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Sánchez-Ruiz MI, Santillana E, Linde D, Romero A, Martínez AT, Ruiz-Dueñas FJ. Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:74. [PMID: 38824538 PMCID: PMC11144326 DOI: 10.1186/s13068-024-02517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure-function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule. RESULTS Two MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD-referred to as Ape-MnP1 and Cst-MnP1, respectively-were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation. CONCLUSIONS Understanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure-function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.
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Affiliation(s)
- María Isabel Sánchez-Ruiz
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Elena Santillana
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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Castaño JD, El Khoury IV, Goering J, Evans JE, Zhang J. Unlocking the distinctive enzymatic functions of the early plant biomass deconstructive genes in a brown rot fungus by cell-free protein expression. Appl Environ Microbiol 2024; 90:e0012224. [PMID: 38567954 PMCID: PMC11205865 DOI: 10.1128/aem.00122-24] [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: 01/23/2024] [Accepted: 03/10/2024] [Indexed: 05/22/2024] Open
Abstract
Saprotrophic fungi that cause brown rot of woody biomass evolved a distinctive mechanism that relies on reactive oxygen species (ROS) to kick-start lignocellulosic polymers' deconstruction. These ROS agents are generated at incipient decay stages through a series of redox relays that shuttle electrons from fungus's central metabolism to extracellular Fenton chemistry. A list of genes has been suggested encoding the enzyme catalysts of the redox processes involved in ROS's function. However, navigating the functions of the encoded enzymes has been challenging due to the lack of a rapid method for protein synthesis. Here, we employed cell-free expression system to synthesize four redox or degradative enzymes, which were identified, by transcriptomic data, as conserved players of the ROS oxidation phase across brown rot fungal species. All four enzymes were successfully expressed and showed activities that enable confident assignment of function, namely, benzoquinone reductase (BQR), ferric reductase, α-L-arabinofuranosidase (ABF), and heme-thiolate peroxidase (HTP). Detailed analysis of their catalytic features within the context of brown rot environments allowed us to interpret their roles during ROS-driven wood decomposition. Specifically, we validated the functions of BQR as the driver redox enzyme of Fenton cycles and reconstructed its interactions with the co-occurring HTP or laccase and ABF. Taken together, this research demonstrated that the cell-free expression platform is adequate for synthesizing functional fungal enzymes and provided an alternative route for the rapid characterization of fungal proteins, escalating our understanding of the distinctive biocatalyst system for plant biomass conversion.IMPORTANCEBrown rot fungi are efficient wood decomposers in nature, and their unique degradative systems harbor untapped catalysts pursued by the biorefinery and bioremediation industries. While the use of "omics" platforms has recently uncovered the key "oxidative-hydrolytic" mechanisms that allow these fungi to attack lignocellulose, individual protein characterization is lagging behind due to the lack of a robust method for rapid synthesis of crucial fungal enzymes. This work delves into the studies of biochemical functions of brown rot enzymes using a rapid, cell-free expression platform, which allowed the successful depictions of enzymes' catalytic features, their interactions with Fenton chemistry, and their roles played during the incipient stage of brown rot when fungus sets off the reactive oxygen species for oxidative degradation. We expect this research could illuminate cell-free protein expression system's use to fulfill the increasing need for functional studies of fungal enzymes, advancing the discoveries of novel biomass-converting catalysts.
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Affiliation(s)
- Jesus D. Castaño
- Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, USA
| | - Irina V. El Khoury
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Joshua Goering
- Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, USA
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Jiwei Zhang
- Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, USA
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Molinelli L, Drula E, Gaillard JC, Navarro D, Armengaud J, Berrin JG, Tron T, Tarrago L. Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay. Appl Environ Microbiol 2024; 90:e0193123. [PMID: 38376171 PMCID: PMC10952391 DOI: 10.1128/aem.01931-23] [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: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.
