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Duran K, Miebach J, van Erven G, Baars JJP, Comans RNJ, Kuyper TW, Kabel MA. Oxidation-driven lignin removal by Agaricus bisporus from wheat straw-based compost at industrial scale. Int J Biol Macromol 2023; 246:125575. [PMID: 37385314 DOI: 10.1016/j.ijbiomac.2023.125575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/09/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023]
Abstract
Fungi are main lignin degraders and the edible white button mushroom, Agaricus bisporus, inhabits lignocellulose-rich environments. Previous research hinted at delignification when A. bisporus colonized pre-composted wheat straw-based substrate in an industrial setting, assumed to aid subsequent release of monosaccharides from (hemi-)cellulose to form fruiting bodies. Yet, structural changes and specific quantification of lignin throughout A. bisporus mycelial growth remain largely unresolved. To elucidate A. bisporus routes of delignification, at six timepoints throughout mycelial growth (15 days), substrate was collected, fractionated, and analyzed by quantitative pyrolysis-GC-MS, 2D-HSQC NMR, and SEC. Lignin decrease was highest between day 6 and day 10 and reached in total 42 % (w/w). The substantial delignification was accompanied by extensive structural changes of residual lignin, including increased syringyl to guaiacyl (S/G) ratios, accumulated oxidized moieties, and depleted intact interunit linkages. Hydroxypropiovanillone and hydroxypropiosyringone (HPV/S) subunits accumulated, which are indicative for β-|O-4' ether cleavage and imply a laccase-driven ligninolysis. We provide compelling evidence that A. bisporus is capable of extensive lignin removal, have obtained insights into mechanisms at play and susceptibilities of various substructures, thus we were contributing to understanding fungal lignin conversion.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Jeanne Miebach
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands; Wageningen Food & Biobased Research, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Johan J P Baars
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, the Netherlands
| | - Rob N J Comans
- Soil Chemistry and Chemical Soil Quality Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Thomas W Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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Li H, Kang X, Yang M, Kasseney BD, Zhou X, Liang S, Zhang X, Wen JL, Yu B, Liu N, Zhao Y, Mo J, Currie CR, Ralph J, Yelle DJ. Molecular insights into the evolution of woody plant decay in the gut of termites. SCIENCE ADVANCES 2023; 9:eadg1258. [PMID: 37224258 DOI: 10.1126/sciadv.adg1258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Plant cell walls represent the most abundant pool of organic carbon in terrestrial ecosystems but are highly recalcitrant to utilization by microbes and herbivores owing to the physical and chemical barrier provided by lignin biopolymers. Termites are a paradigmatic example of an organism's having evolved the ability to substantially degrade lignified woody plants, yet atomic-scale characterization of lignin depolymerization by termites remains elusive. We report that the phylogenetically derived termite Nasutitermes sp. efficiently degrades lignin via substantial depletion of major interunit linkages and methoxyls by combining isotope-labeled feeding experiments and solution-state and solid-state nuclear magnetic resonance spectroscopy. Exploring the evolutionary origin of lignin depolymerization in termites, we reveal that the early-diverging woodroach Cryptocercus darwini has limited capability in degrading lignocellulose, leaving most polysaccharides intact. Conversely, the phylogenetically basal lineages of "lower" termites are able to disrupt the lignin-polysaccharide inter- and intramolecular bonding while leaving lignin largely intact. These findings advance knowledge on the elusive but efficient delignification in natural systems with implications for next-generation ligninolytic agents.
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Affiliation(s)
- Hongjie Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xue Kang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, China
| | - Mengyi Yang
- Xiaoshan Management Center of Termite Control, Hangzhou Xiaoshan Housing Security and Real Estate Management Service Center, Hangzhou 311200, China
| | - Boris Dodji Kasseney
- Department of Zoology, Faculty of Sciences, University of Lomé, 1BP1515 Lomé, Togo
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Shiyou Liang
- Agricultural Information Center of Pingyang, Renmin Road 71, Wenzhou 325400, China
| | - Xiaojie Zhang
- Quzhou Management Center of Termite Control, Quzhou Housing Security and Real Estate Management Service Center, Quzhou 311200, China
| | - Jia-Long Wen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, No. 35 Tsinghua East Road, Beijing, Haidian District 100083, China
| | - Baoting Yu
- National Termite Control Center of China, Moganshan Road 695, Hangzhou 310011, China
| | - Ning Liu
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, China
| | - Jianchu Mo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Cameron R Currie
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison WI 53706, USA
- David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - John Ralph
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Daniel J Yelle
- US Forest Products Laboratory, Forest Service, Madison, WI 53726, USA
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Conversion of lignin-derived 3-methoxycatechol to the natural product purpurogallin using bacterial P450 GcoAB and laccase CueO. Appl Microbiol Biotechnol 2021; 106:593-603. [PMID: 34971410 DOI: 10.1007/s00253-021-11738-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 01/02/2023]
Abstract
Purpurogallin is a natural benzotropolone extracted from Quercus spp, which has antioxidant, anticancer, and anti-inflammatory properties. Purpurogallin is typically synthesized from pyrogallol using enzymatic or metal catalysts, neither economically feasible nor environmentally friendly. 3-Methoxycatechol (3-MC) is a lignin-derived renewable chemical with the potential to be a substrate for the biosynthesis of purpurogallin. In this study, we designed a pathway to produce purpurogallin from 3-MC. We first characterized four bacterial laccases and identified the laccase CueO from Escherichia coli, which converts pyrogallol to purpurogallin. Then, we used CueO and the P450 GcoAB reported to convert 3-MC to pyrogallol, to construct a method for producing purpurogallin directly from 3-MC. A total of 0.21 ± 0.05 mM purpurogallin was produced from 5 mM 3-MC by whole-cell conversion. This study provides a new method to enable efficient and sustainable synthesis of purpurogallin and offers new insights into lignin valorization. KEY POINTS: • Screening four bacterial laccases for converting pyrogallol to purpurogallin. • Laccase CueO from Escherichia coli presenting the activity for purpurogallin yield. • A novel pathway for converting lignin-derived 3-methoxycatechol to purpurogallin.
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Ma J, Li Q, Wu Y, Yue H, Zhang Y, Zhang J, Shi M, Wang S, Liu GQ. Elucidation of ligninolysis mechanism of a newly isolated white-rot basidiomycete Trametes hirsuta X-13. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:189. [PMID: 34563244 PMCID: PMC8466896 DOI: 10.1186/s13068-021-02040-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/11/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignin is a complex aromatic heteropolymer comprising 15-30% dry weight of the lignocellulose. The complex structural characteristic of lignin renders it difficult for value-added utilization. Exploring efficient lignin-degrading microorganisms and investigating their lignin-degradation mechanisms would be beneficial for promoting lignin valorization. In this study, a newly isolated white-rot basidiomycete, Trametes hirsuta X-13, with capacity to utilize alkaline lignin as the sole substrate was investigated. RESULTS The analysis of the fermentation properties of T. hirsuta X-13 using alkaline lignin as the sole substrate, including the mycelial growth, activities of ligninolytic enzymes and the rates of lignin degradation and decolorization confirmed its great ligninolysis capacity. The maximum lignin degradation rate reached 39.8% after 11 days of T. hirsuta X-13 treatment, which was higher than that of reported fungi under the same condition. Fourier transform infrared spectrometry (FTIR), gas chromatography-mass spectrometry (GC-MS) scanning electron micrographs (SEM), two-dimensional heteronuclear single quantum coherence NMR analysis (2D-HSQC NMR) collaborated with pyrolysis gas chromatography-mass spectrometry (py-GC/MS) analyses proved that lignin structure was severely deconstructed along with amounts of monomer aromatics generated. Furthermore, according to those chemical analysis, in addition to canonical Cα-Cβ breakage, the cleavage of lignin interunit linkages of β-β might also occur by T. hirsuta X-13. CONCLUSIONS This study characterized a newly isolated white-rot basidiomycete T. hirsuta X-13 with impressive alkaline lignin degradation ability and provided mechanistic insight into its ligninolysis mechanism, which will be valuable for the development of lignin valorization strategies.
