PMID: 38571309 PMCID: PMC11079946 DOI: 10.1016/j.bpj.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/10/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH-dependent conformation of a second-sphere histidine (His) that we call the stacking histidine, which is conserved in fungal AA9 LPMOs and is speculated to assist catalysis in several of the LPMO reaction pathways. Using constant-pH and accelerated molecular dynamics simulations, we monitored the dynamics of the stacking His in different protonation states for both the resting Cu(II) and active Cu(I) forms of two fungal LPMOs. Consistent with experimental crystallographic and neutron diffraction data, our calculations suggest that the side chain of the protonated and positively charged form is rotated out of the active site toward the solvent. Importantly, only one of the possible neutral states of histidine (HIE state) is observed in the stacking orientation at neutral pH or when bound to cellulose. Our data predict that, in solution, the stacking His may act as a stabilizer (via hydrogen bonding) of the Cu(II)-superoxo complex after the LPMO-Cu(I) has reacted with O2 in solution, which, in fine, leads to H2O2 formation. Also, our data indicate that the HIE-stacking His is a poor acid/base catalyst when bound to the substrate and, in agreement with the literature, may play an important stabilizing role (via hydrogen bonding) during the peroxygenase catalysis. Our study reveals the pH titration midpoint values of the pH-dependent orientation of the stacking His should be considered when modeling and interpreting LPMO reactions, whether it be for classical LPMO kinetics or in industry-oriented enzymatic cocktails, and for understanding LPMO behavior in slightly acidic natural processes such as fungal wood decay.
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Affiliation(s)
- Ingvild Isaksen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway; INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France.
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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6
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Ma H, Liao M, Zhong P, Ding J, Wang X, Gong G, Huang L, Liu J, Wang Q. Diversely regio-oxidative degradation of konjac glucomannan by lytic polysaccharide monooxygenase AA10 and generating antibacterial hydrolysate. Int J Biol Macromol 2024; 266:131094. [PMID: 38537852 DOI: 10.1016/j.ijbiomac.2024.131094] [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: 12/05/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
Konjac glucomannan (KGM) hydrolysate exhibit various biological activities and health-promoting effects. Lytic polysaccharide monooxygenases (LPMOs) play an important role on enzymatic degradation of recalcitrant polysaccharides to obtain fermentable sugars. It is generally accepted that LPMOs exhibits high substrate specificity and oxidation regioselectivity. Here, a bacteria-derived SmAA10A, with chitin-active with strict C1 oxidation, was used to catalyse KGM degradation. Through ethanol precipitation, two hydrolysed KGM components (4 kDa (KGM-1) and 5 kDa (KGM-2)) were obtained that exhibited antibacterial activity against Staphylococcus aureus. In natural KGM, KGM-1, and KGM-2, the molar ratios of mannose to glucose were 1:2.19, 1:3.05, and 1:2.87, respectively, indicating that SmAA10A preferentially degrades mannose in KGM. Fourier-transform infrared spectroscopy and scanning electron microscopy imaging revealed the breakage of glycosylic bonds during enzymatic catalysis. The regioselectivity of SmAA10A for KGM degradation was determined based on the fragmentation behaviour of the KGM-1 and KGM-2 oligosaccharides and their NaBD4-reduced forms. SmAA10A exhibited diverse oxidation degradation of KGM and generated single C1-, single C4-, and C1/C4-double oxidised oligosaccharide forms. This study provides an alternative method for obtaining KGM degradation components with antibacterial functions and expands the substrate specificity and oxidation regioselectivity of bacterial LPMOs.
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Affiliation(s)
- Hongjuan Ma
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China; College of Life Science, Northwest University, Xi'an 710069, China
| | - Minghong Liao
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Peiyun Zhong
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jieqiong Ding
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Xiaoqin Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Guiping Gong
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jianling Liu
- College of Life Science, Northwest University, Xi'an 710069, China.
| | - Qingling Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
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7
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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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8
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Zhao H, Su H, Sun J, Dong H, Mao X. Bioconversion of α-Chitin by a Lytic Polysaccharide Monooxygenase OsLPMO10A Coupled with Chitinases and the Synergistic Mechanism Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7256-7265. [PMID: 38438973 DOI: 10.1021/acs.jafc.3c08688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The whole enzymatic conversion of chitin is a green and promising alternative to current strategies, which are based on lytic polysaccharide monooxygenases (LPMOs) and chitinases. However, the lack of LPMOs with high activity toward α-chitin limits the efficient bioconversion of α-chitin. Herein, we characterized a high chitin-active LPMO from Oceanobacillus sp. J11TS1 (OsLPMO10A), which could promote the decrystallization of the α-chitin surface. Furthermore, when coupled with OsLPMO10A, the conversion rate of α-chitin to N-acetyl chitobiose [(GlcNAc)2] by three chitinases (Serratia marcescens, ChiA, -B, and -C) reached 30.86%, which was 2.03-folds that without the addition of OsLPMO10A. Moreover, the results of synergistic reactions indicated that OsLPMO10A and chitinases promoted the degradation of α-chitin each other mainly on the surface. To the best of our knowledge, this study achieved the highest yield of N-acetyl chitooligosaccharides (N-acetyl COSs) among reported LPMOs-driven bioconversion systems, which could be regarded as a promising candidate for α-chitin bioconversion.
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Affiliation(s)
- Hongjun Zhao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, P. R. China
| | - Haipeng Su
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, P. R. China
| | - Jianan Sun
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, P. R. China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, P. R. China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, P. R. China
| | - Hao Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, P. R. China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, P. R. China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, P. R. China
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P. R. China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, P. R. China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, P. R. China
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9
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Sundararaj R, Mathimaran A, Prabhu D, Ramachandran B, Jeyaraman J, Muthupandian S, Asmelash T. In silico approaches for the identification of potential allergens among hypothetical proteins from Alternaria alternata and its functional annotation. Sci Rep 2024; 14:6696. [PMID: 38509156 PMCID: PMC10954717 DOI: 10.1038/s41598-024-55463-1] [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: 11/01/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Direct exposure to the fungal species Alternaria alternata is a major risk factor for the development of asthma, allergic rhinitis, and inflammation. As of November 23rd 2020, the NCBI protein database showed 11,227 proteins from A. alternata genome as hypothetical proteins (HPs). Allergens are the main causative of several life-threatening diseases, especially in fungal infections. Therefore, the main aim of the study is to identify the potentially allergenic inducible proteins from the HPs in A. alternata and their associated functional assignment for the complete understanding of the complex biological systems at the molecular level. AlgPred and Structural Database of Allergenic Proteins (SDAP) were used for the prediction of potential allergens from the HPs of A. alternata. While analyzing the proteome data, 29 potential allergens were predicted by AlgPred and further screening in SDAP confirmed the allergic response of 10 proteins. Extensive bioinformatics tools including protein family classification, sequence-function relationship, protein motif discovery, pathway interactions, and intrinsic features from the amino acid sequence were used to successfully predict the probable functions of the 10 HPs. The functions of the HPs are characterized as chitin-binding, ribosomal protein P1, thaumatin, glycosyl hydrolase, and NOB1 proteins. The subcellular localization and signal peptide prediction of these 10 proteins has further provided additional information on localization and function. The allergens prediction and functional annotation of the 10 proteins may facilitate a better understanding of the allergenic mechanism of A. alternata in asthma and other diseases. The functional domain level insights and predicted structural features of the allergenic proteins help to understand the pathogenesis and host immune tolerance. The outcomes of the study would aid in the development of specific drugs to combat A. alternata infections.
