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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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302
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303
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Vu VV, Marletta MA. Starch-degrading polysaccharide monooxygenases. Cell Mol Life Sci 2016; 73:2809-19. [PMID: 27170366 PMCID: PMC11108391 DOI: 10.1007/s00018-016-2251-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 01/08/2023]
Abstract
Polysaccharide degradation by hydrolytic enzymes glycoside hydrolases (GHs) is well known. More recently, polysaccharide monooxygenases (PMOs, also known as lytic PMOs or LPMOs) were found to oxidatively degrade various polysaccharides via a copper-dependent hydroxylation. PMOs were previously thought to be either GHs or carbohydrate binding modules (CBMs), and have been re-classified in carbohydrate active enzymes (CAZY) database as auxiliary activity (AA) families. These enzymes include cellulose-active fungal PMOs (AA9, formerly GH61), chitin- and cellulose-active bacterial PMOs (AA10, formerly CBM33), and chitin-active fungal PMOs (AA11). These PMOs significantly boost the activity of GHs under industrially relevant conditions, and thus have great potential in the biomass-based biofuel industry. PMOs that act on starch are the latest PMOs discovered (AA13), which has expanded our perspectives in PMOs studies and starch degradation. Starch-active PMOs have many common structural features and biochemical properties of the PMO superfamily, yet differ from other PMO families in several important aspects. These differences likely correlate, at least in part, to the differences in primary and higher order structures of starch and cellulose, and chitin. In this review we will discuss the discovery, structural features, biochemical and biophysical properties, and possible biological functions of starch-active PMOs, as well as their potential application in the biofuel, food, and other starch-based industries. Important questions regarding various aspects of starch-active PMOs and possible economical driving force for their future studies will also be highlighted.
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Affiliation(s)
- Van V Vu
- NTT Hi-Tech Institute (NHTI), Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City, Vietnam
| | - Michael A Marletta
- Department of Chemistry and Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720-3220, USA.
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304
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Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation. Appl Environ Microbiol 2016; 82:4387-4400. [PMID: 27208101 DOI: 10.1128/aem.00134-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/08/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research. IMPORTANCE This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.
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305
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Garajova S, Mathieu Y, Beccia MR, Bennati-Granier C, Biaso F, Fanuel M, Ropartz D, Guigliarelli B, Record E, Rogniaux H, Henrissat B, Berrin JG. Single-domain flavoenzymes trigger lytic polysaccharide monooxygenases for oxidative degradation of cellulose. Sci Rep 2016; 6:28276. [PMID: 27312718 PMCID: PMC4911613 DOI: 10.1038/srep28276] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022] Open
Abstract
The enzymatic conversion of plant biomass has been recently revolutionized by the discovery of lytic polysaccharide monooxygenases (LPMOs) that carry out oxidative cleavage of polysaccharides. These very powerful enzymes are abundant in fungal saprotrophs. LPMOs require activation by electrons that can be provided by cellobiose dehydrogenases (CDHs), but as some fungi lack CDH-encoding genes, other recycling enzymes must exist. We investigated the ability of AA3_2 flavoenzymes secreted under lignocellulolytic conditions to trigger oxidative cellulose degradation by AA9 LPMOs. Among the flavoenzymes tested, we show that glucose dehydrogenase and aryl-alcohol quinone oxidoreductases are catalytically efficient electron donors for LPMOs. These single-domain flavoenzymes display redox potentials compatible with electron transfer between partners. Our findings extend the array of enzymes which regulate the oxidative degradation of cellulose by lignocellulolytic fungi.
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Affiliation(s)
- Sona Garajova
- INRA, Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, F-13288 Marseille, France.,Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Yann Mathieu
- INRA, Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, F-13288 Marseille, France
| | - Maria Rosa Beccia
- Aix-Marseille Université, CNRS, UMR7281 Unité de Bioénergétique et Ingénierie des Protéines, F-13402 Marseille, France
| | - Chloé Bennati-Granier
- INRA, Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, F-13288 Marseille, France
| | - Frédéric Biaso
- Aix-Marseille Université, CNRS, UMR7281 Unité de Bioénergétique et Ingénierie des Protéines, F-13402 Marseille, France
| | - Mathieu Fanuel
- INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - David Ropartz
- INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Bruno Guigliarelli
- Aix-Marseille Université, CNRS, UMR7281 Unité de Bioénergétique et Ingénierie des Protéines, F-13402 Marseille, France
| | - Eric Record
- INRA, Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, F-13288 Marseille, France
| | - Hélène Rogniaux
- INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, F-44316 Nantes, France
| | - Bernard Henrissat
- CNRS, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France.,INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, F-13288 Marseille, France
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306
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Bischof RH, Ramoni J, Seiboth B. Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei. Microb Cell Fact 2016; 15:106. [PMID: 27287427 PMCID: PMC4902900 DOI: 10.1186/s12934-016-0507-6] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
More than 70 years ago, the filamentous ascomycete Trichoderma reesei was isolated on the Solomon Islands due to its ability to degrade and thrive on cellulose containing fabrics. This trait that relies on its secreted cellulases is nowadays exploited by several industries. Most prominently in biorefineries which use T. reesei enzymes to saccharify lignocellulose from renewable plant biomass in order to produce biobased fuels and chemicals. In this review we summarize important milestones of the development of T. reesei as the leading production host for biorefinery enzymes, and discuss emerging trends in strain engineering. Trichoderma reesei has very recently also been proposed as a consolidated bioprocessing organism capable of direct conversion of biopolymeric substrates to desired products. We therefore cover this topic by reviewing novel approaches in metabolic engineering of T. reesei.
