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Kapich AN, Suzuki H, Hirth KC, Fernández-Fueyo E, Martínez AT, Houtman CJ, Hammel KE. The white rot basidiomycete Gelatoporia subvermispora produces fatty aldehydes that enable fungal manganese peroxidases to degrade recalcitrant lignin structures. Appl Environ Microbiol 2024; 90:e0204423. [PMID: 38483171 PMCID: PMC11022559 DOI: 10.1128/aem.02044-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/26/2024] [Indexed: 04/18/2024] Open
Abstract
The ability of some white rot basidiomycetes to remove lignin selectively from wood indicates that low molecular weight oxidants have a role in ligninolysis. These oxidants are likely free radicals generated by fungal peroxidases from compounds in the biodegrading wood. Past work supports a role for manganese peroxidases (MnPs) in the production of ligninolytic oxidants from fungal membrane lipids. However, the fatty acid alkylperoxyl radicals initially formed during this process are not reactive enough to attack the major structures in lignin. Here, we evaluate the hypothesis that the peroxidation of fatty aldehydes might provide a source of more reactive acylperoxyl radicals. We found that Gelatoporia subvermispora produced trans-2-nonenal, trans-2-octenal, and n-hexanal (a likely metabolite of trans-2,4-decadienal) during the incipient decay of aspen wood. Fungal fatty aldehydes supported the in vitro oxidation by MnPs of a nonphenolic lignin model dimer, and also of the monomeric model veratryl alcohol. Experiments with the latter compound showed that the reactions were partially inhibited by oxalate, the chelator that white rot fungi employ to detach Mn3+ from the MnP active site, but nevertheless proceeded at its physiological concentration of 1 mM. The addition of catalase was inhibitory, which suggests that the standard MnP catalytic cycle is involved in the oxidation of aldehydes. MnP oxidized trans-2-nonenal quantitatively to trans-2-nonenoic acid with the consumption of one O2 equivalent. The data suggest that when Mn3+ remains associated with MnP, it can oxidize aldehydes to their acyl radicals, and the latter subsequently add O2 to become ligninolytic acylperoxyl radicals.IMPORTANCEThe biodegradation of lignin by white rot fungi is essential for the natural recycling of plant biomass and has useful applications in lignocellulose bioprocessing. Although fungal peroxidases have a key role in ligninolysis, past work indicates that biodegradation is initiated by smaller, as yet unidentified oxidants that can infiltrate the substrate. Here, we present evidence that the peroxidase-catalyzed oxidation of naturally occurring fungal aldehydes may provide a source of ligninolytic free radical oxidants.
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Affiliation(s)
| | - Hideki Suzuki
- US Forest Products Laboratory, Madison, Wisconsin, USA
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Kenneth E. Hammel
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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Rajtar NN, Kielsmeier-Cook JC, Held BW, Toapanta-Alban CE, Ordonez ME, Barnes CW, Blanchette RA. Diverse Xylaria in the Ecuadorian Amazon and their mode of wood degradation. BOTANICAL STUDIES 2023; 64:30. [PMID: 37878199 PMCID: PMC10600087 DOI: 10.1186/s40529-023-00403-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Xylaria is a diverse and ecologically important genus in the Ascomycota. This paper describes the xylariaceous fungi present in an Ecuadorian Amazon Rainforest and investigates the decay potential of selected Xylaria species. Fungi were collected at Yasuní National Park, Ecuador during two collection trips to a single hectare plot divided into a 10-m by 10-m grid, providing 121 collection points. All Xylaria fruiting bodies found within a 1.2-m radius of each grid point were collected. Dried fruiting bodies were used for culturing and the internal transcribed spacer region was sequenced to identify Xylaria samples to species level. Agar microcosms were used to assess the decay potential of three selected species, two unknown species referred to as Xylaria 1 and Xylaria 2 and Xylaria curta, on four different types of wood from trees growing in Ecuador including balsa (Ochroma pyramidale), melina (Gmelina arborea), saman (Samanea saman), and moral (Chlorophora tinctoria). ANOVA and post-hoc comparisons were used to test for differences in biomass lost between wood blocks inoculated with Xylaria and uninoculated control blocks. Scanning electron micrographs of transverse sections of each wood and assay fungus were used to assess the type of degradation present. RESULTS 210 Xylaria collections were sequenced, with 106 collections belonging to 60 taxa that were unknown species, all with less than 97% match to NCBI reference sequences. Xylaria with sequence matches of 97% or greater included X. aff. comosa (28 isolates), X. cuneata (9 isolates) X. curta and X. oligotoma (7 isolates), and X. apiculta (6 isolates)., All Xylaria species tested were able to cause type 1 or type 2 soft rot degradation in the four wood types and significant biomass loss was observed compared to the uninoculated controls. Balsa and melina woods had the greatest amount of biomass loss, with as much as 60% and 25% lost, respectively, compared to the controls. CONCLUSIONS Xylaria species were found in extraordinary abundance in the Ecuadorian rainforest studied. Our study demonstrated that the Xylaria species tested can cause a soft rot type of wood decay and with the significant amount of biomass loss that occurred within a short incubation time, it indicates these fungi likely play a significant role in nutrient cycling in the Amazonian rainforest.
