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Semenova MV, Gusakov AV, Telitsin VD, Rozhkova AM, Kondratyeva EG, Sinitsyn AP. Purification and characterization of two forms of the homologously expressed lytic polysaccharide monooxygenase (PvLPMO9A) from Penicillium verruculosum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140297. [DOI: 10.1016/j.bbapap.2019.140297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/17/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022]
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Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
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153
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Cellobiose dehydrogenase. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:457-489. [DOI: 10.1016/bs.enz.2020.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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154
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Filandr F, Man P, Halada P, Chang H, Ludwig R, Kracher D. The H 2O 2-dependent activity of a fungal lytic polysaccharide monooxygenase investigated with a turbidimetric assay. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:37. [PMID: 32158501 PMCID: PMC7057652 DOI: 10.1186/s13068-020-01673-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/01/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent redox enzymes that cleave recalcitrant biopolymers such as cellulose, chitin, starch and hemicelluloses. Although LPMOs receive ample interest in industry and academia, their reaction mechanism is not yet fully understood. Recent studies showed that H2O2 is a more efficient cosubstrate for the enzyme than O2, which could greatly affect the utilization of LPMOs in industrial settings. RESULTS We probe the reactivity of LPMO9C from the cellulose-degrading fungus Neurospora crassa with a turbidimetric assay using phosphoric acid-swollen cellulose (PASC) as substrate and H2O2 as a cosubstrate. The measurements were also followed by continuous electrochemical H2O2 detection and LPMO reaction products were analysed by mass spectrometry. Different systems for the in situ generation of H2O2 and for the reduction of LPMO's active-site copper were employed, including glucose oxidase, cellobiose dehydrogenase, and the routinely used reductant ascorbate. CONCLUSIONS We found for all systems that the supply of H2O2 limited LPMO's cellulose depolymerization activity, which supports the function of H2O2 as the relevant cosubstrate. The turbidimetric assay allowed rapid determination of LPMO activity on a cellulosic substrate without the need for time-consuming and instrumentally elaborate analysis methods.
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Affiliation(s)
- Frantisek Filandr
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague 2, Czech Republic
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Petr Man
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Petr Halada
- BioCeV-Institute of Microbiology, The Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Hucheng Chang
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Kracher
- Biocatalysis and Biosensing Research Group, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- The University of Manchester, Manchester Institute of Biotechnology, Manchester, M1 7DN UK
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155
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Mäkelä MR, Hildén K, Kowalczyk JE, Hatakka A. Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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156
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Zerva A, Pentari C, Grisel S, Berrin JG, Topakas E. A new synergistic relationship between xylan-active LPMO and xylobiohydrolase to tackle recalcitrant xylan. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:142. [PMID: 32793303 PMCID: PMC7419196 DOI: 10.1186/s13068-020-01777-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/29/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Hemicellulose accounts for a significant part of plant biomass, and still poses a barrier to the efficient saccharification of lignocellulose. The recalcitrant part of hemicellulose is a serious impediment to the action of cellulases, despite the use of xylanases in the cellulolytic cocktail mixtures. However, the complexity and variety of hemicelluloses in different plant materials require the use of highly specific enzymes for a complete breakdown. Over the last few years, new fungal enzymes with novel activities on hemicelluloses have emerged. In the present study, we explored the synergistic relationships of the xylan-active AA14 lytic polysaccharide monooxygenase (LPMO), PcAA14B, with the recently discovered glucuronoxylan-specific xylanase TtXyn30A, of the (sub)family GH30_7, displaying xylobiohydrolase activity, and with commercial cellobiohydrolases, on pretreated natural lignocellulosic substrates. RESULTS PcAA14B and TtXyn30A showed a strong synergistic interaction on the degradation of the recalcitrant part of xylan. PcAA14B was able to increase the release of xylobiose from TtXyn30A, showing a degree of synergism (DS) of 3.8 on birchwood cellulosic fibers, and up to 5.7 on pretreated beechwood substrates. The increase in activity was dose- and time- dependent. A screening study on beechwood materials pretreated with different methods showed that the effect of the PcAA14B-TtXyn30A synergism was more prominent on substrates with low hemicellulose content, indicating that PcAA14B is mainly active on the recalcitrant part of xylan, which is in close proximity to the underlying cellulose fibers. Simultaneous addition of both enzymes resulted in higher DS than sequential addition. Moreover, PcAA14B was found to enhance cellobiose release from cellobiohydrolases during hydrolysis of pretreated lignocellulosic substrates, as well as microcrystalline cellulose. CONCLUSIONS The results of the present study revealed a new synergistic relationship not only among two recently discovered xylan-active enzymes, the LPMO PcAA14B, and the GH30_7 glucuronoxylan-active xylobiohydrolase TtXyn30A, but also among PcAA14B and cellobiohydrolases. We hypothesize that PcAA14B creates free ends in the xylan polymer, which can be used as targets for the action of TtXyn30A. The results are of special importance for the design of next-generation enzymatic cocktails, able to efficiently remove hemicelluloses, allowing complete saccharification of cellulose in plant biomass.
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Affiliation(s)
- Anastasia Zerva
- Industrial Biotechnology and Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
- INRAE, Aix Marseille University, Biodiversité Et Biotechnologie Fongiques (BBF), UMR1163, 13009 Marseille, France
| | - Christina Pentari
- Industrial Biotechnology and Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Sacha Grisel
- INRAE, Aix Marseille University, Biodiversité Et Biotechnologie Fongiques (BBF), UMR1163, 13009 Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille University, Biodiversité Et Biotechnologie Fongiques (BBF), UMR1163, 13009 Marseille, France
| | - Evangelos Topakas
- Industrial Biotechnology and Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
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157
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Challacombe JF, Hesse CN, Bramer LM, McCue LA, Lipton M, Purvine S, Nicora C, Gallegos-Graves LV, Porras-Alfaro A, Kuske CR. Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics 2019; 20:976. [PMID: 31830917 PMCID: PMC6909477 DOI: 10.1186/s12864-019-6358-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. RESULTS Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. CONCLUSIONS This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.
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Affiliation(s)
- Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Present address: Colorado State University, College of Agricultural Sciences, 301 University Ave, Fort Collins, CO, 80523, USA.
| | - Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Horticultural Crops Research, USDA ARS, Corvallis, OR, USA
| | - Lisa M Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mary Lipton
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel Purvine
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie Nicora
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | | | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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158
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Laurent CV, Sun P, Scheiblbrandner S, Csarman F, Cannazza P, Frommhagen M, van Berkel WJ, Oostenbrink C, Kabel MA, Ludwig R. Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity. Int J Mol Sci 2019; 20:E6219. [PMID: 31835532 PMCID: PMC6940765 DOI: 10.3390/ijms20246219] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 12/07/2019] [Indexed: 12/29/2022] Open
Abstract
In past years, new lytic polysaccharide monooxygenases (LPMOs) have been discovered as distinct in their substrate specificity. Their unconventional, surface-exposed catalytic sites determine their enzymatic activities, while binding sites govern substrate recognition and regioselectivity. An additional factor influencing activity is the presence or absence of a family 1 carbohydrate binding module (CBM1) connected via a linker to the C-terminus of the LPMO. This study investigates the changes in activity induced by shortening the second active site segment (Seg2) or removing the CBM1 from Neurospora crassa LPMO9C. NcLPMO9C and generated variants have been tested on regenerated amorphous cellulose (RAC), carboxymethyl cellulose (CMC) and xyloglucan (XG) using activity assays, conversion experiments and surface plasmon resonance spectroscopy. The absence of CBM1 reduced the binding affinity and activity of NcLPMO9C, but did not affect its regioselectivity. The linker was found important for the thermal stability of NcLPMO9C and the CBM1 is necessary for efficient binding to RAC. Wild-type NcLPMO9C exhibited the highest activity and strongest substrate binding. Shortening of Seg2 greatly reduced the activity on RAC and CMC and completely abolished the activity on XG. This demonstrates that Seg2 is indispensable for substrate recognition and the formation of productive enzyme-substrate complexes.
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Affiliation(s)
- Christophe V.F.P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Florian Csarman
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
| | - Pietro Cannazza
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Willem J.H. van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands; (P.S.); (M.F.); (W.J.H.v.B.); (M.A.K.)
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU—University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (C.V.F.P.L.); (S.S.); (F.C.); (P.C.)