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Affiliation(s)
- Lise Molinelli
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Elodie Drula
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - David Navarro
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean-Guy Berrin
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Thierry Tron
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
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Zhang X, Feng Q, Cao J, Liu W, Qin Y, Zhu M, Han T. Grazing practices affect soil microbial networks but not diversity and composition in alpine meadows of northeastern Qinghai-Tibetan plateau. ENVIRONMENTAL RESEARCH 2023; 235:116656. [PMID: 37451580 DOI: 10.1016/j.envres.2023.116656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Livestock grazing is the primary practice in alpine meadows and can alter soil microbiomes, which is critical for ecosystem functions and services. Seasonal grazing (SG) and continuous grazing (CG) are two kinds of different grazing practices that dominate alpine meadows on the Qinghai-Tibetan Plateau (QTP), and how they affect soil microbial communities remains in-depth exploration. The present study was conducted to investigate the effects of different grazing practices (i.e., SG and CG) on the diversity, composition, and co-occurrence networks of soil bacteria and fungi in QTP alpine meadows. Soil microbial α- and β-diversity showed no obvious difference between SG and CG grasslands. Grazing practices had little impact on soil microbial composition, except that the relative abundance of Proteobacteria and Ascomycota showed significant difference between SG and CG grasslands. Soil microbial networks were more complex and less stable in SG grasslands than that in CG grasslands, and the bacterial networks were more complex than fungal networks. Soil fungal diversity was more strongly correlated with environmental factors than bacteria, whereas both fungal and bacterial structures were mainly influenced by soil pH, total nitrogen, and ammonium nitrogen. These findings indicate that microbial associations are more sensitive to grazing practices than microbial diversity and composition, and that SG may be a better grazing practice for ecological benefits in alpine meadows.
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Affiliation(s)
- Xiaofang Zhang
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qi Feng
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Jianjun Cao
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou, 730070, China.
| | - Wei Liu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; Qilian Mountains Eco-Environment Research Center in Gansu Province, Lanzhou, 730000, China
| | - Yanyan Qin
- Qilian Mountains Eco-Environment Research Center in Gansu Province, Lanzhou, 730000, China; Key Laboratory of Land Surface Process and Climate Change in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Meng Zhu
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Tuo Han
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
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Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds. Int J Mol Sci 2023; 24:13115. [PMID: 37685920 PMCID: PMC10487439 DOI: 10.3390/ijms241713115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.
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Affiliation(s)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (K.V.M.); (O.S.S.); (T.V.F.)
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Valette N, Legout A, Goodell B, Alfredsen G, Auer L, Gelhaye E, Derrien D. Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zerva A, Siaperas R, Taxeidis G, Kyriakidi M, Vouyiouka S, Zervakis GI, Topakas E. Investigation of Abortiporus biennis lignocellulolytic toolbox, and the role of laccases in polystyrene degradation. CHEMOSPHERE 2023; 312:137338. [PMID: 36423718 DOI: 10.1016/j.chemosphere.2022.137338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
White-rot basidiomycetes are the only microorganisms able to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for degrading all lignocellulose constituents. Their enzymatic machinery makes them ideal for the discovery of novel enzymes with desirable properties. In the present work, Abortiporus biennis, a white-rot fungus, was studied in regard to its lignocellulolytic potential. Secretomics and biochemical analyses were employed to study the strain's enzymatic arsenal, after growth in corn stover cultures and xylose-based defined media. The results revealed the presence of all the necessary enzymatic activities for complete breakdown of biomass, while the prominent role of oxidative enzymes in the lignocellulolytic strategy of the strain became evident. Two novel laccases, AbiLac1 and AbiLac2, were isolated from the culture supernatant with ion-exchange chromatography. Characterization of purified laccases revealed their ability to oxidize a wide variety of phenolic and non-phenolic substrates. AbiLac1 was found to oxidize polystyrene powder, showing high depolymerization potential, based on radical chain scission mechanism as evidenced by molecular weight decrease. The results of the present study demonstrate the biotechnological potential of the unexplored enzymatic machinery of white-rot basidiomycetes, including the design of improved lignocellulolytic cocktails, as well as the degradation and/or valorization of plastic waste materials.
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Affiliation(s)
- Anastasia Zerva
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Romanos Siaperas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - George Taxeidis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Maria Kyriakidi
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Stamatina Vouyiouka
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855, Athens, Greece
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece.
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Shabaev AV, Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. Int J Mol Sci 2022; 23:ijms231810322. [PMID: 36142233 PMCID: PMC9499651 DOI: 10.3390/ijms231810322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins.
