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Walton PH, Davies GJ. On the catalytic mechanisms of lytic polysaccharide monooxygenases. Curr Opin Chem Biol 2016; 31:195-207. [PMID: 27094791 DOI: 10.1016/j.cbpa.2016.04.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/03/2016] [Accepted: 04/05/2016] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered copper-containing oxygenases. LPMOs oxidise recalcitrant polysaccharides such as chitin and cellulose, thereby making these substrates more tractable to canonical chitinase or cellulase action. As such, LPMOs are attracting much attention not only for their capacity to greatly increase the efficiency of production of cellulosic-based biofuels, but also for the new questions they pose about the mechanisms of biological oxidation of recalcitrant substrates. This review draws together the current thinking on the catalytic mechanisms of LPMOs and other copper catalysed oxygenations and provides a blueprint for further investigation into the mechanisms of action of these intriguing enzymes.
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Affiliation(s)
- Paul H Walton
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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202
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Chaplin AK, Wilson MT, Hough MA, Svistunenko DA, Hemsworth GR, Walton PH, Vijgenboom E, Worrall JAR. Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:12838-12850. [PMID: 27129229 DOI: 10.1074/jbc.m116.722447] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/23/2022] Open
Abstract
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively deconstruct polysaccharides. The active site copper in LPMOs is coordinated by a histidine-brace. This utilizes the amino group and side chain of the N-terminal His residue with the side chain of a second His residue to create a T-shaped arrangement of nitrogen ligands. We report a structural, kinetic, and thermodynamic appraisal of copper binding to the histidine-brace in an auxiliary activity family 10 (AA10) LPMO from Streptomyces lividans (SliLPMO10E). Unexpectedly, we discovered the existence of two apo-SliLPMO10E species in solution that can each bind copper at a single site with distinct kinetic and thermodynamic (exothermic and endothermic) properties. The experimental EPR spectrum of copper-bound SliLPMO10E requires the simulation of two different line shapes, implying two different copper-bound species, indicative of three and two nitrogen ligands coordinating the copper. Amino group coordination was probed through the creation of an N-terminal extension variant (SliLPMO10E-Ext). The kinetics and thermodynamics of copper binding to SliLPMO10E-Ext are in accord with copper binding to one of the apo-forms in the wild-type protein, suggesting that amino group coordination is absent in the two-nitrogen coordinate form of SliLPMO10E. Copper binding to SliLPMO10B was also investigated, and again it revealed the presence of two apo-forms with kinetics and stoichiometry of copper binding identical to that of SliLPMO10E. Our findings highlight that heterogeneity exists in the active site copper coordination sphere of LPMOs that may have implications for the mechanism of loading copper in the cell.
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Affiliation(s)
- Amanda K Chaplin
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael T Wilson
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael A Hough
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Dimitri A Svistunenko
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Glyn R Hemsworth
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Paul H Walton
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Erik Vijgenboom
- the Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, P. O. Box 9505, 2300RA Leiden, The Netherlands
| | - Jonathan A R Worrall
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom,.
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203
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Jagadeeswaran G, Gainey L, Prade R, Mort AJ. A family of AA9 lytic polysaccharide monooxygenases in Aspergillus nidulans is differentially regulated by multiple substrates and at least one is active on cellulose and xyloglucan. Appl Microbiol Biotechnol 2016; 100:4535-47. [DOI: 10.1007/s00253-016-7505-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 02/03/2023]
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204
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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205
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Dos Santos Castro L, de Paula RG, Antoniêto ACC, Persinoti GF, Silva-Rocha R, Silva RN. Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. Front Microbiol 2016; 7:175. [PMID: 26909077 PMCID: PMC4754417 DOI: 10.3389/fmicb.2016.00175] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
We defined the role of the transcriptional factor—XYR1—in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the Δxyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the Δxyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields.
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Affiliation(s)
- Lilian Dos Santos Castro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Renato G de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Amanda C C Antoniêto
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Gabriela F Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais Campinas, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
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206
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Forsberg Z, Nelson CE, Dalhus B, Mekasha S, Loose JSM, Crouch LI, Røhr ÅK, Gardner JG, Eijsink VGH, Vaaje-Kolstad G. Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus. J Biol Chem 2016; 291:7300-12. [PMID: 26858252 DOI: 10.1074/jbc.m115.700161] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 01/11/2023] Open
Abstract
Cellvibrio japonicusis a Gram-negative soil bacterium that is primarily known for its ability to degrade plant cell wall polysaccharides through utilization of an extensive repertoire of carbohydrate-active enzymes. Several putative chitin-degrading enzymes are also found among these carbohydrate-active enzymes, such as chitinases, chitobiases, and lytic polysaccharide monooxygenases (LPMOs). In this study, we have characterized the chitin-active LPMO,CjLPMO10A, a tri-modular enzyme containing a catalytic family AA10 LPMO module, a family 5 chitin-binding module, and a C-terminal unclassified module of unknown function. Characterization of the latter module revealed tight and specific binding to chitin, thereby unraveling a new family of chitin-binding modules (classified as CBM73). X-ray crystallographic elucidation of theCjLPMO10A catalytic module revealed that the active site of the enzyme combines structural features previously only observed in either cellulose or chitin-active LPMO10s. Analysis of the copper-binding site by EPR showed a signal signature more similar to those observed for cellulose-cleaving LPMOs. The full-length LPMO shows no activity toward cellulose but is able to bind and cleave both α- and β-chitin. Removal of the chitin-binding modules reduced LPMO activity toward α-chitin compared with the full-length enzyme. Interestingly, the full-length enzyme and the individual catalytic LPMO module boosted the activity of an endochitinase equally well, also yielding similar amounts of oxidized products. Finally, gene deletion studies show thatCjLPMO10A is needed byC. japonicusto obtain efficient growth on both purified chitin and crab shell particles.
