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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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Yotsui I, Matsui H, Miyauchi S, Iwakawa H, Melkonian K, Schlüter T, Michavila S, Kanazawa T, Nomura Y, Stolze SC, Jeon HW, Yan Y, Harzen A, Sugano SS, Shirakawa M, Nishihama R, Ichihashi Y, Ibanez SG, Shirasu K, Ueda T, Kohchi T, Nakagami H. LysM-mediated signaling in Marchantia polymorpha highlights the conservation of pattern-triggered immunity in land plants. Curr Biol 2023; 33:3732-3746.e8. [PMID: 37619565 DOI: 10.1016/j.cub.2023.07.068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Pattern-recognition receptor (PRR)-triggered immunity (PTI) wards off a wide range of pathogenic microbes, playing a pivotal role in angiosperms. The model liverwort Marchantia polymorpha triggers defense-related gene expression upon sensing components of bacterial and fungal extracts, suggesting the existence of PTI in this plant model. However, the molecular components of the putative PTI in M. polymorpha and the significance of PTI in bryophytes have not yet been described. We here show that M. polymorpha has four lysin motif (LysM)-domain-containing receptor homologs, two of which, LysM-receptor-like kinase (LYK) MpLYK1 and LYK-related (LYR) MpLYR, are responsible for sensing chitin and peptidoglycan fragments, triggering a series of characteristic immune responses. Comprehensive phosphoproteomic analysis of M. polymorpha in response to chitin treatment identified regulatory proteins that potentially shape LysM-mediated PTI. The identified proteins included homologs of well-described PTI components in angiosperms as well as proteins whose roles in PTI are not yet determined, including the blue-light receptor phototropin MpPHOT. We revealed that MpPHOT is required for negative feedback of defense-related gene expression during PTI. Taken together, this study outlines the basic framework of LysM-mediated PTI in M. polymorpha and highlights conserved elements and new aspects of pattern-triggered immunity in land plants.
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Affiliation(s)
- Izumi Yotsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Department of BioScience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hidenori Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Okinawa, Japan
| | - Hidekazu Iwakawa
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan
| | | | - Titus Schlüter
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Santiago Michavila
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | | | - Hyung-Woo Jeon
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yijia Yan
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Anne Harzen
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Shigeo S Sugano
- Bioproduction Research Institute, The National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Makoto Shirakawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Nara, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510, Chiba, Japan
| | - Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; RIKEN BioResource Research Center, Tsukuba 305-0074, Ibaraki, Japan
| | - Selena Gimenez Ibanez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Kanagawa, Japan; Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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Affiliation(s)
- Nalin N Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Roy A, Kalita B, Jayaprakash A, Kumar A, Lakshmi PTV. Computational identification and characterization of vascular wilt pathogen ( Fusarium oxysporum f. sp. lycopersici) CAZymes in tomato xylem sap. J Biomol Struct Dyn 2022:1-17. [PMID: 35470778 DOI: 10.1080/07391102.2022.2067236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fusarium oxysporum f. sp. lycopersici is a devastating plant pathogenic fungi known for wilt disease in the tomato plant and secrete cell wall degrading enzymes. These enzymes are collectively known as carbohydrate-active enzymes (CAZymes), crucial for growth, colonization and pathogenesis. Therefore, the present study was aimed to identify and annotate pathogen CAZymes in the xylem sap of a susceptible tomato variety using downstream proteomics and meta servers. Further, structural elucidation and conformational stability analysis of the selected CAZyme families were done through homology modeling and molecular dynamics simulation. Among all the fungal proteins identified, the carbohydrate metabolic process was found to be enriched. Most of the annotated CAZymes belonged to the hydrolase and oxidoreductase families, and 90% were soluble and extracellular. Moreover, using a publically available interactome database, interactions were observed between the families acting on chitin, hemicellulose and pectin. Subsequently, important catalytic residues were identified in the candidate CAZymes belonging to carbohydrate esterase (CE8) and glycosyl hydrolase (GH18 and GH28). Further, essential dynamics after molecular simulation of 100 ns revealed the overall behavior of these CAZymes with distinct global minima and transition states in CE8. Thus, our study identified some of the CAZyme families that assist in pathogenesis and growth through host cell wall deconstruction with further structural insight into the selected CAZyme families.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhijeet Roy
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Barsha Kalita
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Aiswarya Jayaprakash
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Amrendra Kumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - P T V Lakshmi
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Guan R, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. THE ISME JOURNAL 2022; 16:876-889. [PMID: 34686763 PMCID: PMC8857181 DOI: 10.1038/s41396-021-01138-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/05/2022]
Abstract
Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
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Affiliation(s)
- Lisa K. Mahdi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Shingo Miyauchi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Charles Uhlmann
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Ruben Garrido-Oter
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gregor Langen
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Stephan Wawra
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Yulong Niu
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Rui Guan
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Senga Robertson-Albertyn
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Jane E. Parker
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Alga Zuccaro
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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Tomé LMR, da Silva FF, Fonseca PLC, Mendes-Pereira T, Azevedo VADC, Brenig B, Badotti F, Góes-Neto A. Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown. J Fungi (Basel) 2022; 8:jof8020142. [PMID: 35205897 PMCID: PMC8876698 DOI: 10.3390/jof8020142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Felipe Ferreira da Silva
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Paula Luize Camargos Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany;
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte 30421-169, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
- Correspondence: ; Tel.: +55-31-994130996
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A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor. Microorganisms 2021; 9:microorganisms9122612. [PMID: 34946213 PMCID: PMC8708209 DOI: 10.3390/microorganisms9122612] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 02/05/2023] Open
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.