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Affiliation(s)
- Nickolas N Rajtar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
| | | | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Maria E Ordonez
- QCAM Fungarium, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Department of Microbiology and Plant Pathology, University of California, Riverside, 92521, USA
| | - Charles W Barnes
- Forest Health Protection-Region 5, USDA Forest Service, San Bernardino, CA, 92408, USA
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
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Wendt LM, Wahlen BD, Walton MR, Nguyen JA, Lin Y, Brown RM, Zhao H. Exploring filamentous fungi depolymerization of corn stover in the context bioenergy queuing operations. Food Energy Secur 2021. [DOI: 10.1002/fes3.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lynn M. Wendt
- Idaho National Laboratory Idaho Falls Idaho USA
- University of Idaho Idaho Falls Idaho USA
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4
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Wang Y, Van Le Q, Yang H, Lam SS, Yang Y, Gu H, Sonne C, Peng W. Progress in microbial biomass conversion into green energy. CHEMOSPHERE 2021; 281:130835. [PMID: 33992848 DOI: 10.1016/j.chemosphere.2021.130835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
The increase in global population size over the past 100 decades has doubled the requirements for energy resources. To mitigate the limited fossil fuel available, new clean energy sources being environmental sustainable for replacement of traditional energy sources are explored to supplement the current scarcity. Biomass containing lignin and cellulose is the main raw material to replace fossil energy given its abundance and lower emission of greenhouse gases and NOx when transformed into energy. Bacteria, fungi and algae decompose lignocellulose leading to generation of hydrogen, methane, bioethanol and biodiesel being the clean energy used for heating, power generation and the automobile industry. Microbial Fuel Cell (MFC) uses microorganisms to decompose biomass in wastewater to generate electricity and remove heavy metals in wastewater. Biomass contains cellulose, hemicellulose, lignin and other biomacromolecules which need hydrolyzation for conversion into small molecules by corresponding enzymes in order to be utilized by microorganisms. This paper discusses microbial decomposition of biomass into clean energy and the five major ways of clean energy production, and its economic benefits for future renewable energy security.
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Affiliation(s)
- Yacheng Wang
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Quyet Van Le
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Viet Nam
| | - Han Yang
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Su Shiung Lam
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Yafeng Yang
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haiping Gu
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Christian Sonne
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark.
| | - Wanxi Peng
- Henan Province International Collaboration Lab of Forest Resources Utilization, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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Wu B, Gaskell J, Held BW, Toapanta C, Vuong TV, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola". Appl Environ Microbiol 2021; 87:e0032921. [PMID: 34313495 PMCID: PMC8353965 DOI: 10.1128/aem.00329-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jill Gaskell
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - Benjamin W. Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Cristina Toapanta
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thu V. Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Steven Ahrendt
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan S. Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Igor V. Grigoriev
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
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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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7
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Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso MN. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay. Environ Microbiol 2021; 23:5716-5732. [PMID: 33538380 PMCID: PMC8596683 DOI: 10.1111/1462-2920.15423] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022]
Abstract
Because they comprise some of the most efficient wood‐decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin‐like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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Affiliation(s)
- Hayat Hage
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Shingo Miyauchi
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Köln, Germany
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Elodie Drula
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, USC1408, AFMB, Marseille, 13009, France
| | - Byoungnam Min
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Delphine Chaduli
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - David Navarro
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Anne Favel
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Manon Norest
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Laurence Lesage-Meessen
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Laura de Eugenio
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Cenek Novotny
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic.,University of Ostrava, Ostrava, 701 03, Czech Republic
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joey W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, 0316, Norway
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Willian Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hope Hundley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary.,Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
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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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9
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Asemoloye MD, Marchisio MA, Gupta VK, Pecoraro L. Genome-based engineering of ligninolytic enzymes in fungi. Microb Cell Fact 2021; 20:20. [PMID: 33478513 PMCID: PMC7819241 DOI: 10.1186/s12934-021-01510-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/07/2021] [Indexed: 12/23/2022] Open
Abstract
Background Many fungi grow as saprobic organisms and obtain nutrients from a wide range of dead organic materials. Among saprobes, fungal species that grow on wood or in polluted environments have evolved prolific mechanisms for the production of degrading compounds, such as ligninolytic enzymes. These enzymes include arrays of intense redox-potential oxidoreductase, such as laccase, catalase, and peroxidases. The ability to produce ligninolytic enzymes makes a variety of fungal species suitable for application in many industries, including the production of biofuels and antibiotics, bioremediation, and biomedical application as biosensors. However, fungal ligninolytic enzymes are produced naturally in small quantities that may not meet the industrial or market demands. Over the last decade, combined synthetic biology and computational designs have yielded significant results in enhancing the synthesis of natural compounds in fungi. Main body of the abstract In this review, we gave insights into different protein engineering methods, including rational, semi-rational, and directed evolution approaches that have been employed to enhance the production of some important ligninolytic enzymes in fungi. We described the role of metabolic pathway engineering to optimize the synthesis of chemical compounds of interest in various fields. We highlighted synthetic biology novel techniques for biosynthetic gene cluster (BGC) activation in fungo and heterologous reconstruction of BGC in microbial cells. We also discussed in detail some recombinant ligninolytic enzymes that have been successfully enhanced and expressed in different heterologous hosts. Finally, we described recent advance in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) protein systems as the most promising biotechnology for large-scale production of ligninolytic enzymes. Short conclusion Aggregation, expression, and regulation of ligninolytic enzymes in fungi require very complex procedures with many interfering factors. Synthetic and computational biology strategies, as explained in this review, are powerful tools that can be combined to solve these puzzles. These integrated strategies can lead to the production of enzymes with special abilities, such as wide substrate specifications, thermo-stability, tolerance to long time storage, and stability in different substrate conditions, such as pH and nutrients.
