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Sulaeva I, Budischowsky D, Rahikainen J, Marjamaa K, Støpamo FG, Khaliliyan H, Melikhov I, Rosenau T, Kruus K, Várnai A, Eijsink VGH, Potthast A. A novel approach to analyze the impact of lytic polysaccharide monooxygenases (LPMOs) on cellulosic fibres. Carbohydr Polym 2024; 328:121696. [PMID: 38220335 DOI: 10.1016/j.carbpol.2023.121696] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Enzymatic treatment of cellulosic fibres is a green alternative to classical chemical modification. For many applications, mild procedures for cellulose alteration are sufficient, in which the fibre structure and, therefore, the mechanical performance of cellulosic fibres are preserved. Lytic polysaccharide monooxygenases (LPMOs) bear a great potential to become a green reagent for such targeted cellulose modifications. An obstacle for wide implementation of LPMOs in tailored cellulose chemistry is the lack of suitable techniques to precisely monitor the LPMO impact on the polymer. Soluble oxidized cello-oligomers can be quantified using chromatographic and mass-spectrometric techniques. A considerable portion of the oxidized sites, however, remain on the insoluble cellulose fibres, and their quantification is difficult. Here, we describe a method for the simultaneous quantification of oxidized sites on cellulose fibres and changes in their molar mass distribution after treatment with LPMOs. The method is based on quantitative, heterogeneous, carbonyl-selective labelling with a fluorescent label (CCOA) followed by cellulose dissolution and size-exclusion chromatography (SEC). Application of the method to reactions of seven different LPMOs with pure cellulose fibres revealed pronounced functional differences between the enzymes, showing that this CCOA/SEC/MALS method is a promising tool to better understand the catalytic action of LPMOs.
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Affiliation(s)
- Irina Sulaeva
- Core Facility "Analysis of Lignocellulosics" (ALICE), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - David Budischowsky
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Jenni Rahikainen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland
| | - Kaisa Marjamaa
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland
| | - Fredrik Gjerstad Støpamo
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Hajar Khaliliyan
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Ivan Melikhov
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Thomas Rosenau
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
| | - Kristiina Kruus
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 Espoo, Finland; School of Chemical Engineering, Aalto University, P.O. Box 16100, Espoo 00076 AALTO, Finland
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Antje Potthast
- Institute of Chemistry of Renewable Resources, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria.
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Chen K, Zhao X, Zhang P, Long L, Ding S. A novel AA14 LPMO from Talaromyces rugulosus with bifunctional cellulolytic/hemicellulolytic activity boosted cellulose hydrolysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:30. [PMID: 38395898 PMCID: PMC10885436 DOI: 10.1186/s13068-024-02474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/10/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND The recently discovered PcAA14A and B from white-rot basidiomycete Pycnoporus coccineus enriched our understanding of the oxidative degradation of xylan in fungi, however, the unusual mode of action of AA14 LPMOs has sparked controversy. The substrate specificity and functionality of AA14 LPMOs still remain enigmatic and need further investigation. RESULTS In this study, a novel AA14 LPMO was characterized from the ascomycete Talaromyces rugulosus. TrAA14A has a broad substrate specificity with strong oxidative activity on pure amorphous cellulose and xyloglucan. It could simultaneously oxidize cellulose, xylan and xyloglucan in natural hemi/cellulosic substrate such as fibrillated eucalyptus pulp, and released native and oxidized cello-oligosaccharides, xylo-oligosaccharides and xyloglucan oligosaccharides from this substrate, but its cellulolytic/hemicellulolytic activity became weaker as the contents of xylan increase in the alkaline-extracted hemi/cellulosic substrates. The dual cellulolytic/hemicellulolytic activity enables TrAA14A to possess a profound boosting effect on cellulose hydrolysis by cellulolytic enzymes. Structure modelling of TrAA14A revealed that it exhibits a relatively flat active-site surface similar to the active-site surfaces in AA9 LPMOs but quite distinct from PcAA14B, despite TrAA14A is strongly clustered together with AA14 LPMOs. Remarkable difference in electrostatic potentials of L2 and L3 surfaces was also observed among TrAA14A, PcAA14B and NcLPMO9F. We speculated that the unique feature in substrate-binding surface might contribute to the cellulolytic/hemicellulolytic activity of TrAA14A. CONCLUSIONS The extensive cellulolytic/hemicellulolytic activity on natural hemi/cellulosic substrate indicated that TrAA14A from ascomycete is distinctively different from previously characterized xylan-active AA9 or AA14 LPMOs. It may play as a bifunctional enzyme to decompose some specific network structures formed between cellulose and hemicellulose in the plant cell walls. Our findings shed new insights into the novel substrate specificities and biological functionalities of AA14 LPMOs, and will contribute to developing novel bifunctional LPMOs as the booster in commercial cellulase cocktails to efficiently break down the hemicellulose-cellulose matrix in lignocellulose.