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159
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Breslmayr E, Daly S, Požgajčić A, Chang H, Rezić T, Oostenbrink C, Ludwig R. Improved spectrophotometric assay for lytic polysaccharide monooxygenase. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:283. [PMID: 31827611 PMCID: PMC6894463 DOI: 10.1186/s13068-019-1624-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/28/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND The availability of a sensitive and robust activity assay is a prerequisite for efficient enzyme production, purification, and characterization. Here we report on a spectrophotometric assay for lytic polysaccharide monooxygenase (LPMO), which is an advancement of the previously published 2,6-dimethoxyphenol (2,6-DMP)-based LPMO assay. The new assay is based on hydrocoerulignone as substrate and hydrogen peroxide as cosubstrate and aims toward a higher sensitivity at acidic pH and a more reliable detection of LPMO in complex matrices like culture media. RESULTS An LPMO activity assay following the colorimetric oxidation of hydrocoerulignone to coerulignone was developed. This peroxidase activity of LPMO in the presence of hydrogen peroxide can be detected in various buffers between pH 4-8. By reducing the substrate and cosubstrate concentration, the assay has been optimized for minimal autoxidation and enzyme deactivation while maintaining sensitivity. Finally, the optimized and validated LPMO assay was used to follow the recombinant expression of an LPMO in Pichia pastoris and to screen for interfering substances in fermentation media suppressing the assayed reaction. CONCLUSIONS The biphenol hydrocoerulignone is a better substrate for LPMO than the monophenol 2,6-DMP, because of a ~ 30 times lower apparent K M value and a 160 mV lower oxidation potential. This greatly increases the measured LPMO activity when using hydrocoerulignone instead of 2,6-DMP under otherwise similar assay conditions. The improved activity allows the adaptation of the LPMO assay toward a higher sensitivity, different buffers and pH values, more stable assay conditions or to overcome low concentrations of inhibiting substances. The developed assay protocol and optimization guidelines increase the adaptability and applicability of the hydrocoerulignone assay for the production, purification, and characterization of LPMOs.
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Affiliation(s)
- Erik Breslmayr
- Biocatalysis and Biosensor Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Sarah Daly
- Biocatalysis and Biosensor Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alen Požgajčić
- Biocatalysis and Biosensor Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Hucheng Chang
- Biocatalysis and Biosensor Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Tonči Rezić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensor Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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160
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Forsberg Z, Sørlie M, Petrović D, Courtade G, Aachmann FL, Vaaje-Kolstad G, Bissaro B, Røhr ÅK, Eijsink VGH. Polysaccharide degradation by lytic polysaccharide monooxygenases. Curr Opin Struct Biol 2019; 59:54-64. [DOI: 10.1016/j.sbi.2019.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
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161
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Paradisi A, Johnston EM, Tovborg M, Nicoll CR, Ciano L, Dowle A, McMaster J, Hancock Y, Davies GJ, Walton PH. Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H 2O 2. J Am Chem Soc 2019; 141:18585-18599. [PMID: 31675221 PMCID: PMC7007232 DOI: 10.1021/jacs.9b09833] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 01/14/2023]
Abstract
Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)-tyrosyl radical center entails the formation of significant Cu(II)-(●OTyr) overlap, which in turn requires that the plane of the d(x2-y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a "hole-hopping" charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.
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Affiliation(s)
- Alessandro Paradisi
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Esther M. Johnston
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | | | - Callum R. Nicoll
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Luisa Ciano
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Adam Dowle
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Jonathan McMaster
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Y. Hancock
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
- York
Cross-Disciplinary Centre for Systems Analysis, University of York, Heslington,
York YO10 5GE, United Kingdom
| | - Gideon J. Davies
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Paul H. Walton
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
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162
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Malgas S, Mafa MS, Mkabayi L, Pletschke BI. A mini review of xylanolytic enzymes with regards to their synergistic interactions during hetero-xylan degradation. World J Microbiol Biotechnol 2019; 35:187. [PMID: 31728656 DOI: 10.1007/s11274-019-2765-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously) with their distinctive roles in mind to achieve efficient xylan degradation. With respect to homeosynergy, synergism appears to be as a result of β-xylanase and/or oligosaccharide reducing-end β-xylanase liberating xylo-oligomers (XOS) that are preferred substrates of the processive β-xylosidase. With regards to hetero-synergism, two cross relationships appear to exist and seem to be the reason for synergism between the enzymes during xylan degradation. These cross relations are the debranching enzymes such as α-glucuronidase or side-chain cleaving enzymes such as carbohydrate esterases (CE) removing decorations that would have hindered back-bone-cleaving enzymes, while backbone-cleaving-enzymes liberate XOS that are preferred substrates of the debranching and side-chain-cleaving enzymes. This interaction is demonstrated by high yields in co-production of xylan substituents such as arabinose, glucuronic acid and ferulic acid, and XOS. Finally, lytic polysaccharide monooxygenases (LPMO) have also been implicated in boosting whole lignocellulosic biomass or insoluble xylan degradation by glycoside hydrolases (GH) by possibly disrupting entangled xylan residues. Since it has been observed that the same enzyme (same Enzyme Commission, EC, classification) from different GH or CE and/or AA families can display different synergistic interactions with other enzymes due to different substrate specificities and properties, in this review, we propose an approach of enzyme selection (and mode of application thereof) during xylan degradation, as this can improve the economic viability of the degradation of xylan for producing precursors of value added products.
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Affiliation(s)
- Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Mpho S Mafa
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.,Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Wits University, Johannesburg, Gauteng, 2000, South Africa
| | - Lithalethu Mkabayi
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Brett I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.
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163
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Specific Xylan Activity Revealed for AA9 Lytic Polysaccharide Monooxygenases of the Thermophilic Fungus Malbranchea cinnamomea by Functional Characterization. Appl Environ Microbiol 2019; 85:AEM.01408-19. [PMID: 31540984 PMCID: PMC6856335 DOI: 10.1128/aem.01408-19] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/14/2019] [Indexed: 11/20/2022] Open
Abstract
The thermophilic biomass-degrader Malbranchea cinnamomea exhibits poor growth on cellulose but excellent growth on hemicelluloses as the sole carbon source. This is surprising considering that its genome encodes eight lytic polysaccharide monooxygenases (LPMOs) from auxiliary activity family 9 (AA9), enzymes known for their high potential in accelerating cellulose depolymerization. We characterized four of the eight (M. cinnamomea AA9s) McAA9s, namely, McAA9A, McAA9B, McAA9F, and McAA9H, to gain a deeper understanding about their roles in the fungus. The characterized McAA9s were active on hemicelluloses, including xylan, glucomannan, and xyloglucan, and furthermore, in accordance with transcriptomics data, differed in substrate specificity. Of the McAA9s, McAA9H is unique, as it preferentially cleaves residual xylan in phosphoric acid-swollen cellulose (PASC). Moreover, when exposed to cellulose-xylan blends, McAA9H shows a preference for xylan and for releasing (oxidized) xylooligosaccharides. The cellulose dependence of the xylan activity suggests that a flat conformation, with rigidity similar to that of cellulose microfibrils, is a prerequisite for productive interaction between xylan and the catalytic surface of the LPMO. McAA9H showed a similar trend on xyloglucan, underpinning the suggestion that LPMO activity on hemicelluloses strongly depends on the polymers' physicochemical context and conformation. Our results support the notion that LPMO multiplicity in fungal genomes relates to the large variety of copolymeric polysaccharide arrangements occurring in the plant cell wall.IMPORTANCE The Malbranchea cinnamomea LPMOs (McAA9s) showed activity on a broad range of soluble and insoluble substrates, suggesting their involvement in various steps of biomass degradation besides cellulose decomposition. Our results indicate that the fungal AA9 family is more diverse than originally thought and able to degrade almost any kind of plant cell wall polysaccharide. The discovery of an AA9 that preferentially cleaves xylan enhances our understanding of the physiological roles of LPMOs and enables the use of xylan-specific LPMOs in future applications.
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164
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Voshol GP, Punt PJ, Vijgenboom E. Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments. F1000Res 2019; 8:1834. [PMID: 31956399 PMCID: PMC6950343 DOI: 10.12688/f1000research.21104.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
Insight into the inter- and intra-family relationship of protein families is important, since it can aid understanding of substrate specificity evolution and assign putative functions to proteins with unknown function. To study both these inter- and intra-family relationships, the ability to build phylogenetic trees using the most sensitive sequence similarity search methods (e.g. profile hidden Markov model (pHMM)-pHMM alignments) is required. However, existing solutions require a very long calculation time to obtain the phylogenetic tree. Therefore, a faster protocol is required to make this approach efficient for research. To contribute to this goal, we extended the original Profile Comparer program (PRC) for the construction of large pHMM phylogenetic trees at speeds several orders of magnitude faster compared to pHMM-tree. As an example, PRC Extended (PRCx) was used to study the phylogeny of over 10,000 sequences of lytic polysaccharide monooxygenase (LPMO) from over seven families. Using the newly developed program we were able to reveal previously unknown homologs of LPMOs, namely the PFAM Egh16-like family. Moreover, we show that the substrate specificities have evolved independently several times within the LPMO superfamily. Furthermore, the LPMO phylogenetic tree, does not seem to follow taxonomy-based classification.