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Affiliation(s)
- Michael Dare Asemoloye
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
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Liew FJ, Schilling JS. High-efficiency methane capture by living fungi and dried fungal hyphae (necromass). JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:1467-1476. [PMID: 33118202 DOI: 10.1002/jeq2.20136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/19/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Fungi can hasten microbial degradation of hydrophobic compounds by enhancing capture and dissolution into biofilms. For methane (CH4 ) released from natural soils and agricultural systems, prokaryotes are ultimately responsible for oxidation and degradation; however, in many cases Henry's law of gas dissolution, not oxidation, is rate-limiting. Given that fungi can improve capture and bioremediation of other hydrophobic compounds (e.g., toluene), we tested fungi for CH4 capture. We used a batch system of CH4 -flooded vials to screen candidate fungi. We found 79% removal efficiency by Ganoderma lucidum relative to activated carbon. In a follow-up, we found comparable efficiency in other Ganoderma species (G. applanatum, G. meredithae). However, these efficiency gains by Ganoderma species could not be sustained when inoculated wood substrates were placed in "live" soils. Substrates colonized naturally, without preinoculations, performed similarly to those deployed with (native) test strains, likely because inoculated fungi were outcompeted and displaced by native colonizers. Instead of rescreening using more combative fungi, we tested an alternative way to present fungi with high single-strain efficiencies for filtration: in dried form as dead biomass (necromass). In dried biomass trials, dried G. lucidum biomass performed better than when testing living biomass, again with the highest strain-specific removal efficiencies (84% of activated carbon). These results demonstrate the potential for G. lucidum, commonly used in biomaterial production, in a variety of indoor and outdoor biofiltration scenarios. It also implies an overlooked, potentially large role for fungi and their soil necromass in capturing and reducing CH4 emissions from soils in nature.
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Affiliation(s)
- Feng Jin Liew
- Dep. of Bioproducts and Biosystems Engineering, Univ. of Minnesota, 2004 Folwell Ave, Saint Paul, MN, 55108, USA
| | - Jonathan S Schilling
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, 1500 Gortner Ave., Saint Paul, MN, 55108, USA
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11
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Mäkelä MR, Hildén K, Kowalczyk JE, Hatakka A. Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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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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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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14
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Jurak E, Suzuki H, van Erven G, Gandier JA, Wong P, Chan K, Ho CY, Gong Y, Tillier E, Rosso MN, Kabel MA, Miyauchi S, Master ER. Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. BMC Genomics 2018; 19:815. [PMID: 30424733 PMCID: PMC6234650 DOI: 10.1186/s12864-018-5210-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
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Affiliation(s)
- E Jurak
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Department of Aquatic Biotechnology and Bioproduct Engineering, Groningen, The Netherlands
| | - H Suzuki
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - G van Erven
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - J A Gandier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - P Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - K Chan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - C Y Ho
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Y Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - E Tillier
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - M-N Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - M A Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - S Miyauchi
- Laboratory of Excellence ARBRE, INRA, Nancy, Lorraine, France.,Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - E R Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
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15
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Naresh Kumar M, Ravikumar R, Kirupa Sankar M, Thenmozhi S. New insight into the effect of fungal mycelia present in the bio-pretreated paddy straw on their enzymatic saccharification and optimization of process parameters. BIORESOURCE TECHNOLOGY 2018; 267:291-302. [PMID: 30029174 DOI: 10.1016/j.biortech.2018.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/30/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Assessment of Pleurotus florida efficiency on paddy straw pretreatment and optimization of saccharification parameters were studied. P. florida growth was monitored by the estimation of fungal cell wall component (glucosamine). The control bio-pretreatment sample showed high glucosamine content by 397 mg/g in 28 days of incubation. But, the Inhibitor Mediated Biological (IMB) Pretreatment showed 29% lower result due to the inhibition of cellulase enzyme limits mycelial penetration rate inside the paddy straw. Fungal components present inside the pretreated straw renders nonspecific interactions with the hydrolytic enzymes during saccharification process and reducing the hydrolysis efficiency. IMB pretreated paddy straw showed maximum saccharification efficiency up to 75.3% with optimized condition (Biomass loading- 10% (w/v), Enzyme loading- 20 FPU/g and saccharification time - 72 h) than control pretreatment sample. Thus, the study brings out new insight into the effect of fungal residues inside the bio-pretreated paddy straw during enzymatic saccharification to improve the efficiency.
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Affiliation(s)
- Manickam Naresh Kumar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
| | - Rajarathinam Ravikumar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India.
| | - Muthuvelu Kirupa Sankar
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
| | - Senniyappan Thenmozhi
- Bioenergy Research Laboratory, Department of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, TN, India
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16
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Ćilerdžić J, Galić M, Ivanović Ž, Brčeski I, Vukojević J, Stajić M. Stimulation of Wood Degradation by Daedaleopsis confragosa and D. tricolor. Appl Biochem Biotechnol 2018; 187:1371-1383. [PMID: 30229433 DOI: 10.1007/s12010-018-2884-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/09/2018] [Indexed: 11/25/2022]
Abstract
Biological pretreatment of the lignocellulosic residues, in which white-rot fungi have a crucial role, has many advantages compared to the chemical, physical, and physico-chemical methods of delignification and therefore attracts increasing scientific attention. Regarding the fact that properties and capacities of the ligninolytic enzymes of Daedaleopsis spp. are still unknown, the aim of this study was to research how nitrogen sources and inducers affect the potential of Daedaleopsis confragosa and Daedaleopsis tricolor to degrade cherry sawdust. NH4NO3, (NH4)2SO4, and peptone were tested as nitrogen sources, while veratryl alcohol, p-anisidine, vanillic acid, and phenylmethylsulfonyl fluoride were the studied inducers. As Mn-dependent peroxidase and laccase were the leader enzymes and cherry sawdust/peptone medium the best stimulator of their activities, the effect of inducers on delignification potential of these species was studied during fermentation of that substrate. Veratryl alcohol was the best stimulator of laccase and phenylmethylsulfonyl fluoride of Mn-dependent peroxidase activity (27,610.0 and 1338.4 U/L, respectively). These inducers also increased cherry sawdust delignification selectivity, particularly in D. tricolor in the presence of phenylmethylsulfonyl fluoride (lignin:hemicellulose:cellulose = 32.1%:0.9%:11.7%). Owing to the presented results, studied species could have an important role in the phase of lignocellulose pretreatment in various biotechnological processes.