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Affiliation(s)
- Rajamanikandan Sundararaj
- Department of Biochemistry, Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, 641021, India
| | - Amala Mathimaran
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630 004, India
| | - Dhamodharan Prabhu
- Department of Biotechnology, Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, 641021, India
| | - Balajee Ramachandran
- Department of Pharmacology, Physiology & Biophysics, Chobanian & Avedisian School of Medicine, Boston University, 700 Albany Street, Boston, MA, 02118, USA
| | - Jeyakanthan Jeyaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630 004, India
| | - Saravanan Muthupandian
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600077, India
| | - Tsehaye Asmelash
- Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Tigray, Ethiopia.
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10
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Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
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Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
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11
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Yao RA, Reyre JL, Tamburrini KC, Haon M, Tranquet O, Nalubothula A, Mukherjee S, Le Gall S, Grisel S, Longhi S, Madhuprakash J, Bissaro B, Berrin JG. The Ustilago maydis AA10 LPMO is active on fungal cell wall chitin. Appl Environ Microbiol 2023; 89:e0057323. [PMID: 37702503 PMCID: PMC10617569 DOI: 10.1128/aem.00573-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 09/14/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can perform oxidative cleavage of glycosidic bonds in carbohydrate polymers (e.g., cellulose, chitin), making them more accessible to hydrolytic enzymes. 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. The AA10 LPMOs are active on chitin and/or cellulose and mostly found in bacteria and in some viruses and archaea. Interestingly, AA10-encoding genes are also encountered in some pathogenic fungi of the Ustilaginomycetes class, such as Ustilago maydis, responsible for corn smut disease. Transcriptomic studies have shown the overexpression of the AA10 gene during the infectious cycle of U. maydis. In fact, U. maydis has a unique AA10 gene that codes for a catalytic domain appended with a C-terminal disordered region. To date, there is no public report on fungal AA10 LPMOs. In this study, we successfully produced the catalytic domain of this LPMO (UmAA10_cd) in Pichia pastoris and carried out its biochemical characterization. Our results show that UmAA10_cd oxidatively cleaves α- and β-chitin with C1 regioselectivity and boosts chitin hydrolysis by a GH18 chitinase from U. maydis (UmGH18A). Using a biologically relevant substrate, we show that UmAA10_cd exhibits enzymatic activity on U. maydis fungal cell wall chitin and promotes its hydrolysis by UmGH18A. These results represent an important step toward the understanding of the role of LPMOs in the fungal cell wall remodeling process during the fungal life cycle.IMPORTANCELytic polysaccharide monooxygenases (LPMOs) have been mainly studied in a biotechnological context for the efficient degradation of recalcitrant polysaccharides. Only recently, alternative roles and paradigms begin to emerge. In this study, we provide evidence that the AA10 LPMO from the phytopathogen Ustilago maydis is active against fungal cell wall chitin. Given that chitin-active LPMOs are commonly found in microbes, it is important to consider fungal cell wall as a potential target for this enigmatic class of enzymes.
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Affiliation(s)
- Roseline Assiah Yao
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
| | - Jean-Lou Reyre
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
- IFP Energies Nouvelles, Rueil-Malmaison, France
| | - Ketty C. Tamburrini
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
- CNRS, Aix Marseille Univ, UMR 7257 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Mireille Haon
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
- INRAE, Aix Marseille Univ, 3PE Platform, Marseille, France
| | - Olivier Tranquet
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
| | - Akshay Nalubothula
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sophie Le Gall
- INRAE, UR1268 BIA, Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, Nantes, France
| | - Sacha Grisel
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
- INRAE, Aix Marseille Univ, 3PE Platform, Marseille, France
| | - Sonia Longhi
- CNRS, Aix Marseille Univ, UMR 7257 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
- INRAE, Aix Marseille Univ, 3PE Platform, Marseille, France
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12
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Dan M, Zheng Y, Zhao G, Hsieh YSY, Wang D. Current insights of factors interfering the stability of lytic polysaccharide monooxygenases. Biotechnol Adv 2023; 67:108216. [PMID: 37473820 DOI: 10.1016/j.biotechadv.2023.108216] [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: 03/20/2023] [Revised: 06/30/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023]
Abstract
Cellulose and chitin are two of the most abundant biopolymers in nature, but they cannot be effectively utilized in industry due to their recalcitrance. This limitation was overcome by the advent of lytic polysaccharide monooxygenases (LPMOs), which promote the disruption of biopolymers through oxidative mechanism and provide a breakthrough in the action of hydrolytic enzymes. In the application of LPMOs to biomass degradation, the key to consistent and effective functioning lies in their stability. The efficient transformation of biomass resources using LPMOs depends on factors that interfere with their stability. This review discussed three aspects that affect LPMO stability: general external factors, structural factors, and factors in the enzyme-substrate reaction. It explains how these factors impact LPMO stability, discusses the resulting effects, and finally presents relevant measures and considerations, including potential resolutions. The review also provides suggestions for the application of LPMOs in polysaccharide degradation.
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Affiliation(s)
- Meiling Dan
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Guohua Zhao
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden; School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Damao Wang
- College of Food Science, Southwest University, Chongqing 400715, China.
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13
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Singh J, Singh P, Singh AP, Singh PK. Lytic Polysaccharide Monooxygenase Activity of Tma12 Is Critical for Its Toxicity to Whitefly. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13696-13705. [PMID: 37671750 DOI: 10.1021/acs.jafc.3c03208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful redox enzymes that transform complex carbohydrates through oxidation and make them suitable for saccharification by canonical hydrolases. Due to this property, LPMOs are considered to be a valuable component of enzymatic consortia for industrial biorefineries. Tma12 is a fern entomotoxic protein that kills whitefly and has structural similarities with chitinolytic LPMO. However, its enzymatic activity is poorly understood. Studying the role of the LPMO-like activity in the insecticidal function of Tma12 can be of considerable importance. Our results show that Tma12 preferentially binds and digests β-chitin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis shows that the digestion of chitin produces chitin oligosaccharides of various lengths (DP2-DP7). The Michaelis constant (km) and catalytic constant (kcat) for hydrocoerulignone are 0.022 mM and 0.044 s-1, respectively. The attenuation of catalytic activity through diethylpyrocarbonate modification abolishes the insecticidal activity of the protein. Our findings reveal that (a) Tma12 is an active LPMO and (b) LPMO activity is indispensable for its function as a bioinsecticide.