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Affiliation(s)
- Robert H Bischof
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | - Jonas Ramoni
- Molecular Biotechnology, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria
| | - Bernhard Seiboth
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH c/o Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria. .,Molecular Biotechnology, Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060, Vienna, Austria.
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307
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Singh G, Verma AK, Kumar V. Catalytic properties, functional attributes and industrial applications of β-glucosidases. 3 Biotech 2016; 6:3. [PMID: 28330074 PMCID: PMC4697909 DOI: 10.1007/s13205-015-0328-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/19/2015] [Indexed: 12/18/2022] Open
Abstract
β-Glucosidases are diverse group of enzymes with great functional importance to biological systems. These are grouped in multiple glycoside hydrolase families based on their catalytic and sequence characteristics. Most studies carried out on β-glucosidases are focused on their industrial applications rather than their endogenous function in the target organisms. β-Glucosidases performed many functions in bacteria as they are components of large complexes called cellulosomes and are responsible for the hydrolysis of short chain oligosaccharides and cellobiose. In plants, β-glucosidases are involved in processes like formation of required intermediates for cell wall lignification, degradation of endosperm’s cell wall during germination and in plant defense against biotic stresses. Mammalian β-glucosidases are thought to play roles in metabolism of glycolipids and dietary glucosides, and signaling functions. These enzymes have diverse biotechnological applications in food, surfactant, biofuel, and agricultural industries. The search for novel and improved β-glucosidase is still continued to fulfills demand of an industrially suitable enzyme. In this review, a comprehensive overview on detailed functional roles of β-glucosidases in different organisms, their industrial applications, and recent cloning and expression studies with biochemical characterization of such enzymes is presented for the better understanding and efficient use of diverse β-glucosidases.
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Affiliation(s)
- Gopal Singh
- Institute of Himalayan Bioresource Technology, Palampur, 176062, India
| | - A K Verma
- Department of Biochemistry, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Vinod Kumar
- Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, India.
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308
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Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T. Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass. Trends Biochem Sci 2016; 41:633-645. [PMID: 27211037 DOI: 10.1016/j.tibs.2016.04.006] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Lignocellulose, the most abundant renewable carbon source on earth, is the logical candidate to replace fossil carbon as the major biofuel raw material. Nevertheless, the technologies needed to convert lignocellulose into soluble products that can then be utilized by the chemical or fuel industries face several challenges. Enzymatic hydrolysis is of major importance, and we review the progress made in fungal enzyme technology over the past few years with major emphasis on (i) the enzymes needed for the conversion of polysaccharides (cellulose and hemicellulose) into soluble products, (ii) the potential uses of lignin degradation products, and (iii) current progress and bottlenecks for the use of the soluble lignocellulose derivatives in emerging biorefineries.
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Affiliation(s)
- Vijai K Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland Galway, Galway City, Ireland.
| | - Christian P Kubicek
- Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstrasse, 1060 Wien, Austria
| | - Jean-Guy Berrin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - David W Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marie Couturier
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - Alex Berlin
- Novozymes, Inc., 1445 Drew Ave, Davis CA 95618 USA
| | - Edivaldo X F Filho
- Laboratory of Enzymology, Department of Cell Biology, University of Brasilia, Asa Norte, 70910-900 Brasilia, DF Brazil
| | - Thaddeus Ezeji
- Biotechnology and Fermentation Group, Department of Animal Sciences, Ohio State University and Ohio Agricultural Research and Development Center (OARDC), Madison Avenue, Wooster, OH 44691, USA
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309
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Sinitsyn AP, Korotkova OG, Sinitsyna OA, Rozhkova AM, Dotsenko GS, Proskurina OV, Osipov DO, Kondrat’eva EG, Chekushina AV. Optimizing the composition of cellulase enzyme complex from Penicillium verruculosum: Enhancing hydrolytic capabilities via genetic engineering. CATALYSIS IN INDUSTRY 2016. [DOI: 10.1134/s2070050416010128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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310
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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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311
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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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312
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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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313
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Light-driven oxidation of polysaccharides by photosynthetic pigments and a metalloenzyme. Nat Commun 2016; 7:11134. [PMID: 27041218 PMCID: PMC4822002 DOI: 10.1038/ncomms11134] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/23/2016] [Indexed: 12/31/2022] Open
Abstract
Oxidative processes are essential for the degradation of plant biomass. A class of powerful and widely distributed oxidative enzymes, the lytic polysaccharide monooxygenases (LPMOs), oxidize the most recalcitrant polysaccharides and require extracellular electron donors. Here we investigated the effect of using excited photosynthetic pigments as electron donors. LPMOs combined with pigments and reducing agents were exposed to light, which resulted in a never before seen 100-fold increase in catalytic activity. In addition, LPMO substrate specificity was broadened to include both cellulose and hemicellulose. LPMO enzymes and pigment derivatives common in the environment of plant-degrading organisms thus form a highly reactive and stable light-driven system increasing the turnover rate and versatility of LPMOs. This light-driven system may find applications in biotechnology and chemical processing. Lytic polysaccharide monooxygenases are proteins involved in the degradation of plant biomass and are promising biotechnological tools for biofuel production. Here, the authors show that their catalytic activity is significantly boosted when they are combined with photopigments and exposed to light.