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Affiliation(s)
- Jasmina Ćilerdžić
- Faculty of Biology, University of Belgrade, Takovska 43, Belgrade, 11000, Serbia.
| | - Milica Galić
- Faculty of Biology, University of Belgrade, Takovska 43, Belgrade, 11000, Serbia
| | - Žarko Ivanović
- Institute for Plant Protection and Environment, Teodora Drajzera 9, Belgrade, 11000, Serbia
| | - Ilija Brčeski
- Faculty of Chemistry, University of Belgrade, Studentski Trg 12-16, Belgrade, 11000, Serbia
| | - Jelena Vukojević
- Faculty of Biology, University of Belgrade, Takovska 43, Belgrade, 11000, Serbia
| | - Mirjana Stajić
- Faculty of Biology, University of Belgrade, Takovska 43, Belgrade, 11000, Serbia
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17
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Wu B, Gaskell J, Held BW, Toapanta C, Vuong T, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola. Appl Environ Microbiol 2018; 84:e00991-18. [PMID: 29884757 PMCID: PMC6070754 DOI: 10.1128/aem.00991-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/03/2018] [Indexed: 12/20/2022] Open
Abstract
Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jill Gaskell
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Cristina Toapanta
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thu Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Steven Ahrendt
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - David S Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
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18
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Houtman CJ, Maligaspe E, Hunt CG, Fernández-Fueyo E, Martínez AT, Hammel KE. Fungal lignin peroxidase does not produce the veratryl alcohol cation radical as a diffusible ligninolytic oxidant. J Biol Chem 2018; 293:4702-4712. [PMID: 29462790 DOI: 10.1074/jbc.ra117.001153] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Indexed: 11/06/2022] Open
Abstract
Peroxidases are considered essential agents of lignin degradation by white-rot basidiomycetes. However, low-molecular-weight oxidants likely have a primary role in lignin breakdown because many of these fungi delignify wood before its porosity has sufficiently increased for enzymes to infiltrate. It has been proposed that lignin peroxidases (LPs, EC 1.11.1.14) fulfill this role by oxidizing the secreted fungal metabolite veratryl alcohol (VA) to its aryl cation radical (VA+•), releasing it to act as a one-electron lignin oxidant within woody plant cell walls. Here, we attached the fluorescent oxidant sensor BODIPY 581/591 throughout beads with a nominal porosity of 6 kDa and assessed whether peroxidase-generated aryl cation radical systems could oxidize the beads. As positive control, we used the 1,2,4,5-tetramethoxybenzene (TMB) cation radical, generated from TMB by horseradish peroxidase. This control oxidized the beads to depths that increased with the amount of oxidant supplied, ultimately resulting in completely oxidized beads. A reaction-diffusion computer model yielded oxidation profiles that were within the 95% confidence intervals for the data. By contrast, bead oxidation caused by VA and the LPA isozyme of Phanerochaete chrysosporium was confined to a shallow shell of LP-accessible volume at the bead surface, regardless of how much oxidant was supplied. This finding contrasted with the modeling results, which showed that if the LP/VA system were to release VA+•, it would oxidize the bead interiors. We conclude that LPA releases insignificant quantities of VA+• and that a different mechanism produces small ligninolytic oxidants during white rot.
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Affiliation(s)
- Carl J Houtman
- United States Forest Products Laboratory, Madison, Wisconsin 53726
| | - Eranda Maligaspe
- United States Forest Products Laboratory, Madison, Wisconsin 53726
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Kenneth E Hammel
- United States Forest Products Laboratory, Madison, Wisconsin 53726; Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706.
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19
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Abstract
The global push toward an efficient and economical biobased economy has driven research to develop more cost-effective applications for the entirety of plant biomass, including lignocellulosic crops. As discussed elsewhere (Karlsson M, Atanasova L, Funck Jensen D, Zeilinger S, in Heitman J et al. [ed], Tuberculosis and the Tubercle Bacillus, 2nd ed, in press), significant progress has been made in the use of polysaccharide fractions from lignocellulose, cellulose, and various hemicellulose types. However, developing processes for use of the lignin fraction has been more challenging. In this chapter, we discuss characteristics of lignolytic enzymes and the fungi that produce them as well as potential and current uses of lignin-derived products.