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Affiliation(s)
- Kaixiang Chen
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xu Zhao
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Peiyu Zhang
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Liangkun Long
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shaojun Ding
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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de Oliveira Gorgulho Silva C, Vuillemin M, Kabel MA, van Berkel WJH, Meyer AS, Agger JW. Polyphenol Oxidase Products Are Priming Agents for LPMO Peroxygenase Activity. CHEMSUSCHEM 2023; 16:e202300559. [PMID: 37278305 DOI: 10.1002/cssc.202300559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Polyphenol oxidases catalyze the hydroxylation of monophenols to diphenols, which are reducing agents for lytic polysaccharide monooxygenases (LPMOs) in their degradation of cellulose. In particular, the polyphenol oxidase MtPPO7 from Myceliophthora thermophila converts lignocellulose-derived monophenols, and under the new perspective of the peroxygenase reaction catalyzed by LPMOs, we aim to differentiate the role of the catalytic products of MtPPO7 in priming and fueling of LPMO activity. Exemplified by the activity of MtPPO7 towards guaiacol and by using the benchmark LPMO NcAA9C from Neurospora crassa we show that MtPPO7 catalytic products provide the initial electron for the reduction of Cu(II) to Cu(I) but cannot provide the required reducing power for continuous fueling of the LPMO. The priming reaction is shown to occur with catalytic amounts of MtPPO7 products and those compounds do not generate substantial amounts of H2 O2 in situ to fuel the LPMO peroxygenase activity. Reducing agents with a low propensity to generate H2 O2 can provide the means for controlling the LPMO catalysis through exogenous H2 O2 and thereby minimize any enzyme inactivation.
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Affiliation(s)
| | - Marlene Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs Lyngby, Denmark
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs Lyngby, Denmark
| | - Jane W Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs Lyngby, Denmark
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Schwaiger L, Zenone A, Csarman F, Ludwig R. Continuous photometric activity assays for lytic polysaccharide monooxygenase-Critical assessment and practical considerations. Methods Enzymol 2022; 679:381-404. [PMID: 36682872 DOI: 10.1016/bs.mie.2022.08.054] [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] [Indexed: 12/31/2022]
Abstract
Lytic polysaccharide monooxygenase (LPMO) is a monocopper-dependent enzyme that cleaves glycosidic bonds by using an oxidative mechanism. In nature, they act in concert with cellobiohydrolases to facilitate the efficient degradation of lignocellulosic biomass. After more than a decade of LPMO research, it has become evident that LPMOs are abundant in all domains of life and fulfill a diverse range of biological functions. Independent of their biological function and the preferred polysaccharide substrate, studying and characterizing LPMOs is tedious and so far mostly relied on the discontinuous analysis of the solubilized reaction products by HPLC/MS-based methods. In the absence of appropriate substrates, LPMOs can engage in two off-pathway reactions, i.e., an oxidase and a peroxidase-like activity. These futile reactions have been exploited to set up easy-to-use continuous spectroscopic assays. As the natural substrates of newly discovered LPMOs are often unknown, widely applicable, simple, reliable, and robust spectroscopic assays are required to monitor LPMO expression and to perform initial biochemical characterizations, e.g., thermal stability measurements. Here we provide detailed descriptions and practical protocols to perform continuous photometric assays using either 2,6-dimethoxyphenol (2,6-DMP) or hydrocoerulignone as colorimetric substrates as a broadly applicable assay for a range of LPMOs. In addition, a turbidimetric measurement is described as the currently only method available to continuously monitor LPMOs acting on amorphous cellulose.