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Affiliation(s)
- Gerben P. Voshol
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
- Dutch DNA Biotech B.V., Utrecht, 3584CH, The Netherlands
| | - Peter J. Punt
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
- Dutch DNA Biotech B.V., Utrecht, 3584CH, The Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
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165
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Adsul M, Sandhu SK, Singhania RR, Gupta R, Puri SK, Mathur A. Designing a cellulolytic enzyme cocktail for the efficient and economical conversion of lignocellulosic biomass to biofuels. Enzyme Microb Technol 2019; 133:109442. [PMID: 31874688 DOI: 10.1016/j.enzmictec.2019.109442] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022]
Abstract
Concerns about dwindling fossil fuels and their unfavorable environmental impacts shifted the global focus towards the development of biofuels from lignocellulosic feedstocks. The structure of this biomass is very complex due to which variety of enzymes (cellulolytic, hemicellulolytic, auxiliary/AA9) and proteins (e.g. swollenin) required for efficient deconstruction. Major impediments in large-scale commercial production of cellulosic ethanol are the cost of cellulases and inability of any single microorganism to produce all cellulolytic components in sufficient titers. In the recent past, various methods for reducing the enzyme cost during cellulosic ethanol production have been attempted. These include designing optimal synergistic enzyme blends/cocktail, having certain ratios of enzymes from different microbial sources, for efficient hydrolysis of pretreated biomass. However, the mechanisms underlying the development, strategies for production and evaluation of optimal cellulolytic cocktails still remain unclear. This article aims to explore the technical and economic benefits of using cellulolytic enzyme cocktail, basic enzymatic and non-enzymatic components required for its development and various strategies employed for efficient cellulolytic cocktail preparation. Consideration was also given to the ways of evaluation of commercially available and in-house developed cocktails. Discussion about commercially available cellulolytic cocktails, current challenges and possible avenues in the development of cellulolytic cocktails included.
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Affiliation(s)
- Mukund Adsul
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India.
| | - Simranjeet Kaur Sandhu
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Reeta Rani Singhania
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Ravi Gupta
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Suresh K Puri
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Anshu Mathur
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
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166
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Kracher D, Forsberg Z, Bissaro B, Gangl S, Preims M, Sygmund C, Eijsink VGH, Ludwig R. Polysaccharide oxidation by lytic polysaccharide monooxygenase is enhanced by engineered cellobiose dehydrogenase. FEBS J 2019; 287:897-908. [PMID: 31532909 PMCID: PMC7078924 DOI: 10.1111/febs.15067] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/13/2019] [Accepted: 09/16/2019] [Indexed: 11/30/2022]
Abstract
The catalytic function of lytic polysaccharide monooxygenases (LPMOs) to cleave and decrystallize recalcitrant polysaccharides put these enzymes in the spotlight of fundamental and applied research. Here we demonstrate that the demand of LPMO for an electron donor and an oxygen species as cosubstrate can be fulfilled by a single auxiliary enzyme: an engineered fungal cellobiose dehydrogenase (CDH) with increased oxidase activity. The engineered CDH was about 30 times more efficient in driving the LPMO reaction due to its 27 time increased production of H2O2 acting as a cosubstrate for LPMO. Transient kinetic measurements confirmed that intra‐ and intermolecular electron transfer rates of the engineered CDH were similar to the wild‐type CDH, meaning that the mutations had not compromised CDH’s role as an electron donor. These results support the notion of H2O2‐driven LPMO activity and shed new light on the role of CDH in activating LPMOs. Importantly, the results also demonstrate that the use of the engineered CDH results in fast and steady LPMO reactions with CDH‐generated H2O2 as a cosubstrate, which may provide new opportunities to employ LPMOs in biomass hydrolysis to generate fuels and chemicals.
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Affiliation(s)
- Daniel Kracher
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sonja Gangl
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marita Preims
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Roland Ludwig
- Department of Food Science and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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167
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Garron ML, Henrissat B. The continuing expansion of CAZymes and their families. Curr Opin Chem Biol 2019; 53:82-87. [PMID: 31550558 DOI: 10.1016/j.cbpa.2019.08.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/17/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022]
Abstract
Carbohydrate-active enzymes (CAZymes) catalyze the assembly and breakdown of glycans and glycoconjugates. Some have been discovered, studied and exploited for numerous applications long ago. For instance, amylase and invertase were isolated in the second half of the 19th century and lysozyme was the first enzyme whose 3-D structure was determined. In spite of this early start, the number of families of carbohydrate-active enzymes continues to grow steadily in the early 21st century. This review examines the CAZyme families reported during the last two years and posits that the current expansion will continue in the future, progressively uncovering the massive diversity of glycans whose breakdown requires a large diversity of bespoke enzymes.
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Affiliation(s)
- Marie-Line Garron
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France; INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France; INRA, USC 1408 AFMB, 13288, Marseille, France.
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168
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Zhou X, Qi X, Huang H, Zhu H. Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity. Int J Mol Sci 2019; 20:ijms20184594. [PMID: 31533304 PMCID: PMC6771041 DOI: 10.3390/ijms20184594] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xiaohua Qi
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Hongxia Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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169
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Frandsen KEH, Tovborg M, Jørgensen CI, Spodsberg N, Rosso MN, Hemsworth GR, Garman EF, Grime GW, Poulsen JCN, Batth TS, Miyauchi S, Lipzen A, Daum C, Grigoriev IV, Johansen KS, Henrissat B, Berrin JG, Lo Leggio L. Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 2019; 294:17117-17130. [PMID: 31471321 DOI: 10.1074/jbc.ra119.009223] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/22/2019] [Indexed: 01/13/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
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Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark.,INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | | | | | | | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Glyn R Hemsworth
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Geoffrey W Grime
- The Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, United Kingdom
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shingo Miyauchi
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, 13009 Marseille, France.,INRA, USC 1408 AFMB, 13009 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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170
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Petrović DM, Várnai A, Dimarogona M, Mathiesen G, Sandgren M, Westereng B, Eijsink VGH. Comparison of three seemingly similar lytic polysaccharide monooxygenases from Neurospora crassa suggests different roles in plant biomass degradation. J Biol Chem 2019; 294:15068-15081. [PMID: 31431506 DOI: 10.1074/jbc.ra119.008196] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/02/2019] [Indexed: 11/06/2022] Open
Abstract
Many fungi produce multiple lytic polysaccharide monooxygenases (LPMOs) with seemingly similar functions, but the biological reason for this multiplicity remains unknown. To address this question, here we carried out comparative structural and functional characterizations of three cellulose-active C4-oxidizing family AA9 LPMOs from the fungus Neurospora crassa, NcLPMO9A (NCU02240), NcLPMO9C (NCU02916), and NcLPMO9D (NCU01050). We solved the three-dimensional structure of copper-bound NcLPMO9A at 1.6-Å resolution and found that NcLPMO9A and NcLPMO9C, containing a CBM1 carbohydrate-binding module, bind cellulose more strongly and were less susceptible to inactivation than NcLPMO9D, which lacks a CBM. All three LPMOs were active on tamarind xyloglucan and konjac glucomannan, generating similar products but clearly differing in activity levels. Importantly, in some cases, the addition of phosphoric acid-swollen cellulose (PASC) had a major effect on activity: NcLPMO9A was active on xyloglucan only in the presence of PASC, and PASC enhanced NcLPMO9D activity on glucomannan. Interestingly, the three enzymes also exhibited large differences in their interactions with enzymatic electron donors, which could reflect that they are optimized to act with different reducing partners. All three enzymes efficiently used H2O2 as a cosubstrate, yielding product profiles identical to those obtained in O2-driven reactions with PASC, xyloglucan, or glucomannan. Our results indicate that seemingly similar LPMOs act preferentially on different types of copolymeric substructures in the plant cell wall, possibly because these LPMOs are functionally adapted to distinct niches differing in the types of available reductants.
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Affiliation(s)
- Dejan M Petrović
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Maria Dimarogona
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.,Laboratory of Biotechnology and Structural Biology, Department of Chemical Engineering, University of Patras, 26504 Patras, Greece
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Bjørge Westereng
- 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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171
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Zhou H, Li T, Yu Z, Ju J, Zhang H, Tan H, Li K, Yin H. A lytic polysaccharide monooxygenase from Myceliophthora thermophila and its synergism with cellobiohydrolases in cellulose hydrolysis. Int J Biol Macromol 2019; 139:570-576. [PMID: 31381927 DOI: 10.1016/j.ijbiomac.2019.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/22/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have attracted vast attention because of their unique mechanism of oxidative degradation of carbohydrate polymers and the potential application in biorefineries. This study characterized a novel LPMO from Myceliophthora thermophila, denoted MtLPMO9L. The structure model of the enzyme indicated that it belongs to the C1-oxidizing LPMO, which has neither an extra helix in the L3 loop nor extra loop region in the L2 loop. This was confirmed subsequently by the enzymatic assays since MtLPMO9L only acts on cellulose and generates C1-oxidized cello-oligosaccharides. Moreover, synergetic experiments showed that MtLPMO9L significantly improves the efficiency of cellobiohydrolase (CBH) II. In contrast, the inhibitory rather than synergetic effect was observed when combining used MtLPMO9L and CBHI. Changing the incubation time and concentration ratio of MtLPMO9L and CBHI could attenuate the inhibitory effects. This discovery suggests a different synergy detail between MtLPMO9L and two CBHs, which implies that the composition of cellulase cocktails may need reconsideration.