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20
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Nishimura H, Yamaguchi D, Watanabe T. Cerebrosides, extracellular glycolipids secreted by the selective lignin-degrading fungus Ceriporiopsis subvermispora. Chem Phys Lipids 2017; 203:1-11. [PMID: 28062355 DOI: 10.1016/j.chemphyslip.2016.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 12/28/2016] [Accepted: 12/30/2016] [Indexed: 10/20/2022]
Abstract
Ceriporiopsis subvermispora is a selective white-rot fungus that degrades lignin at a site far from the hyphae and extracellular enzymes, without intensive damage to the cellulose. In selective ligninolysis, low molecular mass metabolites play a principal role and amphipathic substances are involved to control the degradation and transport of hydrophobic aromatic molecules, including lignin and lipids; however, secretion of the amphipathic substances by this fungus has not been well understood, except for alk(en)yl itaconates called ceriporic acids, which have a weak amphiphilicity. Herein, we report for the first time that the fungus secretes cerebrosides that are classified as glycosphingolipids. By using liquid chromatography electron spray ionization mass spectrometry (LC-ESI-MS) and nuclear magnetic resonance (NMR) spectroscopy coupled with stable isotope feeding experiments with 13C-glucose and 15N-ammonium sulfate, the cerebrosides were determined to be N-hydroxyoctadecanoyl-1-O-β-d-glucopyranosyl-4E,8E-sphingadienine, N-hydroxyoctadecanoyl-1-O-β-d-glucopyranosyl-4E,8Z-sphingadienine, and N-hydroxyoctadecanoyl-1-O-β-d-glucopyranosyl-9-methyl-4E,8E-sphingadienine. The cerebrosides are strong amphipathic substances and potential metabolites for regulating difference and symbiosis within the microbial community.
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Affiliation(s)
- Hiroshi Nishimura
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, Japan.
| | - Daisuke Yamaguchi
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Takashi Watanabe
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, Japan
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21
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Bi R, Berglund J, Vilaplana F, McKee LS, Henriksson G. The degree of acetylation affects the microbial degradability of mannans. Polym Degrad Stab 2016. [DOI: 10.1016/j.polymdegradstab.2016.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Houtman CJ, Kitin P, Houtman JCD, Hammel KE, Hunt CG. Acridine Orange Indicates Early Oxidation of Wood Cell Walls by Fungi. PLoS One 2016; 11:e0159715. [PMID: 27454126 PMCID: PMC4959780 DOI: 10.1371/journal.pone.0159715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/06/2016] [Indexed: 11/18/2022] Open
Abstract
Colonization of wood blocks by brown and white rot fungi rapidly resulted in detectable wood oxidation, as shown by a reduced phloroglucinol response, a loss of autofluorescence, and acridine orange (AO) staining. This last approach is shown to provide a novel method for identifying wood oxidation. When lignin was mildly oxidized, the association between AO and lignin was reduced such that stained wood sections emitted less green light during fluorescence microscopy. This change was detectable after less than a week, an interval that past work has shown to be too short for significant delignification of wood. Although fungal hyphae were observed in only a few wood lumina, oxidation was widespread, appearing relatively uniform over regions several hundred micrometers from the hyphae. This observation suggests that both classes of fungi release low molecular weight mild oxidants during the first few days of colonization.
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Affiliation(s)
- Carl J. Houtman
- USDA Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin, United States of America
- * E-mail:
| | - Peter Kitin
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jon C. D. Houtman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Kenneth E. Hammel
- USDA Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christopher G. Hunt
- USDA Forest Service, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, Wisconsin, United States of America
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Schneider WDH, Gonçalves TA, Uchima CA, Couger MB, Prade R, Squina FM, Dillon AJP, Camassola M. Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:66. [PMID: 26989443 PMCID: PMC4794826 DOI: 10.1186/s13068-016-0476-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/02/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND The enzymatic degradation of lignocellulosic materials by fungal enzyme systems has been extensively studied due to its effectiveness in the liberation of fermentable sugars for bioethanol production. Recently, variants of the fungus Penicillium echinulatum have been described as a great producer of cellulases and considered a promising strain for the bioethanol industry. RESULTS Penicillium echinulatum, wild-type 2HH and its mutant strain S1M29, were grown on four different carbon sources: cellulose, sugar cane bagasse pretreated by steam explosion (SCB), glucose, and glycerol for 120 h. Samples collected at 24, 96, and 120 h were used for enzymatic measurement, and the 96-h one was also used for secretome analysis by 1D-PAGE LC-MS/MS. A total of 165 proteins were identified, and more than one-third of these proteins belong to CAZy families. Glycosyl hydrolases (GH) are the most abundant group, being represented in larger quantities by GH3, 5, 17, 43, and 72. Cellobiohydrolases, endoglucanases, β-glycosidases, xylanases, β-xylosidases, and mannanases were found, and in minor quantities, pectinases, ligninases, and amylases were also found. Swollenin and esterases were also identified. CONCLUSIONS Our study revealed differences in the two strains of P. echinulatum in several aspects in which the mutation improved the production of enzymes related to lignocellulosic biomass deconstruction. Considering the spectral counting analysis, the mutant strain S1M29 was more efficient in the production of enzymes involved in cellulose and hemicellulose degradation, despite having a nearly identical CAZy enzymatic repertoire. Moreover, S1M29 secretes more quantities of protein on SCB than on cellulose, relevant information when considering the production of cellulases using raw materials at low cost. Glucose, and especially glycerol, were used mainly for the production of amylases and ligninases.
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Affiliation(s)
- Willian Daniel Hahn Schneider
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Thiago Augusto Gonçalves
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
- />Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo Brazil
| | - Cristiane Akemi Uchima
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Matthew Brian Couger
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Rolf Prade
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Fabio Marcio Squina
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Aldo José Pinheiro Dillon
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Marli Camassola
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
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Hori C, Cullen D. Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood. Appl Environ Microbiol 2015; 81:7802-12. [PMID: 26341198 DOI: 10.1128/aem.02064-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022] Open
Abstract
Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe(3+) reduction, and oxidase-catalyzed H2O2 production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis.