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Affiliation(s)
- Lorenz Schwaiger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alice Zenone
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Florian Csarman
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Roland Ludwig
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
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Wu S, Tian J, Xie N, Adnan M, Wang J, Liu G. A sensitive, accurate, and high-throughput gluco-oligosaccharide oxidase-based HRP colorimetric method for assaying lytic polysaccharide monooxygenase activity. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:15. [PMID: 35418300 PMCID: PMC8830019 DOI: 10.1186/s13068-022-02112-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/28/2022] [Indexed: 11/17/2022]
Abstract
Background The AA9 (auxiliary activities) family of lytic polysaccharide monooxygenases (AA9 LPMOs) is a ubiquitous and diverse group of enzymes in the fungal kingdom. They catalyse the oxidative cleavage of glycosidic bonds in lignocellulose and exhibit great potential for biorefinery applications. Robust, high-throughput and direct methods for assaying AA9 LPMO activity, which are prerequisites for screening LPMOs with excellent properties, are still lacking. Here, we present a gluco-oligosaccharide oxidase (GOOX)-based horseradish peroxidase (HRP) colorimetric method for assaying AA9 LPMO activity. Results We cloned and expressed a GOOX gene from Sarocladium strictum in Trichoderma reesei, purified the recombinant SsGOOX, validated its properties, and developed an SsGOOX-based HRP colorimetric method for assaying cellobiose concentrations. Then, we expressed two AA9 LPMOs from Thielavia terrestris, TtAA9F and TtAA9G, in T. reesei, purified the recombinant proteins, and analysed their product profiles and regioselectivity towards phosphoric acid swollen cellulose (PASC). TtAA9F was characterized as a C1-type (class 1) LPMO, while TtAA9G was characterized as a C4-type (class 2) LPMO. Finally, the SsGOOX-based HRP colorimetric method was used to quantify the total concentration of reducing lytic products from the LPMO reaction, and the activities of both the C1- and C4-type LPMOs were analysed. These LPMOs could be effectively analysed with limits of detection (LoDs) less than 30 nmol/L, and standard curves between the A515 and LPMO concentrations with determination coefficients greater than 0.994 were obtained. Conclusions A novel, sensitive and accurate assay method that directly targets the main activity of both C1- and C4-type AA9 LPMOs was established. This method is easy to use and could be performed on a microtiter plate for high-throughput screening of AA9 LPMOs with desirable properties. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02112-2.
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Deletion of AA9 Lytic Polysaccharide Monooxygenases Impacts A. nidulans Secretome and Growth on Lignocellulose. Microbiol Spectr 2022; 10:e0212521. [PMID: 35658600 PMCID: PMC9241910 DOI: 10.1128/spectrum.02125-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, and bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are cosecreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that three target LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose-active enzymes with distinct regioselectivity and activity on cellulose with different proportions of crystalline and amorphous regions. AnLPMO9s deletion and overexpression studies corroborate functional data. The abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G was less abundant and constantly secreted, and acts preferentially on crystalline regions of cellulose, uniquely displaying activity on highly crystalline algae cellulose. Single or double deletion of AnLPMO9s resulted in about 25% reduction in fungal growth on sugarcane straw but not on Avicel, demonstrating the contribution of LPMO9s for the saprophytic fungal lifestyle relies on the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of alternative electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification. IMPORTANCE Fungal lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that boost plant biomass degradation in combination with glycoside hydrolases. Secretion of LPMO9s arsenal by Aspergillus nidulans is influenced by the substrate and time of induction. These findings along with the biochemical characterization of novel fungal LPMO9s have implications on our understanding of their concerted action, allowing rational engineering of fungal strains for biotechnological applications such as plant biomass degradation. Additionally, the role of oxidative players in fungal growth on plant biomass was evaluated by deletion and overexpression experiments using a model fungal system.
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Méndez-Líter JA, Ayuso-Fernández I, Csarman F, de Eugenio LI, Míguez N, Plou FJ, Prieto A, Ludwig R, Martínez MJ. Lytic Polysaccharide Monooxygenase from Talaromyces amestolkiae with an Enigmatic Linker-like Region: The Role of This Enzyme on Cellulose Saccharification. Int J Mol Sci 2021; 22:13611. [PMID: 34948409 PMCID: PMC8703934 DOI: 10.3390/ijms222413611] [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: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022] Open
Abstract
The first lytic polysaccharide monooxygenase (LPMO) detected in the genome of the widespread ascomycete Talaromyces amestolkiae (TamAA9A) has been successfully expressed in Pichia pastoris and characterized. Molecular modeling of TamAA9A showed a structure similar to those from other AA9 LPMOs. Although fungal LPMOs belonging to the genera Penicillium or Talaromyces have not been analyzed in terms of regioselectivity, phylogenetic analyses suggested C1/C4 oxidation which was confirmed by HPAEC. To ascertain the function of a C-terminal linker-like region present in the wild-type sequence of the LPMO, two variants of the wild-type enzyme, one without this sequence and one with an additional C-terminal carbohydrate binding domain (CBM), were designed. The three enzymes (native, without linker and chimeric variant with a CBM) were purified in two chromatographic steps and were thermostable and active in the presence of H2O2. The transition midpoint temperature of the wild-type LPMO (Tm = 67.7 °C) and its variant with only the catalytic domain (Tm = 67.6 °C) showed the highest thermostability, whereas the presence of a CBM reduced it (Tm = 57.8 °C) and indicates an adverse effect on the enzyme structure. Besides, the potential of the different T. amestolkiae LPMO variants for their application in the saccharification of cellulosic and lignocellulosic materials was corroborated.