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Affiliation(s)
- Jyoti Singh
- Insect Defense Laboratory, Molecular Biology, and Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-National Botanical Research Institute (NBRI), 435 Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Pooja Singh
- Insect Defense Laboratory, Molecular Biology, and Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-National Botanical Research Institute (NBRI), 435 Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Ajit Pratap Singh
- Pteridology Laboratory, Plant Diversity, Systematics, and Herbarium Division, Council of Scientific and Industrial Research (CSIR)-National Botanical Research Institute (NBRI), 435 Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Pradhyumna Kumar Singh
- Insect Defense Laboratory, Molecular Biology, and Biotechnology Division, Council of Scientific and Industrial Research (CSIR)-National Botanical Research Institute (NBRI), 435 Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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14
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Kuusk S, Eijsink VGH, Väljamäe P. The "life-span" of lytic polysaccharide monooxygenases (LPMOs) correlates to the number of turnovers in the reductant peroxidase reaction. J Biol Chem 2023; 299:105094. [PMID: 37507015 PMCID: PMC10458328 DOI: 10.1016/j.jbc.2023.105094] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/02/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes that degrade the insoluble crystalline polysaccharides cellulose and chitin. Besides the H2O2 cosubstrate, the cleavage of glycosidic bonds by LPMOs depends on the presence of a reductant needed to bring the enzyme into its reduced, catalytically active Cu(I) state. Reduced LPMOs that are not bound to substrate catalyze reductant peroxidase reactions, which may lead to oxidative damage and irreversible inactivation of the enzyme. However, the kinetics of this reaction remain largely unknown, as do possible variations between LPMOs belonging to different families. Here, we describe the kinetic characterization of two fungal family AA9 LPMOs, TrAA9A of Trichoderma reesei and NcAA9C of Neurospora crassa, and two bacterial AA10 LPMOs, ScAA10C of Streptomyces coelicolor and SmAA10A of Serratia marcescens. We found peroxidation of ascorbic acid and methyl-hydroquinone resulted in the same probability of LPMO inactivation (pi), suggesting that inactivation is independent of the nature of the reductant. We showed the fungal enzymes were clearly more resistant toward inactivation, having pi values of less than 0.01, whereas the pi for SmAA10A was an order of magnitude higher. However, the fungal enzymes also showed higher catalytic efficiencies (kcat/KM(H2O2)) for the reductant peroxidase reaction. This inverse linear correlation between the kcat/KM(H2O2) and pi suggests that, although having different life spans in terms of the number of turnovers in the reductant peroxidase reaction, LPMOs that are not bound to substrates have similar half-lives. These findings have not only potential biological but also industrial implications.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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15
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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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16
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Sørensen HV, Montserrat-Canals M, Loose JSM, Fisher SZ, Moulin M, Blakeley MP, Cordara G, Bjerregaard-Andersen K, Krengel U. Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. ACS OMEGA 2023; 8:29101-29112. [PMID: 37599915 PMCID: PMC10433351 DOI: 10.1021/acsomega.3c02168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen's large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using N-acetylglucosamine-binding protein A (GbpA) from Vibrio cholerae as a target. GbpA is a multifunctional protein that is secreted by the bacteria to colonize and degrade chitin. We developed an efficient deuteration protocol, which yields >10 mg of pure 97% deuterated protein per liter expression media, which was scaled up further at international facilities. The deuterated protein retains its catalytic activity and structure, as demonstrated by small-angle X-ray and neutron scattering studies of full-length GbpA and X-ray crystal structures of its LPMO domain (to 1.1 Å resolution), setting the stage for neutron scattering experiments with its substrate chitin.
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Affiliation(s)
- H. V. Sørensen
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | - Mateu Montserrat-Canals
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
- Centre
for Molecular Medicine Norway, University
of Oslo, NO-0318 Oslo, Norway
| | - Jennifer S. M. Loose
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1340 Ås, Norway
| | - S. Zoë Fisher
- Science
Directorate, European Spallation Source
ERIC, P.O. Box 176, SE-221 00 Lund, Sweden
- Department
of Biology, Lund University, 35 Sölvegatan, SE-223 62 Lund, Sweden
| | - Martine Moulin
- Life Sciences
Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9 Grenoble, France
| | - Matthew P. Blakeley
- Large-Scale
Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Gabriele Cordara
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | | | - Ute Krengel
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
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17
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Arnold ND, Garbe D, Brück TB. Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp. Mar Drugs 2023; 21:448. [PMID: 37623729 PMCID: PMC10455584 DOI: 10.3390/md21080448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
In nature, chitin, the most abundant marine biopolymer, does not accumulate due to the action of chitinolytic organisms, whose saccharification systems provide instructional blueprints for effective chitin conversion. Therefore, discovery and deconstruction of chitinolytic machineries and associated enzyme systems are essential for the advancement of biotechnological chitin valorization. Through combined investigation of the chitin-induced secretome with differential proteomic and transcriptomic analyses, a holistic system biology approach has been applied to unravel the chitin response mechanisms in the Gram-negative Jeongeupia wiesaeckerbachi. Hereby, the majority of the genome-encoded chitinolytic machinery, consisting of various glycoside hydrolases and a lytic polysaccharide monooxygenase, could be detected extracellularly. Intracellular proteomics revealed a distinct translation pattern with significant upregulation of glucosamine transport, metabolism, and chemotaxis-associated proteins. While the differential transcriptomic results suggested the overall recruitment of more genes during chitin metabolism compared to that of glucose, the detected protein-mRNA correlation was low. As one of the first studies of its kind, the involvement of over 350 unique enzymes and 570 unique genes in the catabolic chitin response of a Gram-negative bacterium could be identified through a three-way systems biology approach. Based on the cumulative data, a holistic model for the chitinolytic machinery of Jeongeupia spp. is proposed.
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Affiliation(s)
| | | | - Thomas B. Brück
- TUM School of Natural Sciences, Department of Chemistry, Technical University of Munich, Werner-Siemens Chair for Synthetic Biotechnology (WSSB), Lichtenbergstr. 4, 85748 Garching, Germany; (N.D.A.); (D.G.)
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18
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Tuveng TR, Østby H, Tamburrini KC, Bissaro B, Hegnar OA, Stepnov AA, Várnai A, Berrin JG, Eijsink VGH. Revisiting the AA14 family of lytic polysaccharide monooxygenases and their catalytic activity. FEBS Lett 2023; 597:2086-2102. [PMID: 37418595 DOI: 10.1002/1873-3468.14694] [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: 03/31/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) belonging to the AA14 family are believed to contribute to the enzymatic degradation of lignocellulosic biomass by specifically acting on xylan in recalcitrant cellulose-xylan complexes. Functional characterization of an AA14 LPMO from Trichoderma reesei, TrAA14A, and a re-evaluation of the properties of the previously described AA14 from Pycnoporus coccineus, PcoAA14A, showed that these proteins have oxidase and peroxidase activities that are common for LPMOs. However, we were not able to detect activity on cellulose-associated xylan or any other tested polysaccharide substrate, meaning that the substrate of these enzymes remains unknown. Next to raising questions regarding the true nature of AA14 LPMOs, the present data illustrate possible pitfalls in the functional characterization of these intriguing enzymes.
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Affiliation(s)
- Tina R Tuveng
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Heidi Østby
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ketty C Tamburrini
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Bastien Bissaro
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anton A Stepnov
- 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
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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19
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Thakur D, Bairwa A, Dipta B, Jhilta P, Chauhan A. An overview of fungal chitinases and their potential applications. PROTOPLASMA 2023; 260:1031-1046. [PMID: 36752884 DOI: 10.1007/s00709-023-01839-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 01/30/2023] [Indexed: 06/07/2023]
Abstract
Chitin, the world's second most abundant biopolymer after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) residues. It is the key structural component of many organisms, including crustaceans, mollusks, marine invertebrates, algae, fungi, insects, and nematodes. There has been a significant increase in the generation of chitinous waste from seafood businesses, resulting in a big amount of scrap. Although several organisms, such as plants, crustaceans, insects, nematodes, and animals, produce chitinases, microorganisms are promising candidates and a sustainable option that mediates chitin degradation. Fungi are the dominant group of chitinase producers among microorganisms. In fungi, chitinases are involved in morphogenesis, cell division, autolysis, chitin acquisition for nutritional purposes, and mycoparasitism. Many efficient chitinolytic fungi with potential applications have been identified in a variety of environments, including soil, water, marine wastes, and plants. The current review highlights the key sources of chitinolytic fungi and the characterization of fungal chitinases. It also discusses the applications of fungal chitinases and the cloning of fungal chitinase genes.