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DONALDSON L, KROESE H, HILL S, FRANICH R. Detection of wood cell wall porosity using small carbohydrate molecules and confocal fluorescence microscopy. J Microsc 2015; 259:228-36. [DOI: 10.1111/jmi.12257] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/20/2015] [Indexed: 11/29/2022]
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Mäkelä MR, Marinović M, Nousiainen P, Liwanag AJM, Benoit I, Sipilä J, Hatakka A, de Vries RP, Hildén KS. Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass. ADVANCES IN APPLIED MICROBIOLOGY 2015; 91:63-137. [PMID: 25911233 DOI: 10.1016/bs.aambs.2014.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The biological conversion of plant lignocellulose plays an essential role not only in carbon cycling in terrestrial ecosystems but also is an important part of the production of second generation biofuels and biochemicals. The presence of the recalcitrant aromatic polymer lignin is one of the major obstacles in the biofuel/biochemical production process and therefore microbial degradation of lignin is receiving a great deal of attention. Fungi are the main degraders of plant biomass, and in particular the basidiomycete white rot fungi are of major importance in converting plant aromatics due to their ability to degrade lignin. However, the aromatic monomers that are released from lignin and other aromatic compounds of plant biomass are toxic for most fungi already at low levels, and therefore conversion of these compounds to less toxic metabolites is essential for fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting aromatic monomers. In this review we provide an overview of the aromatic components of plant biomass, and their release and conversion by fungi. Finally, we will summarize the applications of fungal systems related to plant aromatics.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mila Marinović
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Department of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, Helsinki, Finland
| | - April J M Liwanag
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Jussi Sipilä
- Department of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, Helsinki, Finland
| | - Annele Hatakka
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Kristiina S Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Zeng J, Singh D, Gao D, Chen S. Effects of lignin modification on wheat straw cell wall deconstruction by Phanerochaete chrysosporium. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:161. [PMID: 25516769 PMCID: PMC4266972 DOI: 10.1186/s13068-014-0161-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/16/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND A key focus in sustainable biofuel research is to develop cost-effective and energy-saving approaches to increase saccharification of lignocellulosic biomass. Numerous efforts have been made to identify critical issues in cellulose hydrolysis. Aerobic fungal species are an integral part of the carbon cycle, equip the hydrolytic enzyme consortium, and provide a gateway for understanding the systematic degradation of lignin, hemicelluloses, and cellulose. This study attempts to reveal the complex biological degradation process of lignocellulosic biomass by Phanerochaete chrysosporium in order to provide new knowledge for the development of energy-efficient biorefineries. RESULTS In this study, we evaluated the performance of a fungal biodegradation model, Phanerochaete chrysosporium, in wheat straw through comprehensive analysis. We isolated milled straw lignin and cellulase enzyme-treated lignin from fungal-spent wheat straw to determine structural integrity and cellulase absorption isotherms. The results indicated that P. chrysosporium increased the total lignin content in residual biomass and also increased the cellulase adsorption kinetics in the resulting lignin. The binding strength increased from 117.4 mL/g to 208.7 mL/g in milled wood lignin and from 65.3 mL/g to 102.4 mL/g in cellulase enzyme lignin. A detailed structural dissection showed a reduction in the syringyl lignin/guaiacyl lignin ratio and the hydroxycinnamate/lignin ratio as predominant changes in fungi-spent lignin by heteronuclear single quantum coherence spectroscopy. CONCLUSION P. chrysosporium shows a preference for degradation of phenolic terminals without significantly destroying other lignin components to unzip carbohydrate polymers. This is an important step in fungal growth on wheat straw. The phenolics presumably locate at the terminal region of the lignin moiety and/or link with hemicellulose to form the lignin-carbohydrate complex. Findings may inform the development of a biomass hydrolytic enzyme combination to enhance lignocellulosic biomass hydrolysis and modify the targets in plant cell walls.
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Affiliation(s)
- Jijiao Zeng
- Department of Biological Systems Engineering, Bioprocessing and Bioproduct Engineering Laboratory (BBEL), Washington State University, L.J. Smith 213, Pullman, Washington 99163 USA
| | - Deepak Singh
- Department of Biological Systems Engineering, Bioprocessing and Bioproduct Engineering Laboratory (BBEL), Washington State University, L.J. Smith 213, Pullman, Washington 99163 USA
| | - Difeng Gao
- Department of Biological Systems Engineering, Bioprocessing and Bioproduct Engineering Laboratory (BBEL), Washington State University, L.J. Smith 213, Pullman, Washington 99163 USA
| | - Shulin Chen
- Department of Biological Systems Engineering, Bioprocessing and Bioproduct Engineering Laboratory (BBEL), Washington State University, L.J. Smith 213, Pullman, Washington 99163 USA
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Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes. Fungal Genet Biol 2014; 72:124-130. [DOI: 10.1016/j.fgb.2014.05.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 11/20/2022]
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A highly diastereoselective oxidant contributes to Ligninolysis by the white rot basidiomycete Ceriporiopsis subvermispora. Appl Environ Microbiol 2014; 80:7536-44. [PMID: 25261514 DOI: 10.1128/aem.02111-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The white rot basidiomycete Ceriporiopsis subvermispora delignifies wood selectively and has potential biotechnological applications. Its ability to remove lignin before the substrate porosity has increased enough to admit enzymes suggests that small diffusible oxidants contribute to delignification. A key question is whether these unidentified oxidants attack lignin via single-electron transfer (SET), in which case they are expected to cleave its propyl side chains between Cα and Cβ and to oxidize the threo-diastereomer of its predominating β-O-4-linked structures more extensively than the corresponding erythro-diastereomer. We used two-dimensional solution-state nuclear magnetic resonance (NMR) techniques to look for changes in partially biodegraded lignin extracted from spruce wood after white rot caused by C. subvermispora. The results showed that (i) benzoic acid residues indicative of Cα-Cβ cleavage were the major identifiable truncated structures in lignin after decay and (ii) depletion of β-O-4-linked units was markedly diastereoselective with a threo preference. The less selective delignifier Phanerochaete chrysosporium also exhibited this diastereoselectivity on spruce, and a P. chrysosporium lignin peroxidase operating in conjunction with the P. chrysosporium metabolite veratryl alcohol did likewise when cleaving synthetic lignin in vitro. However, C. subvermispora was significantly more diastereoselective than P. chrysosporium or lignin peroxidase-veratryl alcohol. Our results show that the ligninolytic oxidants of C. subvermispora are collectively more diastereoselective than currently known fungal ligninolytic oxidants and suggest that SET oxidation is one of the chemical mechanisms involved.