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Affiliation(s)
- Jiangshan Ma
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Qiang Li
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Yujie Wu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Huimin Yue
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Yanghong Zhang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Jiashun Zhang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Muling Shi
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Sixian Wang
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
- International Cooperation Base of Science and Technology Innovation On Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, 410004 Hunan People’s Republic of China
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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Mao L, van Arkel J, Hendriks WH, Cone JW, de Vos RC, Sonnenberg AS. Assessing the nutritional quality of fungal treated wheat straw: Compounds formed after treatment with Ceriporiopsis subvermispora and Lentinula edodes. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Pecularities and applications of aryl-alcohol oxidases from fungi. Appl Microbiol Biotechnol 2021; 105:4111-4126. [PMID: 33997930 PMCID: PMC8140971 DOI: 10.1007/s00253-021-11337-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
Abstract Aryl-alcohol oxidases (AAOs) are FAD-containing enzymes that oxidize a broad range of aromatic as well as aliphatic allylic alcohols to aldehydes. Their broad substrate spectrum accompanied by the only need for molecular oxygen as cosubstrate and production of hydrogen peroxide as sole by-product makes these enzymes very promising biocatalysts. AAOs were used in the synthesis of flavors, fragrances, and other high-value-added compounds and building blocks as well as in dye decolorization and pulp biobleaching. Furthermore, AAOs offer a huge potential as efficient suppliers of hydrogen peroxide for peroxidase- and peroxygenase-catalyzed reactions. A prerequisite for application as biocatalysts at larger scale is the production of AAOs in sufficient amounts. Heterologous expression of these predominantly fungal enzymes is, however, quite challenging. This review summarizes different approaches aiming at enhancing heterologous expression of AAOs and gives an update on substrates accepted by these promising enzymes as well as potential fields of their application. Key points • Aryl-alcohol oxidases (AAOs) supply ligninolytic peroxidases with H2O2. • AAOs accept a broad spectrum of aromatic and aliphatic allylic alcohols. • AAOs are potential biocatalysts for the production of high-value-added bio-based chemicals.
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9
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Venkatesagowda B, Dekker RFH. Microbial demethylation of lignin: Evidence of enzymes participating in the removal of methyl/methoxyl groups. Enzyme Microb Technol 2021; 147:109780. [PMID: 33992403 DOI: 10.1016/j.enzmictec.2021.109780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 02/27/2021] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
Lignin is an abundant natural plant aromatic biopolymer containing various functional groups that can be exploited for activating lignin for potential commercial applications. Applications are hindered due to the presence of a high content of methyl/methoxyl groups that affects reactiveness. Various chemical and enzymatic approaches have been investigated to increase the functionality in transforming lignin. Among these is demethylation/demethoxylation, which increases the potential numbers of vicinal hydroxyl groups for applications as phenol-formaldehyde resins. Although the chemical route to lignin demethylation is well-studied, the biological route is still poorly explored. Bacteria and fungi have the ability to demethylate lignin and lignin-related compounds. Considering that appropriate microorganisms possess the biochemical machinery to demethylate lignin by cleaving O-methyl groups liberating methanol, and modify lignin by increasing the vicinal diol content that allows lignin to substitute for phenol in organic polymer syntheses. Certain bacteria through the actions of specific O-demethylases can modify various lignin-related compounds generating vicinal diols and liberating methanol or formaldehyde as end-products. The enzymes include: cytochrome P450-aryl-O-demethylase, monooxygenase, veratrate 3-O-demethylase, DDVA O-demethylase (LigX; lignin-related biphenyl 5,5'-dehydrodivanillate (DDVA)), vanillate O-demethylase, syringate O-demethylase, and tetrahydrofolate-dependent-O-demethylase. Although, the fungal counterparts have not been investigated in depth as in bacteria, O-demethylases, nevertheless, have been reported in demethylating various lignin substrates providing evidence of a fungal enzyme system. Few fungi appear to have the ability to secrete O-demethylases. The fungi can mediate lignin demethylation enzymatically (laccase, lignin peroxidase, manganese peroxidase, O-demethylase), or non-enzymatically in brown-rot fungi through the Fenton reaction. This review discusses details on the aspects of microbial (bacterial and fungal) demethylation of lignins and lignin-model compounds and provides evidence of enzymes identified as specific O-demethylases involved in demethylation.
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Affiliation(s)
- Balaji Venkatesagowda
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada.
| | - Robert F H Dekker
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada; Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Engenharia Ambiental, Câmpus Londrina, CEP: 86036-370, Londrina, PR, Brazil.
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10
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Storage temperature and time and its influence on feed quality of fungal treated wheat straw. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2020.114749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Abstract
Aryl-alcohol oxidases (AAO) constitute a family of FAD-containing enzymes, included in the glucose-methanol-choline oxidase/dehydrogenase superfamily of proteins. They are commonly found in fungi, where their eco-physiological role is to produce hydrogen peroxide that activates ligninolytic peroxidases in white-rot (lignin-degrading) basidiomycetes or to trigger the Fenton reactions in brown-rot (carbohydrate-degrading) basidiomycetes. These enzymes catalyze the oxidation of a plethora of aromatic, and some aliphatic, polyunsaturated alcohols bearing conjugated primary hydroxyl group. Besides, the enzymes show activity on the hydrated forms of the corresponding aldehydes. Some AAO features, such as the broad range of substrates that it can oxidize (with the only need of molecular oxygen as co-substrate) and its stereoselective mechanism, confer good properties to these enzymes as industrial biocatalysts. In fact, AAO can be used for different biotechnological applications, such as flavor synthesis, secondary alcohol deracemization and oxidation of furfurals for the production of furandicarboxylic acid as a chemical building block. Also, AAO can participate in processes of interest in the wood biorefinery and textile industries as an auxiliary enzyme providing hydrogen peroxide to ligninolytic or dye-decolorizing peroxidases. Both rational design and directed molecular evolution have been employed to engineer AAO for some of the above biotechnological applications.
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Affiliation(s)
- Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain.
| | - Juan Carro
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain.
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12
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van Erven G, Wang J, Sun P, de Waard P, van der Putten J, Frissen GE, Gosselink RJA, Zinovyev G, Potthast A, van Berkel WJH, Kabel MA. Structural Motifs of Wheat Straw Lignin Differ in Susceptibility to Degradation by the White-Rot Fungus Ceriporiopsis subvermispora. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2019; 7:20032-20042. [PMID: 31867146 PMCID: PMC6921689 DOI: 10.1021/acssuschemeng.9b05780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/29/2019] [Indexed: 05/11/2023]
Abstract
The white-rot fungus Ceriporiopsis subvermispora delignifies plant biomass extensively and selectively and, therefore, has great biotechnological potential. We previously demonstrated that after 7 weeks of fungal growth on wheat straw 70% w/w of lignin was removed and established the underlying degradation mechanisms via selectively extracted diagnostic substructures. In this work, we fractionated the residual (more intact) lignin and comprehensively characterized the obtained isolates to determine the susceptibility of wheat straw lignin's structural motifs to fungal degradation. Using 13C IS pyrolysis gas chromatography-mass spectrometry (py-GC-MS), heteronuclear single quantum coherence (HSQC) and 31P NMR spectroscopy, and size-exclusion chromatography (SEC) analyses, it was shown that β-O-4' ethers and the more condensed phenylcoumarans and resinols were equally susceptible to fungal breakdown. Interestingly, for β-O-4' ether substructures, marked cleavage preferences could be observed: β-O-4'-syringyl substructures were degraded more frequently than their β-O-4'-guaiacyl and β-O-4'-tricin analogues. Furthermore, diastereochemistry (threo > erythro) and γ-acylation (γ-OH > γ-acyl) influenced cleavage susceptibility. These results indicate that electron density of the 4'-O-coupled ring and local steric hindrance are important determinants of oxidative β-O-4' ether degradation. Our findings provide novel insight into the delignification mechanisms of C. subvermispora and contribute to improving the valorization of lignocellulosic biomass.