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Affiliation(s)
- Zarah Forsberg
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Cassandra E Nelson
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Bjørn Dalhus
- the Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, and
| | - Sophanit Mekasha
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jennifer S M Loose
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Lucy I Crouch
- the Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Åsmund K Røhr
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jeffrey G Gardner
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Vincent G H Eijsink
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway,
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207
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Patel I, Kracher D, Ma S, Garajova S, Haon M, Faulds CB, Berrin JG, Ludwig R, Record E. Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:108. [PMID: 27213015 PMCID: PMC4875668 DOI: 10.1186/s13068-016-0520-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/06/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) belong to the "auxiliary activities (AA)" enzyme class of the CAZy database. They are known to strongly improve the saccharification process and boost soluble sugar yields from lignocellulosic biomass, which is a key step in the efficient production of sustainable economic biofuels. To date, most LPMOs have been characterized from terrestrial fungi, but novel fungal LPMOs isolated from more extreme environments such as an estuary mangrove ecosystem could offer enzymes with unique properties in terms of salt tolerance and higher stability under harsh condition. RESULTS Two LPMOs secreted by the mangrove-associated fungus Pestalotiopsis sp. NCi6 (PsLPMOA and PsLPMOB) were expressed in the yeast Pichia pastoris and produced in a bioreactor with >85 mg L(-1) for PsLPMOA and >260 mg L(-1) for PsLPMOB. Structure-guided homology modeling of the PsLPMOs showed a high abundance of negative surface charges, enabling enhanced protein stability and activity in the presence of sea salt. Both PsLPMOs were activated by a cellobiose dehydrogenase (CDH) from Neurospora crassa, with an apparent optimum of interaction at pH 5.5. Investigation into their regioselective mode of action revealed that PsLPMOA released C1- and C4-oxidized cello-oligosaccharide products, while PsLPMOB released only C4-oxidized products. PsLPMOA was found to cleave polymeric cellulose in the presence of up to 6 % sea salt, which emphasizes the use of sea water in the industrial saccharification process with improved ecological footprints. CONCLUSIONS Two new LPMOs from the mangrove fungus Pestalotiopsis sp. NCi6 were found to be fully reactive against cellulose. The combined hydrolytic activities of these salt-responsive LPMOs could therefore facilitate the saccharification process using sea water as a reaction medium for large-scale biorefineries.
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Affiliation(s)
- Ilabahen Patel
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Daniel Kracher
- />Department of Food Sciences and Technology, Food Biotechnology Laboratory, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, 1190 Austria
| | - Su Ma
- />Department of Food Sciences and Technology, Food Biotechnology Laboratory, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, 1190 Austria
| | - Sona Garajova
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Mireille Haon
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Craig B. Faulds
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Jean-Guy Berrin
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Roland Ludwig
- />Department of Food Sciences and Technology, Food Biotechnology Laboratory, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, 1190 Austria
| | - Eric Record
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, Polytech Marseille, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- />UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy-Polytech Marseille, Aix-Marseille Université, 163 Avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
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209
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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210
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Moses V, Hatherley R, Tastan Bishop Ö. Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:239. [PMID: 27833654 PMCID: PMC5101804 DOI: 10.1186/s13068-016-0655-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/25/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Due to the impending depletion of fossil fuels, it has become important to identify alternative energy sources. The biofuel industry has proven to be a promising alternative. However, owing to the complex nature of plant biomass, hence the degradation, biofuel production remains a challenge. The copper-dependent Auxiliary Activity family 9 (AA9) proteins have been found to act synergistically with other cellulose-degrading enzymes resulting in an increased rate of cellulose breakdown. AA9 proteins are lytic polysaccharide monooxygenase (LPMO) enzymes, otherwise known as polysaccharide monooxygenases (PMOs). They are further classified as Type 1, 2 or 3 PMOs, depending on the different cleavage products formed. As AA9 proteins are known to exhibit low sequence conservation, the analysis of unique features of AA9 domains of these enzymes should provide insights for the better understanding of how different AA9 PMO types function. RESULTS Bioinformatics approaches were used to identify features specific to the catalytic AA9 domains of each type of AA9 PMO. Sequence analysis showed the N terminus to be highly variable with type-specific inserts evident in this region. Phylogenetic analysis was performed to cluster AA9 domains based on their types. Motif analysis enabled the identification of sub-groups within each AA9 PMO type with the majority of these motifs occurring within the highly variable N terminus of AA9 domains. AA9 domain structures were manually docked to crystalline cellulose and used to analyze both the type-specific inserts and motifs at a structural level. The results indicated that these regions influence the AA9 domain active site topology and may contribute to the regioselectivity displayed by different AA9 PMO types. Physicochemical property analysis was performed and detected significant differences in aromaticity, isoelectric point and instability index between certain AA9 PMO types. CONCLUSIONS In this study, a type-specific characterisation of AA9 domains was performed using various bioinformatics approaches. These highly variable proteins were found to have a greater degree of conservation within their respective types. Type-specific features were identified for AA9 domains, which could be observed at a sequence, structural and physicochemical level. This provides a basis under which to identify and group new AA9 LPMOs in future.
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Affiliation(s)
- Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - Rowan Hatherley
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
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211
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Gregory RC, Hemsworth GR, Turkenburg JP, Hart SJ, Walton PH, Davies GJ. Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens. Dalton Trans 2016; 45:16904-16912. [DOI: 10.1039/c6dt02793h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels.
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212
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Song W, Han X, Qian Y, Liu G, Yao G, Zhong Y, Qu Y. Proteomic analysis of the biomass hydrolytic potentials of Penicillium oxalicum lignocellulolytic enzyme system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:68. [PMID: 26997974 PMCID: PMC4797192 DOI: 10.1186/s13068-016-0477-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/02/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND The mining of high-performance enzyme systems is necessary to develop industrial lignocellulose bioconversion. Large amounts of cellulases and hemicellulases can be produced by Penicillium oxalicum. Hence, the enzyme system of this hypercellulolytic fungus should be elucidated to help design optimum enzyme systems for effective biomass hydrolysis. RESULTS The cellulolytic and xylanolytic activities of an SP enzyme system prepared from P. oxalicum JU-A10 were comparatively analyzed. Results indicated that the fungus possesses a complete cellulolytic-xylanolytic enzyme system. The cellobiohydrolase- and xylanase-specific activities of this system were higher than those of two other enzyme systems, i.e., ST from Trichoderma reesei SN1 and another commercial preparation Celluclast 1.5L. Delignified corncob residue (DCCR) could be hydrolyzed by SP to a greater extent than corncob residue (CCR). Beta-glucosidase (BG) supplemented in SP increased the ability of the system to hydrolyze DCCR and CCR, and resulted in a 64 % decrease in enzyme dosage with the same glucose yield. The behaviors of the enzyme components in the hydrolysis of CCR were further investigated by monitoring individual enzyme dynamics. The total protein concentrations and cellobiohydrolase (CBH), endoglucanase (EG), and filter paper activities in the supernatants significantly decreased during saccharification. These findings were more evident in SP than in the other enzyme systems. The comparative proteomic analysis of the enzyme systems revealed that both SP and ST were rich in carbohydrate-degrading enzymes and multiple non-hydrolytic proteins. A larger number of carbohydrate-binding modules 1 (CBM1) were also identified in SP than in ST. This difference might be linked to the greater adsorption to substrates and lower hydrolysis efficiency of SP enzymes than ST during lignocellulose saccharification, because CBM1 not only targets enzymes to insoluble cellulose but also leads to non-productive adsorption to lignin. CONCLUSIONS Penicillium oxalicum can be applied to the biorefinery of lignocellulosic biomass. Its ability to degrade lignocellulosic substrates could be further improved by modifying its enzyme system on the basis of enzyme activity measurement and proteomic analysis. The proposed strategy may also be applied to other lignocellulolytic enzyme systems to enhance their hydrolytic performances rationally.