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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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Akin DE. Linen most useful: perspectives on structure, chemistry, and enzymes for retting flax. ISRN BIOTECHNOLOGY 2012; 2013:186534. [PMID: 25969769 PMCID: PMC4403609 DOI: 10.5402/2013/186534] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/07/2012] [Indexed: 11/23/2022]
Abstract
The components of flax (Linum usitatissimum) stems are described and illustrated, with reference to the anatomy and chemical makeup and to applications in processing and products. Bast fiber, which is a major economic product of flax along with linseed and linseed oil, is described with particular reference to its application in textiles, composites, and specialty papers. A short history of retting methods, which is the separation of bast fiber from nonfiber components, is presented with emphasis on water retting, field retting (dew retting), and experimental methods. Past research on enzyme retting, particularly by the use of pectinases as a potential replacement for the current commercial practice of field retting, is reviewed. The importance and mechanism of Ca2+ chelators with pectinases in retting are described. Protocols are provided for retting of both fiber-type and linseed-type flax stems with different types of pectinases. Current and future applications are listed for use of a wide array of enzymes to improve processed fibers and blended yarns. Finally, potential lipid and aromatic coproducts derived from the dust and shive waste streams of fiber processing are indicated.
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Affiliation(s)
- Danny E Akin
- Russell Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30606, USA
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35
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Characterization of extracellular lignocellulolytic enzymes of Coniochaeta sp. during corn stover bioconversion. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fungal pretreatment of lignocellulosic biomass. Biotechnol Adv 2012; 30:1447-57. [DOI: 10.1016/j.biotechadv.2012.03.003] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/25/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
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Babič J, Likozar B, Pavko A. Optimization of ligninolytic enzyme activity and production rate with Ceriporiopsis subvermispora for application in bioremediation by varying submerged media composition and growth immobilization support. Int J Mol Sci 2012; 13:11365-11384. [PMID: 23109859 PMCID: PMC3472751 DOI: 10.3390/ijms130911365] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/23/2012] [Accepted: 09/05/2012] [Indexed: 11/21/2022] Open
Abstract
Response surface methodology (central composite design of experiments) was employed to simultaneously optimize enzyme production and productivities of two ligninolytic enzymes produced by Ceriporiopsis subvermispora. Concentrations of glucose, ammonium tartrate and Polysorbate 80 were varied to establish the optimal composition of liquid media (OLM), where the highest experimentally obtained activities and productivities were 41 U L−1 and 16 U L−1 day−1 for laccase (Lac), and 193 U L−1 and 80 U L−1 day−1 for manganese peroxidase (MnP). Considering culture growth in OLM on various types of immobilization support, the best results were obtained with 1 cm beech wood cubes (BWCM). Enzyme activities in culture filtrate were 152 U L−1 for Lac and 58 U L−1 for MnP, since the chemical composition of this immobilization material induced higher Lac activity. Lower enzyme activities were obtained with polyurethane foam. Culture filtrates of OLM and BWCM were applied for dye decolorization. Remazol Brilliant Blue R (RBBR) was decolorized faster and more efficiently than Copper(II)phthalocyanine (CuP) with BWCM (80% and 60%), since Lac played a crucial role. Decolorization of CuP was initially faster than that of RBBR, due to higher MnP activities in OLM. The extent of decolorization after 14 h was 60% for both dyes.
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Affiliation(s)
- Janja Babič
- Chair of Chemical, Biochemical and Environmental Engineering, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia; E-Mail:
| | - Blaž Likozar
- Laboratory of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; E-Mail:
| | - Aleksander Pavko
- Chair of Chemical, Biochemical and Environmental Engineering, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +386-1-24-19-506; Fax: +386-1-24-19-530
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Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A 2012; 109:5458-63. [PMID: 22434909 DOI: 10.1073/pnas.1119912109] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.
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Arantes V, Jellison J, Goodell B. Peculiarities of brown-rot fungi and biochemical Fenton reaction with regard to their potential as a model for bioprocessing biomass. Appl Microbiol Biotechnol 2012; 94:323-38. [DOI: 10.1007/s00253-012-3954-y] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/24/2022]
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Adav SS, Chao LT, Sze SK. Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol Cell Proteomics 2012; 11:M111.012419. [PMID: 22355001 DOI: 10.1074/mcp.m111.012419] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Trichoderma reesei is a mesophilic, filamentous fungus, and it is a major industrial source of cellulases, but its lignocellulolytic protein expressions on lignocellulosic biomass are poorly explored at present. The extracellular proteins secreted by T. reesei QM6a wild-type and hypercellulolytic mutant Rut C30 grown on natural lignocellulosic biomasses were explored using a quantitative proteomic approach with 8-plex high throughput isobaric tags for relative and absolute quantification (iTRAQ) and analyzed by liquid chromatography tandem mass spectrometry. We quantified 230 extracellular proteins, including cellulases, hemicellulases, lignin-degrading enzymes, proteases, protein-translocating transporter, and hypothetical proteins. Quantitative iTRAQ results suggested that the expressions and regulations of these lignocellulolytic proteins in the secretome of T. reesei wild-type and mutant Rut C30 were dependent on both nature and complexity of different lignocellulosic carbon sources. Therefore, we discuss here the essential lignocellulolytic proteins for designing an enzyme mixture for optimal lignocellulosic biomass hydrolysis.