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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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9
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Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
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10
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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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11
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Marqués‐Gálvez JE, Miyauchi S, Paolocci F, Navarro‐Ródenas A, Arenas F, Pérez‐Gilabert M, Morin E, Auer L, Barry KW, Kuo A, Grigoriev IV, Martin FM, Kohler A, Morte A. Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle. THE NEW PHYTOLOGIST 2021; 229:2917-2932. [PMID: 33118170 PMCID: PMC7898904 DOI: 10.1111/nph.17044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.
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Affiliation(s)
- José Eduardo Marqués‐Gálvez
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Shingo Miyauchi
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Francesco Paolocci
- CNR‐IBBRIstituto di Bioscienze e BiorisorseUOS di PerugiaPerugia06128Italy
| | - Alfonso Navarro‐Ródenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Francisco Arenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Manuela Pérez‐Gilabert
- Departamento de Bioquímica y Biología Molecular‐AUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Emmanuelle Morin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Lucas Auer
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Kerrie W. Barry
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Alan Kuo
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCA94598USA
| | - Francis M. Martin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Annegret Kohler
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Asunción Morte
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
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12
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Fasim A, More VS, More SS. Large-scale production of enzymes for biotechnology uses. Curr Opin Biotechnol 2020; 69:68-76. [PMID: 33388493 DOI: 10.1016/j.copbio.2020.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023]
Abstract
Enzymes are biocatalysts that speed up the chemical reaction to obtain the final valuable product/s. Biotechnology has revolutionized the use of traditional enzymes to be applicable in industries such as food, beverage, personal and household care, agriculture, bioenergy, pharmaceutical, and various other segments. With respect to the exponential growth of enzymes in biotech industries, it becomes important to highlight the advancements and impact of enzyme technology over recent years. In this review article, we discuss the existing and emerging production approaches, applications, developments, and global need for enzymes. Special emphasis is given to the predominantly utilized hydrolytic microbial enzymes in industrial bioprocesses.
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Affiliation(s)
- Aneesa Fasim
- School of Basic and Applied Sciences, Dayananda Sagar University, Bengaluru 560 111, Karnataka, India
| | - Veena S More
- Department of Biotechnology, Sapthagiri College of Engineering, Bengaluru 560 057 Karnataka, India
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, Bengaluru 560 111, Karnataka, India.