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314
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Attia M, Stepper J, Davies GJ, Brumer H. Functional and structural characterization of a potent GH74 endo-xyloglucanase from the soil saprophyte Cellvibrio japonicus unravels the first step of xyloglucan degradation. FEBS J 2016; 283:1701-19. [PMID: 26929175 DOI: 10.1111/febs.13696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 11/27/2022]
Abstract
UNLABELLED The heteropolysaccharide xyloglucan (XyG) comprises up to one-quarter of the total carbohydrate content of terrestrial plant cell walls and, as such, represents a significant reservoir in the global carbon cycle. The complex composition of XyG requires a consortium of backbone-cleaving endo-xyloglucanases and side-chain cleaving exo-glycosidases for complete saccharification. The biochemical basis for XyG utilization by the model Gram-negative soil saprophytic bacterium Cellvibrio japonicus is incompletely understood, despite the recent characterization of associated side-chain cleaving exo-glycosidases. We present a detailed functional and structural characterization of a multimodular enzyme encoded by gene locus CJA_2477. The CJA_2477 gene product comprises an N-terminal glycoside hydrolase family 74 (GH74) endo-xyloglucanase module in train with two carbohydrate-binding modules (CBMs) from families 10 and 2 (CBM10 and CBM2). The GH74 catalytic domain generates Glc4 -based xylogluco-oligosaccharide (XyGO) substrates for downstream enzymes through an endo-dissociative mode of action. X-ray crystallography of the GH74 module, alone and in complex with XyGO products spanning the entire active site, revealed a broad substrate-binding cleft specifically adapted to XyG recognition, which is composed of two seven-bladed propeller domains characteristic of the GH74 family. The appended CBM10 and CBM2 members notably did not bind XyG, nor other soluble polysaccharides, and instead were specific cellulose-binding modules. Taken together, these data shed light on the first step of xyloglucan utilization by C. japonicus and expand the repertoire of GHs and CBMs for selective biomass analysis and utilization. DATABASE Structural data have been deposited in the RCSB protein database under the Protein Data Bank codes: 5FKR, 5FKS, 5FKT and 5FKQ.
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Affiliation(s)
- Mohamed Attia
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | | | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
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315
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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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316
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Frandsen KEH, Simmons TJ, Dupree P, Poulsen JCN, Hemsworth GR, Ciano L, Johnston EM, Tovborg M, Johansen KS, von Freiesleben P, Marmuse L, Fort S, Cottaz S, Driguez H, Henrissat B, Lenfant N, Tuna F, Baldansuren A, Davies GJ, Lo Leggio L, Walton PH. The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases. Nat Chem Biol 2016; 12:298-303. [PMID: 26928935 DOI: 10.1038/nchembio.2029] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/12/2016] [Indexed: 12/27/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that oxidatively break down recalcitrant polysaccharides such as cellulose and chitin. Since their discovery, LPMOs have become integral factors in the industrial utilization of biomass, especially in the sustainable generation of cellulosic bioethanol. We report here a structural determination of an LPMO-oligosaccharide complex, yielding detailed insights into the mechanism of action of these enzymes. Using a combination of structure and electron paramagnetic resonance spectroscopy, we reveal the means by which LPMOs interact with saccharide substrates. We further uncover electronic and structural features of the enzyme active site, showing how LPMOs orchestrate the reaction of oxygen with polysaccharide chains.