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Affiliation(s)
- Gijs van Erven
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Jianli Wang
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Peicheng Sun
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Pieter de Waard
- MAGNEFY
(MAGNEtic Resonance Research FacilitY), Wageningen University & Research, Stippeneng 4, 6708
WE Wageningen, The Netherlands
| | - Jacinta van der Putten
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Guus E. Frissen
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Richard J. A. Gosselink
- Wageningen
Food and Biobased Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Grigory Zinovyev
- Department
of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences, Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria
| | - Antje Potthast
- Department
of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences, Konrad-Lorenz-Strasse 24, A-3430 Tulln, Austria
| | - Willem J. H. van Berkel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory
of Food Chemistry, Wageningen University
& Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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13
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Venkatesagowda B. Enzymatic demethylation of lignin for potential biobased polymer applications. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2019.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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Nayan N, van Erven G, Kabel MA, Sonnenberg ASM, Hendriks WH, Cone JW. Evaluation of fungal degradation of wheat straw cell wall using different analytical methods from ruminant nutrition perspective. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:4054-4062. [PMID: 30737799 PMCID: PMC6593870 DOI: 10.1002/jsfa.9634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND White rot fungi have been used to improve the nutritive value of lignocellulose for ruminants. In feed analysis, the Van Soest method is widely used to determine the cell wall contents. To assess the reliability of this method (Method A) for determination of cell wall contents in fungal-treated wheat straw, we compared a combined monosaccharide analysis and pyrolysis coupled to gas chromatography with mass spectrometry (Py-GC/MS) (Method B). Ruminal digestibility, measured as in vitro gas production (IVGP), was subsequently used to examine which method explains best the effect of fungal pretreatment on the digestibility of wheat straw. RESULTS Both methods differed considerably in the mass recoveries of the individual cell wall components, which changed on how we assess their degradation characteristics. For example, Method B gave a higher degradation of lignin (61.9%), as compared to Method A (33.2%). Method A, however, showed a better correlation of IVGP with the ratio of lignin to total structural carbohydrates, as compared to Method B (Pearson's r of -0.84 versus -0.69). Nevertheless, Method B provides a more accurate quantification of lignin, reflecting its actual modification and degradation. With the information on the lignin structural features, Method B presents a substantial advantage in understanding the underlying mechanisms of lignin breakdown. Both methods, however, could not accurately quantify the cellulose contents - among others, due to interference of fungal biomass. CONCLUSION Method A only accounts for the recalcitrant residue and therefore is more suitable for evaluating ruminal digestibility. Method B allows a more accurate quantification of cell wall, required to understand and better explains the actual modification of the cell wall. The suitability of both methods, therefore, depends on their intended purposes. © 2019 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Nazri Nayan
- Animal Nutrition GroupWageningen University & ResearchWageningenThe Netherlands
| | - Gijs van Erven
- Laboratory of Food ChemistryWageningen University & ResearchWageningenThe Netherlands
| | - Mirjam A Kabel
- Laboratory of Food ChemistryWageningen University & ResearchWageningenThe Netherlands
| | | | - Wouter H Hendriks
- Animal Nutrition GroupWageningen University & ResearchWageningenThe Netherlands
| | - John W Cone
- Animal Nutrition GroupWageningen University & ResearchWageningenThe Netherlands
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15
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Adesogan AT, Arriola KG, Jiang Y, Oyebade A, Paula EM, Pech-Cervantes AA, Romero JJ, Ferraretto LF, Vyas D. Symposium review: Technologies for improving fiber utilization. J Dairy Sci 2019; 102:5726-5755. [PMID: 30928262 DOI: 10.3168/jds.2018-15334] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022]
Abstract
The forage lignocellulosic complex is one of the greatest limitations to utilization of the nutrients and energy in fiber. Consequently, several technologies have been developed to increase forage fiber utilization by dairy cows. Physical or mechanical processing techniques reduce forage particle size and gut fill and thereby increase intake. Such techniques increase the surface area for microbial colonization and may increase fiber utilization. Genetic technologies such as brown midrib mutants (BMR) with less lignin have been among the most repeatable and practical strategies to increase fiber utilization. Newer BMR corn hybrids are better yielding than the early hybrids and recent brachytic dwarf BMR sorghum hybrids avoid lodging problems of early hybrids. Several alkalis have been effective at increasing fiber digestibility. Among these, ammoniation has the added benefit of increasing the nitrogen concentration of the forage. However, few of these have been widely adopted due to the cost and the caustic nature of the chemicals. Urea treatment is more benign but requires sufficient urease and moisture for efficacy. Ammonia-fiber expansion technology uses high temperature, moisture, and pressure to degrade lignocellulose to a greater extent than ammoniation alone, but it occurs in reactors and is therefore not currently usable on farms. Biological technologies for increasing fiber utilization such as application of exogenous fibrolytic enzymes, live yeasts, and yeast culture have had equivocal effects on forage fiber digestion in individual studies, but recent meta-analyses indicate that their overall effects are positive. Nonhydrolytic expansin-like proteins act in synergy with fibrolytic enzymes to increase fiber digestion beyond that achieved by the enzyme alone due to their ability to expand cellulose microfibrils allowing greater enzyme penetration of the cell wall matrix. White-rot fungi are perhaps the biological agents with the greatest potential for lignocellulose deconstruction, but they require aerobic conditions and several strains degrade easily digestible carbohydrates. Less ruminant nutrition research has been conducted on brown rot fungi that deconstruct lignocellulose by generating highly destructive hydroxyl radicals via the Fenton reaction. More research is needed to increase the repeatability, efficacy, cost effectiveness, and on-farm applicability of technologies for increasing fiber utilization.
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Affiliation(s)
- A T Adesogan
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611.
| | - K G Arriola
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - Y Jiang
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - A Oyebade
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - E M Paula
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - A A Pech-Cervantes
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - J J Romero
- Animal and Veterinary Sciences Program, School of Food and Agriculture, University of Maine, Orono 04469
| | - L F Ferraretto
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
| | - D Vyas
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32611
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16
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Cellular level chemical changes in Scots pine heartwood during incipient brown rot decay. Sci Rep 2019; 9:5188. [PMID: 30914737 PMCID: PMC6435796 DOI: 10.1038/s41598-019-41735-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
The heartwoods of many wood species have natural resistance to wood decay due to the accumulation of antifungal heartwood extractives. The natural durability of heartwoods has been extensively investigated, yet very little information is available on the initiation of heartwood decay. This experiment examined the onset of Rhodonia placenta brown rot decay in Scots pine heartwood in order to identify the key changes leading to heartwood decay. An imaging approach based on Raman imaging and multivariate image analysis revealed that the degradation of heartwood began in the innermost cell wall layers and then spread into the remaining cell walls and the middle lamella. Pinosylvins were extensively degraded in the cell walls, middle lamella and extractive deposits, while unidentified material most likely consisting of hemicelluloses and/or lipophilic extractives was removed from the inner cell wall layers. Changes similar to inner cell wall degradation were seen in the remaining cell walls in more advanced decay. The results indicate that the key change in incipient heartwood decay is the degradation of antifungal heartwood extractives. The inner cell wall degradation seen in this experiment may serve a nutritive purpose or facilitate the penetration of degradative agents into the cell walls and middle lamella.