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Affiliation(s)
- Wenxia Song
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Xiaolong Han
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Yuanchao Qian
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Guodong Liu
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Guangshan Yao
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Yaohua Zhong
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
| | - Yinbo Qu
- />State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
- />National Glycoengineering Research Center, Shandong University, No.27 Shanda South Road, Jinan, 250100 Shandong China
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213
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Mekasha S, Forsberg Z, Dalhus B, Bacik JP, Choudhary S, Schmidt-Dannert C, Vaaje-Kolstad G, Eijsink VGH. Structural and functional characterization of a small chitin-active lytic polysaccharide monooxygenase domain of a multi-modular chitinase fromJonesia denitrificans. FEBS Lett 2015; 590:34-42. [DOI: 10.1002/1873-3468.12025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Sophanit Mekasha
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Zarah Forsberg
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry; Institute for Clinical Medicine; University of Oslo; Norway
- Department of Microbiology; Clinic for Diagnostics and Intervention; Oslo University Hospital, Rikshospitalet; Norway
| | - John-Paul Bacik
- Bioscience Division; Protein Crystallography Station; Los Alamos National Laboratory; NM USA
| | - Swati Choudhary
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota; St. Paul MN USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics; University of Minnesota; St. Paul MN USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
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214
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A novel bio-electronic tongue using different cellobiose dehydrogenases to resolve mixtures of various sugars and interfering analytes. Biosens Bioelectron 2015; 79:515-21. [PMID: 26748369 DOI: 10.1016/j.bios.2015.12.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/15/2015] [Accepted: 12/20/2015] [Indexed: 11/22/2022]
Abstract
A novel application of cellobiose dehydrogenase (CDH) as sensing element for a Bioelectronic Tongue (BioET) system has been tested. In this work CDHs from various fungi, which exhibit different substrate specificities, were used to discriminate between lactose and glucose in presence of the interfering matrix compound Ca(2+) in various mixtures. This work exploits the advantage of an electronic tongue system with practically zero pre-treatment of samples and operation at low voltages in a direct electron transfer mode. The Artificial Neural Network (ANN) used in the BioET system to interpret the voltammetric data was able to provide a correct prediction of the concentrations of the analytes considered. Correlation coefficients in the comparison of obtained vs. expected concentrations were highly significant, especially for lactose (R(2)=0.975) and Ca(2+) (R(2)=0.945). This BioET application has a high potential especially for the food and dairy industry and also, if further miniaturised in screen printed format, for its in-situ use.
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215
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Lytic Polysaccharide Monooxygenases in Biomass Conversion. Trends Biotechnol 2015; 33:747-761. [DOI: 10.1016/j.tibtech.2015.09.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
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216
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Udatha DBRKG, Topakas E, Salazar M, Olsson L, Andersen MR, Panagiotou G. Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. BMC SYSTEMS BIOLOGY 2015; 9:77. [PMID: 26573537 PMCID: PMC4647334 DOI: 10.1186/s12918-015-0224-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/28/2015] [Indexed: 12/30/2022]
Abstract
Background The gene expression and secretion of fungal lignocellulolytic enzymes are tightly controlled at the transcription level using independent mechanisms to respond to distinct inducers from plant biomass. An advanced systems-level understanding of transcriptional regulatory networks is required to rationally engineer filamentous fungi for more efficient bioconversion of different types of biomass. Results In this study we focused on ten chemically defined inducers to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae and shed light on the complex network of transcriptional activators required. The chemical diversity analysis of the inducers, based on 186 chemical descriptors calculated from the structure, resulted into three clusters, however, the global, metabolic and extracellular protein transcription of the A. oryzae genome were only partially explained by the chemical similarity of the enzyme inducers. Genes encoding enzymes that have attracted considerable interest such as cellobiose dehydrogenases and copper-dependent polysaccharide mono-oxygenases presented a substrate-specific induction. Several homology-model structures were derived using ab-initio multiple threading alignment in our effort to elucidate the interplay of transcription factors involved in regulating plant-deconstructing enzymes and metabolites. Systematic investigation of metabolite-protein interactions, using the 814 unique reactants involved in 2360 reactions in the genome scale metabolic network of A. oryzae, was performed through a two-step molecular docking against the binding pockets of the transcription factors AoXlnR and AoAmyR. A total of six metabolites viz., sulfite (H2SO3), sulfate (SLF), uroporphyrinogen III (UPGIII), ethanolamine phosphate (PETHM), D-glyceraldehyde 3-phosphate (T3P1) and taurine (TAUR) were found as strong binders, whereas the genes involved in the metabolic reactions that these metabolites appear were found to be significantly differentially expressed when comparing the inducers with glucose. Conclusions Based on our observations, we believe that specific binding of sulfite to the regulator of the cellulase gene expression, AoXlnR, may be the molecular basis for the connection of sulfur metabolism and cellulase gene expression in filamentous fungi. Further characterization and manipulation of the regulatory network components identified in this study, will enable rational engineering of industrial strains for improved production of the sophisticated set of enzymes necessary to break-down chemically divergent plant biomass. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0224-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D B R K Gupta Udatha
- The Norwegian Structural Biology Centre, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15780, Greece.
| | - Margarita Salazar
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| | - Lisbeth Olsson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Søltofts plads 223, DK-2800, Lyngby, Denmark.
| | - Gianni Panagiotou
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Hong Kong, China.
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217
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Bacik JP, Mekasha S, Forsberg Z, Kovalevsky A, Nix JC, Cuneo MJ, Coates L, Vaaje-Kolstad G, Chen JCH, Eijsink VGH, Unkefer CJ. Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase. Acta Crystallogr F Struct Biol Commun 2015; 71:1448-52. [PMID: 26527275 PMCID: PMC4631597 DOI: 10.1107/s2053230x15019743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1-3 mm(3)) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space group P212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.
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Affiliation(s)
- John-Paul Bacik
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
| | - Sophanit Mekasha
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Zarah Forsberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Jay C. Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Matthew J. Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Julian C.-H. Chen
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Clifford J. Unkefer
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
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218
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Proskurina OV, Korotkova OG, Rozhkova AM, Kondrat’eva EG, Matys VY, Zorov IN, Koshelev AV, Okunev ON, Nemashkalov VA, Bubnova TV, Sinitsyn AP. Use of endoglucanase IV from Trichoderma reesei to enhance the hydrolytic activity of a cellulase complex from the fungus Penicillium verruculosum. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815060125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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219
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Direct target network of the Neurospora crassa plant cell wall deconstruction regulators CLR-1, CLR-2, and XLR-1. mBio 2015; 6:e01452-15. [PMID: 26463163 PMCID: PMC4620465 DOI: 10.1128/mbio.01452-15] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Fungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. In Neurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. When N. crassa is exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog in Saccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex. Understanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.