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Affiliation(s)
| | - Thomas J Simmons
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Luisa Ciano
- Department of Chemistry, University of York, York, UK
| | | | | | | | | | - Laurence Marmuse
- Centre de Recherches sur les Macromolecules Végétales (CERMAV), Université de Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Sébastien Fort
- Centre de Recherches sur les Macromolecules Végétales (CERMAV), Université de Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Sylvain Cottaz
- Centre de Recherches sur les Macromolecules Végétales (CERMAV), Université de Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Hugues Driguez
- Centre de Recherches sur les Macromolecules Végétales (CERMAV), Université de Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France.,Institut National de la Recherche Agronomique (INRA), AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Lenfant
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France.,Institut National de la Recherche Agronomique (INRA), AFMB, Marseille, France
| | - Floriana Tuna
- Engineering and Physical Sciences Research Council (EPSRC) National EPR Facility, School of Chemistry and Photon Science Institute, University of Manchester, Manchester, UK
| | - Amgalanbaatar Baldansuren
- Engineering and Physical Sciences Research Council (EPSRC) National EPR Facility, School of Chemistry and Photon Science Institute, University of Manchester, Manchester, UK
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Paul H Walton
- Department of Chemistry, University of York, York, UK
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317
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dos Santos LV, de Barros Grassi MC, Gallardo JCM, Pirolla RAS, Calderón LL, de Carvalho-Netto OV, Parreiras LS, Camargo ELO, Drezza AL, Missawa SK, Teixeira GS, Lunardi I, Bressiani J, Pereira GAG. Second-Generation Ethanol: The Need is Becoming a Reality. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2015.0017] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | | | | | - Luige Llerena Calderón
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | | | - Lucas Salera Parreiras
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | | | | | - Sílvia Kazue Missawa
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | - Gleidson Silva Teixeira
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
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318
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Crouch LI, Labourel A, Walton PH, Davies GJ, Gilbert HJ. The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:7439-49. [PMID: 26801613 PMCID: PMC4817175 DOI: 10.1074/jbc.m115.702365] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass is a sustainable industrial substrate. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) contribute to the degradation of lignocellulose and increase the efficiency of biofuel production. LPMOs can contain non-catalytic carbohydrate binding modules (CBMs), but their role in the activity of these enzymes is poorly understood. Here we explored the importance of CBMs in LPMO function. The family 2a CBMs of two monooxygenases,CfLPMO10 andTbLPMO10 fromCellulomonas fimiandThermobispora bispora, respectively, were deleted and/or replaced with CBMs from other proteins. The data showed that the CBMs could potentiate and, surprisingly, inhibit LPMO activity, and that these effects were both enzyme-specific and substrate-specific. Removing the natural CBM or introducingCtCBM3a, from theClostridium thermocellumcellulosome scaffoldin CipA, almost abolished the catalytic activity of the LPMOs against the cellulosic substrates. The deleterious effect of CBM removal likely reflects the importance of prolonged presentation of the enzyme on the surface of the substrate for efficient catalytic activity, as only LPMOs appended to CBMs bound tightly to cellulose. The negative impact ofCtCBM3a is in sharp contrast with the capacity of this binding module to potentiate the activity of a range of glycoside hydrolases including cellulases. The deletion of the endogenous CBM fromCfLPMO10 or the introduction of a family 10 CBM fromCellvibrio japonicusLPMO10B intoTbLPMO10 influenced the quantity of non-oxidized products generated, demonstrating that CBMs can modulate the mode of action of LPMOs. This study demonstrates that engineered LPMO-CBM hybrids can display enhanced industrially relevant oxygenations.
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Affiliation(s)
- Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
| | - Paul H Walton
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Newcastle upon Tyne NE2 4HH and
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319
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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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321
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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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322
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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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323
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Principles and Challenges Involved in the Enzymatic Hydrolysis of Cellulosic Materials at High Total Solids. GREEN FUELS TECHNOLOGY 2016. [DOI: 10.1007/978-3-319-30205-8_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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324
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Fungal Biotechnology for Industrial Enzyme Production: Focus on (Hemi)cellulase Production Strategies, Advances and Challenges. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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325
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Zhu N, Liu J, Yang J, Lin Y, Yang Y, Ji L, Li M, Yuan H. Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:42. [PMID: 26900401 PMCID: PMC4761152 DOI: 10.1186/s13068-016-0461-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum. RESULTS Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins. CONCLUSIONS Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification in parallel with the synergistic system of various polysaccharide-degrading enzymes. Furthermore, the complex enzyme system of S. commune holds significant potential for application in biomass saccharification. These discoveries will help unveil the diversity of natural lignocellulose-degrading mechanisms, and advance the design of more efficient enzyme mixtures for the deconstruction of lignocellulosic feedstocks.