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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de Oliveira Júnior SD, Dos Santos Gouvêa PR, de Aguiar LVB, Pessoa VA, Dos Santos Cruz Costa CL, Chevreuil LR, Dedo BritoNascimento LB, Dos Santos ES, Sales-Campos C. Production of Lignocellulolytic Enzymes and Phenolic Compounds by Lentinus strigosus from the Amazon Using Solid-State Fermentation (SSF) of Guarana (Paullinia cupana) Residue. Appl Biochem Biotechnol 2022; 194:2882-2900. [PMID: 35286593 DOI: 10.1007/s12010-022-03851-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
The Amazon rainforest has a rich biodiversity, and studies of Basidiomycete fungi that have biomolecules of biotechnological interest are relevant. The use of lignocellulosic biomass in biotechnological processes proposes an alternative use, and also adds value to the material when employed in the bioconversion of agro-industrial waste. In this context, this study evaluate the production of lignocellulolytic enzymes (carboxymethylcellulases (CMCase), xylanase, pectinase, laccase) as well as phenolic compounds and proteases by solid-state fermentation (SSF) using the fungus Lentinus strigosus isolated from Amazon. The guarana (Paullinia cupana) residue was characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). SSF was carried out with 60% humidification of the residue, at 30 °C, for 10 days. The lignocellulosic biomass presented fragmented structures with irregular shapes and porosities, and was mainly constituted by cellulose (19.16%), hemicellulose (32.83%), and lignin (6.06%). During the SSF, significant values of CMCase (0.84 U/g) on the 8th day, xylanase (1.00 U/g) on the 7th day, pectinase (2.19 U/g) on the 6th day, laccase (176.23 U/mL) on the 5th day, phenolic compounds (10.27 μg/mL) on the 1st day, soluble proteins (0.08 mg/mL) on the 5th day, and protease (8.30 U/mL) on the 6th day were observed. In general, the agro-industrial residue used provided promising results as a viable alternative for use as a substrate in biotechnological processes.
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Affiliation(s)
| | - Paula Romenya Dos Santos Gouvêa
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil.,Post-Graduate Program in Biotechnology, Federal University of Amazonas (UFAM), Manaus, Amazonas, 69067-005, Brazil
| | - Lorena Vieira Bentolila de Aguiar
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil.,Post-Graduate Program in Biodiversity and Biotechnology of the BIONORTE, Amazonas State University (UEA), Manaus, Amazonas, 69065-001, Brazil
| | - Vitor Alves Pessoa
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil.,Post-Graduate Program in Biotechnology and Natural Resources, Amazonas State University (UEA), Manaus, Amazonas, 69065-001, Brazil
| | | | - Larissa Ramos Chevreuil
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil
| | - Larissa Batista Dedo BritoNascimento
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil.,Post-Graduate Program in Biotechnology, Federal University of Amazonas (UFAM), Manaus, Amazonas, 69067-005, Brazil
| | - Everaldo Silvino Dos Santos
- Laboratory of Biochemical Engineering, Chemical Engineering Department, Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, 59064-741, Brazil.
| | - Ceci Sales-Campos
- Edible Mushroom Cultivation Laboratory, National Institute for Amazonian Research (INPA), Manaus, Amazonas, 69067-375, Brazil
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Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
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Ahmad F, Yang GY, Liang SY, Zhou QH, Gaal HA, Mo JC. Multipartite symbioses in fungus-growing termites (Blattodea: Termitidae, Macrotermitinae) for the degradation of lignocellulose. INSECT SCIENCE 2021; 28:1512-1529. [PMID: 33236502 DOI: 10.1111/1744-7917.12890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Fungus-growing termites are among the most successful herbivorous animals and improve crop productivity and soil fertility. A range of symbiotic organisms can be found inside their nests. However, interactions of termites with these symbionts are poorly understood. This review provides detailed information on the role of multipartite symbioses (between termitophiles, termites, fungi, and bacteria) in fungus-growing termites for lignocellulose degradation. The specific functions of each component in the symbiotic system are also discussed. Based on previous studies, we argue that the enzymatic contribution from the host, fungus, and bacteria greatly facilitates the decomposition of complex polysaccharide plant materials. The host-termitophile interaction protects the termite nest from natural enemies and maintains the stability of the microenvironment inside the colony.
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Affiliation(s)
- Farhan Ahmad
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Entomology Section, Central Cotton Research Institute, Sakrand, Shaheed Benazirabad, Sindh, Pakistan
| | - Gui-Ying Yang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shi-You Liang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi-Huan Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hassan Ahmed Gaal
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Entomology, Faculty of Veterinary and Animal Husbandry, Somali National University, Mogadishu, Somalia
| | - Jian-Chu Mo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
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13
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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14
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Castaño JD, Zhou M, Schilling J. Towards an Understanding of Oxidative Damage in an α-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach. Appl Biochem Biotechnol 2021; 193:3287-3300. [PMID: 34125378 DOI: 10.1007/s12010-021-03594-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Trichoderma reesei is a "workhorse" fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on α-L-arabinofuranosidase, an enzyme important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render this enzyme inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of the protein when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized protein. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized protein, implying a less favorable reaction pathway. These results reveal the basis for loss of function in this carbohydrate active enzyme (CAZY) in the commercially relevant fungus T. reesei.