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Affiliation(s)
- Deepali Thakur
- Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Aarti Bairwa
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
| | - Prakriti Jhilta
- Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Anjali Chauhan
- Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
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20
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The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases. Essays Biochem 2023; 67:551-559. [PMID: 36876880 DOI: 10.1042/ebc20220156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
In nature, enzymatic degradation of recalcitrant polysaccharides such as chitin and cellulose takes place by a synergistic interaction between glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The two different families of carbohydrate-active enzymes use two different mechanisms when breaking glycosidic bonds between sugar moieties. GHs employ a hydrolytic activity and LPMOs are oxidative. Consequently, the topologies of the active sites differ dramatically. GHs have tunnels or clefts lined with a sheet of aromatic amino acid residues accommodating single polymer chains being threaded into the active site. LPMOs are adapted to bind to the flat crystalline surfaces of chitin and cellulose. It is believed that the LPMO oxidative mechanism provides new chain ends that the GHs can attach to and degrade, often in a processive manner. Indeed, there are many reports of synergies as well as rate enhancements when LPMOs are applied in concert with GHs. Still, these enhancements vary in magnitude with respect to the nature of the GH and the LPMO. Moreover, impediment of GH catalysis is also observed. In the present review, we discuss central works where the interplay between LPMOs and GHs has been studied and comment on future challenges to be addressed to fully use the potential of this interplay to improve enzymatic polysaccharide degradation.
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21
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Kommedal EG, Angeltveit CF, Klau LJ, Ayuso-Fernández I, Arstad B, Antonsen SG, Stenstrøm Y, Ekeberg D, Gírio F, Carvalheiro F, Horn SJ, Aachmann FL, Eijsink VGH. Visible light-exposed lignin facilitates cellulose solubilization by lytic polysaccharide monooxygenases. Nat Commun 2023; 14:1063. [PMID: 36828821 PMCID: PMC9958194 DOI: 10.1038/s41467-023-36660-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze oxidative cleavage of crystalline polysaccharides such as cellulose and are crucial for the conversion of plant biomass in Nature and in industrial applications. Sunlight promotes microbial conversion of plant litter; this effect has been attributed to photochemical degradation of lignin, a major redox-active component of secondary plant cell walls that limits enzyme access to the cell wall carbohydrates. Here, we show that exposing lignin to visible light facilitates cellulose solubilization by promoting formation of H2O2 that fuels LPMO catalysis. Light-driven H2O2 formation is accompanied by oxidation of ring-conjugated olefins in the lignin, while LPMO-catalyzed oxidation of phenolic hydroxyls leads to the required priming reduction of the enzyme. The discovery that light-driven abiotic reactions in Nature can fuel H2O2-dependent redox enzymes involved in deconstructing lignocellulose may offer opportunities for bioprocessing and provides an enzymatic explanation for the known effect of visible light on biomass conversion.
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Affiliation(s)
- Eirik G Kommedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Camilla F Angeltveit
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Leesa J Klau
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Bjørnar Arstad
- SINTEF Industry, Process Chemistry and Functional Materials, 0373, Oslo, Norway
| | - Simen G Antonsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Yngve Stenstrøm
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Dag Ekeberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Francisco Gírio
- National Laboratory of Energy and Geology (LNEG), 1649-038, Lisboa, Portugal
| | | | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Finn Lillelund Aachmann
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway.
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22
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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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23
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Zhang H, Zhou H, Zhao Y, Li T, Yin H. Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis. PeerJ 2023; 11:e14670. [PMID: 36684673 PMCID: PMC9851047 DOI: 10.7717/peerj.14670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023] Open
Abstract
Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B.
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Affiliation(s)
- Huiyan Zhang
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Zhao
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tang Li
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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24
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Cordas CM, Valério GN, Stepnov A, Kommedal E, Kjendseth ÅR, Forsberg Z, Eijsink VGH, Moura JJG. Electrochemical characterization of a family AA10 LPMO and the impact of residues shaping the copper site on reactivity. J Inorg Biochem 2023; 238:112056. [PMID: 36332410 DOI: 10.1016/j.jinorgbio.2022.112056] [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: 08/27/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Research on enzymes for lignocellulose biomass degradation has progressively increased in recent years due to the interest in taking advantage of this natural resource. Among these enzymes are the lytic polysaccharide monooxygenases (LPMOs) that oxidatively depolymerize crystalline cellulose using a reactive oxygen species generated in a reduced mono‑copper active site. The copper site comprises of a highly conserved histidine-brace, providing three equatorial nitrogen ligands, whereas less conserved residues close to the copper contribute to shaping and confining the site. The catalytic copper site is exposed to the solvent and to the crystalline substrates, and as so, the influence of the copper environment on LPMO properties, including the redox potential, is of great interest. In the current work, a direct electrochemical study of an LPMO (ScLPMO10C) was conducted allowing to retrieve kinetic and thermodynamic data associated with the redox transition in the catalytic centre. Moreover, two residues that do not bind to the copper but shape the copper sites were mutated, and the properties of the mutants were compared with those of the wild-type enzyme. The direct electrochemical studies, using cyclic voltammetry, yielded redox potentials in the +200 mV range, well in line with LPMO redox potentials determined by other methods. Interestingly, while the mutations hardly affected the formal redox potential of the enzyme, they drastically affected the reactivity of the copper site and enzyme functionality.
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Affiliation(s)
- Cristina M Cordas
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
| | - Gabriel N Valério
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Anton Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Eirik Kommedal
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Åsmund R Kjendseth
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
| | - José J G Moura
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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25
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On the impact of carbohydrate-binding modules (CBMs) in lytic polysaccharide monooxygenases (LPMOs). Essays Biochem 2022; 67:561-574. [PMID: 36504118 PMCID: PMC10154629 DOI: 10.1042/ebc20220162] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022]
Abstract
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have revolutionized our understanding of how enzymes degrade insoluble polysaccharides. Compared with the substantial knowledge developed on the structure and mode of action of the catalytic LPMO domains, the (multi)modularity of LPMOs has received less attention. The presence of other domains, in particular carbohydrate-binding modules (CBMs), tethered to LPMOs has profound implications for the catalytic performance of the full-length enzymes. In the last few years, studies on LPMO modularity have led to advancements in elucidating how CBMs, other domains, and linker regions influence LPMO structure and function. This mini review summarizes recent literature, with particular focus on comparative truncation studies, to provide an overview of the diversity in LPMO modularity and the functional implications of this diversity.