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Affiliation(s)
- Ning Zhu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jiawen Liu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jinshui Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yujian Lin
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yi Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Lei Ji
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Meng Li
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
| | - Hongli Yuan
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
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326
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Hori C, Cullen D. Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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327
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Shida Y, Yamaguchi K, Nitta M, Nakamura A, Takahashi M, Kidokoro SI, Mori K, Tashiro K, Kuhara S, Matsuzawa T, Yaoi K, Sakamoto Y, Tanaka N, Morikawa Y, Ogasawara W. The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:230. [PMID: 26719764 PMCID: PMC4696228 DOI: 10.1186/s13068-015-0420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/15/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina) produces increased cellulase expression when grown on cellulose or its derivatives as a sole carbon source. It has been believed that β-glucosidases of T. reesei not only metabolize cellobiose but also contribute in the production of inducers of cellulase gene expression by their transglycosylation activity. The cellulase hyper-producing mutant PC-3-7 developed in Japan has enhanced cellulase production ability when cellobiose is used as the inducer. The comparative genomics analysis of PC-3-7 and its parent revealed a single-nucleotide mutation within the bgl2 gene encoding intracellular β-glucosidase II (BGLII/Cel1a), giving rise to an amino acid substitution in PC-3-7, which could potentially account for the enhanced cellulase expression when these strains are cultivated on cellulose and cellobiose. RESULTS To analyze the effects of the BGLII mutation in cellulase induction, we constructed both a bgl2 revertant and a disruptant. Enzymatic analysis of the transformant lysates showed that the strain expressing mutant BGLII exhibited weakened cellobiose hydrolytic activity, but produced some transglycosylation products, suggesting that the SNP in bgl2 strongly diminished cellobiase activity, but did not result in complete loss of function of BGLII. The analysis of the recombinant BGLII revealed that transglycosylation products might be oligosaccharides, composed probably of glucose linked β-1,4, β-1,3, or a mixture of both. PC-3-7 revertants of bgl2 exhibited reduced expression and inducibility of cellulase during growth on cellulose and cellobiose substrates. Furthermore, the effect of this bgl2 mutation was reproduced in the common strain QM9414 in which the transformants showed cellulase production comparable to that of PC-3-7. CONCLUSION We conclude that BGLII plays an important role in cellulase induction in T. reesei and that the bgl2 mutation in PC-3-7 brought about enhanced cellulase expression on cellobiose. The results of the investigation using PC-3-7 suggested that other mutation(s) in PC-3-7 could also contribute to cellulase induction. Further investigation is essential to unravel the mechanism responsible for cellulase induction in T. reesei.
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Affiliation(s)
- Yosuke Shida
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kaori Yamaguchi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Mikiko Nitta
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
- />Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Ayana Nakamura
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Machiko Takahashi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Shun-ichi Kidokoro
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kazuki Mori
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Tomohiko Matsuzawa
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Katsuro Yaoi
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Yasumitsu Sakamoto
- />School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694 Japan
| | - Nobutada Tanaka
- />School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555 Japan
| | - Yasushi Morikawa
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Wataru Ogasawara
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
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328
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Westereng B, Cannella D, Wittrup Agger J, Jørgensen H, Larsen Andersen M, Eijsink VG, Felby C. Enzymatic cellulose oxidation is linked to lignin by long-range electron transfer. Sci Rep 2015; 5:18561. [PMID: 26686263 PMCID: PMC4685257 DOI: 10.1038/srep18561] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/20/2015] [Indexed: 12/25/2022] Open
Abstract
Enzymatic oxidation of cell wall polysaccharides by lytic polysaccharide monooxygenases (LPMOs) plays a pivotal role in the degradation of plant biomass. While experiments have shown that LPMOs are copper dependent enzymes requiring an electron donor, the mechanism and origin of the electron supply in biological systems are only partly understood. We show here that insoluble high molecular weight lignin functions as a reservoir of electrons facilitating LPMO activity. The electrons are donated to the enzyme by long-range electron transfer involving soluble low molecular weight lignins present in plant cell walls. Electron transfer was confirmed by electron paramagnetic resonance spectroscopy showing that LPMO activity on cellulose changes the level of unpaired electrons in the lignin. The discovery of a long-range electron transfer mechanism links the biodegradation of cellulose and lignin and sheds new light on how oxidative enzymes present in plant degraders may act in concert.
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Affiliation(s)
- Bjørge Westereng
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
- University of Copenhagen, Faculty of Science, Department of Geoscience and Natural Resources Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - David Cannella
- University of Copenhagen, Faculty of Science, Department of Geoscience and Natural Resources Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Jane Wittrup Agger
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Henning Jørgensen
- University of Copenhagen, Faculty of Science, Department of Geoscience and Natural Resources Rolighedsvej 23, 1958 Frederiksberg C, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, 2800 Lyngby, Denmark
| | - Mogens Larsen Andersen
- University of Copenhagen, Faculty of Science, Department of Food Science Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| | - Vincent G.H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Claus Felby
- University of Copenhagen, Faculty of Science, Department of Geoscience and Natural Resources Rolighedsvej 23, 1958 Frederiksberg C, Denmark
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329
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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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330
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The framework of polysaccharide monooxygenase structure and chemistry. Curr Opin Struct Biol 2015; 35:93-9. [PMID: 26615470 DOI: 10.1016/j.sbi.2015.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023]
Abstract
Polysaccharide monooxygenases, or PMOs (also known as lytic PMOs or LPMOs), are a group of enzymes discovered in recent years to catalyze the oxidative degradation of carbohydrate polymers. The PMO catalytic domain has a β-sandwich fold that bears a strong resemblance to both immunoglobulin (Ig) and fibronectin type III (FnIII) domains. PMOs are secreted by fungi and bacteria, and there is recent evidence for their roles in pathogenesis, in addition to biomass processing. This review addresses the biological origins and functions of emerging PMO families, as well as describes the aspects of PMO structure that support the chemistry of copper-catalyzed, oxidative polysaccharide degradation.