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Affiliation(s)
- Jesus D Castaño
- Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
- Marine and Coastal Research Institute, INVEMAR, Santa Marta, Colombia, 470006
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jonathan Schilling
- Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
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15
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Kölle M, Crivelente Horta MA, Benz JP, Pilgård A. Comparative Transcriptomics During Brown Rot Decay in Three Fungi Reveals Strain-Specific Degradative Strategies and Responses to Wood Acetylation. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:701579. [PMID: 37744145 PMCID: PMC10512373 DOI: 10.3389/ffunb.2021.701579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/12/2021] [Indexed: 09/26/2023]
Abstract
Brown rot fungi degrade wood in a two-step process in which enzymatic hydrolysis is preceded by an oxidative degradation phase. While a detailed understanding of the molecular processes during brown rot decay is mandatory for being able to better protect wooden products from this type of degradation, the underlying mechanisms are still not fully understood. This is particularly true for wood that has been treated to increase its resistance against rot. In the present study, the two degradation phases were separated to study the impact of wood acetylation on the behavior of three brown rot fungi commonly used in wood durability testing. Transcriptomic data from two strains of Rhodonia placenta (FPRL280 and MAD-698) and Gloeophyllum trabeum were recorded to elucidate differences between the respective decay strategies. Clear differences were found between the two decay stages in all fungi. Moreover, strategies varied not only between species but also between the two strains of the same species. The responses to wood acetylation showed that decay is generally delayed and that parts of the process are attenuated. By hierarchical clustering, we could localize several transcription factors within gene clusters that were heavily affected by acetylation, especially in G. trabeum. The results suggest that regulatory circuits evolve rapidly and are probably the major cause behind the different decay strategies as observed even between the two strains of R. placenta. Identifying key genes in these processes can help in decay detection and identification of the fungi by biomarker selection, and also be informative for other fields, such as fiber modification by biocatalysts and the generation of biochemical platform chemicals for biorefinery applications.
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Affiliation(s)
- Martina Kölle
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Maria Augusta Crivelente Horta
- Professorship of Fungal Biotechnology in Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - J. Philipp Benz
- Professorship of Fungal Biotechnology in Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Advanced Study, Technical University of Munich, Munich, Germany
| | - Annica Pilgård
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Biobased Materials, Bioeconomy, RISE Research Institutes of Sweden, Borås, Sweden
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16
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Abstract
Brown rot fungi release massive amounts of carbon from forest deadwood, particularly at high latitudes. These fungi degrade wood by generating small reactive oxygen species (ROS) to loosen lignocellulose, to then selectively remove carbohydrates. The ROS mechanism has long been considered the key adaptation defining brown rot wood decomposition, but recently, we found preliminary evidence that fungal glycoside hydrolases (GHs) implicated in early cell wall loosening might have been adapted to tolerate ROS stress and to synergize with ROS to loosen woody lignocellulose. In the current study, we found more specifically that side chain hemicellulases that help in the early deconstruction of the lignocellulosic complex are significantly more tolerant of ROS in the brown rot fungus Rhodonia placenta than in a white rot fungus (Trametes versicolor) and a soft rot fungus (Trichoderma reesei). Using proteomics to understand the extent of tolerance, we found that significant oxidation of secreted R. placenta proteins exposed to ROS was less than half of the oxidation observed for T. versicolor or T. reesei. The principal oxidative modifications observed in all cases were monooxidation and dioxidation/trioxidation (mainly in methionine and tryptophan residues), some of which were critical for enzyme activity. At the peptide level, we found that GHs in R. placenta were the least ROS affected among our tested fungi. These results confirm and describe underlying mechanisms of tolerance in early-secreted brown rot fungal hemicellulases. These enzymatic adaptations may have been as important as nonenzymatic ROS pathway adaptations in brown rot fungal evolution.
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17
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Abstract
Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.
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18
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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19
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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20
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Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi. J Fungi (Basel) 2021; 7:jof7040265. [PMID: 33807430 PMCID: PMC8065597 DOI: 10.3390/jof7040265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/23/2022] Open
Abstract
Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities.
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21
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Sahu N, Merényi Z, Bálint B, Kiss B, Sipos G, Owens RA, Nagy LG. Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species. Microorganisms 2021; 9:149. [PMID: 33440901 PMCID: PMC7827401 DOI: 10.3390/microorganisms9010149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/01/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.