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220
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Guerriero G, Hausman J, Strauss J, Ertan H, Siddiqui KS. Lignocellulosic bioma
ss
: Biosynthesis, degradation, and industrial utilization. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400196] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN) Luxembourg Institute of Science and Technology (LIST) Esch/Alzette Luxembourg
| | - Jean‐Francois Hausman
- Environmental Research and Innovation (ERIN) Luxembourg Institute of Science and Technology (LIST) Esch/Alzette Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology Fungal Genetics and Genomics Unit University of Natural Resources and Life Sciences Vienna (BOKU) University and Research Center Campus Tulln‐Technopol Tulln/Donau Austria
- Health and Environment Department Austrian Institute of Technology GmbH ‐ AIT University and Research Center Campus Tulln‐Technopol Tulln/Donau Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney Australia
- Department of Molecular Biology and Genetics Istanbul University Istanbul Turkey
| | - Khawar Sohail Siddiqui
- Life Sciences Department King Fahd University of Petroleum and Minerals (KFUPM) Dhahran Kingdom of Saudi Arabia
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221
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Jung S, Song Y, Kim HM, Bae HJ. Enhanced lignocellulosic biomass hydrolysis by oxidative lytic polysaccharide monooxygenases (LPMOs) GH61 from Gloeophyllum trabeum. Enzyme Microb Technol 2015; 77:38-45. [DOI: 10.1016/j.enzmictec.2015.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023]
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222
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Tanghe M, Danneels B, Camattari A, Glieder A, Vandenberghe I, Devreese B, Stals I, Desmet T. Recombinant Expression of Trichoderma reesei Cel61A in Pichia pastoris: Optimizing Yield and N-terminal Processing. Mol Biotechnol 2015; 57:1010-7. [DOI: 10.1007/s12033-015-9887-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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223
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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224
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Borisova AS, Isaksen T, Dimarogona M, Kognole AA, Mathiesen G, Várnai A, Røhr ÅK, Payne CM, Sørlie M, Sandgren M, Eijsink VGH. Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity. J Biol Chem 2015; 290:22955-69. [PMID: 26178376 DOI: 10.1074/jbc.m115.660183] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/02/2023] Open
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose β-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu(2+) center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4-oxidized products show an intermediate situation.
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Affiliation(s)
- Anna S Borisova
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Trine Isaksen
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Maria Dimarogona
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Abhishek A Kognole
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Geir Mathiesen
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Anikó Várnai
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Åsmund K Røhr
- the Department of Biosciences, University of Oslo, N-0316 Oslo, Norway, and
| | - Christina M Payne
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden, the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Mats Sandgren
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden,
| | - Vincent G H Eijsink
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway,
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225
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Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, Hällberg BM, Ludwig R, Divne C. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat Commun 2015; 6:7542. [PMID: 26151670 PMCID: PMC4507011 DOI: 10.1038/ncomms8542] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.
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Affiliation(s)
- Tien-Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Daniel Kracher
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Rosaria Gandini
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Roman Kittl
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - B. Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22603, Germany; and Centre for Structural Systems Biology (CSSB), DESY-Campus, Hamburg 22603, Germany
| | - Roland Ludwig
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
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Morales-Cruz A, Amrine KCH, Blanco-Ulate B, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. BMC Genomics 2015; 16:469. [PMID: 26084502 PMCID: PMC4472170 DOI: 10.1186/s12864-015-1624-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development. RESULTS The integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution. CONCLUSIONS This study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Katherine C H Amrine
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Daniel P Lawrence
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
| | - Renaud Travadon
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA.
| | - Kendra Baumgartner
- United States Department of Agriculture - Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA.
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
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227
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Research advances in expansins and expansion-like proteins involved in lignocellulose degradation. Biotechnol Lett 2015; 37:1541-51. [DOI: 10.1007/s10529-015-1842-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/29/2015] [Indexed: 12/12/2022]
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228
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Classification of fungal and bacterial lytic polysaccharide monooxygenases. BMC Genomics 2015; 16:368. [PMID: 25956378 PMCID: PMC4424831 DOI: 10.1186/s12864-015-1601-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These enzymes were originally designated glycoside hydrolase family 61 and carbohydrate-binding module family 33 but are now classified as auxiliary activities 9, 10 and 11 in the CAZy database. To obtain a systematic analysis of the divergent families of lytic polysaccharide monooxygenases we used Peptide Pattern Recognition to divide 5396 protein sequences resembling enzymes from families AA9 (1828 proteins), AA10 (2799 proteins) and AA11 (769 proteins) into subfamilies. Results The results showed that the lytic polysaccharide monooxygenases have two conserved regions identified by conserved peptides specific for each AA family. The peptides were used for in silico PCR discovery of the lytic polysaccharide monooxygenases in 79 fungal and 95 bacterial genomes. The bacterial genomes encoded 0 – 7 AA10s (average 0.6). No AA9 or AA11 were found in the bacteria. The fungal genomes encoded 0 – 40 AA9s (average 7) and 0 – 15 AA11s (average 2) and two of the fungi possessed a gene encoding a putative AA10. The AA9s were mainly found in plant cell wall-degrading asco- and basidiomycetes in agreement with the described role of AA9 enzymes. In contrast, the AA11 proteins were found in 36 of the 39 ascomycetes and in only two of the 32 basidiomycetes and their abundance did not correlate to the degradation of cellulose and hemicellulose. Conclusions These results provides an overview of the sequence characteristics and occurrence of the divergent AA9, AA10 and AA11 families and pave the way for systematic investigations of the of lytic polysaccharide monooxygenases and for structure-function studies of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1601-6) contains supplementary material, which is available to authorized users.
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229
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Kim IJ, Nam KH, Yun EJ, Kim S, Youn HJ, Lee HJ, Choi IG, Kim KH. Optimization of synergism of a recombinant auxiliary activity 9 from Chaetomium globosum with cellulase in cellulose hydrolysis. Appl Microbiol Biotechnol 2015; 99:8537-47. [PMID: 25936375 PMCID: PMC4768223 DOI: 10.1007/s00253-015-6592-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/14/2015] [Accepted: 04/01/2015] [Indexed: 01/16/2023]
Abstract
Auxiliary activity family 9 (AA9, formerly known as glycoside hydrolase family 61 or polysaccharide monooxygenase) is a group of fungal proteins that were recently found to have a significant synergism with cellulase in cellulose hydrolysis via the oxidative cleavage of glycosidic bonds of cellulose chains. In this study, we report the active expression of a recombinant fungal AA9 from Chaetomium globosum (CgAA9) in a bacterial host, Escherichia coli, and the optimization of its synergistic activity in cellulose hydrolysis by using cellulase. The recombinant CgAA9 (0.9 mg/g cellulose) exhibited 1.7-fold synergism in the hydrolysis of Avicel when incubated with 0.9 filter paper units of Celluclast 1.5 L/g cellulose. The first study of the active expression of AA9 using a bacterial host and its synergistic optimization could be useful for the industrial application of AA9 for the saccharification of lignocellulose.