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331
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Lehmann L, Rønnest NP, Jørgensen CI, Olsson L, Stocks SM, Jørgensen HS, Hobley T. Linking hydrolysis performance to Trichoderma reesei cellulolytic enzyme profile. Biotechnol Bioeng 2015; 113:1001-10. [PMID: 26524197 DOI: 10.1002/bit.25871] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 11/07/2022]
Abstract
Trichoderma reesei expresses a large number of enzymes involved in lignocellulose hydrolysis and the mechanism of how these enzymes work together is too complex to study by traditional methods, for example, by spiking with single enzymes and monitoring hydrolysis performance. In this study, a multivariate approach, partial least squares regression, was used to see whether it could help explain the correlation between enzyme profile and hydrolysis performance. Diverse enzyme mixtures were produced by T. reesei Rut-C30 by exploiting various fermentation conditions and used for hydrolysis of washed pretreated corn stover as a measure of enzyme performance. In addition, the enzyme mixtures were analyzed by liquid chromatography-tandem mass spectrometry to identify and quantify the different proteins. A multivariate model was applied for the prediction of enzyme performance based on the combination of different proteins present in an enzyme mixture. The multivariate model was used for identification of candidate proteins that are correlated to enzyme performance on pretreated corn stover. A very large variation in hydrolysis performance was observed and this was clearly caused by the difference in fermentation conditions. Besides β-glucosidase, the multivariate model identified several xylanases, Cip1 and Cip2, as relevant proteins to study further.
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Affiliation(s)
- Linda Lehmann
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Nanna P Rønnest
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | | | | | - Timothy Hobley
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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332
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Sun FF, Hong J, Hu J, Saddler JN, Fang X, Zhang Z, Shen S. Accessory enzymes influence cellulase hydrolysis of the model substrate and the realistic lignocellulosic biomass. Enzyme Microb Technol 2015; 79-80:42-8. [DOI: 10.1016/j.enzmictec.2015.06.020] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 11/28/2022]
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333
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Kumar A, Henrissat B, Arvas M, Syed MF, Thieme N, Benz JP, Sørensen JL, Record E, Pöggeler S, Kempken F. De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster. PLoS One 2015; 10:e0140398. [PMID: 26505484 PMCID: PMC4624724 DOI: 10.1371/journal.pone.0140398] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/24/2015] [Indexed: 01/10/2023] Open
Abstract
The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.
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Affiliation(s)
- Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France
- Centre National de la Recherche Scientifique, CNRS UMR 7257, 13288 Marseille, France
| | - Mikko Arvas
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 VTT, Espoo, Finland
| | - Muhammad Fahad Syed
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, FI-02044 VTT, Espoo, Finland
- Biocomputing Platforms Ltd, Tekniikantie 14, FI-02150, Espoo, Finland
| | - Nils Thieme
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J. Philipp Benz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, DK-6700 Esbjerg, Denmark
| | - Eric Record
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
- Aix-Marseille Université, INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Faculté des Sciences de Luminy-Polytech, CP 925, 13288 Marseille Cedex 09, France
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany
| | - Frank Kempken
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
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334
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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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335
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Hudson CM, Kirton E, Hutchinson MI, Redfern JL, Simmons B, Ackerman E, Singh S, Williams KP, Natvig DO, Powell AJ. Lignin‐modifying processes in the rhizosphere of arid land grasses. Environ Microbiol 2015; 17:4965-78. [DOI: 10.1111/1462-2920.13020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 01/23/2023]
Affiliation(s)
| | | | | | | | - Blake Simmons
- Sandia National Laboratories Livermore CA USA
- Joint BioEnergy Institute Emeryville CA USA
| | - Eric Ackerman
- Computational Simulation Sandia National Laboratories Albuquerque NM USA
| | - Seema Singh
- Sandia National Laboratories Livermore CA USA
- Joint BioEnergy Institute Emeryville CA USA
| | | | - Donald O. Natvig
- Department of Biology University of New Mexico Albuquerque NM USA
| | - Amy J. Powell
- Computational Simulation Sandia National Laboratories Albuquerque NM USA
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336
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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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337
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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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338