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Affiliation(s)
- Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, Singapore
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Quantitative proteomic analysis of lignocellulolytic enzymes by Phanerochaete chrysosporium on different lignocellulosic biomass. J Proteomics 2012; 75:1493-504. [DOI: 10.1016/j.jprot.2011.11.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/29/2011] [Accepted: 11/17/2011] [Indexed: 11/23/2022]
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Mode of coniferous wood decay by the white rot fungus Phanerochaete carnosa as elucidated by FTIR and ToF-SIMS. Appl Microbiol Biotechnol 2012; 94:1303-11. [DOI: 10.1007/s00253-011-3830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 12/03/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
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Nishimura H, Sasaki M, Seike H, Nakamura M, Watanabe T. Alkadienyl and alkenyl itaconic acids (ceriporic acids G and H) from the selective white-rot fungus Ceriporiopsis subvermispora: a new class of metabolites initiating ligninolytic lipid peroxidation. Org Biomol Chem 2012; 10:6432-42. [DOI: 10.1039/c2ob25415h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nishimura H, Murayama K, Watanabe T, Honda Y, Watanabe T. Diverse rare lipid-related metabolites including ω-7 and ω-9 alkenylitaconic acids (ceriporic acids) secreted by a selective white rot fungus, Ceriporiopsis subvermispora. Chem Phys Lipids 2012; 165:97-104. [DOI: 10.1016/j.chemphyslip.2011.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/22/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022]
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Abstract
Over the past three decades, the activities of four kinds of enzyme have been purported to furnish the mechanistic foundations for macromolecular lignin depolymerization in decaying plant cell walls. The pertinent fungal enzymes comprise lignin peroxidase (with a relatively high redox potential), manganese peroxidase, an alkyl aryl etherase, and laccase. The peroxidases and laccase, but not the etherase, are expressed extracellularly by white-rot fungi. A number of these microorganisms exhibit a marked preference toward lignin in their degradation of lignocellulose. Interestingly, some white-rot fungi secrete both kinds of peroxidase but no laccase, while others that are equally effective express extracellular laccase activity but no peroxidases. Actually, none of these enzymes has been reported to possess significant depolymerase activity toward macromolecular lignin substrates that are derived with little chemical modification from the native biopolymer. Here, the assays commonly employed for monitoring the traditional fungal peroxidases, alkyl aryl etherase, and laccase are described in their respective contexts. A soluble native polymeric substrate that can be isolated directly from a conventional milled-wood lignin preparation is characterized in relation to its utility in next-generation lignin-depolymerase assays.
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Affiliation(s)
- Yi-ru Chen
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, USA
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Epoxy ceriporic acid produced by selective lignin-degrading fungus Ceriporiopsis subvermispora. Chem Phys Lipids 2011; 164:707-12. [PMID: 21864516 DOI: 10.1016/j.chemphyslip.2011.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/13/2011] [Accepted: 07/22/2011] [Indexed: 11/23/2022]
Abstract
Ceriporiopsis subvermispora is a selective white rot basidiomycete which degrades lignin in wood at a distance far from enzymes. Low molecular mass metabolites play a central role in the oxidative degradation of lignin. To understand the unique wood-decaying mechanism, we surveyed the oxidized derivatives of ceriporic acids (alk(en)ylitaconic acids) produced by C. subvermispora using high-resolution liquid chromatography multiple-stage mass spectrometry (HR-LC/MS(n)). The analysis of the precursor and product ions from the extract suggested that an epoxidized derivative of ceriporic acid is produced by the fungus. To identify the new metabolite, an authentic compound of ceriporic acid epoxide was synthesized in vitro by reacting (R)-3-[(Z)-hexadec-7-enyl]-itaconic acid (ceriporic acid C) with m-chloroperbenzoic acid. The precursor and product ions from the natural metabolite and authentic epoxide were identical and distinguishable from those of hydroxy and hydroperoxy derivatives after reduction with NaBD(4). Feeding experiments with [U-(13)C]-glucose, 99% and the subsequent analyses of the first and second generation product ions demonstrated that the oxidized ceriporic acid was (R)-3-(7,8-epoxy-hexadecyl)-itaconic acid. To our knowledge, this study is the first to report that natural alkylitaconic acid bears an epoxy group on its side chain.
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Co-cultured Production of Lignin-Modifying Enzymes with White-Rot Fungi. Appl Biochem Biotechnol 2011; 165:700-18. [DOI: 10.1007/s12010-011-9289-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 05/16/2011] [Indexed: 10/18/2022]
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Ohashi Y, Uno Y, Amirta R, Watanabe T, Honda Y, Watanabe T. Alkoxyl- and carbon-centered radicals as primary agents for degrading non-phenolic lignin-substructure model compounds. Org Biomol Chem 2011; 9:2481-91. [DOI: 10.1039/c0ob00797h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Lignocellulosic polysaccharides and lignin degradation by wood decay fungi: the relevance of nonenzymatic Fenton-based reactions. J Ind Microbiol Biotechnol 2010; 38:541-55. [DOI: 10.1007/s10295-010-0798-2] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 07/22/2010] [Indexed: 11/26/2022]
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50
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Wan C, Li Y. Microbial delignification of corn stover by Ceriporiopsis subvermispora for improving cellulose digestibility. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.04.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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