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Affiliation(s)
- Haichuan Zhou
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zuochen Yu
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jiu Ju
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huiyan Zhang
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haidong Tan
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kuikui Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian 116023, China.
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172
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Deshors M, Guais O, Neugnot-Roux V, Cameleyre X, Fillaudeau L, Francois JM. Combined in situ Physical and ex-situ Biochemical Approaches to Investigate in vitro Deconstruction of Destarched Wheat Bran by Enzymes Cocktail Used in Animal Nutrition. Front Bioeng Biotechnol 2019; 7:158. [PMID: 31297370 PMCID: PMC6607472 DOI: 10.3389/fbioe.2019.00158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Abstract
Wheat bran is a foodstuff containing more than 40% of non-starch polysaccharides (NSPs) that are hardly digestible by monogastric animals. Therefore, cocktails enriched of hydrolytic enzymes (termed NSPases) are commonly provided as feed additives in animal nutrition. However, how these enzymes cocktails contribute to NSPs deconstruction remains largely unknown. This question was addressed by employing an original methodology that makes use of a multi-instrumented bioreactor that allows to dynamically monitor enzymes in action and to extract in-situ physical and ex-situ biochemical data from this monitoring. We report here that the deconstruction of destarched wheat bran by an industrial enzymes cocktail termed Rovabio® was entailed by two concurrent events: a particles fragmentation that caused in <2 h a 70% drop of the suspension viscosity and a solubilization that released <30 % of the wheat bran NSPs. Upon longer exposure, the fragmentation of particles continued at a very slow rate without any further solubilization. Contrary to this cocktail, xylanase C alone caused a moderate 25% drop of viscosity and a very weak fragmentation. However, the amount of xylose and arabinose from solubilized sugars after 6 h treatment with this enzyme was similar to that obtained after 2 h with Rovabio®. Altogether, this multi-scale analysis supported the synergistic action of enzymes mixture to readily solubilize complex polysaccharides, and revealed that in spite of the richness and diversity of hydrolytic enzymes in the cocktail, the deconstruction of NSPs in wheat bran was largely incomplete.
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Affiliation(s)
- Marine Deshors
- LISBP, UMR INSA-CNRS 5504 & INRA 792, Toulouse, France.,Cinabio-Adisseo France S.A.S., Toulouse, France
| | | | | | | | - Luc Fillaudeau
- LISBP, UMR INSA-CNRS 5504 & INRA 792, Toulouse, France.,Fédération de Recherche FERMAT (Fluides, Energie, Réacteurs, Matériaux et Transferts), Université de Toulouse, CNRS, INPT, INSA, UPS, Toulouse, France
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174
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Valadares F, Gonçalves TA, Damasio A, Milagres AM, Squina FM, Segato F, Ferraz A. The secretome of two representative lignocellulose-decay basidiomycetes growing on sugarcane bagasse solid-state cultures. Enzyme Microb Technol 2019; 130:109370. [PMID: 31421724 DOI: 10.1016/j.enzmictec.2019.109370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022]
Abstract
Secretome evaluations of lignocellulose-decay basidiomycetes can reveal new enzymes in selected fungal species that degrade specific substrates. Proteins discovered in such studies can support biorefinery development. Brown-rot (Gloeophyllum trabeum) and white-rot (Pleurotus ostreatus) fungi growing in sugarcane bagasse solid-state cultures produced 119 and 63 different extracellular proteins, respectively. Several of the identified enzymes are suitable for in vitro biomass conversion, including a range of cellulases (endoglucanases, cellobiohydrolases and β-glucosidases), hemicellulases (endoxylanases, α-arabinofuranosidases, α-glucuronidases and acetylxylan esterases) and carbohydrate-active auxiliary proteins, such as AA9 lytic polysaccharide monooxygenase, AA1 laccase and AA2 versatile peroxidase. Extracellular oxalate decarboxylase was also detected in both fungal species, exclusively in media containing sugarcane bagasse. Interestingly, intracellular AA6 quinone oxidoreductases were also exclusively produced under sugarcane bagasse induction in both fungi. These enzymes promote quinone redox cycling, which is used to produce Fenton's reagents by lignocellulose-decay fungi. Hitherto undiscovered hypothetical proteins that are predicted in lignocellulose-decay fungi genomes appeared in high relative abundance in the cultures containing sugarcane bagasse, which suggests undisclosed, new biochemical mechanisms that are used by lignocellulose-decay fungi to degrade sugarcane biomass. In general, lignocellulose-decay fungi produce a number of canonical hydrolases, as well as some newly observed enzymes, that are suitable for in vitro biomass digestion in a biorefinery context.
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Affiliation(s)
- Fernanda Valadares
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - Thiago A Gonçalves
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, 18023-000 Sorocaba, SP, Brazil; Institute of Biology, University of Campinas (UNICAMP), 13080-655, Campinas, SP, Brazil
| | - André Damasio
- Institute of Biology, University of Campinas (UNICAMP), 13080-655, Campinas, SP, Brazil
| | - Adriane Mf Milagres
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Fernando Segato
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - André Ferraz
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil.
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175
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Vu VV, Hangasky JA, Detomasi TC, Henry SJW, Ngo ST, Span EA, Marletta MA. Substrate selectivity in starch polysaccharide monooxygenases. J Biol Chem 2019; 294:12157-12166. [PMID: 31235519 DOI: 10.1074/jbc.ra119.009509] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/21/2019] [Indexed: 11/06/2022] Open
Abstract
Degradation of polysaccharides is central to numerous biological and industrial processes. Starch-active polysaccharide monooxygenases (AA13 PMOs) oxidatively degrade starch and can potentially be used with industrial amylases to convert starch into a fermentable carbohydrate. The oxidative activities of the starch-active PMOs from the fungi Neurospora crassa and Myceliophthora thermophila, NcAA13 and MtAA13, respectively, on three different starch substrates are reported here. Using high-performance anion-exchange chromatography coupled with pulsed amperometry detection, we observed that both enzymes have significantly higher oxidative activity on amylose than on amylopectin and cornstarch. Analysis of the product distribution revealed that NcAA13 and MtAA13 more frequently oxidize glycosidic linkages separated by multiples of a helical turn consisting of six glucose units on the same amylose helix. Docking studies identified important residues that are involved in amylose binding and suggest that the shallow groove that spans the active-site surface of AA13 PMOs favors the binding of helical amylose substrates over nonhelical substrates. Truncations of NcAA13 that removed its native carbohydrate-binding module resulted in diminished binding to amylose, but truncated NcAA13 still favored amylose oxidation over other starch substrates. These findings establish that AA13 PMOs preferentially bind and oxidize the helical starch substrate amylose. Moreover, the product distributions of these two enzymes suggest a unique interaction with starch substrates.
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Affiliation(s)
- Van V Vu
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam.
| | - John A Hangasky
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Skylar J W Henry
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
| | - Elise A Span
- Biophysics Graduate Group, University of California, Berkeley, California 94720
| | - Michael A Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720; Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.
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176
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Wang B, Walton PH, Rovira C. Molecular Mechanisms of Oxygen Activation and Hydrogen Peroxide Formation in Lytic Polysaccharide Monooxygenases. ACS Catal 2019; 9:4958-4969. [PMID: 32051771 PMCID: PMC7007194 DOI: 10.1021/acscatal.9b00778] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/17/2019] [Indexed: 12/26/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes for the degradation of recalcitrant polysaccharides such as chitin and cellulose. Unlike classical hydrolytic enzymes (cellulases), LPMOs catalyze the cleavage of the glycosidic bond via an oxidative mechanism using oxygen and a reductant. The full enzymatic molecular mechanisms, starting from the initial electron transfer from a reductant to oxygen activation and hydrogen peroxide formation, are not yet understood. Using quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, we have uncovered the oxygen activation mechanisms by LPMO in the presence of ascorbic acid, one of the most-used reductants in LPMOs assays. Our simulations capture the sequential formation of Cu(II)-O2 - and Cu(II)-OOH- intermediates via facile H atom abstraction from ascorbate. By investigating all the possible reaction pathways from the Cu(II)-OOH- intermediate, we ruled out Cu(II)-O• - formation via direct O-O cleavage of Cu(II)-OOH-. Meanwhile, we identified a possible pathway in which the proximal O atom of Cu(II)-OOH- abstracts a hydrogen atom from ascorbate, leading to Cu(I) and H2O2. The in-situ-generated H2O2 either converts to LPMO-Cu(II)-O• - via a homolytic reaction, or diffuses into the bulk water in an uncoupled pathway. The competition of these two pathways is strongly dependent on the binding of the carbohydrate substrate, which plays a role in barricading the in-situ-generated H2O2 molecule, preventing its diffusion from the active site into the bulk water. Based on the present results, we propose a catalytic cycle of LPMOs that is consistent with the experimental information available. In particular, it explains the enigmatic substrate dependence of the reactivity of the LPMO with H2O2.