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Affiliation(s)
- Juan Antonio Méndez-Líter
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.); (A.P.)
| | - Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1462 Ås, Norway;
| | - Florian Csarman
- Department of Food Science and Technology, BOKU–University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (F.C.); (R.L.)
| | - Laura Isabel de Eugenio
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.); (A.P.)
| | - Noa Míguez
- Instituto de Catálisis y Petroleoquímica, Spanish National Research Council (CSIC), Marie Curie 2, 28049 Madrid, Spain; (N.M.); (F.J.P.)
| | - Francisco J. Plou
- Instituto de Catálisis y Petroleoquímica, Spanish National Research Council (CSIC), Marie Curie 2, 28049 Madrid, Spain; (N.M.); (F.J.P.)
| | - Alicia Prieto
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.); (A.P.)
| | - Roland Ludwig
- Department of Food Science and Technology, BOKU–University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (F.C.); (R.L.)
| | - María Jesús Martínez
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.); (A.P.)
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Calderaro F, Bevers LE, van den Berg MA. Oxidative Power: Tools for Assessing LPMO Activity on Cellulose. Biomolecules 2021; 11:biom11081098. [PMID: 34439765 PMCID: PMC8391687 DOI: 10.3390/biom11081098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cellulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have been elucidated, the need for fast and reliable methods to assess its activity have become clear. Several aspects such as its co-substrates, electron donors, inhibiting factors, and the inhomogeneity of lignocellulose had to be considered during experimental design and data interpretation, as they can impact and often hamper outcomes. This review provides an overview of the currently available methods to measure LPMO activity, including their potential and limitations, and it is illustrated with practical examples.
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Affiliation(s)
- Federica Calderaro
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
- Molecular Enzymolog y Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Correspondence: ; Tel.: +31-6-36028569
| | - Loes E. Bevers
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
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Wang D, Li Y, Zheng Y, Hsieh YSY. Recent Advances in Screening Methods for the Functional Investigation of Lytic Polysaccharide Monooxygenases. Front Chem 2021; 9:653754. [PMID: 33912540 PMCID: PMC8072006 DOI: 10.3389/fchem.2021.653754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.
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Affiliation(s)
- Damao Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Yanping Li
- College of Food Science, Southwest University, Chongqing, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.,School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Ferreira Filho JA, Horta MAC, Dos Santos CA, Almeida DA, Murad NF, Mendes JS, Sforça DA, Silva CBC, Crucello A, de Souza AP. "Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)". BMC Genomics 2020; 21:757. [PMID: 33138770 PMCID: PMC7607812 DOI: 10.1186/s12864-020-07158-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/18/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters. RESULTS We used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multiomics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 being CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in Trichoderma spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family. CONCLUSIONS Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes.
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Affiliation(s)
- Jaire A Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Maria Augusta C Horta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
- Holzforshung München, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Clelton A Dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Deborah A Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | - Natália F Murad
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Juliano S Mendes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Danilo A Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Claudio Benício C Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Aline Crucello
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Anete P de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Department of Plant Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil.
- Dept. de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, CEP 13083-875, Brazil.