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Affiliation(s)
- In Jung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Eun Ju Yun
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Sooah Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Hak Jin Youn
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Hee Jin Lee
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 136-713, Republic of Korea.
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230
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Vermaas JV, Crowley MF, Beckham GT, Payne CM. Effects of lytic polysaccharide monooxygenase oxidation on cellulose structure and binding of oxidized cellulose oligomers to cellulases. J Phys Chem B 2015; 119:6129-43. [PMID: 25785779 DOI: 10.1021/acs.jpcb.5b00778] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In nature, polysaccharide glycosidic bonds are cleaved by hydrolytic enzymes for a vast array of biological functions. Recently, a new class of enzymes that utilize an oxidative mechanism to cleave glycosidic linkages was discovered; these enzymes are called lytic polysaccharide monooxygenases (LPMO). These oxidative enzymes are synergistic with cocktails of hydrolytic enzymes and are thought to act primarily on crystalline regions, in turn providing new sites of productive attachment and detachment for processive hydrolytic enzymes. In the case of cellulose, the homopolymer of β-1,4-d-glucose, enzymatic oxidation occurs at either the reducing end or the nonreducing end of glucose, depending on enzymatic specificity, and results in the generation of oxidized chemical substituents at polymer chain ends. LPMO oxidation of cellulose is thought to produce either a lactone at the reducing end of glucose that can spontaneously or enzymatically convert to aldonic acid or 4-keto-aldose at the nonreducing end that may further oxidize to a geminal diol. Here, we use molecular simulation to examine the effect of oxidation on the structure of crystalline cellulose. The simulations highlight variations in behaviors depending on the chemical identity of the oxidized species and its location within the cellulose fibril, as different oxidized species introduce steric effects that disrupt local crystallinity and in some cases reduce the work needed for polymer decrystallization. Reducing-end oxidations are easiest to decrystallize when located at the end of the fibril, whereas nonreducing end oxidations readily decrystallize from internal cleavage sites despite their lower solvent accessibility. The differential in decrystallization free energy suggests a molecular mechanism consistent with experimentally observed LPMO/cellobiohydrolase synergy. Additionally, the soluble oxidized cellobiose products released by hydrolytic cellulases may bind to the active sites of cellulases with different affinities relative to cellobiose itself, which potentially affects hydrolytic turnover through product inhibition. To examine the effect of oxidation on cello-oligomer binding, we use thermodynamic integration to compute the relative change in binding free energy between the hydrolyzed and oxidized products in the active site of Family 7 and Family 6 processive glycoside hydrolases, Trichoderma reesei Cel7A and Cel6A, which are key industrial cellulases and commonly used model systems for fungal cellulases. Our results suggest that the equilibrium between the two reducing end oxidized products, favoring the linear aldonic acid, may increase product inhibition, which would in turn reduce processive substrate turnover. In the case of LMPO action at the nonreducing end, oxidation appears to lower affinity with the nonreducing end specific cellulase, reducing product inhibition and potentially promoting processive cellulose turnover. Overall, this suggests that oxidation of recalcitrant polysaccharides by LPMOs accelerates degradation not only by increasing the concentration of chain termini but also by reducing decrystallization work, and that product inhibition may be somewhat reduced as a result.
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Affiliation(s)
- Josh V Vermaas
- †Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,‡National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael F Crowley
- §Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gregg T Beckham
- ‡National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Christina M Payne
- ∥Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States.,⊥Center for Computational Science, University of Kentucky, Lexington, Kentucky 40506, United States
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231
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Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist EA, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proc Natl Acad Sci U S A 2015; 112:3451-6. [PMID: 25733908 PMCID: PMC4371944 DOI: 10.1073/pnas.1424293112] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.
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Affiliation(s)
- Braham Dhillon
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
| | - Andrea L Aerts
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Stéphanie Beauseigle
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Louis Bernier
- Centre d'Étude de la Forêt, Université Laval, Québec, QC, Canada G1V 0A6
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Adam Foster
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7
| | - Navdeep Gill
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Bernard Henrissat
- UMR 7257 Centre National de la Recherche Scientifique, Aix-Marseille University, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Padmini Herath
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Kurt M LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Anthony Levasseur
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France
| | - Erika A Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Eline Majoor
- Fungal Physiology, Centraalbureau voor Schimmelcultures-Royal Netherlands Academy of Arts and Sciences Fungal Biodiversity Centre (CBS-KNAW), 3584 CT, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | | | - Amadeus Pribowo
- Forest Products Biotechnology and Bioenergy, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4; and
| | - John N Saddler
- Forest Products Biotechnology and Bioenergy, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4; and
| | - Monique L Sakalidis
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Ronald P de Vries
- Fungal Physiology, Centraalbureau voor Schimmelcultures-Royal Netherlands Academy of Arts and Sciences Fungal Biodiversity Centre (CBS-KNAW), 3584 CT, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Stephen B Goodwin
- US Department of Agriculture-Agricultural Research Service Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN 47907-2054
| | - Philippe Tanguay
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7;
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232
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Takeda K, Matsumura H, Ishida T, Samejima M, Ohno H, Yoshida M, Igarashi K, Nakamura N. Characterization of a novel PQQ-dependent quinohemoprotein pyranose dehydrogenase from Coprinopsis cinerea classified into auxiliary activities family 12 in carbohydrate-active enzymes. PLoS One 2015; 10:e0115722. [PMID: 25679509 PMCID: PMC4332668 DOI: 10.1371/journal.pone.0115722] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
Abstract
The basidiomycete Coprinopsis cinerea contains a quinohemoprotein (CcPDH named as CcSDH in our previous paper), which is a new type of pyrroloquinoline-quinone (PQQ)-dependent pyranose dehydrogenase and is the first found among all eukaryotes. This enzyme has a three-domain structure consisting of an N-terminal heme b containing a cytochrome domain that is homologous to the cytochrome domain of cellobiose dehydrogenase (CDH; EC 1.1.99.18) from the wood-rotting basidiomycete Phanerochaete chrysosporium, a C-terminal family 1-type carbohydrate-binding module, and a novel central catalytic domain containing PQQ as a cofactor. Here, we describe the biochemical and electrochemical characterization of recombinant CcPDH. UV-vis and resonance Raman spectroscopic studies clearly reveal characteristics of a 6-coordinated low-spin heme b in both the ferric and ferrous states, as well as intramolecular electron transfer from the PQQ to heme b. Moreover, the formal potential of the heme was evaluated to be 130 mV vs. NHE by cyclic voltammetry. These results indicate that the cytochrome domain of CcPDH possesses similar biophysical properties to that in CDH. A comparison of the conformations of monosaccharides as substrates and the associated catalytic efficiency (kcat/Km) of CcPDH indicates that the enzyme prefers monosaccharides with equatorial C-2, C-3 hydroxyl groups and an axial C-4 hydroxyl group in the 1C4 chair conformation. Furthermore, a binding study shows a high binding affinity of CcPDH for cellulose, suggesting that CcPDH function is related to the enzymatic degradation of plant cell wall.