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Affiliation(s)
- Neha Sahu
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Merényi
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Balázs Bálint
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Brigitta Kiss
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - György Sipos
- Research Center for Forestry and Wood Industry, Functional Genomics and Bioinformatics Group, University of Sopron, 9400 Sopron, Hungary;
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Rebecca A. Owens
- Department of Biology, Maynooth University, W23 F2H6 Kildare, Ireland;
| | - László G. Nagy
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
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22
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Vos AM, Bleichrodt R, Herman KC, Ohm RA, Scholtmeijer K, Schmitt H, Lugones LG, Wösten HAB. Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus. Environ Microbiol 2021; 23:224-238. [PMID: 33140552 PMCID: PMC7894533 DOI: 10.1111/1462-2920.15297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
Abstract
Wood and litter degrading fungi are the main decomposers of lignocellulose and thus play a key role in carbon cycling in nature. Here, we provide evidence for a novel lignocellulose degradation strategy employed by the litter degrading fungus Agaricus bisporus (known as the white button mushroom). Fusion of hyphae allows this fungus to synchronize the activity of its mycelium over large distances (50 cm). The synchronized activity has a 13-h interval that increases to 20 h before becoming irregular and it is associated with a 3.5-fold increase in respiration, while compost temperature increases up to 2°C. Transcriptomic analysis of this burst-like phenomenon supports a cyclic degradation of lignin, deconstruction of (hemi-) cellulose and microbial cell wall polymers, and uptake of degradation products during vegetative growth of A. bisporus. Cycling in expression of the ligninolytic system, of enzymes involved in saccharification, and of proteins involved in nutrient uptake is proposed to provide an efficient way for degradation of substrates such as litter.
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Affiliation(s)
- Aurin M. Vos
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
- Wageningen Plant ResearchWageningen URWageningenthe Netherlands
| | | | - Koen C. Herman
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Robin A. Ohm
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Karin Scholtmeijer
- Plant BreedingWageningen University and ResearchWageningenthe Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment SciencesUtrecht UniversityUtrechtthe Netherlands
| | - Luis G. Lugones
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Han A. B. Wösten
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
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Transcriptome analysis of the brown rot fungus Gloeophyllum trabeum during lignocellulose degradation. PLoS One 2020; 15:e0243984. [PMID: 33315957 PMCID: PMC7735643 DOI: 10.1371/journal.pone.0243984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Brown rot fungi have great potential in biorefinery wood conversion systems because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Comparison to the gene expression on glucose, 1,129 genes were upregulated on cellulose and 1,516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included glycoside hyrolase family 12 (GH12), GH131, carbohydrate esterase family 1 (CE1), auxiliary activities family 3 subfamily 1 (AA3_1), AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these gene products in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
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24
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Presley GN, Zhang J, Purvine SO, Schilling JS. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. Front Microbiol 2020; 11:1646. [PMID: 32849338 PMCID: PMC7399148 DOI: 10.3389/fmicb.2020.01646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023] Open
Abstract
Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
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Affiliation(s)
- Gerald N Presley
- Department of Wood Science and Engineering, Oregon State University, Corvallis, OR, United States
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
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25
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Alfaro M, Majcherczyk A, Kües U, Ramírez L, Pisabarro AG. Glucose counteracts wood-dependent induction of lignocellulolytic enzyme secretion in monokaryon and dikaryon submerged cultures of the white-rot basidiomycete Pleurotus ostreatus. Sci Rep 2020; 10:12421. [PMID: 32709970 PMCID: PMC7381666 DOI: 10.1038/s41598-020-68969-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The secretome complexity and lignocellulose degrading capacity of Pleurotus ostreatus monokaryons mkPC9 and mkPC15 and mated dikaryon dkN001 were studied in submerged liquid cultures containing wood, glucose, and wood plus glucose as carbon sources. The study revealed that this white-rot basidiomycete attacks all the components of the plant cell wall. P. ostreatus secretes a variety of glycoside hydrolases, carbohydrate esterases, and polysaccharide lyases, especially when wood is the only carbon source. The presence of wood increased the secretome complexity, whereas glucose diminished the secretion of enzymes involved in cellulose, hemicellulose and pectin degradation. In contrast, the presence of glucose did not influence the secretion of redox enzymes or proteases, which shows the specificity of glucose on the secretion of cellulolytic enzymes. The comparison of the secretomes of monokaryons and dikaryons reveals that secretome complexity is unrelated to the nuclear composition of the strain.
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Affiliation(s)
- Manuel Alfaro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Andrzej Majcherczyk
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain.