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26
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Tamburino R, Marcolongo L, Sannino L, Ionata E, Scotti N. Plastid Transformation: New Challenges in the Circular Economy Era. Int J Mol Sci 2022; 23:ijms232315254. [PMID: 36499577 PMCID: PMC9736159 DOI: 10.3390/ijms232315254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In a circular economy era the transition towards renewable and sustainable materials is very urgent. The development of bio-based solutions, that can ensure technological circularity in many priority areas (e.g., agriculture, biotechnology, ecology, green industry, etc.), is very strategic. The agricultural and fishing industry wastes represent important feedstocks that require the development of sustainable and environmentally-friendly industrial processes to produce and recover biofuels, chemicals and bioactive molecules. In this context, the replacement, in industrial processes, of chemicals with enzyme-based catalysts assures great benefits to humans and the environment. In this review, we describe the potentiality of the plastid transformation technology as a sustainable and cheap platform for the production of recombinant industrial enzymes, summarize the current knowledge on the technology, and display examples of cellulolytic enzymes already produced. Further, we illustrate several types of bacterial auxiliary and chitinases/chitin deacetylases enzymes with high biotechnological value that could be manufactured by plastid transformation.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | | | - Lorenza Sannino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | - Elena Ionata
- CNR-IRET, Research Institute on Terrestrial Ecosystems, 80131 Naples, Italy
| | - Nunzia Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
- Correspondence:
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27
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Guo X, An Y, Liu F, Lu F, Wang B. Lytic polysaccharide monooxygenase - A new driving force for lignocellulosic biomass degradation. BIORESOURCE TECHNOLOGY 2022; 362:127803. [PMID: 35995343 DOI: 10.1016/j.biortech.2022.127803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) can catalyze polysaccharides by oxidative cleavage of glycosidic bonds and have catalytic activity for cellulose, hemicellulose, chitin, starch and pectin, thus playing an important role in the biomass conversion of lignocellulose. The catalytic substrates of LPMOs are different and the specific catalytic mechanism has not been fully elucidated. Although there have been many studies related to LPMOs, few have actually been put into industrial biomass conversion, which poses a challenge for their expression, regulation and application. In this review, the origin, substrate specificity, structural features, and the relationship between structure and function of LPMOs are described. Additionally, the catalytic mechanism and electron donor of LPMOs and their heterologous expression and regulation are discussed. Finally, the synergistic degradation of biomass by LPMOs with other polysaccharide hydrolases is reviewed, and their current problems and future research directions are pointed out.
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Affiliation(s)
- Xiao Guo
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China; Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Yajing An
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300450, PR China
| | - Bo Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China.
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28
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Yurtsever A, Wang PX, Priante F, Morais Jaques Y, Miyata K, MacLachlan MJ, Foster AS, Fukuma T. Probing the Structural Details of Chitin Nanocrystal-Water Interfaces by Three-Dimensional Atomic Force Microscopy. SMALL METHODS 2022; 6:e2200320. [PMID: 35686343 DOI: 10.1002/smtd.202200320] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Chitin is one of the most abundant and renewable natural biopolymers. It exists in the form of crystalline microfibrils and is the basic structural building block of many biological materials. Its surface crystalline structure is yet to be reported at the molecular level. Herein, atomic force microscopy (AFM) in combination with molecular dynamics simulations reveals the molecular-scale structural details of the chitin nanocrystal (chitin NC)-water interface. High-resolution AFM images reveal the molecular details of chitin chain arrangements at the surfaces of individual chitin NCs, showing highly ordered, stable crystalline structures almost free of structural defects or disorder. 3D-AFM measurements with submolecular spatial resolution demonstrate that chitin NC surfaces interact strongly with interfacial water molecules creating stable, well-ordered hydration layers. Inhomogeneous encapsulation of the underlying chitin substrate by these hydration layers reflects the chitin NCs' multifaceted surface character with different chain arrangements and molecular packing. These findings provide important insights into chitin NC structures at the molecular level, which is critical for developing the properties of chitin-based nanomaterials. Furthermore, these results will contribute to a better understanding of the chemical and enzymatic hydrolysis of chitin and other native polysaccharides, which is also essential for the enzymatic conversion of biomass.
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Affiliation(s)
- Ayhan Yurtsever
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Pei-Xi Wang
- Department of Chemistry, University of British Columbia 2036 Main Mall, Vancouver, V6T 1Z1, Canada
| | - Fabio Priante
- Department of Applied Physics, Aalto University, FI-00076, Helsinki, Finland
| | - Ygor Morais Jaques
- Department of Applied Physics, Aalto University, FI-00076, Helsinki, Finland
| | - Kazuki Miyata
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Mark J MacLachlan
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Department of Chemistry, University of British Columbia 2036 Main Mall, Vancouver, V6T 1Z1, Canada
| | - Adam S Foster
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Department of Applied Physics, Aalto University, FI-00076, Helsinki, Finland
| | - Takeshi Fukuma
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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29
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Moon M, Lee JP, Park GW, Lee JS, Park HJ, Min K. Lytic polysaccharide monooxygenase (LPMO)-derived saccharification of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 359:127501. [PMID: 35753567 DOI: 10.1016/j.biortech.2022.127501] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Given that traditional biorefineries have been based on microbial fermentation to produce useful fuels, materials, and chemicals as metabolites, saccharification is an important step to obtain fermentable sugars from biomass. It is well-known that glycosidic hydrolases (GHs) are responsible for the saccharification of recalcitrant polysaccharides through hydrolysis, but the discovery of lytic polysaccharide monooxygenase (LPMO), which is a kind of oxidative enzyme involved in cleaving polysaccharides and boosting GH performance, has profoundly changed the understanding of enzyme-based saccharification. This review briefly introduces the classification, structural information, and catalytic mechanism of LPMOs. In addition to recombinant expression strategies, synergistic effects with GH are comprehensively discussed. Challenges and perspectives for LPMO-based saccharification on a large scale are also briefly mentioned. Ultimately, this review can provide insights for constructing an economically viable lignocellulose-based biorefinery system and a closed-carbon loop to cope with climate change.
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Affiliation(s)
- Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
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30
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Natural photoredox catalysts promote light-driven lytic polysaccharide monooxygenase reactions and enzymatic turnover of biomass. Proc Natl Acad Sci U S A 2022; 119:e2204510119. [PMID: 35969781 PMCID: PMC9407654 DOI: 10.1073/pnas.2204510119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze oxidative cleavage of crystalline polysaccharides such as cellulose and chitin and are important for biomass conversion in the biosphere as well as in biorefineries. The target polysaccharides of LPMOs naturally occur in copolymeric structures such as plant cell walls and insect cuticles that are rich in phenolic compounds, which contribute rigidity and stiffness to these materials. Since these phenolics may be photoactive and since LPMO action depends on reducing equivalents, we hypothesized that LPMOs may enable light-driven biomass conversion. Here, we show that redox compounds naturally present in shed insect exoskeletons enable harvesting of light energy to drive LPMO reactions and thus biomass conversion. The primary underlying mechanism is that irradiation of exoskeletons with visible light leads to the generation of H2O2, which fuels LPMO peroxygenase reactions. Experiments with a cellulose model substrate show that the impact of light depends on both light and exoskeleton dosage and that light-driven LPMO activity is inhibited by a competing H2O2-consuming enzyme. Degradation experiments with the chitin-rich exoskeletons themselves show that solubilization of chitin by a chitin-active LPMO is promoted by light. The fact that LPMO reactions, and likely reactions catalyzed by other biomass-converting redox enzymes, are fueled by light-driven abiotic reactions in nature provides an enzyme-based explanation for the known impact of visible light on biomass conversion.