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13
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PsAA9A, a C1-specific AA9 lytic polysaccharide monooxygenase from the white-rot basidiomycete Pycnoporus sanguineus. Appl Microbiol Biotechnol 2020; 104:9631-9643. [DOI: 10.1007/s00253-020-10911-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
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14
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Li X, Han C, Li W, Chen G, Wang L. Insights into the cellulose degradation mechanism of the thermophilic fungus Chaetomium thermophilum based on integrated functional omics. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:143. [PMID: 32817759 PMCID: PMC7425565 DOI: 10.1186/s13068-020-01783-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant and renewable biomass resource on the planet. Lignocellulose can be converted into biofuels and high-value compounds; however, its recalcitrance makes its breakdown a challenge. Lytic polysaccharide monooxygenases (LPMOs) offer tremendous promise for the degradation of recalcitrant polysaccharides. Chaetomium thermophilum, having many LPMO-coding genes, is a dominant thermophilic fungus in cellulose-rich and self-heating habitats. This study explores the genome, secretomes and transcript levels of specific genes of C. thermophilum. RESULTS The genome of C. thermophilum encoded a comprehensive set of cellulose- and xylan-degrading enzymes, especially 18 AA9 LPMOs that belonged to different subfamilies. Extracellular secretomes showed that arabinose and microcrystalline cellulose (MCC) could specifically induce the secretion of carbohydrate-active enzymes (CAZymes), especially AA9 LPMOs, by C. thermophilum under different carbon sources. Temporal analyses of secretomes and transcripts revealed that arabinose induced the secretion of xylanases by C. thermophilum, which was obviously different from other common filamentous fungi. MCC could efficiently induce the specific secretion of LPMO2s, possibly because the insert in loop3 on the substrate-binding surface of LPMO2s strengthened its binding capacity to cellulose. LPMO2s, cellobio hydrolases (CBHs) and cellobiose dehydrogenases (CDHs) were cosecreted, forming an efficient cellulose degradation system of oxidases and hydrolases under thermophilic conditions. CONCLUSIONS The specific expression of LPMO2s and cosecretion of hydrolases and oxidases by the thermophilic fungus C. thermophilum play an important role in cellulose degradation. This insight increases our understanding of the cellulose degradation under thermophilic conditions and may inspire the design of the optimal enzyme cocktails for more efficient exploration of biomass resources in industrial applications.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Chao Han
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Weiguang Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Jimo Binhai Road, Qingdao, 266237 Shandong People’s Republic of China
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15
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Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
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16
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Basso V, Kohler A, Miyauchi S, Singan V, Guinet F, Šimura J, Novák O, Barry KW, Amirebrahimi M, Block J, Daguerre Y, Na H, Grigoriev IV, Martin F, Veneault-Fourrey C. An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots. PLANT, CELL & ENVIRONMENT 2020; 43:1047-1068. [PMID: 31834634 DOI: 10.1111/pce.13702] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.
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Affiliation(s)
- Veronica Basso
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Annegret Kohler
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Shingo Miyauchi
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Vasanth Singan
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Frédéric Guinet
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Jan Šimura
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Ondřej Novák
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Kerrie W Barry
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Mojgan Amirebrahimi
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Jonathan Block
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Yohann Daguerre
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Hyunsoo Na
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Igor V Grigoriev
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
| | - Francis Martin
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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17
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Dai Y, Li X, Song B, Sun L, Yang C, Zhang X, Wang Y, Zhang Z, Fu Y, Li Y. Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species. Front Microbiol 2019; 10:2255. [PMID: 31632371 PMCID: PMC6786273 DOI: 10.3389/fmicb.2019.02255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
Species in the genus Auricularia play important roles for people’s food and nutrition especially Auricularia cornea and A. heimuer. To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of Auricularia cornea and the corresponding comparative genomic analysis. The genome size of A. cornea was similar to Auricularia subglabra, but 1.5 times larger than that of A. heimuer. Several factors were responsible for genome size variation including gene numbers, repetitive elements, and gene lengths. Phylogenomic analysis revealed that the estimated divergence time between A. heimuer and other Auricularia is ∼79.1 million years ago (Mya), while the divergence between A. cornea and A. subglabra occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of A. cornea and A. heimuer, indicating that their populations fluctuated over time with global climate change during Marine Isotope Stage 5-2. Moreover, despite the highly similar external morphologies of A. cornea and A. heimuer, their genomic properties were remarkably different. The A. cornea genome only shared 14% homologous syntenic blocks with A. heimuer and possessed more genes encoding carbohydrate-active enzymes and secondary metabolite biosynthesis proteins. The cross-taxa transferability rates of simple sequence repeat (SSR) and insertion or deletion (InDel) markers within the genus Auricularia were also lower than that previously observed for species within the same genus. Taken together, these results indicate a high level of genetic differentiation between these two Auricularia species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of Auricularia species that will facilitate future genetic breeding.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xiao Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Chentao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xin Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yanfeng Wang
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun, China
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18
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Frandsen KEH, Tovborg M, Jørgensen CI, Spodsberg N, Rosso MN, Hemsworth GR, Garman EF, Grime GW, Poulsen JCN, Batth TS, Miyauchi S, Lipzen A, Daum C, Grigoriev IV, Johansen KS, Henrissat B, Berrin JG, Lo Leggio L. Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 2019; 294:17117-17130. [PMID: 31471321 DOI: 10.1074/jbc.ra119.009223] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/22/2019] [Indexed: 01/13/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
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Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark.,INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | | | | | | | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Glyn R Hemsworth
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Geoffrey W Grime
- The Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, United Kingdom
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shingo Miyauchi
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, 13009 Marseille, France.,INRA, USC 1408 AFMB, 13009 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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19
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Anasontzis GE, Lebrun MH, Haon M, Champion C, Kohler A, Lenfant N, Martin F, O'Connell RJ, Riley R, Grigoriev IV, Henrissat B, Berrin JG, Rosso MN. Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants. Environ Microbiol 2019; 21:2724-2739. [PMID: 30887618 DOI: 10.1111/1462-2920.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/17/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.