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Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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177
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de Gouvêa PF, Gerolamo LE, Bernardi AV, Pereira LMS, Uyemura SA, Dinamarco TM. Lytic Polysaccharide Monooxygenase from Aspergillus fumigatus can Improve Enzymatic Cocktail Activity During Sugarcane Bagasse Hydrolysis. Protein Pept Lett 2019; 26:377-385. [DOI: 10.2174/0929866526666190228163629] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022]
Abstract
Background:
Lytic Polysaccharide Monooxygenases (LPMOs) are auxiliary accessory
enzymes that act synergistically with cellulases and which are increasingly being used in secondgeneration
bioethanol production from biomasses. Several LPMOs have been identified in various
filamentous fungi, including Aspergillus fumigatus. However, many LPMOs have not been characterized
yet.
Objective:
To report the role of uncharacterized A. fumigatus AfAA9_B LPMO.
Methods:
qRT-PCR analysis was employed to analyze the LPMO gene expression profile in different
carbon sources. The gene encoding an AfAA9_B (Afu4g07850) was cloned into the vector pET-
28a(+), expressed in the E. coli strain RosettaTM (DE3) pLysS, and purified by a Ni2+-nitrilotriacetic
(Ni-NTA) agarose resin. To evaluate the specific LPMO activity, the purified protein peroxidase
activity was assessed. The auxiliary LPMO activity was investigated by the synergistic activity in
Celluclast 1.5L enzymatic cocktail.
Results:
LPMO was highly induced in complex biomass like sugarcane bagasse (SEB), Avicel®
PH-101, and CM-cellulose. The LPMO gene encoded a protein comprising 250 amino acids, without
a CBM domain. After protein purification, the AfAA9_B molecular mass estimated by SDSPAGE
was 35 kDa. The purified protein specific peroxidase activity was 8.33 ± 1.9 U g-1. Upon
addition to Celluclast 1.5L, Avicel® PH-101 and SEB hydrolysis increased by 18% and 22%, respectively.
Conclusion:
A. fumigatus LPMO is a promising candidate to enhance the currently available enzymatic
cocktail and can therefore be used in second-generation ethanol production.
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Affiliation(s)
- Paula Fagundes de Gouvêa
- Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Luis Eduardo Gerolamo
- Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Aline Vianna Bernardi
- Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Lucas Matheus Soares Pereira
- Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sergio Akira Uyemura
- Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Taisa Magnani Dinamarco
- Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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178
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Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 2019; 20:430. [PMID: 31138126 PMCID: PMC6540522 DOI: 10.1186/s12864-019-5817-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. RESULTS The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. CONCLUSIONS The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
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Affiliation(s)
- Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.,Present address: VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Jaana Kuuskeri
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland.,Present address: Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.
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179
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Corrêa TLR, Júnior AT, Wolf LD, Buckeridge MS, dos Santos LV, Murakami MT. An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:117. [PMID: 31168322 PMCID: PMC6509861 DOI: 10.1186/s13068-019-1449-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/22/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) opened a new horizon for biomass deconstruction. They use a redox mechanism not yet fully understood and the range of substrates initially envisaged to be the crystalline polysaccharides is steadily expanding to non-crystalline ones. RESULTS The enzyme KpLPMO10A from the actinomycete Kitasatospora papulosa was cloned and overexpressed in Escherichia coli cells in the functional form with native N-terminal. The enzyme can release oxidized species from chitin (C1-type oxidation) and cellulose (C1/C4-type oxidation) similarly to other AA10 members from clade II (subclade A). Interestingly, KpLPMO10A also cleaves isolated xylan (not complexed with cellulose, C4-type oxidation), a rare activity among LPMOs not described yet for the AA10 family. The synergistic effect of KpLPMO10A with Celluclast® and an endo-β-1,4-xylanase also supports this finding. The crystallographic elucidation of KpLPMO10A at 1.6 Å resolution along with extensive structural analyses did not indicate any evident difference with other characterized AA10 LPMOs at the catalytic interface, tempting us to suggest that these enzymes might also be active on xylan or that the ability to attack both crystalline and non-crystalline substrates involves yet obscure mechanisms of substrate recognition and binding. CONCLUSIONS This work expands the spectrum of substrates recognized by AA10 family, opening a new perspective for the understanding of the synergistic effect of these enzymes with canonical glycoside hydrolases to deconstruct ligno(hemi)cellulosic biomass.
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Affiliation(s)
- Thamy Lívia Ribeiro Corrêa
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Atílio Tomazini Júnior
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Lúcia Daniela Wolf
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | | | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
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180
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Basotra N, Dhiman SS, Agrawal D, Sani RK, Tsang A, Chadha BS. Characterization of a novel Lytic Polysaccharide Monooxygenase from Malbranchea cinnamomea exhibiting dual catalytic behavior. Carbohydr Res 2019; 478:46-53. [DOI: 10.1016/j.carres.2019.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
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181
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Hangasky JA, Detomasi TC, Marletta MA. Glycosidic Bond Hydroxylation by Polysaccharide Monooxygenases. TRENDS IN CHEMISTRY 2019. [DOI: 10.1016/j.trechm.2019.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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182
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Karnaouri A, Antonopoulou I, Zerva A, Dimarogona M, Topakas E, Rova U, Christakopoulos P. Thermophilic enzyme systems for efficient conversion of lignocellulose to valuable products: Structural insights and future perspectives for esterases and oxidative catalysts. BIORESOURCE TECHNOLOGY 2019; 279:362-372. [PMID: 30685134 DOI: 10.1016/j.biortech.2019.01.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/12/2019] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Thermophilic enzyme systems are of major importance nowadays in all industrial processes due to their great performance at elevated temperatures. In the present review, an overview of the current knowledge on the properties of thermophilic and thermotolerant carbohydrate esterases and oxidative enzymes with great thermostability is provided, with respect to their potential use in biotechnological applications. A special focus is given to the lytic polysaccharide monooxygenases that are able to oxidatively cleave lignocellulose through the use of oxygen or hydrogen peroxide as co-substrate and a reducing agent as electron donor. Structural characteristics of the enzymes, including active site conformation and surface properties are discussed and correlated with their substrate specificity and thermostability properties.
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Affiliation(s)
- Anthi Karnaouri
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| | - Io Antonopoulou
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Anastasia Zerva
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Maria Dimarogona
- Section of Process and Environmental Engineering, Department of Chemical Engineering, University of Patras, 26504 Rio, Patras, Greece
| | - Evangelos Topakas
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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183
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Chylenski P, Bissaro B, Sørlie M, Røhr ÅK, Várnai A, Horn SJ, Eijsink VG. Lytic Polysaccharide Monooxygenases in Enzymatic Processing of Lignocellulosic Biomass. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00246] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr Chylenski
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Svein J. Horn
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
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184
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Anasontzis GE, Lebrun MH, Haon M, Champion C, Kohler A, Lenfant N, Martin F, O'Connell RJ, Riley R, Grigoriev IV, Henrissat B, Berrin JG, Rosso MN. Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants. Environ Microbiol 2019; 21:2724-2739. [PMID: 30887618 DOI: 10.1111/1462-2920.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/17/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.
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Affiliation(s)
- George E Anasontzis
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.,CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Marc-Henri Lebrun
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Mireille Haon
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Charlotte Champion
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Annegret Kohler
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Nicolas Lenfant
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Francis Martin
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Richard J O'Connell
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Bernard Henrissat
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France.,INRA, USC 1408, AFMB, Marseille, France
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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185
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Laurent CFP, Breslmayr E, Tunega D, Ludwig R, Oostenbrink C. Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase. Biochemistry 2019; 58:1226-1235. [PMID: 30715860 PMCID: PMC6404106 DOI: 10.1021/acs.biochem.8b01178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/24/2019] [Indexed: 01/10/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are ubiquitous oxidoreductases, facilitating the degradation of polymeric carbohydrates in biomass. Cellobiose dehydrogenase (CDH) is a biologically relevant electron donor in this process, with the electrons resulting from cellobiose oxidation being shuttled from the CDH dehydrogenase domain to its cytochrome domain and then to the LPMO catalytic site. In this work, we investigate the interaction of four Neurospora crassa LPMOs and five CDH cytochrome domains from different species using computational methods. We used HADDOCK to perform protein-protein docking experiments on all 20 combinations and subsequently to select four complexes for extensive molecular dynamics simulations. The potential of mean force is computed for a rotation of the cytochrome domain relative to LPMO. We find that the LPMO loops are largely responsible for the preferred orientations of the cytochrome domains. This leads us to postulate a hybrid version of NcLPMO9F, with exchanged loops and predicted altered cytochrome binding preferences for this variant. Our work provides insight into the possible mechanisms of electron transfer between the two protein systems, in agreement with and complementary to previously published experimental data.