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31
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Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species. Appl Environ Microbiol 2022; 88:e0096822. [PMID: 35862679 PMCID: PMC9361826 DOI: 10.1128/aem.00968-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cellulomonas flavigena is a saprotrophic bacterium that encodes, within its genome, four predicted lytic polysaccharide monooxygenases (LPMOs) from Auxiliary Activity family 10 (AA10). We showed previously that three of these cleave the plant polysaccharide cellulose by oxidation at carbon-1 (J. Li, L. Solhi, E.D. Goddard-Borger, Y. Mattieu et al., Biotechnol Biofuels 14:29, 2021, https://doi.org/10.1186/s13068-020-01860-3). Here, we present the biochemical characterization of the fourth C. flavigena AA10 member (CflaLPMO10D) as a chitin-active LPMO. Both the full-length CflaLPMO10D-Carbohydrate-Binding Module family 2 (CBM2) and catalytic module-only proteins were produced in Escherichia coli using the native general secretory (Sec) signal peptide. To quantify chitinolytic activity, we developed a high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method as an alternative to the established hydrophilic interaction liquid ion chromatography coupled with UV detection (HILIC-UV) method for separation and detection of released oxidized chito-oligosaccharides. Using this method, we demonstrated that CflaLPMO10D is strictly active on the β-allomorph of chitin, with optimal activity at pH 5 to 6 and a preference for ascorbic acid as the reducing agent. We also demonstrated the importance of the CBM2 member for both mediating enzyme localization to substrates and prolonging LPMO activity. Together with previous work, the present study defines the distinct substrate specificities of the suite of C. flavigena AA10 members. Notably, a cross-genome survey of AA10 members indicated that chitinolytic LPMOs are, in fact, rare among Cellulomonas bacteria. IMPORTANCE Species from the genus Cellulomonas have a long history of study due to their roles in biomass recycling in nature and corresponding potential as sources of enzymes for biotechnological applications. Although Cellulomonas species are more commonly associated with the cleavage and utilization of plant cell wall polysaccharides, here, we show that C. flavigena produces a unique lytic polysaccharide monooxygenase with activity on β-chitin, which is found, for example, in arthropods. The limited distribution of orthologous chitinolytic LPMOs suggests adaptation of individual cellulomonads to specific nutrient niches present in soil ecosystems. This research provides new insight into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria, and it raises new questions about the physiological function of these enzymes.
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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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Qu M, Guo X, Tian S, Yang Q, Kim M, Mun S, Noh MY, Kramer KJ, Muthukrishnan S, Arakane Y. AA15 lytic polysaccharide monooxygenase is required for efficient chitinous cuticle turnover during insect molting. Commun Biol 2022; 5:518. [PMID: 35641660 PMCID: PMC9156745 DOI: 10.1038/s42003-022-03469-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of crystalline polysaccharides including chitin and cellulose. The discovery of a large assortment of LPMO-like proteins widely distributed in insect genomes suggests that they could be involved in assisting chitin degradation in the exoskeleton, tracheae and peritrophic matrix during development. However, the physiological functions of insect LPMO-like proteins are still undetermined. To investigate the functions of insect LPMO15 subgroup I-like proteins (LPMO15-1s), two evolutionarily distant species, Tribolium castaneum and Locusta migratoria, were chosen. Depletion by RNAi of T. castaneum TcLPMO15-1 caused molting arrest at all developmental stages, whereas depletion of the L. migratoria LmLPMO15-1, prevented only adult eclosion. In both species, LPMO15-1-deficient animals were unable to shed their exuviae and died. TEM analysis revealed failure of turnover of the chitinous cuticle, which is critical for completion of molting. Purified recombinant LPMO15-1-like protein from Ostrinia furnacalis (rOfLPMO15-1) exhibited oxidative cleavage activity and substrate preference for chitin. These results reveal the physiological importance of catalytically active LPMO15-1-like proteins from distant insect species and provide new insight into the enzymatic mechanism of cuticular chitin turnover during molting.
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Affiliation(s)
- Mingbo Qu
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Xiaoxi Guo
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Shuang Tian
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
| | - Myeongjin Kim
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Seulgi Mun
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Department of Forest Resources, AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61186, South Korea
| | - Karl J Kramer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Yasuyuki Arakane
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea.
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Rajput M, Kumar M, Pareek N. Myco-chitinases as versatile biocatalysts for translation of coastal residual resources to eco-competent chito-bioactives. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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Molecular analysis of genes involved in chitin degradation from the chitinolytic bacterium Bacillus velezensis. Antonie van Leeuwenhoek 2022; 115:215-231. [PMID: 35001244 DOI: 10.1007/s10482-021-01697-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
Abstract
Bacillus velezensis RB.IBE29 is a potent biocontrol agent with high chitinase activity isolated from the rhizosphere of black pepper cultivated in the Central Highlands, Vietnam. Genome sequences revealed that this species possesses some GH18 chitinases and AA10 protein(s); however, these enzymes have not been experimentally characterized. In this work, three genes were identified from the genomic DNA of this bacterium and cloned in Escherichia coli. Sequence analysis exhibited that the ORF of chiA consists of 1,203 bp and encodes deduced 45.46 kDa-chitinase A of 400 aa. The domain structure of chitinase A is composed of a CBM 50 domain at the N-terminus and a catalytic domain at the C-terminus. The ORF of chiB includes 1,263 bp and encodes deduced 47.59 kDa-chitinase B of 420 aa. Chitinase B consists of two CBM50 domains at the N-terminus and a catalytic domain at the C-terminus. The ORF of lpmo10 is 621 bp and encodes a deduced 22.44 kDa-AA10 protein, BvLPMO10 of 206 aa. BvLPMO10 contains a signal peptide and an AA10 catalytic domain. Chitinases A and B were grouped into subfamily A of family 18 chitinases. Amino acid sequences in their catalytic domains lack aromatic residues (Trp, Phe, Tyr) probably involved in processivity and substrate binding compared with well-known bacterial GH18 chitinases. chiB was successfully expressed in E. coli. Purified rBvChiB degraded insoluble chitin and was responsible for inhibition of fungal spore-germination and egg hatching of plant-parasitic nematode. This is the first report describing the analysis of the chitinase system from B. velezensis.
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Rieder L, Stepnov AA, Sørlie M, Eijsink VG. Fast and Specific Peroxygenase Reactions Catalyzed by Fungal Mono-Copper Enzymes. Biochemistry 2021; 60:3633-3643. [PMID: 34738811 PMCID: PMC8638258 DOI: 10.1021/acs.biochem.1c00407] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/27/2021] [Indexed: 11/28/2022]
Abstract
The copper-dependent lytic polysaccharide monooxygenases (LPMOs) are receiving attention because of their role in the degradation of recalcitrant biomass and their intriguing catalytic properties. The fundamentals of LPMO catalysis remain somewhat enigmatic as the LPMO reaction is affected by a multitude of LPMO- and co-substrate-mediated (side) reactions that result in a complex reaction network. We have performed kinetic studies with two LPMOs that are active on soluble substrates, NcAA9C and LsAA9A, using various reductants typically employed for LPMO activation. Studies with NcAA9C under "monooxygenase" conditions showed that the impact of the reductant on catalytic activity is correlated with the hydrogen peroxide-generating ability of the LPMO-reductant combination, supporting the idea that a peroxygenase reaction is taking place. Indeed, the apparent monooxygenase reaction could be inhibited by a competing H2O2-consuming enzyme. Interestingly, these fungal AA9-type LPMOs were found to have higher oxidase activity than bacterial AA10-type LPMOs. Kinetic analysis of the peroxygenase activity of NcAA9C on cellopentaose revealed a fast stoichiometric conversion of high amounts of H2O2 to oxidized carbohydrate products. A kcat value of 124 ± 27 s-1 at 4 °C is 20 times higher than a previously described kcat for peroxygenase activity on an insoluble substrate (at 25 °C) and some 4 orders of magnitude higher than typical "monooxygenase" rates. Similar studies with LsAA9A revealed differences between the two enzymes but confirmed fast and specific peroxygenase activity. These results show that the catalytic site arrangement of LPMOs provides a unique scaffold for highly efficient copper redox catalysis.