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Affiliation(s)
- George E Anasontzis
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.,CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Marc-Henri Lebrun
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Mireille Haon
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Charlotte Champion
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Annegret Kohler
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Nicolas Lenfant
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Francis Martin
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Richard J O'Connell
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Bernard Henrissat
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France.,INRA, USC 1408, AFMB, Marseille, France
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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20
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Jurak E, Suzuki H, van Erven G, Gandier JA, Wong P, Chan K, Ho CY, Gong Y, Tillier E, Rosso MN, Kabel MA, Miyauchi S, Master ER. Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. BMC Genomics 2018; 19:815. [PMID: 30424733 PMCID: PMC6234650 DOI: 10.1186/s12864-018-5210-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
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Affiliation(s)
- E Jurak
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Department of Aquatic Biotechnology and Bioproduct Engineering, Groningen, The Netherlands
| | - H Suzuki
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - G van Erven
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - J A Gandier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - P Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - K Chan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - C Y Ho
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Y Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - E Tillier
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - M-N Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - M A Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - S Miyauchi
- Laboratory of Excellence ARBRE, INRA, Nancy, Lorraine, France.,Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - E R Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
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21
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Lesage-Meessen L, Bou M, Ginies C, Chevret D, Navarro D, Drula E, Bonnin E, del Río JC, Odinot E, Bisotto A, Berrin JG, Sigoillot JC, Faulds CB, Lomascolo A. Lavender- and lavandin-distilled straws: an untapped feedstock with great potential for the production of high-added value compounds and fungal enzymes. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:217. [PMID: 30083230 PMCID: PMC6071384 DOI: 10.1186/s13068-018-1218-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Lavender (Lavandula angustifolia) and lavandin (a sterile hybrid of L. angustifolia × L. latifolia) essential oils are among those most commonly used in the world for various industrial purposes, including perfumes, pharmaceuticals and cosmetics. The solid residues from aromatic plant distillation such as lavender- and lavandin-distilled straws are generally considered as wastes, and consequently either left in the fields or burnt. However, lavender- and lavandin-distilled straws are a potentially renewable plant biomass as they are cheap, non-food materials that can be used as raw feedstocks for green chemistry industry. The objective of this work was to assess different pathways of valorization of these straws as bio-based platform chemicals and fungal enzymes of interest in biorefinery. RESULTS Sugar and lignin composition analyses and saccharification potential of the straw fractions revealed that these industrial by-products could be suitable for second-generation bioethanol prospective. The solvent extraction processes, developed specifically for these straws, released terpene derivatives (e.g. τ-cadinol, β-caryophyllene), lactones (e.g. coumarin, herniarin) and phenolic compounds of industrial interest, including rosmarinic acid which contributed to the high antioxidant activity of the straw extracts. Lavender and lavandin straws were also suitable inducers for the secretion of a wide panel of lignocellulose-acting enzymes (cellulases, hemicellulases and oxido-reductases) from the white-rot model fungus Pycnoporus cinnabarinus. Interestingly, high amounts of laccase and several lytic polysaccharide monooxygenases were identified in the lavender and lavandin straw secretomes using proteomics. CONCLUSIONS The present study demonstrated that the distilled straws of lavender and lavandin are lignocellulosic-rich materials that can be used as raw feedstocks for producing high-added value compounds (antioxidants, aroma) and fungal oxidative enzymes, which represent opportunities to improve the decomposition of recalcitrant lignocellulose into biofuel. Hence, the structure and the physico-chemical properties of these straws clearly open new perspectives for use in biotechnological processes involving especially filamentous fungi. These approaches represent sustainable strategies to foster the development of a local circular bioeconomy.