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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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339
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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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340
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Romero J, Ma Z, Gonzalez C, Adesogan A. Effect of adding cofactors to exogenous fibrolytic enzymes on preingestive hydrolysis, in vitro digestibility, and fermentation of bermudagrass haylage. J Dairy Sci 2015; 98:4659-72. [DOI: 10.3168/jds.2014-8849] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 03/20/2015] [Indexed: 11/19/2022]
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341
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Nam YW, Nihira T, Arakawa T, Saito Y, Kitaoka M, Nakai H, Fushinobu S. Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes. J Biol Chem 2015; 290:18281-92. [PMID: 26041776 DOI: 10.1074/jbc.m115.664664] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 01/02/2023] Open
Abstract
The microbial oxidative cellulose degradation system is attracting significant research attention after the recent discovery of lytic polysaccharide mono-oxygenases. A primary product of the oxidative and hydrolytic cellulose degradation system is cellobionic acid (CbA), the aldonic acid form of cellobiose. We previously demonstrated that the intracellular enzyme belonging to glycoside hydrolase family 94 from cellulolytic fungus and bacterium is cellobionic acid phosphorylase (CBAP), which catalyzes reversible phosphorolysis of CbA into glucose 1-phosphate and gluconic acid (GlcA). In this report, we describe the biochemical characterization and the three-dimensional structure of CBAP from the marine cellulolytic bacterium Saccharophagus degradans. Structures of ligand-free and complex forms with CbA, GlcA, and a synthetic disaccharide product from glucuronic acid were determined at resolutions of up to 1.6 Å. The active site is located near the dimer interface. At subsite +1, the carboxylate group of GlcA and CbA is recognized by Arg-609 and Lys-613. Additionally, one residue from the neighboring protomer (Gln-190) is involved in the carboxylate recognition of GlcA. A mutational analysis indicated that these residues are critical for the binding and catalysis of the aldonic and uronic acid acceptors GlcA and glucuronic acid. Structural and sequence comparisons with other glycoside hydrolase family 94 phosphorylases revealed that CBAPs have a unique subsite +1 with a distinct amino acid residue conservation pattern at this site. This study provides molecular insight into the energetically efficient metabolic pathway of oxidized sugars that links the oxidative cellulolytic pathway to the glycolytic and pentose phosphate pathways in cellulolytic microbes.
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Affiliation(s)
- Young-Woo Nam
- From the Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takanori Nihira
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan, and
| | - Takatoshi Arakawa
- From the Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuka Saito
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan, and
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan, and
| | - Shinya Fushinobu
- From the Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan,
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342
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Hu J, Chandra R, Arantes V, Gourlay K, Susan van Dyk J, Saddler JN. The addition of accessory enzymes enhances the hydrolytic performance of cellulase enzymes at high solid loadings. BIORESOURCE TECHNOLOGY 2015; 186:149-153. [PMID: 25812819 DOI: 10.1016/j.biortech.2015.03.055] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/05/2023]
Abstract
The pretreatment process used and the nature of the biomass feedstock will influence the role that accessory enzymes can play in synergistically interacting with cellulases to effectively deconstruct the substrate. The work reported here assessed the possible boosting effects of the xylanase and lytic polysaccharide monooxygenase (AA9, formerly known as GH61) on the hydrolytic potential of cellulase enzyme mixtures during hydrolysis of steam pretreated poplar and corn stover at high (10-20% w/v) substrate concentrations. A higher proportion of xylanase was required when the substrate had a relatively high xylan content and at high substrate concentrations. In contrast, a relatively small amount of AA9 (about 2 mg/g cellulose) was enough, regardless of the nature or concentration of the substrate. The overall protein loading required to achieve effective hydrolysis of high concentrations of pretreated biomass substrates could be substantially reduced by optimizing the ratio of enzymes in the "cellulase" mixture.
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Affiliation(s)
- Jinguang Hu
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada
| | - Richard Chandra
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada
| | - Valdeir Arantes
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada
| | - Keith Gourlay
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada
| | - J Susan van Dyk
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada
| | - Jack N Saddler
- Forest Products Biotechnology and Bioenergy Group, University of British Columbia, Vancouver, BC, Canada.
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343
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Abstract
Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.