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Affiliation(s)
- Christophe
V. F. P. Laurent
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Erik Breslmayr
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Daniel Tunega
- Institute
of Soil Research, BOKU-University of Natural
Resources and Life Sciences, 1190 Vienna, Austria
| | - Roland Ludwig
- Vienna
Institute of BioTechnology, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute
of Molecular Modeling and Simulation, BOKU-University
of Natural Resources and Life Sciences, 1190 Vienna, Austria
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186
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pH-Dependent Relationship between Catalytic Activity and Hydrogen Peroxide Production Shown via Characterization of a Lytic Polysaccharide Monooxygenase from Gloeophyllum trabeum. Appl Environ Microbiol 2019; 85:AEM.02612-18. [PMID: 30578267 DOI: 10.1128/aem.02612-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/20/2018] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that perform oxidative cleavage of recalcitrant polysaccharides. We have purified and characterized a recombinant family AA9 LPMO, LPMO9B, from Gloeophyllum trabeum (GtLPMO9B) which is active on both cellulose and xyloglucan. Activity of the enzyme was tested in the presence of three different reductants: ascorbic acid, gallic acid, and 2,3-dihydroxybenzoic acid (2,3-DHBA). Under standard aerobic conditions typically used in LPMO experiments, the first two reductants could drive LPMO catalysis whereas 2,3-DHBA could not. In agreement with the recent discovery that H2O2 can drive LPMO catalysis, we show that gradual addition of H2O2 allowed LPMO activity at very low, substoichiometric (relative to products formed) reductant concentrations. Most importantly, we found that while 2,3-DHBA is not capable of driving the LPMO reaction under standard aerobic conditions, it can do so in the presence of externally added H2O2 At alkaline pH, 2,3-DHBA is able to drive the LPMO reaction without externally added H2O2, and this ability overlaps entirely the endogenous generation of H2O2 by GtLPMO9B-catalyzed oxidation of 2,3-DHBA. These findings support the notion that H2O2 is a cosubstrate of LPMOs and provide insight into how LPMO reactions depend on, and may be controlled by, the choice of pH and reductant.IMPORTANCE Lytic polysaccharide monooxygenases promote enzymatic depolymerization of lignocellulosic materials by microorganisms due to their ability to oxidatively cleave recalcitrant polysaccharides. The properties of these copper-dependent enzymes are currently of high scientific and industrial interest. We describe a previously uncharacterized fungal LPMO and show how reductants, which are needed to prime the LPMO by reducing Cu(II) to Cu(I) and to supply electrons during catalysis, affect enzyme efficiency and stability. The results support claims that H2O2 is a natural cosubstrate for LPMOs by demonstrating that when certain reductants are used, catalysis can be driven only by H2O2 and not by O2 Furthermore, we show how auto-inactivation resulting from endogenous generation of H2O2 in the LPMO-reductant system may be prevented. Finally, we identified a reductant that leads to enzyme activation without any endogenous H2O2 generation, allowing for improved control of LPMO reactivity and providing a valuable tool for future LPMO research.
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187
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Ahmad M, Yousaf M, Nasir A, Bhatti IA, Mahmood A, Fang X, Jian X, Kalantar-Zadeh K, Mahmood N. Porous Eleocharis@MnPE Layered Hybrid for Synergistic Adsorption and Catalytic Biodegradation of Toxic Azo Dyes from Industrial Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2161-2170. [PMID: 30673285 DOI: 10.1021/acs.est.8b05866] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The effective treatment of industrial wastewater to protect freshwater reserves for the survival of life is a primary focus of current research. Herein, a multicomponent Eleocharis-manganese peroxidase enzyme (Eleocharis@MnPE) layered hybrid with high surface area (1200 m2/m3), with a strong synergistic adsorption and catalytic biodegradation (SACB), has been developed through a facile method. A combination of outer porous (Eleocharis) and inner catalytically active (MnPE) components of the hybrid resulted in highly efficient SACB system, evidenced by high removal rate of 15 kg m-3 day-1 (100%) and complete degradation of toxic Orange II (OR) azo dye into nontoxic products (gases and weak acids). The Eleocharis@MnPE layered hybrid efficiently degraded both OR in synthetic wastewater and also other azo dyes (red, pink, and yellow dyes) present in three different textile industrial effluents. For the industrial effluents, these were evidenced by the color disappearance and reduction in biological oxygen demand (BOD), chemical oxygen demand (COD), and total organic carbon (TOC) of up to 97%, 92%, and 76%, respectively. Furthermore, reduced toxicity of treated wastewater was confirmed by decreased cell toxicity to 0.1%-1% and increased cell viability to 90%. We believe that designing a hybrid system with strong ability of SACB could be highly effective for industrial-scale treatment of wastewater.
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Affiliation(s)
- Muhammad Ahmad
- Department of Structure and Environmental Engineering , University of Agriculture Faisalabad , Faisalabad , Punjab 38040 , Pakistan
- Department of Environmental Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education , Peking University , Beijing 100871 , China
| | - Maryam Yousaf
- Department of Chemistry , University of Agriculture Faisalabad , Faisalabad , Punjab 38040 , Pakistan
| | - Abdul Nasir
- Department of Structure and Environmental Engineering , University of Agriculture Faisalabad , Faisalabad , Punjab 38040 , Pakistan
| | - Ijaz Ahmad Bhatti
- Department of Chemistry , University of Agriculture Faisalabad , Faisalabad , Punjab 38040 , Pakistan
| | - Asif Mahmood
- Department of Physics , South University of Sciences and Technology , Shenzhen 518055 , People's Republic of China
| | - Xiaocui Fang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , People's Republic of China
| | - Xian Jian
- School of Materials and Energy, National Engineering Research Centre of Electromagnetic Radiation Control Materials, Center for Applied Chemistry, University of Electronic Science and Technology , Chengdu 611731 , People's Republic of China
| | - Kourosh Kalantar-Zadeh
- School of Chemical Engineering , University of New South Wales (UNSW) , 2052 Kensington , New South Wales , Australia
| | - Nasir Mahmood
- School of Engineering , RMIT University , 124 La Trobe Street , 3001 Melbourne , Victoria , Australia
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188
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Assessment of white rot fungus mediated hardwood degradation by FTIR spectroscopy and multivariate analysis. J Microbiol Methods 2019; 157:123-130. [DOI: 10.1016/j.mimet.2019.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 01/26/2023]
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189
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Kont R, Pihlajaniemi V, Borisova AS, Aro N, Marjamaa K, Loogen J, Büchs J, Eijsink VGH, Kruus K, Väljamäe P. The liquid fraction from hydrothermal pretreatment of wheat straw provides lytic polysaccharide monooxygenases with both electrons and H 2O 2 co-substrate. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:235. [PMID: 31624497 PMCID: PMC6781412 DOI: 10.1186/s13068-019-1578-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Enzyme-aided valorization of lignocellulose represents a green and sustainable alternative to the traditional chemical industry. The recently discovered lytic polysaccharide monooxygenases (LPMOs) are important components of the state-of-the art enzyme cocktails for cellulose conversion. Yet, these monocopper enzymes are poorly characterized in terms of their kinetics, as exemplified by the growing evidence for that H2O2 may be a more efficient co-substrate for LPMOs than O2. LPMOs need external electron donors and one key question of relevance for bioprocess development is whether the required reducing power may be provided by the lignocellulosic substrate. RESULTS Here, we show that the liquid fraction (LF) resulting from hydrothermal pretreatment of wheat straw supports LPMO activity on both chitin and cellulose. The initial, transient activity burst of the LPMO reaction was caused by the H2O2 present in the LF before addition of LPMO, while the steady-state rate of LPMO reaction was limited by the LPMO-independent production of H2O2 in the LF. H2O2 is an intermediate of LF oxidation as evidenced by a slow H2O2 accumulation in LF, despite high H2O2 production rates. This H2O2 scavenging ability of LF is important since high concentrations of H2O2 may lead to irreversible inactivation of LPMOs. CONCLUSIONS Our results support the growing understanding that fine-tuned control over the rates of H2O2 production and consumption in different, enzymatic and non-enzymatic reactions is essential for harnessing the full catalytic potential of LPMOs in lignocellulose valorization.