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17
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Venkatesagowda B, Dekker RFH. A rapid method to detect and estimate the activity of the enzyme, alcohol oxidase by the use of two chemical complexes - acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine). J Microbiol Methods 2019; 158:71-79. [PMID: 30716345 DOI: 10.1016/j.mimet.2019.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/10/2019] [Accepted: 01/17/2019] [Indexed: 12/18/2022]
Abstract
A rapid and sensitive method has been devised in order to detect and estimate the synthesis of the enzyme alcohol oxidase (AOX) by fungi, by way of the use of two chemical complexes, namely, acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine). This method involves the use of the AOX enzyme that could specifically oxidize methanol, giving rise to equimolar equivalents each of formaldehyde (HCHO) and hydrogen peroxide (H2O2) as the end products. Further, the formaldehyde, thus produced was allowed to interact with the neutral solutions of acetylacetone and the ammonium salt, gradually developing a yellow color, owing to the synthesis and release of 3,5-diacetyl-1,4-dihydrolutidine (yellow product; λ = 420 nm; λex/em = 390/470 nm) and the product, so generated was quantified spectrophotometrically by measureing its absorbance at 412 nm. In another set up, the amount of formaldehyde produced as a sequel to the oxidation of methanol by the AOX enzyme was determined by allowing it to react with the acetylacetanilide reagent, after which the volume of the fluorescent product - 3,5-di-N-phenylacetyl-1,4-dihydrolutidine (colorless product; λex/em = 390/470 nm) that was generated was estimated by measuring its emission at 460 nm (excitation wavelength at 360 nm) in a spectrophotometer. Of the various substrates tested, a commercial source of the AOX enzyme appreciably oxidizes methanol, thereby generating formaldehyde, and further reacts with acetylacetone, to give rise to a bright yellow complex, displaying a maximum activity of 1402 U/mL. Determination of the AOX activity by the use of acetylacetone and acetylacetanilide could serve as a viable alternative to the conventional alcohol oxidase-peroxidase-2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid (AOX-POD-ABTS) based method. In view of this, this method appears to be invaluable for application at the various food, pharmaceutical, fuel, biosensor, biorefinery, biopolymer, biomaterial, platform chemical, and biodiesel industries.
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Affiliation(s)
- Balaji Venkatesagowda
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada.
| | - Robert F H Dekker
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada
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18
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You T, Li X, Wang R, Zhang X, Xu F. Effects of synergistic fungal pretreatment on structure and thermal properties of lignin from corncob. BIORESOURCE TECHNOLOGY 2019; 272:123-129. [PMID: 30317155 DOI: 10.1016/j.biortech.2018.09.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/28/2018] [Accepted: 09/30/2018] [Indexed: 05/14/2023]
Abstract
Synergistic fungal pretreatment involving white-rot and brown-rot fugal pretreatment has shown great potential for enhancing the yield of sugars from biomass time-effectively and environmentally benign. In this work, the effects of this integrated fungal pretreatment on lignin characteristics and thermal behavior of corncob were examined in the view of whole plant valorization. The results show that an efficient deconstruction of lignin was achieved by white-rot fungus, and subsequent brown-rot fungus promoted the preferential breakdown of guaiacyl units, further enhancing lignin extraction efficiency (62.3%). Consequently, less phenolic hydroxyl, methoxyl, tricin, ester-linked p-coumaric acid, more carboxylic acid, ratio of syringyl to guaiacyl units, β-O-4' linkage and molecular weight were found in W-BL. Thermal stability was improved and the increased phenol and alkyl-phenols contents in pyrolysis products demonstrated that synergistic fungal pretreatment definitely improved the lignin oil quality. These discoveries provide new insights into set strategy for microbial screening, pretreatment and lignin processing.
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Affiliation(s)
- Tingting You
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China
| | - Xin Li
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China
| | - Ruizhen Wang
- Institute of Chemical Industry of Forestry Products, Chinese Academy Forestry, Nanjing 210042, Jiangsu, PR China
| | - Xueming Zhang
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China
| | - Feng Xu
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing 100083, PR China.
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19
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Venkatesagowda B. Enzymatic Kraft lignin demethylation and fungal O-demethylases like vanillate-O-demethylase and syringate O-demethylase catalyzed catechol-Fe 3+ complexation method. J Microbiol Methods 2018; 152:126-134. [PMID: 30076868 DOI: 10.1016/j.mimet.2018.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/29/2018] [Accepted: 07/31/2018] [Indexed: 12/16/2022]
Abstract
The ability of enzymatic Kraft Lignin (KL) demethylation was determined using catechol and ferric ion coordination (catechol-Fe3+ complexes) by reduction of Fe3+ to Fe2+ and formation of mono, bis- and/or tris-catechol-Fe3+ complexes has been investigated to identify enzyme that can strip-off O-methyl groups from lignin such as O-demethylase. To detect fungal demethylation and release of catechol-like structures, these were demonstrated using catechol, gallic acid and caffeic acid as standard model compounds to forms mono, bis- and/or tris-catechol-Fe3+ complexes. The catechol-Fe3+ complexes formation controlled by pH via the deprotonation of the catechol hydroxyls was investigated at pH 2.5, 8.0 and 10.0 and demonstrated that catechol formed mono, bis- and/or tris-catechol-Fe3+ complexes, and showed maximum absorbance at 547 nm. Lignin demethylation (O-demethylase) and formation of pyrocatecholic structures was detected using Aspergillus sp. and Galerina autumnalis culture filtrates as the enzyme source. The produced aromatic vicinal diol groups in lignin model compounds (LMCs) and KL were determined using different catecholic-binding reagents with the influence of H2O2, along with 4-antiaminopyrine reagent, was analyzed by the following: i) Fe3+-catechol complexation method, ii) HNO2 method, iii) FAS (Ferric Ammonium-Sulfate) method, iv) Ti(III)-NTA (Titanium (III)- Nitrilotriacetate) method for hydrolytic zone formation. Among the tested methods showing lytic zone formation was Fe3+-catechol complexation. The LMCs and KL treated using Aspergillus sp. culture filtrate showed maximum Fe3+-catechol complexes with 3-methoxy catechol (91 μmol/mL), o-vanillin (44 μmol/mL) and KL (100 μmol/mL). In addition, Galerina autumnalis culture filtrate showed demethylation of vanillin (48 μmol/mL), 3-methoxy catechol (82 μmol/mL), o-vanillin, (33 μmol/mL), 3 4-dimethoxybenzyl alcohol (49 μmol/mL) and KL (41 μmol/mL). The results suggest that lignin demethylation (O-demethylases) activity that strip-off methyl groups in LMCs and KL and produced vicinal diols that covalently bind with Fe3+ to form Fe3+-catechol complexes. The new Fe3+-catechol complexation method has the ability to characterize pyrocatechol and galloyl structures in chemically or biologically modified lignins and to detect O-demethylase activity.
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Affiliation(s)
- Balaji Venkatesagowda
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada.
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20
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Łucejko JJ, Mattonai M, Zborowska M, Tamburini D, Cofta G, Cantisani E, Kúdela J, Cartwright C, Colombini MP, Ribechini E, Modugno F. Deterioration effects of wet environments and brown rot fungus Coniophora puteana on pine wood in the archaeological site of Biskupin (Poland). Microchem J 2018. [DOI: 10.1016/j.microc.2017.12.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Kameshwar AKS, Qin W. Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data. Int J Biol Sci 2018; 14:237-252. [PMID: 29559843 PMCID: PMC5859471 DOI: 10.7150/ijbs.22868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/09/2018] [Indexed: 11/05/2022] Open
Abstract
To understand the common gene expression patterns employed by P. placenta during lignocellulose degradation, we have retrieved genome wide transcriptome datasets from NCBI GEO database and analyzed using customized analysis pipeline. We have retrieved the top differentially expressed genes and compared the common significant genes among two different growth conditions. Genes encoding for cellulolytic (GH1, GH3, GH5, GH12, GH16, GH45) and hemicellulolytic (GH10, GH27, GH31, GH35, GH47, GH51, GH55, GH78, GH95) glycoside hydrolase classes were commonly up regulated among all the datasets. Fenton's reaction enzymes (iron homeostasis, reduction, hydrogen peroxide generation) were significantly expressed among all the datasets under lignocellulolytic conditions. Due to the evolutionary loss of genes coding for various lignocellulolytic enzymes (including several cellulases), P. placenta employs hemicellulolytic glycoside hydrolases and Fenton's reactions for the rapid depolymerization of plant cell wall components. Different classes of enzymes involved in aromatic compound degradation, stress responsive and detoxification mechanisms (cytochrome P450 monoxygenases) were found highly expressed in complex plant biomass substrates. We have reported the genome wide expression patterns of genes coding for information, storage and processing (KOG), tentative and predicted molecular networks involved in cellulose, hemicellulose degradation and list of significant protein-ID's commonly expressed among different lignocellulolytic growth conditions.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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22
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Tarmadi D, Tobimatsu Y, Yamamura M, Miyamoto T, Miyagawa Y, Umezawa T, Yoshimura T. NMR studies on lignocellulose deconstructions in the digestive system of the lower termite Coptotermes formosanus Shiraki. Sci Rep 2018; 8:1290. [PMID: 29358744 PMCID: PMC5778066 DOI: 10.1038/s41598-018-19562-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Termites represent one of the most efficient lignocellulose decomposers on earth. The mechanism by which termites overcome the recalcitrant lignin barrier to gain access to embedded polysaccharides for assimilation and energy remains largely unknown. In the present study, softwood, hardwood, and grass lignocellulose diets were fed to Coptotermes formosanus workers, and structural differences between the original lignocellulose diets and the resulting feces were examined by solution-state multidimensional nuclear magnetic resonance (NMR) techniques as well as by complementary wet-chemical methods. Overall, our data support the view that lignin polymers are partially decomposed during their passage through the termite gut digestive system, although polysaccharide decomposition clearly dominates the overall lignocellulose deconstruction process and the majority of lignin polymers remain intact in the digestive residues. High-resolution NMR structural data suggested preferential removal of syringyl aromatic units in hardwood lignins, but non-acylated guaiacyl units as well as tricin end-units in grass lignins. In addition, our data suggest that termites and/or their gut symbionts may favor degradation of C-C-bonded β-5 and resinol-type β-β lignin inter-monomeric units over degradation of ether-bonded β-O-4 units, which is in contrast to what has been observed in typical lignin biodegradation undertaken by wood-decaying fungi.