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Affiliation(s)
- Kouta Takeda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hirotoshi Matsumura
- Department of Biomaterials Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Ishida
- Department of Biomaterials Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Samejima
- Department of Biomaterials Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ohno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Makoto Yoshida
- Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- * E-mail: (MY); (KI); (NN)
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail: (MY); (KI); (NN)
| | - Nobuhumi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- * E-mail: (MY); (KI); (NN)
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233
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O'Neill EC, Field RA. Enzymatic synthesis using glycoside phosphorylases. Carbohydr Res 2015; 403:23-37. [PMID: 25060838 PMCID: PMC4336185 DOI: 10.1016/j.carres.2014.06.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 05/29/2014] [Accepted: 06/09/2014] [Indexed: 01/10/2023]
Abstract
Carbohydrate phosphorylases are readily accessible but under-explored catalysts for glycoside synthesis. Their use of accessible and relatively stable sugar phosphates as donor substrates underlies their potential. A wide range of these enzymes has been reported of late, displaying a range of preferences for sugar donors, acceptors and glycosidic linkages. This has allowed this class of enzymes to be used in the synthesis of diverse carbohydrate structures, including at the industrial scale. As more phosphorylase enzymes are discovered, access to further difficult to synthesise glycosides will be enabled. Herein we review reported phosphorylase enzymes and the glycoside products that they have been used to synthesise.
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Affiliation(s)
- Ellis C O'Neill
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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234
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Paspaliari DK, Loose JSM, Larsen MH, Vaaje-Kolstad G. Listeria monocytogeneshas a functional chitinolytic system and an active lytic polysaccharide monooxygenase. FEBS J 2015; 282:921-36. [DOI: 10.1111/febs.13191] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Dafni K. Paspaliari
- Department of Veterinary Disease Biology; Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Jennifer S. M. Loose
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Marianne H. Larsen
- Department of Veterinary Disease Biology; Faculty of Health and Medical Sciences; University of Copenhagen; Denmark
| | - Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
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235
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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236
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Dhar D, Tolman WB. Hydrogen atom abstraction from hydrocarbons by a copper(III)-hydroxide complex. J Am Chem Soc 2015; 137:1322-9. [PMID: 25581555 PMCID: PMC4311965 DOI: 10.1021/ja512014z] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 12/17/2022]
Abstract
With the aim of understanding the basis for the high rate of hydrogen atom abstraction (HAT) from dihydroanthracene (DHA) by the complex LCuOH (1; L = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridinedicarboxamide), the bond dissociation enthalpy of the reaction product LCu(H2O) (2) was determined through measurement of its pK(a) and E(1/2) in THF solution. In so doing, an equilibrium between 2 and LCu(THF) was characterized by UV-vis and EPR spectroscopy and cyclic voltammetry (CV). A high pK(a) of 18.8 ± 1.8 and a low E(1/2) of -0.074 V vs Fc/Fc(+) in THF combined to yield an O-H BDE for 2 of 90 ± 3 kcal mol(-1) that is large relative to values for most transition metal oxo/hydroxo complexes. By taking advantage of the increased stability of 1 observed in 1,2-difluorobenzene (DFB) solvent, the kinetics of the reactions of 1 with a range of substrates with varying BDE values for their C-H bonds were measured. The oxidizing power of 1 was revealed through the accelerated decay of 1 in the presence of the substrates, including THF (BDE = 92 kcal mol(-1)) and cyclohexane (BDE = 99 kcal mol(-1)). CV experiments in THF solvent showed that 1 reacted with THF via rate-determining attack at the THF C-H(D) bonds with a kinetic isotope effect of 10.2. Analysis of the kinetic and thermodynamic data provides new insights into the basis for the high reactivity of 1 and the possible involvement of species like 1 in oxidation catalysis.
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Affiliation(s)
- Debanjan Dhar
- Department of Chemistry and
Center for Metals in Biocatalysis, University
of Minnesota, 207 Pleasant
Street SE, Minneapolis, Minnesota 55455, United States
| | - William B. Tolman
- Department of Chemistry and
Center for Metals in Biocatalysis, University
of Minnesota, 207 Pleasant
Street SE, Minneapolis, Minnesota 55455, United States
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237
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Lo Leggio L, Simmons TJ, Poulsen JCN, Frandsen KEH, Hemsworth GR, Stringer MA, von Freiesleben P, Tovborg M, Johansen KS, De Maria L, Harris PV, Soong CL, Dupree P, Tryfona T, Lenfant N, Henrissat B, Davies GJ, Walton PH. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat Commun 2015; 6:5961. [PMID: 25608804 PMCID: PMC4338556 DOI: 10.1038/ncomms6961] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 11/25/2014] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have significant industrial importance. We report here the activity, spectroscopy and three-dimensional structure of a starch-active LPMO, a representative of the new CAZy AA13 family. We demonstrate that these enzymes generate aldonic acid-terminated malto-oligosaccharides from retrograded starch and boost significantly the conversion of this recalcitrant substrate to maltose by β-amylase. The detailed structure of the enzyme's active site yields insights into the mechanism of action of this important class of enzymes.
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Affiliation(s)
- Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Thomas J. Simmons
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Kristian E. H. Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | | | | | | | | | | | | | - Paul V. Harris
- Novozymes, Inc., 1445 Drew Avenue, Davis, California 95618, USA
| | - Chee-Leong Soong
- Novozymes North America Inc., 77 Perrys Chapel Church Road, Franklinton, North Carolina 27525, USA
| | - Paul Dupree
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Theodora Tryfona
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Nicolas Lenfant
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Paul H. Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
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238
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Yao G, Li Z, Gao L, Wu R, Kan Q, Liu G, Qu Y. Redesigning the regulatory pathway to enhance cellulase production in Penicillium oxalicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:71. [PMID: 25949521 PMCID: PMC4422585 DOI: 10.1186/s13068-015-0253-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/09/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND In cellulolytic fungi, induction and repression mechanisms synchronously regulate the synthesis of cellulolytic enzymes for accurate responses to carbon sources in the environment. Many proteins, particularly transcription regulatory factors involved in these processes, were identified and genetically engineered in Penicillium oxalicum and other cellulolytic fungi. Despite such great efforts, its effect of modifying a single target to improve the production of cellulase is highly limited. RESULTS In this study, we developed a systematic strategy for the genetic engineering of P. oxalicum to enhance cellulase yields, by enhancing induction (by blocking intracellular inducer hydrolysis and increasing the activator level) and relieving the repression. We obtained a trigenic recombinant strain named 'RE-10' by deleting bgl2 and creA, along with over-expressing the gene clrB. The cellulolytic ability of RE-10 was significantly improved; the filter paper activity and extracellular protein concentration increased by up to over 20- and 10-fold, respectively, higher than those of the wild-type (WT) strain 114-2 both on pure cellulose and complex wheat bran media. Most strikingly, the cellulolytic ability of RE-10 was comparable with that of the industrial P. oxalicum strain JU-A10-T obtained by random mutagenesis. Comparative proteomics analysis provided further insights into the differential secretomes between RE-10 and WT strains. In particular, the enzymes and accessory proteins involved in lignocellulose degradation were elevated specifically and dramatically in the recombinant, thereby confirming the importance of them in biomass deconstruction and implying a possible co-regulatory mechanism. CONCLUSIONS We established a novel route to substantially improve cellulolytic enzyme production up to the industrial level in P. oxalicum by combinational manipulation of three key genes to amplify the induction along with derepression, representing a milestone in strain engineering of filamentous fungi. Given the conservation in the mode of cellulose expression regulation among filamentous fungi, this strategy could be compatible with other cellulase-producing fungi.