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26
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Kölle M, Horta MAC, Nowrousian M, Ohm RA, Benz JP, Pilgård A. Degradative Capacity of Two Strains of Rhodonia placenta: From Phenotype to Genotype. Front Microbiol 2020; 11:1338. [PMID: 32625194 PMCID: PMC7314958 DOI: 10.3389/fmicb.2020.01338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 01/23/2023] Open
Abstract
Brown rot fungi, such as Rhodonia placenta (previously Postia placenta), occur naturally in northern coniferous forest ecosystems and are known to be the most destructive group of decay fungi, degrading wood faster and more effectively than other wood-degrading organisms. It has been shown that brown rot fungi not only rely on enzymatic degradation of lignocellulose, but also use low molecular weight oxidative agents in a non-enzymatic degradation step prior to the enzymatic degradation. R. placenta is used in standardized decay tests in both Europe and North America. However, two different strains are employed (FPRL280 and MAD-698, respectively) for which differences in colonization-rate, mass loss, as well as in gene expression have been observed, limiting the comparability of results. To elucidate the divergence between both strains, we investigated the phenotypes in more detail and compared their genomes. Significant phenotypic differences were found between the two strains, and no fusion was possible. MAD-698 degraded scots pine more aggressively, had a more constant growth rate and produced mycelia faster than FPRL280. After sequencing the genome of FPRL280 and comparing it with the published MAD-698 genome we found 660,566 SNPs, resulting in 98.4% genome identity. Specific analysis of the carbohydrate-active enzymes, encoded by the genome (CAZome) identified differences in many families related to plant biomass degradation, including SNPs, indels, gaps or insertions within structural domains. Four genes belonging to the AA3_2 family could not be found in or amplified from FPRL280 gDNA, suggesting the absence of these genes. Differences in other CAZy encoding genes that could potentially affect the lignocellulolytic activity of the strains were also predicted by comparison of genome assemblies (e.g., GH2, GH3, GH5, GH10, GH16, GH78, GT2, GT15, and CBM13). Overall, these mutations help to explain the phenotypic differences observed between both strains as they could interfere with the enzymatic activities, substrate binding ability or protein folding. The investigation of the molecular reasons that make these two strains distinct contributes to the understanding of the development of this important brown rot reference species and will help to put the data obtained from standardized decay tests across the globe into a better biological context.
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Affiliation(s)
- Martina Kölle
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Maria Augusta Crivelente Horta
- Professorship for Wood Bioprocesses, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| | - Robin A Ohm
- Department of Biology, Microbiology, Utrecht University, Utrecht, Netherlands
| | - J Philipp Benz
- Professorship for Wood Bioprocesses, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Institute of Advanced Study, Technical University of Munich, Garching, Germany
| | - Annica Pilgård
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.,Biobased Materials, Bioeconomy, RISE Research Institutes of Sweden, Borås, Sweden
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27
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Mali T, Mäki M, Hellén H, Heinonsalo J, Bäck J, Lundell T. Decomposition of spruce wood and release of volatile organic compounds depend on decay type, fungal interactions and enzyme production patterns. FEMS Microbiol Ecol 2020; 95:5554004. [PMID: 31494677 PMCID: PMC6736282 DOI: 10.1093/femsec/fiz135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/22/2019] [Indexed: 01/18/2023] Open
Abstract
Effect of three wood-decaying fungi on decomposition of spruce wood was studied in solid-state cultivation conditions for a period of three months. Two white rot species (Trichaptum abietinum and Phlebia radiata) were challenged by a brown rot species (Fomitopsis pinicola) in varying combinations. Wood decomposition patterns as determined by mass loss, carbon to nitrogen ratio, accumulation of dissolved sugars and release of volatile organic compounds (VOCs) were observed to depend on both fungal combinations and growth time. Similar dependence of fungal species combination, either white or brown rot dominated, was observed for secreted enzyme activities on spruce wood. Fenton chemistry suggesting reduction of Fe3+ to Fe2+ was detected in the presence of F. pinicola, even in co-cultures, together with substantial degradation of wood carbohydrates and accumulation of oxalic acid. Significant correlation was perceived with two enzyme activity patterns (oxidoreductases produced by white rot fungi; hydrolytic enzymes produced by the brown rot fungus) and wood degradation efficiency. Moreover, emission of four signature VOCs clearly grouped the fungal combinations. Our results indicate that fungal decay type, either brown or white rot, determines the loss of wood mass and decomposition of polysaccharides as well as the pattern of VOCs released upon fungal growth on spruce wood.