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Affiliation(s)
- Didi Tarmadi
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan.,Research Center for Biomaterials, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor KM.46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan.
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan
| | - Takuji Miyamoto
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan
| | - Yasuyuki Miyagawa
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan.,Research Unit for Development and Global Sustainability, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Tsuyoshi Yoshimura
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho Uji, Kyoto, 611-0011, Japan.
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23
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Multi-analysis of chemical transformations of lignin macromolecules from waterlogged archaeological wood. Int J Biol Macromol 2017; 109:407-416. [PMID: 29274420 DOI: 10.1016/j.ijbiomac.2017.12.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 11/24/2022]
Abstract
A large number of archaeological wooden building poles have been excavated from the Hai Menkou site (Yunnan province, China). Lignin can be transformed and altered accompanied with significant loss of carbohydrates during this process. Elucidation of chemical and structural transformations of lignin is of primary importance for understanding both the nature of degradation processes and the structure of waterlogged archaeological wood, and crucial for developing proper consolidation technology and restoring artifacts of historical and cultural value. In this study, state-of-the-art analytical techniques, including SEM, FT-IR, XRD, CP-MAS 13C NMR, 2D-HSQC NMR, 31P-NMR, CRM, GPC and TG analysis, were all employed to elucidate the structural characteristics of lignin in waterlogged and reference Pinus wood. The results interpreted by NMR analysis demonstrated the depolymerization of lignin via cleavage of β-O-4, β-5, -OCH3 and some LCC linkages, leading to a higher amount of free phenol OH groups in the lignin from the ancient waterlogged wood as compared to that of the reference wood. Microscopically, it was found that extensive degradation of carbohydrates in cell walls was mainly occurred in secondary cell walls, while the lignin concentrations were relatively increased in CCML and S regions in the plant cell wall of the ancient wood.
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A critical evaluation of the degradation state of dry archaeological wood from Egypt by SEM, ATR-FTIR, wet chemical analysis and Py(HMDS)-GC-MS. Polym Degrad Stab 2017. [DOI: 10.1016/j.polymdegradstab.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Kong W, Fu X, Wang L, Alhujaily A, Zhang J, Ma F, Zhang X, Yu H. A novel and efficient fungal delignification strategy based on versatile peroxidase for lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:218. [PMID: 28924453 PMCID: PMC5598073 DOI: 10.1186/s13068-017-0906-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/07/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND The selective lignin-degrading white-rot fungi are regarded to be the best lignin degraders and have been widely used for reducing the saccharification recalcitrance of lignocellulose. However, the biological delignification and conversion of lignocellulose in biorefinery is still limited. It is necessary to develop novel and more efficient bio-delignification systems. RESULTS Physisporinus vitreus relies on a new versatile peroxidase (VP)-based delignification strategy to remove enzymatic recalcitrance of corn stover efficiently, so that saccharification of corn stover was significantly enhanced to 349.1 mg/g biomass (yield of glucose) and 91.5% (hydrolysis yield of cellulose) at 28 days, as high as levels reached by thermochemical treatment. Analysis of the lignin structure using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) showed that the total abundance of lignin-derived compounds decreased by 54.0% and revealed a notable demethylation during lignin degradation by P. vitreus. Monomeric and dimeric lignin model compounds were used to confirm the ligninolytic capabilities of extracellular ligninases secreted by P. vitreus. The laccase (Lac) from P. vitreus could not oxidize nonphenolic lignin compounds and polymerized β-O-4 and 5-5' dimers to precipitate which had a negative effect on the enzymatic hydrolysis of corn stover in vitro. However, the VP from P. vitreus could oxidize both phenolic and nonphenolic lignin model compounds as well as break the β-O-4 and 5-5' dimers into monomeric compounds, which were measured by high-performance liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). Moreover, we showed that addition of purified VP in vitro improved the enzymatic hydrolysis of corn stover by 14.1%. CONCLUSIONS From the highly efficient system of enzymatic recalcitrance removal by new white-rot fungus, we identified a new delignification strategy based on VP which could oxidize both phenolic and nonphenolic lignin units and break different linkages in lignin. In addition, this is the first evidence that VP could break 5-5' linkage efficiently in vitro. Moreover, VP improved the enzymatic hydrolysis of corn stover in vitro. The remarkable lignin-degradative potential makes VP attractive for biotechnological applications.
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Affiliation(s)
- Wen Kong
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xiao Fu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Lei Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Ahmad Alhujaily
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Jingli Zhang
- College of Life Science and Technology, WuHan University of Technology, Wuhan, 430070 People’s Republic of China
| | - Fuying Ma
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xiaoyu Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Hongbo Yu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
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Hermosilla E, Schalchli H, Mutis A, Diez MC. Combined effect of enzyme inducers and nitrate on selective lignin degradation in wheat straw by Ganoderma lobatum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:21984-21996. [PMID: 28785941 DOI: 10.1007/s11356-017-9841-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
Lignin is one of the main barriers to obtaining added-value products from cellulosic fraction of lignocellulosic biomass due to its random aromatic structure and strong association with cellulose and hemicellulose. Inorganic and organic compounds have been used as enzyme inducers to increase the ligninolytic potential of white-rot fungi, without considering their effect on the selectivity of degradation. In this study, the selective lignin degradation in wheat straw by Ganoderma lobatum was optimized using a central composite design to evaluate the combined effect of Fe2+ and Mn2+ as inducers of ligninolytic enzymes and NO3- as an additional nitrogen source. Selective lignin degradation was promoted to maximize lignin degradation and minimize weight losses. The optimal conditions were 0.18 M NO3-, 0.73 mM Fe2+, and 1 mM Mn2+, which resulted in 50.0% lignin degradation and 18.5% weight loss after 40 days of fungal treatment. A decrease in absorbance at 1505 and 900 cm-1 in fungal-treated samples was observed in the FTIR spectra, indicating lignin and cellulose degradation in fungal-treated wheat straw, respectively. The main ligninolytic enzymes detected during lignin degradation were manganese-dependent and manganese-independent peroxidases. Additionally, confocal laser scanning microscopy revealed that lignin degradation in wheat straw by G. lobatum resulted in higher cellulose accessibility. We concluded that the addition of enzyme inducers and NO3- promotes selective lignin degradation in wheat straw by G. lobatum.