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Affiliation(s)
- Guangshan Yao
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Zhonghai Li
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
- />Qingdao Vland Biotech Group Co. Ltd., Shandong Expressway Mansion, Miaoling Road, Qingdao, Shandong China
| | - Liwei Gao
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Ruimei Wu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Qinbiao Kan
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Guodong Liu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Yinbo Qu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
- />National Glycoengineering Research Center, Shandong University, Jinan City, Shandong Province 250100 China
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Frommhagen M, Sforza S, Westphal AH, Visser J, Hinz SWA, Koetsier MJ, van Berkel WJH, Gruppen H, Kabel MA. Discovery of the combined oxidative cleavage of plant xylan and cellulose by a new fungal polysaccharide monooxygenase. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:101. [PMID: 26185526 PMCID: PMC4504452 DOI: 10.1186/s13068-015-0284-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/08/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Many agricultural and industrial food by-products are rich in cellulose and xylan. Their enzymatic degradation into monosaccharides is seen as a basis for the production of biofuels and bio-based chemicals. Lytic polysaccharide monooxygenases (LPMOs) constitute a group of recently discovered enzymes, classified as the auxiliary activity subgroups AA9, AA10, AA11 and AA13 in the CAZy database. LPMOs cleave cellulose, chitin, starch and β-(1 → 4)-linked substituted and non-substituted glucosyl units of hemicellulose under formation of oxidized gluco-oligosaccharides. RESULTS Here, we demonstrate a new LPMO, obtained from Myceliophthora thermophila C1 (MtLPMO9A). This enzyme cleaves β-(1 → 4)-xylosyl bonds in xylan under formation of oxidized xylo-oligosaccharides, while it simultaneously cleaves β-(1 → 4)-glucosyl bonds in cellulose under formation of oxidized gluco-oligosaccharides. In particular, MtLPMO9A benefits from the strong interaction between low substituted linear xylan and cellulose. MtLPMO9A shows a strong synergistic effect with endoglucanase I (EGI) with a 16-fold higher release of detected oligosaccharides, compared to the oligosaccharides release of MtLPMO9A and EGI alone. CONCLUSION Now, for the first time, we demonstrate the activity of a lytic polysaccharide monooxygenase (MtLPMO9A) that shows oxidative cleavage of xylan in addition to cellulose. The ability of MtLPMO9A to cleave these rigid regions provides a new paradigm in the understanding of the degradation of xylan-coated cellulose. In addition, MtLPMO9A acts in strong synergism with endoglucanase I. The mode of action of MtLPMO9A is considered to be important for loosening the rigid xylan-cellulose polysaccharide matrix in plant biomass, enabling increased accessibility to the matrix for hydrolytic enzymes. This discovery provides new insights into how to boost plant biomass degradation by enzyme cocktails for biorefinery applications.
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Affiliation(s)
- Matthias Frommhagen
- />Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Stefano Sforza
- />Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
- />Department of Food Science, University of Parma, Parco Area delle Scienze 59a, University Campus, 43124 Parma, Italy
| | - Adrie H Westphal
- />Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Jaap Visser
- />Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Sandra W A Hinz
- />Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Martijn J Koetsier
- />Dyadic Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | | | - Harry Gruppen
- />Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A Kabel
- />Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Moroz OV, Maranta M, Shaghasi T, Harris PV, Wilson KS, Davies GJ. The three-dimensional structure of the cellobiohydrolase Cel7A from Aspergillus fumigatus at 1.5 Å resolution. Acta Crystallogr F Struct Biol Commun 2015; 71:114-20. [PMID: 25615982 PMCID: PMC4304761 DOI: 10.1107/s2053230x14027307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/15/2014] [Indexed: 01/09/2023] Open
Abstract
The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of the Aspergillus fumigatus CBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts.
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Affiliation(s)
- Olga V. Moroz
- Department of Chemistry, University of York, York Structural Biology Laboratory, York YO10 5DD, England
| | | | | | | | - Keith S. Wilson
- Department of Chemistry, University of York, York Structural Biology Laboratory, York YO10 5DD, England
| | - Gideon J. Davies
- Department of Chemistry, University of York, York Structural Biology Laboratory, York YO10 5DD, England
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241
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Bennati-Granier C, Garajova S, Champion C, Grisel S, Haon M, Zhou S, Fanuel M, Ropartz D, Rogniaux H, Gimbert I, Record E, Berrin JG. Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:90. [PMID: 26136828 PMCID: PMC4487207 DOI: 10.1186/s13068-015-0274-3] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/12/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND The understanding of enzymatic polysaccharide degradation has progressed intensely in the past few years with the identification of a new class of fungal-secreted enzymes, the lytic polysaccharide monooxygenases (LPMOs) that enhance cellulose conversion. In the fungal kingdom, saprotrophic fungi display a high number of genes encoding LPMOs from family AA9 but the functional relevance of this redundancy is not fully understood. RESULTS In this study, we investigated a set of AA9 LPMOs identified in the secretomes of the coprophilous ascomycete Podospora anserina, a biomass degrader of recalcitrant substrates. Their activity was assayed on cellulose in synergy with the cellobiose dehydrogenase from the same organism. We showed that the total release of oxidized oligosaccharides from cellulose was higher for PaLPMO9A, PaLPMO9E, and PaLPMO9H that harbored a carbohydrate-binding module from the family CBM1. Investigation of their regioselective mode of action revealed that PaLPMO9A and PaLPMO9H oxidatively cleaved at both C1 and C4 positions while PaLPMO9E released only C1-oxidized products. Rapid cleavage of cellulose was observed using PaLPMO9H that was the most versatile in terms of substrate specificity as it also displayed activity on cello-oligosaccharides and β-(1,4)-linked hemicellulose polysaccharides (e.g., xyloglucan, glucomannan). CONCLUSIONS This study provides insights into the mode of cleavage and substrate specificities of fungal AA9 LPMOs that will facilitate their application for the development of future biorefineries.