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Affiliation(s)
- Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | | | - Nina Aro
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Judith Loogen
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- Department of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | | | - Kristiina Kruus
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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190
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Eijsink VGH, Petrovic D, Forsberg Z, Mekasha S, Røhr ÅK, Várnai A, Bissaro B, Vaaje-Kolstad G. On the functional characterization of lytic polysaccharide monooxygenases (LPMOs). BIOTECHNOLOGY FOR BIOFUELS 2019; 12:58. [PMID: 30923566 PMCID: PMC6423801 DOI: 10.1186/s13068-019-1392-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are abundant in nature and best known for their role in the enzymatic conversion of recalcitrant polysaccharides such as chitin and cellulose. LPMO activity requires an oxygen co-substrate, which was originally thought to be O2, but which may also be H2O2. Functional characterization of LPMOs is not straightforward because typical reaction mixtures will promote side reactions, including auto-catalytic inactivation of the enzyme. For example, despite some recent progress, there is still limited insight into the kinetics of the LPMO reaction. Recent discoveries concerning the role of H2O2 in LPMO catalysis further complicate the picture. Here, we review commonly used methods for characterizing LPMOs, with focus on benefits and potential pitfalls, rather than on technical details. We conclude by pointing at a few key problems and potential misconceptions that should be taken into account when interpreting existing data and planning future experiments.
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Affiliation(s)
- Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Dejan Petrovic
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Sophanit Mekasha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1432 Ås, Norway
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191
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Courtade G, Aachmann FL. Chitin-Active Lytic Polysaccharide Monooxygenases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:115-129. [PMID: 31102244 DOI: 10.1007/978-981-13-7318-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the cleavage of 1,4-glycosidic bonds various plant cell wall polysaccharides and chitin. In contrast to glycoside hydrolases, LPMOs are active on the crystalline regions of polysaccharides and thus synergize with hydrolytic enzymes. This synergism leads to an overall increase in the biomass-degradation activity of enzyme mixtures. Chitin-active LPMOs were discovered in 2010 and are currently classified in families AA10, AA11, and AA15 of the Carbohydrate-Active enZYmes database, which include LPMOs from bacteria, fungi, insects, and viruses. LPMOs have become important enzymes both industrially and scientifically and, in this chapter, we provide a brief introduction to chitin-active LPMOs including a summary of the 20+ chitin-active LPMOs that have been characterized so far. Then, we describe their structural features, catalytic mechanism, and appended carbohydrate modules. Finally, we show how chitin-active LPMOs can be used to perform chemo-enzymatic modification of chitin substrates.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
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192
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Myco-Degradation of Lignocellulose: An Update on the Reaction Mechanism and Production of Lignocellulolytic Enzymes by Fungi. Fungal Biol 2019. [DOI: 10.1007/978-3-030-23834-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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193
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Moreau C, Tapin-Lingua S, Grisel S, Gimbert I, Le Gall S, Meyer V, Petit-Conil M, Berrin JG, Cathala B, Villares A. Lytic polysaccharide monooxygenases (LPMOs) facilitate cellulose nanofibrils production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:156. [PMID: 31249619 PMCID: PMC6589874 DOI: 10.1186/s13068-019-1501-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/15/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that cleave polysaccharides through an oxidative mechanism. These enzymes are major contributors to the recycling of carbon in nature and are currently used in the biorefinery industry. LPMOs are commonly used in synergy with cellulases to enhance biomass deconstruction. However, there are few examples of the use of monocomponent LPMOs as a tool for cellulose fibrillation. In this work, we took advantage of the LPMO action to facilitate disruption of wood cellulose fibers as a strategy to produce nanofibrillated cellulose (NFC). RESULTS The fungal LPMO from AA9 family (PaLPMO9E) was used in this study as it displays high specificity toward cellulose and its recombinant production in bioreactor is easily upscalable. The treatment of birchwood fibers with PaLPMO9E resulted in the release of a mixture of C1-oxidized oligosaccharides without any apparent modification in fiber morphology and dimensions. The subsequent mechanical shearing disintegrated the LPMO-pretreated samples yielding nanoscale cellulose elements. Their gel-like aspect and nanometric dimensions demonstrated that LPMOs disrupt the cellulose structure and facilitate the production of NFC. CONCLUSIONS This study demonstrates the potential use of LPMOs as a pretreatment in the NFC production process. LPMOs weaken fiber cohesion and facilitate fiber disruption while maintaining the crystallinity of cellulose.
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Affiliation(s)
- Céline Moreau
- UR1268 Biopolymères Interactions Assemblages, INRA, 44316 Nantes, France
| | - Sandra Tapin-Lingua
- InTechFibres Division, FCBA, Domaine Universitaire, CS 90252, 39044 Grenoble Cedex 9, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille University, UMR1163, 13009 Marseille, France
| | - Isabelle Gimbert
- Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille University, UMR1163, 13009 Marseille, France
| | - Sophie Le Gall
- UR1268 Biopolymères Interactions Assemblages, INRA, 44316 Nantes, France
| | - Valérie Meyer
- CTP, Domaine Universitaire, CS 90252, 39044 Grenoble Cedex 9, France
| | | | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille University, UMR1163, 13009 Marseille, France
| | - Bernard Cathala
- UR1268 Biopolymères Interactions Assemblages, INRA, 44316 Nantes, France
| | - Ana Villares
- UR1268 Biopolymères Interactions Assemblages, INRA, 44316 Nantes, France
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194
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Chalak A, Villares A, Moreau C, Haon M, Grisel S, d’Orlando A, Herpoël-Gimbert I, Labourel A, Cathala B, Berrin JG. Influence of the carbohydrate-binding module on the activity of a fungal AA9 lytic polysaccharide monooxygenase on cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:206. [PMID: 31508147 PMCID: PMC6721207 DOI: 10.1186/s13068-019-1548-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/24/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cellulose-active lytic polysaccharide monooxygenases (LPMOs) secreted by filamentous fungi play a key role in the degradation of recalcitrant lignocellulosic biomass. They can occur as multidomain proteins fused to a carbohydrate-binding module (CBM). From a biotech perspective, LPMOs are promising innovative tools for producing nanocelluloses and biofuels, but their direct action on cellulosic substrates is not fully understood. RESULTS In this study, we probed the role of the CBM from family 1 (CBM1) appended to the LPMO9H from Podospora anserina (PaLPMO9H) using model cellulosic substrates. Deletion of the CBM1 weakened the binding to cellulose nanofibrils, amorphous and crystalline cellulose. Although the release of soluble sugars from cellulose was drastically reduced under standard conditions, the truncated LPMO retained some activity on soluble oligosaccharides. The cellulolytic action of the truncated LPMO was demonstrated using synergy experiments with a cellobiohydrolase (CBH). The truncated LPMO was still able to improve the efficiency of the CBH on cellulose nanofibrils in the same range as the full-length LPMO. Increasing the substrate concentration enhanced the performance of PaLPMO9H without CBM in terms of product release. Interestingly, removing the CBM also altered the regioselectivity of PaLPMO9H, significantly increasing cleavage at the C1 position. Analysis of the insoluble fraction of cellulosic substrates evaluated by optical and atomic force microscopy confirmed that the CBM1 module was not strictly required to promote disruption of the cellulose network. CONCLUSIONS Absence of the CBM1 does not preclude the activity of the LPMO on cellulose but its presence has an important role in driving the enzyme to the substrate and releasing more soluble sugars (both oxidized and non-oxidized), thus facilitating the detection of LPMO activity at low substrate concentration. These results provide insights into the mechanism of action of fungal LPMOs on cellulose to produce nanocelluloses and biofuels.
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Affiliation(s)
- Amani Chalak
- Biopolymères Interactions Assemblages, INRA, Nantes, France
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Ana Villares
- Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Celine Moreau
- Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Mireille Haon
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | | | - Isabelle Herpoël-Gimbert
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Aurore Labourel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | | | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
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Filiatrault-Chastel C, Navarro D, Haon M, Grisel S, Herpoël-Gimbert I, Chevret D, Fanuel M, Henrissat B, Heiss-Blanquet S, Margeot A, Berrin JG. AA16, a new lytic polysaccharide monooxygenase family identified in fungal secretomes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:55. [PMID: 30923563 PMCID: PMC6420742 DOI: 10.1186/s13068-019-1394-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulosic biomass is considered as a promising alternative to fossil resources for the production of fuels, materials and chemicals. Efficient enzymatic systems are needed to degrade the plant cell wall and overcome its recalcitrance. A widely used producer of cellulolytic cocktails is the ascomycete Trichoderma reesei, but this organism secretes a limited set of enzymes. To improve the saccharification yields, one strategy is to upgrade the T. reesei enzyme cocktail with enzymes produced by other biomass-degrading filamentous fungi isolated from biodiversity. RESULTS In this study, the enzymatic cocktails secreted by five strains from the genus Aspergillus (Aspergillus japonicus strains BRFM 405, 1487, 1489, 1490 and Aspergillus niger strain BRFM 430) were tested for their ability to boost a T. reesei reference cocktail for the saccharification of pretreated biomass. Proteomic analysis of fungal secretomes that significantly improved biomass degradation showed that the presence of proteins belonging to a putative LPMO family previously identified by genome analysis and awaiting experimental demonstration of activity. Members of this novel LPMO family, named AA16, are encountered in fungi and oomycetes with life styles oriented toward interactions with plant biomass. One AA16 protein from Aspergillus aculeatus (AaAA16) was produced to high level in Pichia pastoris. LPMO-type enzyme activity was demonstrated on cellulose with oxidative cleavage at the C1 position of the glucose unit. AaAA16 LPMO was found to significantly improve the activity of T. reesei CBHI on cellulosic substrates. CONCLUSIONS Although Aspergillus spp. has been investigated for decades for their CAZymes diversity, we identified members of a new fungal LPMO family using secretomics and functional assays. Properties of the founding member of the AA16 family characterized herein could be of interest for use in biorefineries.