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Affiliation(s)
- Edward Hermosilla
- Biotechnological Research Center Applied to the Environment (CIBAMA-BIOREN), Universidad de La Frontera, Temuco, Chile
- Doctoral Program in Sciences of Natural Resources, Universidad de La Frontera, Temuco, Chile
| | - Heidi Schalchli
- Biotechnological Research Center Applied to the Environment (CIBAMA-BIOREN), Universidad de La Frontera, Temuco, Chile
- Chemical Engineering Department, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Ana Mutis
- Biotechnological Research Center Applied to the Environment (CIBAMA-BIOREN), Universidad de La Frontera, Temuco, Chile
- Chemical Science and Natural Resource Department, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - María Cristina Diez
- Biotechnological Research Center Applied to the Environment (CIBAMA-BIOREN), Universidad de La Frontera, Temuco, Chile.
- Chemical Engineering Department, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
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Nicolás C, Almeida JP, Ellström M, Bahr A, Bone SE, Rosenstock NP, Bargar JR, Tunlid A, Persson P, Wallander H. Chemical changes in organic matter after fungal colonization in a nitrogen fertilized and unfertilized Norway spruce forest. PLANT AND SOIL 2017; 419:113-126. [PMID: 32009679 PMCID: PMC6959379 DOI: 10.1007/s11104-017-3324-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/22/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Decomposition and transformation of organic matter (OM) in forest soils are conducted by the concomitant action of saprotrophic and mycorrhizal fungi. Here, we examine chemical changes in OM after fungal colonization in nitrogen fertilized and unfertilized soils from a Norway spruce forest. METHODS Sand-filled bags amended with composted maize leaves were placed in the forest soil and harvested after 17 months. Infrared and near edge X-ray absorption fine structure spectroscopies were used to study the chemical changes in the OM. Fungal community composition of the bags was also evaluated. RESULTS The proportion of ectomycorrhizal fungi declined in the fertilized plots, but the overall fungal community composition was similar between N treatments. Decomposition of the OM was, independently of the N level or soil horizon, accompanied by an increase of C/N ratio of the mesh-bag content. Moreover, the proportions of carboxylic compounds in the incubated OM increased in the mineral horizon, while heterocyclic-N compounds decreased, especially in unfertilized plots with higher N demand from the trees. CONCLUSIONS Our results indicate that more oxidized organic C and less heterocyclic-N proportions in the OM remain after fungal colonization in the mineral layers, and suggest that ectomycorrhizal fungi transfer less heterocyclic-N from the mesh bags to the host trees under high N levels.
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Affiliation(s)
- César Nicolás
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Department of Biology, Ecology Building, Lund University, SE 22362 Lund, Sweden
| | - Juan P. Almeida
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Magnus Ellström
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Adam Bahr
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Sharon E. Bone
- Chemistry and Catalysis Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Nicholas P. Rosenstock
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - John R. Bargar
- Chemistry and Catalysis Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Per Persson
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Håkan Wallander
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
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Abstract
Depolymerizing lignin, the complex phenolic polymer fortifying plant cell walls, is an essential but challenging starting point for the lignocellulosics industries. The variety of ether- and carbon-carbon interunit linkages produced via radical coupling during lignification limit chemical and biological depolymerization efficiency. In an ancient fungus-cultivating termite system, we reveal unprecedentedly rapid lignin depolymerization and degradation by combining laboratory feeding experiments, lignocellulosic compositional measurements, electron microscopy, 2D-NMR, and thermochemolysis. In a gut transit time of under 3.5 h, in young worker termites, poplar lignin sidechains are extensively cleaved and the polymer is significantly depleted, leaving a residue almost completely devoid of various condensed units that are traditionally recognized to be the most recalcitrant. Subsequently, the fungus-comb microbiome preferentially uses xylose and cleaves polysaccharides, thus facilitating final utilization of easily digestible oligosaccharides by old worker termites. This complementary symbiotic pretreatment process in the fungus-growing termite symbiosis reveals a previously unappreciated natural system for efficient lignocellulose degradation.
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Saha BC, Kennedy GJ, Qureshi N, Cotta MA. Biological pretreatment of corn stover withPhlebia brevisporaNRRL-13108 for enhanced enzymatic hydrolysis and efficient ethanol production. Biotechnol Prog 2017; 33:365-374. [DOI: 10.1002/btpr.2420] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/17/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Badal C. Saha
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Gregory J. Kennedy
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Nasib Qureshi
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
| | - Michael A. Cotta
- U.S. Department of Agriculture; Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service; Peoria IL 61604
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Yan K, Liu F, Chen Q, Ke M, Huang X, Hu W, Zhou B, Zhang X, Yu H. Pyrolysis characteristics and kinetics of lignin derived from enzymatic hydrolysis residue of bamboo pretreated with white-rot fungus. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:76. [PMID: 27034714 PMCID: PMC4815148 DOI: 10.1186/s13068-016-0489-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/18/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND The lignocellulose biorefinery based on the sugar platform usually focuses on polysaccharide bioconversion, while lignin is only burned for energy recovery. Pyrolysis can provide a novel route for the efficient utilization of residual lignin obtained from the enzymatic hydrolysis of lignocellulose. The pyrolysis characteristics of residual lignin are usually significantly affected by the pretreatment process because of structural alteration of lignin during pretreatment. In recent years, biological pretreatment using white-rot fungi has attracted extensive attention, but there are only few reports on thermal conversion of lignin derived from enzymatic hydrolysis residue (EHRL) of the bio-pretreated lignocellulose. Therefore, the study investigated the pyrolysis characteristics and kinetics of EHRL obtained from bamboo pretreated with Echinodontium taxodii in order to evaluate the potential of thermal conversion processes of EHRL. RESULTS Fourier transform infrared spectroscopy spectra showed that EHRL of bamboo treated with E. taxodii had the typical lignin structure, but aromatic skeletal carbon and side chain of lignin were partially altered by the fungus. Thermogravimetric analysis indicated that EHRL pyrolysis at different heating rates could be divided into two depolymerization stages and covered a wide temperature range from 500 to 900 K. The thermal decomposition reaction can be well described by two third-order reactions. The kinetics study indicated that the EHRL of bamboo treated with white-rot fungus had lower apparent activation energies, lower peak temperatures of pyrolysis reaction, and higher char residue than the EHRL of raw bamboo. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) was applied to characterize the fast pyrolysis products of EHRL at 600 ℃. The ratios of guaiacyl-type to syringyl-type derivatives yield (G/S) and guaiacyl-type to p-hydroxy-phenylpropane-type derivatives yield (G/H) for the treated sample were increased by 33.18 and 25.30 % in comparison with the raw bamboo, respectively. CONCLUSIONS The structural alterations of lignin during pretreatment can decrease the thermal stability of EHRL from the bio-treated bamboo and concentrate the guaiacyl-type derivatives in the fast pyrolysis products. Thus, the pyrolysis can be a promising route for effective utilization of the enzymatic hydrolysis residue from bio-pretreated lignocellulose.
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Affiliation(s)
- Keliang Yan
- />Technology Center of China Tobacco, Yunnan Industrial Co., Ltd, Kunming, 650000 People’s Republic of China
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Fang Liu
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Qing Chen
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Ming Ke
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xin Huang
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Weiyao Hu
- />Technology Center of China Tobacco, Yunnan Industrial Co., Ltd, Kunming, 650000 People’s Republic of China
| | - Bo Zhou
- />Technology Center of China Tobacco, Yunnan Industrial Co., Ltd, Kunming, 650000 People’s Republic of China
| | - Xiaoyu Zhang
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Hongbo Yu
- />College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
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Carro J, Serrano A, Ferreira P, Martínez AT. Fungal Aryl-Alcohol Oxidase in Lignocellulose Degradation and Bioconversion. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2016. [DOI: 10.1007/978-3-319-43679-1_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Fungal demethylation of Kraft lignin. Enzyme Microb Technol 2015; 73-74:44-50. [DOI: 10.1016/j.enzmictec.2015.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/05/2015] [Accepted: 04/06/2015] [Indexed: 11/22/2022]
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Kües U, Nelson DR, Liu C, Yu GJ, Zhang J, Li J, Wang XC, Sun H. Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles. PHYTOCHEMISTRY 2015; 114:18-37. [PMID: 25682509 DOI: 10.1016/j.phytochem.2014.11.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 06/04/2023]
Abstract
Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of Ganoderma species. The current review carries out a detailed comparison of the nuclear genomes, mitochondrial genomes and transcriptomes from several Ganoderma species. Genes involved in biosynthetic pathways such as CYP450 genes and in cellular development such as matA and matB genes are characterized and compared in detail, as examples to demonstrate the usefulness of comparative genomic analyses for the identification of critical genes. Resources needed for future data integration and exploitation are also discussed.