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Affiliation(s)
- Chloé Bennati-Granier
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Sona Garajova
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
- />Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Charlotte Champion
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Sacha Grisel
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Mireille Haon
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Simeng Zhou
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Mathieu Fanuel
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - David Ropartz
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Hélène Rogniaux
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Isabelle Gimbert
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Eric Record
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Jean-Guy Berrin
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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243
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Liaud N, Giniés C, Navarro D, Fabre N, Crapart S, Gimbert IH, Levasseur A, Raouche S, Sigoillot JC. RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger. Fungal Biol Biotechnol 2014; 1:1-14. [PMID: 26457194 PMCID: PMC4599204 DOI: 10.1186/s40694-014-0003-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/23/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers. RESULTS In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. CONCLUSIONS By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production.
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Affiliation(s)
- Nadège Liaud
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Christian Giniés
- INRA, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- INSERM, UMR 1062, « Nutrition, Obésité et Risque Thrombotique », Marseille, F-13385 France
- Université d’Aix-Marseille, UMR 1260, « Nutrition, Obésité et Risque Thrombotique », Faculté de Médecine, Marseille, F-13385 France
| | - David Navarro
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- INRA, International Center for Microbial Resources collection-Filamentous fungi CIRM-CF, Marseille, F-13288 France
| | - Nicolas Fabre
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Sylvaine Crapart
- ARD, Agro-Industry Research and Development, Pômacle, F-51100 France
| | - Isabelle Herpoël- Gimbert
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Anthony Levasseur
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
| | - Sana Raouche
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Polytech’ Marseille (ex ESIL), UMR 1163 BCF - INRA / AMU, 163 Avenue de Luminy CP 925, Marseille, F-13288 France
| | - Jean-Claude Sigoillot
- INRA, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
- Aix Marseille Université, UMR1163 Biotechnology of Filamentous Fungi, Marseille, F-13288 France
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Engineering Neurospora crassa for improved cellobiose and cellobionate production. Appl Environ Microbiol 2014; 81:597-603. [PMID: 25381238 DOI: 10.1128/aem.02885-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report engineering Neurospora crassa to improve the yield of cellobiose and cellobionate from cellulose. A previously engineered strain of N. crassa (F5) with six of seven β-glucosidase (bgl) genes knocked out was shown to produce cellobiose and cellobionate directly from cellulose without the addition of exogenous cellulases. In this study, the F5 strain was further modified to improve the yield of cellobiose and cellobionate from cellulose by increasing cellulase production and decreasing product consumption. The effects of two catabolite repression genes, cre-1 and ace-1, on cellulase production were investigated. The F5 Δace-1 mutant showed no improvement over the wild type. The F5 Δcre-1 and F5 Δace-1 Δcre-1 strains showed improved cellobiose dehydrogenase and exoglucanase expression. However, this improvement in cellulase expression did not lead to an improvement in cellobiose or cellobionate production. The cellobionate phosphorylase gene (ndvB) was deleted from the genome of F5 Δace-1 Δcre-1 to prevent the consumption of cellobiose and cellobionate. Despite a slightly reduced hydrolysis rate, the F5 Δace-1 Δcre-1 ΔndvB strain converted 75% of the cellulose consumed to the desired products, cellobiose and cellobionate, compared to 18% converted by the strain F5 Δace-1 Δcre-1.
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Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genet Biol 2014; 72:168-181. [DOI: 10.1016/j.fgb.2014.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 12/30/2022]
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246
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Peterson RL, Ginsbach JW, Cowley RE, Qayyum MF, Himes RA, Siegler MA, Moore CD, Hedman B, Hodgson KO, Fukuzumi S, Solomon EI, Karlin KD. Stepwise protonation and electron-transfer reduction of a primary copper-dioxygen adduct. J Am Chem Soc 2014; 135:16454-67. [PMID: 24164682 DOI: 10.1021/ja4065377] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The protonation–reduction of a dioxygen adduct with [LCu(I)][B(C6F5)4], cupric superoxo complex [LCu(II)(O2(•–))]+ (1) (L = TMG3tren (1,1,1-tris[2-[N(2)-(1,1,3,3-tetramethylguanidino)]ethyl]amine)) has been investigated. Trifluoroacetic acid (HOAcF) reversibly associates with the superoxo ligand in ([LCu(II)(O2(•–))]+) in a 1:1 adduct [LCu(II)(O2(•–))(HOAcF)](+) (2), as characterized by UV–visible, resonance Raman (rR), nuclear magnetic resonance (NMR), and X-ray absorption (XAS) spectroscopies, along with density functional theory (DFT) calculations. Chemical studies reveal that for the binding of HOAcF with 1 to give 2, Keq = 1.2 × 10(5) M(–1) (−130 °C) and ΔH° = −6.9(7) kcal/mol, ΔS° = −26(4) cal mol(–1) K(–1)). Vibrational (rR) data reveal a significant increase (29 cm(–1)) in vO–O (= 1149 cm(–1)) compared to that known for [LCu(II)(O2(•–))](+) (1). Along with results obtained from XAS and DFT calculations, hydrogen bonding of HOAcF to a superoxo O-atom in 2 is established. Results from NMR spectroscopy of 2 at −120 °C in 2-methyltetrahydrofuran are also consistent with 1/HOAcF = 1:1 formulation of 2 and with this complex possessing a triplet (S = 1) ground state electronic configuration, as previously determined for 1. The pre-equilibrium acid association to 1 is followed by outer-sphere electron-transfer reduction of 2 by decamethylferrocene (Me10Fc) or octamethylferrocene (Me8Fc), leading to the products H2O2, the corresponding ferrocenium salt, and [LCu(II)(OAcF)](+). Second-order rate constants for electron transfer (ket) were determined to be 1365 M(–1) s(–1) (Me10Fc) and 225 M(–1) s(–1) (Me8Fc) at −80 °C. The (bio)chemical relevance of the proton-triggered reduction of the metal-bound dioxygen-derived fragment is discussed.
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Ortiz R, Ludwig R, Gorton L. Highly Efficient Membraneless Glucose Bioanode Based onCorynascus thermophilusCellobiose Dehydrogenase on Aryl Diazonium-Activated Single-Walled Carbon Nanotubes. ChemElectroChem 2014. [DOI: 10.1002/celc.201402197] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ghatge SS, Telke AA, Waghmode TR, Lee Y, Lee KW, Oh DB, Shin HD, Kim SW. Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose. Appl Microbiol Biotechnol 2014; 99:3041-55. [DOI: 10.1007/s00253-014-6116-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022]
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Castillo I, Neira AC, Nordlander E, Zeglio E. Bis(benzimidazolyl)amine copper complexes with a synthetic ‘histidine brace’ structural motif relevant to polysaccharide monooxygenases. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.06.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Morgenstern I, Powlowski J, Tsang A. Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family. Brief Funct Genomics 2014; 13:471-81. [PMID: 25217478 PMCID: PMC4239789 DOI: 10.1093/bfgp/elu032] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
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