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Affiliation(s)
- Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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344
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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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345
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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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346
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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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347
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Courtade G, Balzer S, Forsberg Z, Vaaje-Kolstad G, Eijsink VGH, Aachmann FL. (1)H, (13)C, (15)N resonance assignment of the chitin-active lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:207-10. [PMID: 25204609 DOI: 10.1007/s12104-014-9575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/02/2014] [Indexed: 05/02/2023]
Abstract
The chitin-active 19.2 kDa lytic polysaccharide monooxygenase BlLPMO10A from Bacillus licheniformis has been isotopically labeled and recombinantly expressed. In this paper, we report the (1)H, (13)C, (15)N resonance assignment of BlLPMO10A.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælands vei 6/8, 7491, Trondheim, Norway
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348
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Beeson WT, Vu VV, Span EA, Phillips CM, Marletta MA. Cellulose degradation by polysaccharide monooxygenases. Annu Rev Biochem 2015; 84:923-46. [PMID: 25784051 DOI: 10.1146/annurev-biochem-060614-034439] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharide monooxygenases (PMOs), also known as lytic PMOs (LPMOs), enhance the depolymerization of recalcitrant polysaccharides by hydrolytic enzymes and are found in the majority of cellulolytic fungi and actinomycete bacteria. For more than a decade, PMOs were incorrectly annotated as family 61 glycoside hydrolases (GH61s) or family 33 carbohydrate-binding modules (CBM33s). PMOs have an unusual surface-exposed active site with a tightly bound Cu(II) ion that catalyzes the regioselective hydroxylation of crystalline cellulose, leading to glycosidic bond cleavage. The genomes of some cellulolytic fungi contain more than 20 genes encoding cellulose-active PMOs, suggesting a diversity of biological activities. PMOs show great promise in reducing the cost of conversion of lignocellulosic biomass to fermentable sugars; however, many questions remain about their reaction mechanism and biological function. This review addresses, in depth, the structural and mechanistic aspects of oxidative depolymerization of cellulose by PMOs and considers their biological function and phylogenetic diversity.
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Affiliation(s)
- William T Beeson
- Department of Chemistry, University of California, Berkeley, California 94720
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349
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Shrestha P, Ibáñez AB, Bauer S, Glassman SI, Szaro TM, Bruns TD, Taylor JW. Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:38. [PMID: 25784958 PMCID: PMC4362644 DOI: 10.1186/s13068-015-0221-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/04/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage of the cost of bioethanol production from non-starch (i.e., lignocellulosic) components of energy crops and agricultural residues. We, and others, have reasoned that fungi that naturally deconstruct plant walls may provide the best enzymes for bioconversion of energy crops. RESULTS Previously, we have reported on the isolation of 106 fungi from decaying leaves of Miscanthus and sugarcane (Appl Environ Microbiol 77:5490-504, 2011). Here, we thoroughly analyze 30 of these fungi including those most often found on decaying leaves and stems of these plants, as well as four fungi chosen because they are well-studied for their plant cell wall deconstructing enzymes, for wood decay, or for genetic regulation of plant cell wall deconstruction. We extend our analysis to assess not only their ability over an 8-week period to bioconvert Miscanthus cell walls but also their ability to secrete total protein, to secrete enzymes with the activities of xylanases, exocellulases, endocellulases, and beta-glucosidases, and to remove specific parts of Miscanthus cell walls, that is, glucan, xylan, arabinan, and lignin. CONCLUSION This study of fungi that bioconvert energy crops is significant because 30 fungi were studied, because the fungi were isolated from decaying energy grasses, because enzyme activity and removal of plant cell wall components were recorded in addition to biomass conversion, and because the study period was 2 months. Each of these factors make our study the most thorough to date, and we discovered fungi that are significantly superior on all counts to the most widely used, industrial bioconversion fungus, Trichoderma reesei. Many of the best fungi that we found are in taxonomic groups that have not been exploited for industrial bioconversion and the cultures are available from the Centraalbureau voor Schimmelcultures in Utrecht, Netherlands, for all to use.
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Affiliation(s)
- Prachand Shrestha
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Ana B Ibáñez
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Stefan Bauer
- />Energy Biosciences Institute, University of California, Berkeley, CA 94720 USA
| | - Sydney I Glassman
- />Department of Environmental Science Policy and Management, University of California, Berkeley, CA 94720 USA
| | - Timothy M Szaro
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - Thomas D Bruns
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
| | - John W Taylor
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
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350
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Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J, Lipzen A, Tritt A, Sun H, Haridas S, LaButti K, Ohm RA, Kües U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol 2015; 76:78-92. [PMID: 25683379 DOI: 10.1016/j.fgb.2015.02.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/26/2014] [Accepted: 02/05/2015] [Indexed: 11/17/2022]
Abstract
Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.
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Affiliation(s)
- Dimitrios Floudas
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA; MEMEG, Ecology Building Sölvegatan 37, 223 62, Lund, Sweden.
| | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108-6030, USA.
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Laszlo G Nagy
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA; Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Gage Koehler
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Anthony S Ransdell
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Hina Younus
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Julianna Chow
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Jennifer Chiniquy
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Hui Sun
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Sajeet Haridas
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Robin A Ohm
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA; Microbiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Ursula Kües
- Institute for Forest Botany, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108-6030, USA.
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Robert E Minto
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - David S Hibbett
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA.
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