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Affiliation(s)
- Tuulia Mali
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
| | - Mari Mäki
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Heidi Hellén
- Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jussi Heinonsalo
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland.,Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jaana Bäck
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
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28
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Floudas D, Bentzer J, Ahrén D, Johansson T, Persson P, Tunlid A. Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi. ISME JOURNAL 2020; 14:2046-2059. [PMID: 32382073 PMCID: PMC7368018 DOI: 10.1038/s41396-020-0667-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 04/10/2020] [Accepted: 04/23/2020] [Indexed: 12/22/2022]
Abstract
Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.
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Affiliation(s)
- Dimitrios Floudas
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden.
| | - Johan Bentzer
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Dag Ahrén
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Per Persson
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden.,Centre for Environmental and Climate Research (CEC), Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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29
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Brischke C, Alfredsen G. Wood-water relationships and their role for wood susceptibility to fungal decay. Appl Microbiol Biotechnol 2020; 104:3781-3795. [PMID: 32144473 PMCID: PMC8326242 DOI: 10.1007/s00253-020-10479-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
Wood in service is sequestering carbon, but it is principally prone to deterioration where different fungi metabolize wood, and carbon dioxide is released back to the atmosphere. A key prerequisite for fungal degradation of wood is the presence of moisture. Conversely, keeping wood dry is the most effective way to protect wood from wood degradation and for long-term binding of carbon. Wood is porous and hygroscopic; it can take up water in liquid and gaseous form, and water is released from wood through evaporation following a given water vapour pressure gradient. During the last decades, the perception of wood-water relationships changed significantly and so did the view on moisture-affected properties of wood. Among the latter is its susceptibility to fungal decay. This paper reviews findings related to wood-water relationships and their role for fungal wood decomposition. These are complex interrelationships not yet fully understood, and current knowledge gaps are therefore identified. Studies with chemically and thermally modified wood are included as examples of fungal wood substrates with altered moisture properties. Quantification and localization of capillary and cell wall water - especially in the over-hygroscopic range - is considered crucial for determining minimum moisture thresholds (MMThr) of wood-decay fungi. The limitations of the various methods and experimental set-ups to investigate wood-water relationships and their role for fungal decay are manifold. Hence, combining techniques from wood science, mycology, biotechnology and advanced analytics is expected to provide new insights and eventually a breakthrough in understanding the intricate balance between fungal decay and wood-water relations. KEY POINTS: • Susceptibility to wood-decay fungi is closely linked to their physiological needs. • Content, state and distribution of moisture in wood are keys for fungal activity. • Quantification and localization of capillary and cell wall water in wood is needed. • New methodological approaches are expected to provide new insights.
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Affiliation(s)
- Christian Brischke
- Department of Wood Biology and Wood Products, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Buesgenweg 4, D-37077, Goettingen, Germany.
| | - Gry Alfredsen
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Forest and Forest Resources, Wood Technology, Høgskoleveien 8, 1433, Ås, Norway
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30
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Mattila HK, Mäkinen M, Lundell T. Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:26. [PMID: 32123543 PMCID: PMC7038570 DOI: 10.1186/s13068-020-01677-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fungal decomposition of wood is considered as a strictly aerobic process. However, recent findings on wood-decaying fungi to produce ethanol from various lignocelluloses under oxygen-depleted conditions lead us to question this. We designed gene expression study of the white rot fungus Phlebia radiata (isolate FBCC0043) by adopting comparative transcriptomics and functional genomics on solid lignocellulose substrates under varying cultivation atmospheric conditions. RESULTS Switch to fermentative conditions was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides. Changes in the expression profiles of CAZy (carbohydrate-active enzyme) encoding genes upon oxygen depletion, lead into an alternative wood decomposition strategy. Surprisingly, we noticed higher cellulolytic activity under fermentative conditions in comparison to aerobic cultivation. In addition, our results manifest how oxygen depletion affects over 200 genes of fungal primary metabolism including several transcription factors. We present new functions for acetate generating phosphoketolase pathway and its potential regulator, Adr1 transcription factor, in carbon catabolism under oxygen depletion. CONCLUSIONS Physiologically resilient wood-decomposing Basidiomycota species P. radiata is capable of thriving under respirative and fermentative conditions utilizing only untreated lignocellulose as carbon source. Hypoxia-response mechanism in the fungus is, however, divergent from the regulation described for Ascomycota fermenting yeasts or animal-pathogenic species of Basidiomycota.