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Affiliation(s)
- Camille Filiatrault-Chastel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - David Navarro
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Mireille Haon
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Isabelle Herpoël-Gimbert
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Didier Chevret
- Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Institut Micalis, UMR1319, INRA, Agro-ParisTech, Jouy-En-Josas, France
| | - Mathieu Fanuel
- UR1268, INRA, Biopolymères Interactions Assemblages, Nantes, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, CNRS, Aix Marseille Université, Marseille, France
- USC1408, INRA, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
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196
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Muderspach SJ, Tandrup T, Frandsen KEH, Santoni G, Poulsen JCN, Leggio LL. Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family. ACTA ACUST UNITED AC 2019. [DOI: 10.1515/amylase-2019-0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered copper enzymes that cleave recalcitrant polysaccharides by oxidation. The structure of an Aspergillus oryzae LPMO from the starch degrading family AA13 (AoAA13) has previously been determined from an orthorhombic crystal grown in the presence of copper, which is photoreduced in the structure. Here we describe how crystals reliably grown in presence of Zn can be Cu-loaded post crystallization. A partly photoreduced structure was obtained by severely limiting the X-ray dose, showing that this LPMO is much more prone to photoreduction than others. A serial synchrotron crystallography structure was also obtained, showing that this technique may be promising for further studies, to reduce even further photoreduction. We additionally present a triclinic structure of AoAA13, which has less occluded ligand binding site than the orthorhombic one. The availability of the triclinic crystals prompted new ligand binding studies, which lead us to the conclusion that small starch analogues do not bind to AoAA13 to an appreciable extent. A number of disordered conformations of the metal binding histidine brace have been encountered in this and other studies, and we have previously hypothesized that this disorder may be a consequence of loss of copper. We performed molecular dynamics in the absence of active site metal, and showed that the dynamics in solution differ somewhat from the disorder observed in the crystal, though the extent is equally dramatic.
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197
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Dixit P, Basu B, Puri M, Tuli DK, Mathur AS, Barrow CJ. A screening approach for assessing lytic polysaccharide monooxygenase activity in fungal strains. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:185. [PMID: 31360222 PMCID: PMC6643308 DOI: 10.1186/s13068-019-1526-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/07/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Efforts to develop efficient lignocellulose-degrading enzymatic preparations have led to the relatively recent discovery of a new class of novel cellulase boosters, termed lytic polysaccharide monoxygenases (LPMOs). These enzymes are copper-dependent metalloenzymes that initiate the biomass deconstruction process and subsequently work together with cellulases, hemicellulases, and other accessory enzymes to enhance their hydrolytic action. Given their wide distribution and diversity, screening and isolation of potent LPMOs from natural fungal diversity may provide an important avenue for increasing the efficiency of cellulases and thereby decreasing cellulosic ethanol production costs. However, methods for quick screening and detection are still not widely available. In this article, a simple and sensitive method is described by combining nonhydrolytic activity enhancement followed by LC-MS-based quantitation of LPMOs. RESULTS In this study, a screening approach has been developed for the detection of nonhydrolytic cellulase-enhancing enzymes in crude fungal supernatants. With the application of a saturating benchmark cocktail of Celluclast 1.5L, fungal isolates were selected which had the capability of hydrolyzing pretreated rice straw by their synergistic enzyme fractions. Subsequently, these fungal extracts along with an LPMO-enriched commercial enzyme were investigated for their ability to produce Type I LPMO activity. An LC-MS-based methodology was applied to quantitate gluconic acid in enzymatic hydrolysates as an indirect measurement of Type I LPMO activity. CONCLUSION The present study describes an LC-MS-based separation method to detect and quantitate LPMO activity in a commercial enzyme. This method was also applied to screen fungal extracts. The developed screening strategy has enabled detection of LPMO activity in two industrially important Penicillium strains.
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Affiliation(s)
- Pooja Dixit
- DBT-IOC Centre for Bioenergy Research, R&D Centre, Indian Oil Corporation Limited, Faridabad, India
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC Australia
| | - Biswajit Basu
- DBT-IOC Centre for Bioenergy Research, R&D Centre, Indian Oil Corporation Limited, Faridabad, India
| | - Munish Puri
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC Australia
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Deepak Kumar Tuli
- DBT-IOC Centre for Bioenergy Research, R&D Centre, Indian Oil Corporation Limited, Faridabad, India
| | - Anshu Shankar Mathur
- DBT-IOC Centre for Bioenergy Research, R&D Centre, Indian Oil Corporation Limited, Faridabad, India
| | - Colin James Barrow
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC Australia
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198
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Arora R, Bharval P, Sarswati S, Sen TZ, Yennamalli RM. Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region. J Mol Graph Model 2018; 88:1-10. [PMID: 30612037 DOI: 10.1016/j.jmgm.2018.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), which are found in fungi, bacteria, and viruses, are redox enzymes utilizing copper to break glycosidic bonds in recalcitrant crystalline form of polysaccharides, such as chitin and cellulose. They are classified by the Carbohydrate-Active enZYmes (CAZy) database under various families. LPMOs's structure with a flat substrate binding region has been shown to contribute to its function, however, the role that LPMOs structural dynamics play during polysaccharide degradation and its mechanism of binding towards substrate are relatively unknown. Here, we report an exhaustive implementation of coarse-grained simulations using Elastic Network Models on multiple LPMO structures to shed light on how their structural dynamics contribute to their chemical function. Using Gaussian network models and Anisotropic network models, we show that the substrate binding region is highly flexible with significant and sustained micro-scale level conformational changes. Significantly, the loops on the binding side of the substrate are most mobile, in concert with the dynamic modes influencing the motions during binding. We also observed dynamic differences between four families of LPMO, namely AA9, AA10, AA11, and AA13 that consist of more than one structure. Specifically, the patterns of motion in the loop regions among the AA9 structures are distinct from those in the AA10 structures.
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Affiliation(s)
- Radhika Arora
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Priya Bharval
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Sheena Sarswati
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Taner Z Sen
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA; Iowa State University, Department of Genetics, Development, and Cell Biology, Ames, IA, 50011, USA
| | - Ragothaman M Yennamalli
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India.
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199
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Zhang J, Mitchell HD, Markillie LM, Gaffrey MJ, Orr G, Schilling J. Reference genes for accurate normalization of gene expression in wood-decomposing fungi. Fungal Genet Biol 2018; 123:33-40. [PMID: 30529285 DOI: 10.1016/j.fgb.2018.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/08/2018] [Accepted: 11/27/2018] [Indexed: 12/28/2022]
Abstract
Wood-decomposing fungi efficiently decompose plant lignocellulose, and there is increasing interest in characterizing and perhaps harnessing the fungal gene regulation strategies that enable wood decomposition. Proper interpretation of these fungal mechanisms relies on accurate quantification of gene expression, demanding reliable internal control genes (ICGs) as references. Commonly used ICGs such as actin, however, fluctuate among wood-decomposing fungi under defined conditions. In this study, by mining RNA-seq data in silico and validating ICGs in vitro using qRT-PCR, we targeted more reliable ICGs for studying transcriptional responses in wood-decomposing fungi, particularly responses to changing environments (e.g., carbon sources, decomposition stages) in various culture conditions. Using the model brown rot fungus Postia placenta in a first-pass study, our mining efforts yielded 15 constitutively-expressed genes robust in variable carbon sources (e.g., no carbon, glucose, cellobiose, aspen) and cultivation stages (e.g., 15 h, 72 h) in submerged cultures. Of these, we found 7 genes as most suitable ICGs. Expression stabilities of these newly selected ICGs were better than commonly used ICGs, analyzed by NormFinder algorithm and qRT-PCR. In a second-pass, multi-species study in solid wood, our RNA-seq mining efforts revealed hundreds of highly constitutively expressed genes among four wood-decomposing fungi with varying nutritional modes (brown rot, white rot), including a shared core set of ICGs numbering 11 genes. Together, the newly selected ICGs highlighted here will increase reliability when studying gene regulatory mechanisms of wood-decomposing fungi.
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Affiliation(s)
- Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
| | - Hugh D Mitchell
- Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Matthew J Gaffrey
- Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Galya Orr
- Earth and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jonathan Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States.
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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