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Affiliation(s)
- Laurence Lesage-Meessen
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Marine Bou
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Christian Ginies
- UMR408 SQPOV Sécurité et Qualité des Produits d’Origine Végétale, INRA, Université d’Avignon, 33 rue Louis Pasteur, 84029 Avignon, France
| | - Didier Chevret
- UMR1319 MICALIS Microbiologie de l’Alimentation au Service de la Santé Humaine, PAPPSO, INRA, 78352 Jouy-en-Josas Cedex, France
| | - David Navarro
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Elodie Drula
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
- USC1408 AFMB Architecture et Fonction des Macromolécules Biologiques, INRA, 13288 Marseille, France
| | - Estelle Bonnin
- UR 1268 BIA Biopolymères, Interactions, Assemblage, INRA, 44316 Nantes, France
| | - José C. del Río
- Department of Plant Biotechnology, IRNAS, CSIC, Avda. Reina Mercedes, 10, 41012 Seville, Spain
| | - Elise Odinot
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Alexandra Bisotto
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Jean-Guy Berrin
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Jean-Claude Sigoillot
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Craig B. Faulds
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
| | - Anne Lomascolo
- UMR1163 BBF Biodiversité et Biotechnologie Fongiques, INRA, Aix Marseille Univ, 13288 Marseille Cedex 09, France
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22
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Miyauchi S, Rancon A, Drula E, Hage H, Chaduli D, Favel A, Grisel S, Henrissat B, Herpoël-Gimbert I, Ruiz-Dueñas FJ, Chevret D, Hainaut M, Lin J, Wang M, Pangilinan J, Lipzen A, Lesage-Meessen L, Navarro D, Riley R, Grigoriev IV, Zhou S, Raouche S, Rosso MN. Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:201. [PMID: 30061923 PMCID: PMC6055342 DOI: 10.1186/s13068-018-1198-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. RESULTS We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners. CONCLUSION As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.
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Affiliation(s)
- Shingo Miyauchi
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Laboratoire d’Excellence ARBRE, UMR 1136, INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Champenoux, France
| | - Anaïs Rancon
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Elodie Drula
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Hayat Hage
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Delphine Chaduli
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Anne Favel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Sacha Grisel
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Bernard Henrissat
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isabelle Herpoël-Gimbert
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | | | - Didier Chevret
- INRA, UMR1319, Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Matthieu Hainaut
- UMR 7257, CNRS, Aix-Marseille Univ, Marseille, France
- INRA, USC 1408, AFMB, Marseille, France
| | - Junyan Lin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Laurence Lesage-Meessen
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - David Navarro
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- CIRM-CF, UMR1163, INRA, Aix-Marseille Univ, Marseille, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | - Simeng Zhou
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- Present Address: Institut des Sciences Moléculaires de Marseille, UMR 7313, CNRS, Aix-Marseille Université, Marseille, France
| | - Sana Raouche
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- Aix Marseille Univ, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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Niderhaus C, Garrido M, Insani M, Campos E, Wirth S. Heterologous production and characterization of a thermostable GH10 family endo-xylanase from Pycnoporus sanguineus BAFC 2126. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. Nat Chem Biol 2018; 14:306-310. [DOI: 10.1038/nchembio.2558] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022]
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25
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Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes. Fungal Genet Biol 2017; 112:40-46. [PMID: 28803908 DOI: 10.1016/j.fgb.2017.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/25/2017] [Accepted: 08/07/2017] [Indexed: 01/21/2023]
Abstract
Basidiomycete fungi can degrade a wide range of plant biomass, including living and dead trees, forest litter, crops, and plant matter in soils. Understanding the process of plant biomass decay by basidiomycetes could facilitate their application in various industrial sectors such as food & feed, detergents and biofuels, and also provide new insights into their essential biological role in the global carbon cycle. The fast expansion of basidiomycete genomic and functional genomics data (e.g. transcriptomics, proteomics) has facilitated exploration of key genes and regulatory mechanisms of plant biomass degradation. In this study, we comparatively analyzed 22 transcriptome datasets from basidiomycetes related to plant biomass degradation, and identified 328 commonly induced genes and 318 repressed genes, and defined a core set of carbohydrate active enzymes (CAZymes), which was shared by most of the basidiomycete species. High conservation of these CAZymes in genomes and similar regulation pattern in transcriptomics data from lignocellulosic substrates indicate their key role in plant biomass degradation and need for their further biochemical investigation.
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Berrin JG, Rosso MN, Abou Hachem M. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases. Carbohydr Res 2017; 448:155-160. [DOI: 10.1016/j.carres.2017.05.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/29/2022]
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27
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Miyauchi S, Navarro D, Grisel S, Chevret D, Berrin JG, Rosso MN. The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PLoS One 2017; 12:e0175528. [PMID: 28394946 PMCID: PMC5386290 DOI: 10.1371/journal.pone.0175528] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/27/2017] [Indexed: 01/22/2023] Open
Abstract
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.
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Affiliation(s)
- Shingo Miyauchi
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - David Navarro
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Sacha Grisel
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Didier Chevret
- PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Guy Berrin
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noelle Rosso
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- * E-mail:
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