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Affiliation(s)
- Hans Kristian Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
| | - Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
- Present Address: VTT Technical Research Centre of Finland Ltd, 02044 VTT Espoo, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
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31
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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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32
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Barbi F, Kohler A, Barry K, Baskaran P, Daum C, Fauchery L, Ihrmark K, Kuo A, LaButti K, Lipzen A, Morin E, Grigoriev IV, Henrissat B, Lindahl BD, Martin F. Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers. Environ Microbiol 2019; 22:1089-1103. [DOI: 10.1111/1462-2920.14873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/23/2019] [Accepted: 11/20/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Barbi
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014, SE‐750 07 Uppsala Sweden
| | - Annegret Kohler
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Preetisri Baskaran
- Department of Ecology Swedish University of Agricultural Sciences Box 7044, SE‐750 07 Uppsala Sweden
| | - Chris Daum
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Laure Fauchery
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Box 7026, 750 07 Uppsala Sweden
| | - Alan Kuo
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
| | - Emmanuelle Morin
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
- Department of Plant and Microbial Biology University of California, Berkeley Berkeley CA 94720 USA
| | - Bernard Henrissat
- CNRS UMR 7257, Aix‐Marseille University 13288 Marseille France
- INRA, USC 1408 AFMB 13288 Marseille France
- Department of Biological Sciences King Abdulaziz University Jeddah Saudi Arabia
| | - Björn D. Lindahl
- Department of Soil and Environment Swedish University of Agricultural Sciences Box 7014, SE‐750 07 Uppsala Sweden
| | - Francis Martin
- Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand‐Est Université de Lorraine, INRA, UMR Interactions Arbres/Microorganismes (IAM) 54280 Champenoux France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry University 35 Qinghua East Road, Haidian Qu Beijing Shi 100083 China
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33
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Moiseenko KV, Glazunova OA, Shakhova NV, Savinova OS, Vasina DV, Tyazhelova TV, Psurtseva NV, Fedorova TV. Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. Microorganisms 2019; 7:E527. [PMID: 31694151 PMCID: PMC6921079 DOI: 10.3390/microorganisms7110527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.
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Affiliation(s)
- Konstantin V. Moiseenko
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Natalia V. Shakhova
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Olga S. Savinova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Daria V. Vasina
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
| | - Tatiana V. Tyazhelova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119071, Russia;
| | - Nadezhda V. Psurtseva
- Komarov Botanical Institute of the Russian Academy of Sciences, Professor Popov St. 2, St. Petersburg 197376, Russia;
| | - Tatiana V. Fedorova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (O.A.G.); (O.S.S.); (D.V.V.)
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34
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A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase. Appl Environ Microbiol 2019; 85:AEM.02803-18. [PMID: 30824433 DOI: 10.1128/aem.02803-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs), a class of copper-dependent enzymes, play a crucial role in boosting the enzymatic decomposition of polysaccharides. Here, we reveal that LPMOs might be associated with a lignin degradation pathway. An LPMO from white-rot fungus Pleurotus ostreatus, LPMO9A (PoLPMO9A), was shown to be able to efficiently drive the activity of class II lignin-degrading peroxidases in vitro through H2O2 production regardless of the presence or absence of a cellulose substrate. An LPMO-driven peroxidase reaction can degrade β-O-4 and 5-5' types of lignin dimer with 46.5% and 37.7% degradation, respectively, as well as alter the structure of natural lignin and kraft lignin. H2O2 generated by PoLPMO9A was preferentially utilized for the peroxidase from Physisporinus sp. strain P18 (PsVP) reaction rather than cellulose oxidation, indicating that white-rot fungi may have a strategy for preferential degradation of resistant lignin. This discovery shows that LPMOs may be involved in lignin oxidation as auxiliary enzymes of lignin-degrading peroxidases during the white-rot fungal decay process.IMPORTANCE The enzymatic biodegradation of structural polysaccharides is affected by the degree of delignification of lignocellulose during the white-rot fungal decay process. The lignin matrix decreases accessibility to the substrates for LPMOs. H2O2 has been studied as a cosubstrate for LPMOs, but the formation and utilization of H2O2 in the reactions still represent an intriguing focus of current research. Lignin-degrading peroxidases and LPMOs usually coexist during fungal decay, and therefore, the relationship between H2O2-dependent lignin-degrading peroxidases and LPMOs should be considered during the wood decay process. The current study revealed that white-rot fungal LPMOs may be involved in the degradation of lignin through driving a versatile form of peroxidase activity in vitro and that H2O2 generated by PoLPMO9A was preferentially used for lignin oxidation by lignin-degrading peroxidase (PsVP). These findings reveal a potential relationship between LPMOs and lignin degradation, which will be of great significance for further understanding the contribution of LPMOs to the white-rot fungal decay process.
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