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Affiliation(s)
- Ursula Kües
- University of Göttingen, Büsgen-Institute, Department for Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, D-37077 Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave., Memphis, TN 38163, USA
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
| | - Guo-Jun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Jianhui Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jianqin Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
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Can laccases catalyze bond cleavage in lignin? Biotechnol Adv 2015; 33:13-24. [DOI: 10.1016/j.biotechadv.2014.12.008] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/06/2014] [Accepted: 12/25/2014] [Indexed: 11/13/2022]
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35
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Gai YP, Zhang WT, Mu ZM, Ji XL. Involvement of ligninolytic enzymes in degradation of wheat straw by Trametes trogii. J Appl Microbiol 2014; 117:85-95. [DOI: 10.1111/jam.12529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/27/2014] [Accepted: 04/15/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Y.-P. Gai
- State Key Laboratory of Crop Biology; Shandong Agricultural University; Taian Shan-dong China
| | - W.-T. Zhang
- College of Forestry; Shandong Agricultural University; Taian Shandong China
| | - Z.-M. Mu
- College of Forestry; Shandong Agricultural University; Taian Shandong China
| | - X.-L. Ji
- State Key Laboratory of Crop Biology; Shandong Agricultural University; Taian Shan-dong China
- College of Forestry; Shandong Agricultural University; Taian Shandong China
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37
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Impact of Hot-Water Extraction on Acetone-Water Oxygen Delignification of Paulownia Spp. and Lignin Recovery. ENERGIES 2014. [DOI: 10.3390/en7020857] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Navarro D, Rosso MN, Haon M, Olivé C, Bonnin E, Lesage-Meessen L, Chevret D, Coutinho PM, Henrissat B, Berrin JG. Fast solubilization of recalcitrant cellulosic biomass by the basidiomycete fungus Laetisaria arvalis involves successive secretion of oxidative and hydrolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:143. [PMID: 25320637 PMCID: PMC4197297 DOI: 10.1186/s13068-014-0143-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/18/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Enzymatic breakdown of lignocellulosic biomass is a known bottleneck for the production of high-value molecules and biofuels from renewable sources. Filamentous fungi are the predominant natural source of enzymes acting on lignocellulose. We describe the extraordinary cellulose-deconstructing capacity of the basidiomycete Laetisaria arvalis, a soil-inhabiting fungus. RESULTS The L. arvalis strain displayed the capacity to grow on wheat straw as the sole carbon source and to fully digest cellulose filter paper. The cellulolytic activity exhibited in the secretomes of L. arvalis was up to 7.5 times higher than that of a reference Trichoderma reesei industrial strain, resulting in a significant improvement of the glucose release from steam-exploded wheat straw. Global transcriptome and secretome analyses revealed that L. arvalis produces a unique repertoire of carbohydrate-active enzymes in the fungal taxa, including a complete set of enzymes acting on cellulose. Temporal analyses of secretomes indicated that the unusual degradation efficiency of L. arvalis relies on its early response to the carbon source, and on the finely tuned sequential secretion of several lytic polysaccharide monooxygenases and hydrolytic enzymes targeting cellulose. CONCLUSIONS The present study illustrates the adaptation of a litter-rot fungus to the rapid breakdown of recalcitrant plant biomass. The cellulolytic capabilities of this basidiomycete fungus result from the rapid, selective and successive secretion of oxidative and hydrolytic enzymes. These enzymes expressed at critical times during biomass degradation may inspire the design of improved enzyme cocktails for the conversion of plant cell wall resources into fermentable sugars.
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Affiliation(s)
- David Navarro
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />CIRM-CF, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Marie-Noëlle Rosso
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Mireille Haon
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Caroline Olivé
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Estelle Bonnin
- />INRA, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Laurence Lesage-Meessen
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
| | - Didier Chevret
- />INRA, UMR1319 Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, 78352 Jouy-en-Josas, France
| | - Pedro M Coutinho
- />CNRS, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
- />Aix-Marseille Université, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
| | - Bernard Henrissat
- />Aix-Marseille Université, UMR7257 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
- />Department of Biological Sciences, King Abdulaziz University, Abdullah Sulayman, Jeddah, 22254 Saudi Arabia
| | - Jean-Guy Berrin
- />INRA, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
- />Aix-Marseille Université, Polytech Marseille, UMR1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France
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39
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Kim H, Ralph J. A gel-state 2D-NMR method for plant cell wall profiling and analysis: a model study with the amorphous cellulose and xylan from ball-milled cotton linters. RSC Adv 2014. [DOI: 10.1039/c3ra46338a] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amorphous cellulose and xylan structures were analyzed using high-resolution 2D-NMR, and the NMR data were obtained in a DMSO-d6/pyridine-d5 (4 : 1) solvent system.
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Affiliation(s)
- Hoon Kim
- Department of Biochemistry and the DOE Great Lakes Bioenergy Research Center
- Wisconsin Energy Institute
- University of Wisconsin
- Madison, USA
| | - John Ralph
- Department of Biochemistry and the DOE Great Lakes Bioenergy Research Center
- Wisconsin Energy Institute
- University of Wisconsin
- Madison, USA
- Department of Biological Systems Engineering
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40
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Arantes V, Goodell B. Current Understanding of Brown-Rot Fungal Biodegradation Mechanisms: A Review. ACS SYMPOSIUM SERIES 2014. [DOI: 10.1021/bk-2014-1158.ch001] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Valdeir Arantes
- University of British Columbia, 4035-2424 Main Mall, V6T 1Z4, Vancouver BC, Canada
- Virginia Polytechnic Institute and State University (Virginia Tech), 216 ICTAS II Building (0917), 1075 Life Sciences Circle, Blacksburg VA 24061, United States
| | - Barry Goodell
- University of British Columbia, 4035-2424 Main Mall, V6T 1Z4, Vancouver BC, Canada
- Virginia Polytechnic Institute and State University (Virginia Tech), 216 ICTAS II Building (0917), 1075 Life Sciences Circle, Blacksburg VA 24061, United States
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41
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Salame TM, Knop D, Levinson D, Mabjeesh SJ, Yarden O, Hadar Y. Inactivation of a Pleurotus ostreatus versatile peroxidase-encoding gene (mnp2) results in reduced lignin degradation. Environ Microbiol 2013; 16:265-77. [PMID: 24119015 DOI: 10.1111/1462-2920.12279] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/29/2013] [Accepted: 09/01/2013] [Indexed: 11/27/2022]
Abstract
Lignin biodegradation by white-rot fungi is pivotal to the earth's carbon cycle. Manganese peroxidases (MnPs), the most common extracellular ligninolytic peroxidases produced by white-rot fungi, are considered key in ligninolysis. Pleurotus ostreatus, the oyster mushroom, is a preferential lignin degrader occupying niches rich in lignocellulose such as decaying trees. Here, we provide direct, genetically based proof for the functional significance of MnP to P. ostreatus ligninolytic capacity under conditions mimicking its natural habitat. When grown on a natural lignocellulosic substrate of cotton stalks under solid-state culture conditions, gene and isoenzyme expression profiles of its short MnP and versatile peroxidase (VP)-encoding gene family revealed that mnp2 was predominately expressed. mnp2, encoding the versatile short MnP isoenzyme 2 was disrupted. Inactivation of mnp2 resulted in three interrelated phenotypes, relative to the wild-type strain: (i) reduction of 14% and 36% in lignin mineralization of stalks non-amended and amended with Mn(2+), respectively; (ii) marked reduction of the bioconverted lignocellulose sensitivity to subsequent bacterial hydrolyses; and (iii) decrease in fungal respiration rate. These results may serve as the basis to clarify the roles of the various types of fungal MnPs and VPs in their contribution to white-rot decay of wood and lignocellulose in various ecosystems.