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Affiliation(s)
- Lukas Rieder
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Anton A. Stepnov
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
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Støpamo FG, Røhr ÅK, Mekasha S, Petrović DM, Várnai A, Eijsink VGH. Characterization of a lytic polysaccharide monooxygenase from Aspergillus fumigatus shows functional variation among family AA11 fungal LPMOs. J Biol Chem 2021; 297:101421. [PMID: 34798071 PMCID: PMC8668981 DOI: 10.1016/j.jbc.2021.101421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
The discovery of oxidative cleavage of recalcitrant polysaccharides by lytic polysaccharide monooxygenases (LPMOs) has affected the study and industrial application of enzymatic biomass processing. Despite being widespread in fungi, LPMOs belonging to the auxiliary activity (AA) family AA11 have been understudied. While these LPMOs are considered chitin active, some family members have little or no activity toward chitin, and the only available crystal structure of an AA11 LPMO lacks features found in bacterial chitin-active AA10 LPMOs. Here, we report structural and functional characteristics of a single-domain AA11 LPMO from Aspergillus fumigatus, AfAA11A. The crystal structure shows a substrate-binding surface with features resembling those of known chitin-active LPMOs. Indeed, despite the absence of a carbohydrate-binding module, AfAA11A has considerable affinity for α-chitin and, more so, β-chitin. AfAA11A is active toward both these chitin allomorphs and enhances chitin degradation by an endoacting chitinase, in particular for α-chitin. The catalytic activity of AfAA11A on chitin increases when supplying reactions with hydrogen peroxide, showing that, like LPMOs from other families, AfAA11A has peroxygenase activity. These results show that, in stark contrast to the previously characterized AfAA11B from the same organism, AfAA11A likely plays a role in fungal chitin turnover. Thus, members of the hitherto rather enigmatic family of AA11 LPMOs show considerable structural and functional differences and may have multiple roles in fungal physiology.
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Affiliation(s)
- Fredrik Gjerstad Støpamo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Åsmund Kjendseth Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sophanit Mekasha
- 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
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Eigenfeld M, Kerpes R, Becker T. Recombinant protein linker production as a basis for non-invasive determination of single-cell yeast age in heterogeneous yeast populations. RSC Adv 2021; 11:31923-31932. [PMID: 35495491 PMCID: PMC9041608 DOI: 10.1039/d1ra05276d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
The physiological and metabolic diversity of a yeast culture is the sum of individual cell phenotypes. As well as environmental conditions, genetics, and numbers of cell divisions, a major factor influencing cell characteristics is cell age. A postcytokinesis bud scar on the mother cell, a benchmark in the replicative life span, is a quantifiable indicator of cell age, characterized by significant amounts of chitin. We developed a binding process for visualizing the bud scars of Saccharomyces pastorianus var. carlsbergensis using a protein linker containing a polyhistidine tag, a superfolder green fluorescent protein (sfGFP), and a chitin-binding domain (His6-SUMO-sfGFP-ChBD). The binding did not affect yeast viability; thus, our method provides the basis for non-invasive cell age determination using flow cytometry. The His6-SUMO-sfGFP-ChBD protein was synthesized in Escherichia coli, purified using two-stage chromatography, and checked for monodispersity and purity. Linker-cell binding and the characteristics of the bound complex were determined using flow cytometry and confocal laser scanning microscopy (CLSM). Flow cytometry showed that protein binding increased to 60 455 ± 2706 fluorescence units per cell. The specific coupling of the linker to yeast cells was additionally verified by CLSM and adsorption isotherms using yeast cells, E. coli cells, and chitin resin. We found a relationship between the median bud scar number, the median of the fluorescence units, and the chitin content of yeast cells. A fast measurement of yeast population dynamics by flow cytometry is possible, using this protein binding technique. Rapid qualitative determination of yeast cell age distribution can therefore be performed.
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Affiliation(s)
- Marco Eigenfeld
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
| | - Roland Kerpes
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
| | - Thomas Becker
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
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Rieder L, Petrović D, Väljamäe P, Eijsink VG, Sørlie M. Kinetic Characterization of a Putatively Chitin-Active LPMO Reveals a Preference for Soluble Substrates and Absence of Monooxygenase Activity. ACS Catal 2021; 11:11685-11695. [PMID: 34567832 PMCID: PMC8453653 DOI: 10.1021/acscatal.1c03344] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/24/2021] [Indexed: 12/23/2022]
Abstract
![]()
Enzymes known as
lytic polysaccharide monooxygenases (LPMOs) are
recognized as important contributors to aerobic enzymatic degradation
of recalcitrant polysaccharides such as chitin and cellulose. LPMOs
are remarkably abundant in nature, with some fungal species possessing
more than 50 LPMO genes, and the biological implications of this diversity
remain enigmatic. For example, chitin-active LPMOs have been encountered
in biological niches where chitin conversion does not seem to take
place. We have carried out an in-depth kinetic characterization of
a putatively chitin-active LPMO from Aspergillus fumigatus (AfAA11B), which, as we show here, has multiple
unusual properties, such as a low redox potential and high oxidase
activity. Furthermore, AfAA11B is hardly active on
chitin, while being very active on soluble oligomers of N-acetylglucosamine. In the presence of chitotetraose, the enzyme
can withstand considerable amounts of H2O2,
which it uses to efficiently and stoichiometrically convert this substrate.
The unique properties of AfAA11B allowed experiments
showing that it is a strict peroxygenase and does not catalyze a monooxygenase
reaction. This study shows that nature uses LPMOs for breaking glycosidic
bonds in non-polymeric substrates in reactions that depend on H2O2. The quest for the true substrates of these
enzymes, possibly carbohydrates in the cell wall of the fungus or
its competitors, will be of major interest.
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Affiliation(s)
- Lukas Rieder
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås N-1432, Norway
| | - Dejan Petrović
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås N-1432, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås N-1432, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås N-1432, Norway
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Madland E, Forsberg Z, Wang Y, Lindorff-Larsen K, Niebisch A, Modregger J, Eijsink VGH, Aachmann FL, Courtade G. Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. J Biol Chem 2021; 297:101084. [PMID: 34411561 PMCID: PMC8449059 DOI: 10.1016/j.jbc.2021.101084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022] Open
Abstract
Among the extensive repertoire of carbohydrate-active enzymes, lytic polysaccharide monooxygenases (LPMOs) have a key role in recalcitrant biomass degradation. LPMOs are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides such as cellulose and chitin. Several LPMOs contain carbohydrate-binding modules (CBMs) that are known to promote LPMO efficiency. However, structural and functional properties of some CBMs remain unknown, and it is not clear why some LPMOs, like CjLPMO10A from the soil bacterium Cellvibrio japonicus, have multiple CBMs (CjCBM5 and CjCBM73). Here, we studied substrate binding by these two CBMs to shine light on their functional variation and determined the solution structures of both by NMR, which constitutes the first structure of a member of the CBM73 family. Chitin-binding experiments and molecular dynamics simulations showed that, while both CBMs bind crystalline chitin with Kd values in the micromolar range, CjCBM73 has higher affinity for chitin than CjCBM5. Furthermore, NMR titration experiments showed that CjCBM5 binds soluble chitohexaose, whereas no binding of CjCBM73 to this chitooligosaccharide was detected. These functional differences correlate with distinctly different arrangements of three conserved aromatic amino acids involved in substrate binding. In CjCBM5, these residues show a linear arrangement that seems compatible with the experimentally observed affinity for single chitin chains. On the other hand, the arrangement of these residues in CjCBM73 suggests a wider binding surface that may interact with several chitin chains. Taken together, these results provide insight into natural variation among related chitin-binding CBMs and the possible functional implications of such variation.