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12
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Forsberg Z, Stepnov AA, Nærdal GK, Klinkenberg G, Eijsink VGH. Engineering lytic polysaccharide monooxygenases (LPMOs). Methods Enzymol 2020; 644:1-34. [PMID: 32943141 DOI: 10.1016/bs.mie.2020.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze the hydroxylation of glycosidic bonds found in the most abundant and recalcitrant polysaccharides on Earth. Since their discovery in 2010, these enzymes have received extensive attention in both fundamental and applied research due to their remarkable oxidative power and synergistic interplay with hydrolytic enzymes. The harsh and unnatural conditions used in industrial enzymatic saccharification processes and the sensitivity of LPMOs for damage induced by reactive oxygen species call for enzyme engineering to develop LPMOs to become robust industrial biocatalysts. Other engineering targets include improved catalytic activity, adjusted substrate specificity and the introduction of completely new activities. Reaching these targets not only requires appropriate methods for measuring enzyme activity, but also requires in-depth knowledge of the active site and the reaction mechanism, which is yet to be achieved in the LPMO field. Here we describe what has been done in the LPMO engineering field so far. Furthermore, we address the difficulties involved in properly assessing LPMO functionality, which are due to common side reactions taking place in LPMO reactions and which complicate screening methods.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Guro Kruge Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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13
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Monclaro AV, Petrović DM, Alves GSC, Costa MMC, Midorikawa GEO, Miller RNG, Filho EXF, Eijsink VGH, Várnai A. Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity. PLoS One 2020; 15:e0235642. [PMID: 32640001 PMCID: PMC7343150 DOI: 10.1371/journal.pone.0235642] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/19/2020] [Indexed: 11/23/2022] Open
Abstract
Aspergillus tamarii grows abundantly in naturally composting waste fibers of the textile industry and has a great potential in biomass decomposition. Amongst the key (hemi)cellulose-active enzymes in the secretomes of biomass-degrading fungi are the lytic polysaccharide monooxygenases (LPMOs). By catalyzing oxidative cleavage of glycoside bonds, LPMOs promote the activity of other lignocellulose-degrading enzymes. Here, we analyzed the catalytic potential of two of the seven AA9-type LPMOs that were detected in recently published transcriptome data for A. tamarii, namely AtAA9A and AtAA9B. Analysis of products generated from cellulose revealed that AtAA9A is a C4-oxidizing enzyme, whereas AtAA9B yielded a mixture of C1- and C4-oxidized products. AtAA9A was also active on cellopentaose and cellohexaose. Both enzymes also cleaved the β-(1→4)-glucan backbone of tamarind xyloglucan, but with different cleavage patterns. AtAA9A cleaved the xyloglucan backbone only next to unsubstituted glucosyl units, whereas AtAA9B yielded product profiles indicating that it can cleave the xyloglucan backbone irrespective of substitutions. Building on these new results and on the expanding catalog of xyloglucan- and oligosaccharide-active AA9 LPMOs, we discuss possible structural properties that could underlie the observed functional differences. The results corroborate evidence that filamentous fungi have evolved AA9 LPMOs with distinct substrate specificities and regioselectivities, which likely have complementary functions during biomass degradation.
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Affiliation(s)
- Antonielle V. Monclaro
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Dejan M. Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriel S. C. Alves
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Marcos M. C. Costa
- Brazilian Agricultural Research Corporation, Embrapa CENARGEN, Brasília, Brazil
| | - Glaucia E. O. Midorikawa
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Robert N. G. Miller
- Laboratory of Microbiology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Edivaldo X. F. Filho
- Laboratory of Enzymology, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Drzeżdżon J, Jacewicz D, Sielicka A, Chmurzyński L. MALDI-MS for polymer characterization – Recent developments and future prospects. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Eijsink VGH, Petrovic D, Forsberg Z, Mekasha S, Røhr ÅK, Várnai A, Bissaro B, Vaaje-Kolstad G. On the functional characterization of lytic polysaccharide monooxygenases (LPMOs). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:58. [PMID: 30923566 PMCID: PMC6423801 DOI: 10.1186/s13068-019-1392-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are abundant in nature and best known for their role in the enzymatic conversion of recalcitrant polysaccharides such as chitin and cellulose. LPMO activity requires an oxygen co-substrate, which was originally thought to be O2, but which may also be H2O2. Functional characterization of LPMOs is not straightforward because typical reaction mixtures will promote side reactions, including auto-catalytic inactivation of the enzyme. For example, despite some recent progress, there is still limited insight into the kinetics of the LPMO reaction. Recent discoveries concerning the role of H2O2 in LPMO catalysis further complicate the picture. Here, we review commonly used methods for characterizing LPMOs, with focus on benefits and potential pitfalls, rather than on technical details. We conclude by pointing at a few key problems and potential misconceptions that should be taken into account when interpreting existing data and planning future experiments.
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Affiliation(s)
- Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Dejan Petrovic
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Sophanit Mekasha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
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