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Affiliation(s)
- Tomer M Salame
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel
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42
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Komatsu T, Kikuchi J. Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR. Anal Chem 2013; 85:8857-65. [PMID: 24010724 DOI: 10.1021/ac402197h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A multidimensional solution NMR method has been developed using various pulse programs including HCCH-COSY and (13)C-HSQC-NOESY for the structural characterization of commercially available (13)C labeled lignocellulose from potatoes (Solanum tuberosum L.), chicory (Cichorium intybus), and corn (Zea mays). This new method allowed for 119 of the signals in the (13)C-HSQC spectrum of lignocelluloses to be assigned and was successfully used to characterize the structures of lignocellulose samples from three plants in terms of their xylan and xyloglucan structures, which are the major hemicelluloses in angiosperm. Furthermore, this new method provided greater insight into fine structures of lignin by providing a high resolution to the aromatic signals of the β-aryl ether and resinol moieties, as well as the diastereomeric signals of the β-aryl ether. Finally, the (13)C chemical shifts assigned in this study were compared with those from solid-state NMR and indicated the presence of heterogeneous dynamics in the polysaccharides where rigid cellulose and mobile hemicelluloses moieties existed together.
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Affiliation(s)
- Takanori Komatsu
- RIKEN Center for Sustainable Resource Science , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 235-0045, Japan
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43
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Ruiz-Dueñas FJ, Lundell T, Floudas D, Nagy LG, Barrasa JM, Hibbett DS, Martínez AT. Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Mycologia 2013; 105:1428-44. [PMID: 23921235 DOI: 10.3852/13-059] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species representing the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequenced B. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)-oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.
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44
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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45
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Ogura T, Date Y, Kikuchi J. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota. PLoS One 2013; 8:e66919. [PMID: 23840554 PMCID: PMC3686774 DOI: 10.1371/journal.pone.0066919] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 05/10/2013] [Indexed: 02/01/2023] Open
Abstract
Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an "ECOMICS" web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.
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Affiliation(s)
- Tatsuki Ogura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yasuhiro Date
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- Biomass Engineering Program, RIKEN Research Cluster for Innovation, Wako, Saitama, Japan
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46
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Doddapaneni H, Subramanian V, Fu B, Cullen D. A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus. Fungal Genet Biol 2013; 55:22-31. [DOI: 10.1016/j.fgb.2013.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 03/22/2013] [Accepted: 03/23/2013] [Indexed: 12/24/2022]
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47
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Syringyl-rich lignin renders poplars more resistant to degradation by wood decay fungi. Appl Environ Microbiol 2013; 79:2560-71. [PMID: 23396333 DOI: 10.1128/aem.03182-12] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing an Arabidopsis gene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.
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48
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Wen JL, Sun SL, Xue BL, Sun RC. Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology. MATERIALS 2013; 6:359-391. [PMID: 28809313 PMCID: PMC5452107 DOI: 10.3390/ma6010359] [Citation(s) in RCA: 468] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/04/2013] [Accepted: 01/18/2013] [Indexed: 11/16/2022]
Abstract
The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (insitu), as well as their applications are reviewed.
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Affiliation(s)
- Jia-Long Wen
- Beijing key laboratory of lignocellulosic chemistry, Beijing Forestry University, Beijing 100000, China.
| | - Shao-Long Sun
- Beijing key laboratory of lignocellulosic chemistry, Beijing Forestry University, Beijing 100000, China.
| | - Bai-Liang Xue
- Beijing key laboratory of lignocellulosic chemistry, Beijing Forestry University, Beijing 100000, China.
| | - Run-Cang Sun
- Beijing key laboratory of lignocellulosic chemistry, Beijing Forestry University, Beijing 100000, China.
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510000, China.
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49
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Hastrup ACS, Howell C, Larsen FH, Sathitsuksanoh N, Goodell B, Jellison J. Differences in crystalline cellulose modification due to degradation by brown and white rot fungi. Fungal Biol 2012; 116:1052-63. [DOI: 10.1016/j.funbio.2012.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/11/2012] [Accepted: 07/27/2012] [Indexed: 10/28/2022]
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50
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Rineau F, Roth D, Shah F, Smits M, Johansson T, Canbäck B, Olsen PB, Persson P, Grell MN, Lindquist E, Grigoriev IV, Lange L, Tunlid A. The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. Environ Microbiol 2012; 14:1477-87. [PMID: 22469289 PMCID: PMC3440587 DOI: 10.1111/j.1462-2920.2012.02736.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/16/2012] [Accepted: 03/07/2012] [Indexed: 01/25/2023]
Abstract
Soils in boreal forests contain large stocks of carbon. Plants are the main source of this carbon through tissue residues and root exudates. A major part of the exudates are allocated to symbiotic ectomycorrhizal fungi. In return, the plant receives nutrients, in particular nitrogen from the mycorrhizal fungi. To capture the nitrogen, the fungi must at least partly disrupt the recalcitrant organic matter-protein complexes within which the nitrogen is embedded. This disruption process is poorly characterized. We used spectroscopic analyses and transcriptome profiling to examine the mechanism by which the ectomycorrhizal fungus Paxillus involutus degrades organic matter when acquiring nitrogen from plant litter. The fungus partially degraded polysaccharides and modified the structure of polyphenols. The observed chemical changes were consistent with a hydroxyl radical attack, involving Fenton chemistry similar to that of brown-rot fungi. The set of enzymes expressed by Pa. involutus during the degradation of the organic matter was similar to the set of enzymes involved in the oxidative degradation of wood by brown-rot fungi. However, Pa. involutus lacked transcripts encoding extracellular enzymes needed for metabolizing the released carbon. The saprotrophic activity has been reduced to a radical-based biodegradation system that can efficiently disrupt the organic matter-protein complexes and thereby mobilize the entrapped nutrients. We suggest that the released carbon then becomes available for further degradation and assimilation by commensal microbes, and that these activities have been lost in ectomycorrhizal fungi as an adaptation to symbiotic growth on host photosynthate. The interdependence of ectomycorrhizal symbionts and saprophytic microbes would provide a key link in the turnover of nutrients and carbon in forest ecosystems.
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Affiliation(s)
- Francois Rineau
- Department of Biology, Microbial Ecology Group, Ecology BuildingSE-22362 Lund, Sweden
| | - Doris Roth
- Department of Biotechnology and Chemistry, Aalborg UniversityLautrupvang 15, DK-2750, Ballerup, Denmark
| | - Firoz Shah
- Department of Biology, Microbial Ecology Group, Ecology BuildingSE-22362 Lund, Sweden
| | - Mark Smits
- Centre for Environmental Sciences, Hasselt UniversityBuilding D, Agoralaan, 3590 Diepenbeek, Limburg, Belgium
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Ecology BuildingSE-22362 Lund, Sweden
| | - Björn Canbäck
- Department of Biology, Microbial Ecology Group, Ecology BuildingSE-22362 Lund, Sweden
| | | | - Per Persson
- Department of Chemistry, Umeå UniversitySE-901 87 Umeå, Sweden
| | - Morten Nedergaard Grell
- Department of Biotechnology and Chemistry, Aalborg UniversityLautrupvang 15, DK-2750, Ballerup, Denmark
| | - Erika Lindquist
- US Department of Energy, Joint Genome Institute2800 Mitchell Avenue, Walnut Creek, CA94598, USA
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute2800 Mitchell Avenue, Walnut Creek, CA94598, USA
| | - Lene Lange
- Department of Biotechnology and Chemistry, Aalborg UniversityLautrupvang 15, DK-2750, Ballerup, Denmark
| | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Ecology BuildingSE-22362 Lund, Sweden
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