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Affiliation(s)
- Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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The fish pathogen Aliivibrio salmonicida LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway. Appl Environ Microbiol 2021; 87:e0052921. [PMID: 34319813 DOI: 10.1128/aem.00529-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fish pathogen Aliivibrio (Vibrio) salmonicida LFI1238 is thought to be incapable of utilizing chitin as a nutrient source since approximately half of the genes representing the chitinolytic pathway are disrupted by insertion sequences. In the present study, we combined a broad set of analytical methods to investigate this hypothesis. Cultivation studies revealed that Al. salmonicida grew efficiently on N-acetylglucosamine (GlcNAc) and chitobiose ((GlcNAc)2), the primary soluble products resulting from enzymatic chitin hydrolysis. The bacterium was also able to grow on chitin particles, albeit at a lower rate compared to the soluble substrates. The genome of the bacterium contains five disrupted chitinase genes (pseudogenes) and three intact genes encoding a glycoside hydrolase family 18 (GH18) chitinase and two auxiliary activity family 10 (AA10) lytic polysaccharide monooxygenases (LPMOs). Biochemical characterization showed that the chitinase and LPMOs were able to depolymerize both α- and β-chitin to (GlcNAc)2 and oxidized chitooligosaccharides, respectively. Notably, the chitinase displayed up to 50-fold lower activity compared to other well-studied chitinases. Deletion of the genes encoding the intact chitinolytic enzymes showed that the chitinase was important for growth on β-chitin, whereas the LPMO gene-deletion variants only showed minor growth defects on this substrate. Finally, proteomic analysis of Al. salmonicida LFI1238 growth on β-chitin showed expression of all three chitinolytic enzymes, and intriguingly also three of the disrupted chitinases. In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present study we demonstrate that Al. salmonicida can degrade and metabolize chitin, the most abundant biopolymer in the ocean. Our findings shed new light on the environmental adaption of this fish pathogen.
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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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45
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Lorentzen SB, Arntzen MØ, Hahn T, Tuveng TR, Sørlie M, Zibek S, Vaaje-Kolstad G, Eijsink VGH. Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes. J Proteome Res 2021; 20:4041-4052. [PMID: 34191517 PMCID: PMC8802321 DOI: 10.1021/acs.jproteome.1c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Chitin is an abundant natural polysaccharide
that is hard to degrade
because of its crystalline nature and because it is embedded in robust
co-polymeric materials containing other polysaccharides, proteins,
and minerals. Thus, it is of interest to study the enzymatic machineries
of specialized microbes found in chitin-rich environments. We describe
a genomic and proteomic analysis of Andreprevotia ripae, a chitinolytic Gram-negative bacterium isolated from an anthill.
The genome of A. ripae encodes four secreted
family GH19 chitinases of which two were detected and upregulated
during growth on chitin. In addition, the genome encodes as many as
25 secreted GH18 chitinases, of which 17 were detected and 12 were
upregulated during growth on chitin. Finally, the single lytic polysaccharide
monooxygenase (LPMO) was strongly upregulated during growth on chitin.
Whereas 66% of the 29 secreted chitinases contained two carbohydrate-binding
modules (CBMs), this fraction was 93% (13 out of 14) for the upregulated
chitinases, suggesting an important role for these CBMs. Next to an
unprecedented multiplicity of upregulated chitinases, this study reveals
several chitin-induced proteins that contain chitin-binding CBMs but
lack a known catalytic function. These proteins are interesting targets
for discovery of enzymes used by nature to convert chitin-rich biomass.
The MS proteomic data have been deposited in the PRIDE database with
accession number PXD025087.
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Affiliation(s)
- Silje B Lorentzen
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
| | - Thomas Hahn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Tina R Tuveng
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, N-1433 Ås, Norway
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46
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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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47
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Monge EC, Gardner JG. Efficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicus. Mol Microbiol 2021; 116:366-380. [PMID: 33735458 DOI: 10.1111/mmi.14717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin utilization by microbes plays a significant role in biosphere carbon and nitrogen cycling, and studying the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade a broad range of recalcitrant polysaccharides. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and nonredundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics and bacterial genetics using ecologically relevant substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in C. japonicus. Using RNAseq analysis we found a coordinated expression of genes that encode polysaccharide-degrading enzymes. Mutational analysis determined that the hex20B gene product, predicted to encode a hexosaminidase, was required for efficient utilization of chito-oligosaccharides. Furthermore, two gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were also essential for chito-oligosaccharides utilization. This study further develops our model of C. japonicus chitin metabolism and may be predictive for other environmentally or industrially important bacteria.
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Affiliation(s)
- Estela C Monge
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
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48
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Jagadeeswaran G, Veale L, Mort AJ. Do Lytic Polysaccharide Monooxygenases Aid in Plant Pathogenesis and Herbivory? TRENDS IN PLANT SCIENCE 2021; 26:142-155. [PMID: 33097402 DOI: 10.1016/j.tplants.2020.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes mainly found in fungi, bacteria, and viruses, are responsible for enabling plant infection and degradation processes. Since their discovery 10 years ago, significant progress has been made in understanding the major role these enzymes play in biomass conversion. The recent discovery of additional LPMO families in fungi and oomycetes (AA16) as well as insects (AA15) strongly suggests that LPMOs might also be involved in biological processes such as overcoming plant defenses. In this review, we aim to give a comprehensive overview of the potential role of different LPMO families from the perspective of plant defense and their multiple implications in devising new strategies for achieving crop protection from plant pathogens and insect pests.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Lawrie Veale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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Montroni D, Sparla F, Fermani S, Falini G. Influence of proteins on mechanical properties of a natural chitin-protein composite. Acta Biomater 2021; 120:81-90. [PMID: 32439612 DOI: 10.1016/j.actbio.2020.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/04/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
In many biogenic materials, chitin chains are assembled in fibrils that are wrapped by a protein fold. In them, the mechanical properties are supposed to be related to intra- and inter- interactions among chitin and proteins. This hypothesis has been poorly investigated. Here, this research theme is studied using the pen of Loligo vulgaris as a model material of chitin-protein composites. Chemical treatments were used to change the interactions involving only the proteic phase, through unfolding and/or degradation processes. Successively, structural and mechanical parameters were examined using spectroscopy, microscopy, X-ray diffractometry, and tensile tests. The data analysis showed that chemical treatments did not modify the structure of the chitin matrix. This allowed to derive from the mechanical test analysis the following conclusions: (i) the maximum stress (σmax) relies on the presence of the disulfide bonds; (ii) the Young's modulus (E) relies on the overall correct folding of the proteins; (iii) the whole removal of proteins induces a decrease of E (> 90%) and σmax (> 80%), and an increase in the maximum elongation. These observations indicate that in the chitin matrix the proteins act as a strengthener, which efficacy is controlled by the presence of disulfide bridges. This reinforcement links the chitin fibrils avoiding them to slide one on the other and maximizing their resistance and stiffness. In conclusion, this knowledge can explain the physio-chemical properties of other biogenic polymeric composites and inspire the design of new materials. STATEMENT OF SIGNIFICANCE: To date, no study has addressed on how proteins influence chitin-composite material's mechanical properties. Here we show that the Young's modulus and the maximum stress mainly rely on protein disulfide bonds, the inter-proteins ones and those controlling the folding of chitin-binding domains. The removal of protein matrix induce a reduction of Young's modulus and maximum stress, leaving the chitin matrix structurally unaltered. The measure of the maximum elongation shows that the chitin fibrils slide on each other only after removing the protein matrix. In conclusion, this research shows that the proteins act as a stiff matrix reinforced by di-sulfide bridges that link crystalline chitin fibrils avoiding them to slide one on the other.
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50
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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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