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1. A single workflow for multi-species blood transcriptomics

Author

Elody Orcel, Hayat Hage, May Taha, Noémie Boucher, Emilie Chautard, Virginie Courtois, and Adrien Saliou

Subjects
Preclinical models, Clinical models, Blood samples, RNA extraction, Library preparation, Total RNA sequencing, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Blood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for applications in diagnostics and monitoring of the immune response to vaccines. However, multi-species transcriptomic analysis is still a challenge from a technological point of view and a standardized workflow is urgently needed to allow interspecies comparisons. Results Here, we propose a single and complete total RNA-Seq workflow to generate reliable transcriptomic data from blood samples from humans and from animals typically used in preclinical models. Blood samples from a maximum of six individuals and four different species (rabbit, non-human primate, mouse and human) were extracted and sequenced in triplicates. The workflow was evaluated using different wet-lab and dry-lab criteria, including RNA quality and quantity, the library molarity, the number of raw sequencing reads, the Phred-score quality, the GC content, the performance of ribosomal-RNA and globin depletion, the presence of residual DNA, the strandness, the percentage of coding genes, the number of genes expressed, and the presence of saturation plateau in rarefaction curves. We identified key criteria and their associated thresholds to be achieved for validating the transcriptomic workflow. In this study, we also generated an automated analysis of the transcriptomic data that streamlines the validation of the dataset generated. Conclusions Our study has developed an end-to-end workflow that should improve the standardization and the inter-species comparison in blood transcriptomics studies. In the context of vaccines and drug development, RNA sequencing data from preclinical models can be directly compared with clinical data and used to identify potential biomarkers of value to monitor safety and efficacy.

Published
2024
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2. Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Author

Céline Elie, Magali Perret, Hayat Hage, Erwin Sentausa, Amy Hesketh, Karen Louis, Asmaà Fritah-Lafont, Philippe Leissner, Carole Vachon, Hervé Rostaing, Frédéric Reynier, Gaspard Gervasi, and Adrien Saliou

Subjects
Medicine, Science
Abstract

Abstract The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.

Published
2023
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3. Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass

Author

Shingo Miyauchi, Anaïs Rancon, Elodie Drula, Hayat Hage, Delphine Chaduli, Anne Favel, Sacha Grisel, Bernard Henrissat, Isabelle Herpoël-Gimbert, Francisco J. Ruiz-Dueñas, Didier Chevret, Matthieu Hainaut, Junyan Lin, Mei Wang, Jasmyn Pangilinan, Anna Lipzen, Laurence Lesage-Meessen, David Navarro, Robert Riley, Igor V. Grigoriev, Simeng Zhou, Sana Raouche, and Marie-Noëlle Rosso

Subjects
Solid-state fermentation, Lignin degradation, Polyporus brumalis, Plant biomass transformation, Fuel, TP315-360, Biotechnology, TP248.13-248.65
Abstract

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.

Published
2018
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4. Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers

Author

Hayat Hage and Marie-Noëlle Rosso

Subjects
CAZyme, fungal ecology, evolution, plant-cell wall, plant biomass, Biology (General), QH301-705.5
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.

Published
2021
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5. An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi

Author

Hayat Hage, Julie Couillaud, Asaf Salamov, Margot Loussouarn-Yvon, Fabien Durbesson, Elena Ormeño, Sacha Grisel, Katia Duquesne, Renaud Vincentelli, Igor Grigoriev, Gilles Iacazio, Marie-Noëlle Rosso, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Carnot 3BCAR, INRAE, MICA Division, Ecole Doctorale Sciences Chimiques ED 250 - Aix Marseille Université, A*midex Foundation, IM2B - Institute of Microbiology, Bioenergies and Biotechnology, Department of Energy Joint Genome Institute, and IMBE - Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale

Subjects
sesquiterpene, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], terpene synthase, General Medicine, fungi, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Polyporales, genome, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract

Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.

Published
2023

6. Tandem metalloenzymes gate plant cell entry by pathogenic fungi

Author

Bastien Bissaro, Sayo Kodama, Takumi Nishiuchi, Anna Maria Díaz-Rovira, Hayat Hage, David Ribeaucourt, Mireille Haon, Sacha Grisel, A. Jalila Simaan, Fred Beisson, Stephanie M. Forget, Harry Brumer, Marie-Noëlle Rosso, Victor Guallar, Richard O’Connell, Mickaël Lafond, Yasuyuki Kubo, Jean-Guy Berrin, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté d’agriculture, Université Setsunan, 573-0101 Osaka, Japon., Division de génomique fonctionnelle, Centre de recherche scientifique avancée, Université de Kanazawa, 920-0934 Kanazawa, Japon., Barcelona Supercomputing, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Michael Smith Laboratories, Université de la Colombie-Britannique, ICREA, Passeig Lluís Companys, BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculté d’agriculture, Université Setsunan, and Barcelona Supercomputing Center

Subjects
Fungal Proteins, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Genòmica, Multidisciplinary, Fungal plant diseases, Crop protection, Virulence, Plant Cells, Metalloproteins, Fungi, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Enzims, Fungal phytopathogens
Abstract

Global food security is endangered by fungal phytopathogens causing devastating crop production losses. Many of these pathogens use specialized appressoria cells to puncture plant cuticles. Here, we unveil a pair of alcohol oxidase–peroxidase enzymes to be essential for pathogenicity. Using Colletotrichum orbiculare, we show that the enzyme pair is cosecreted by the fungus early during plant penetration and that single and double mutants have impaired penetration ability. Molecular modeling, biochemical, and biophysical approaches revealed a fine-tuned interplay between these metalloenzymes, which oxidize plant cuticular long-chain alcohols into aldehydes. We show that the enzyme pair is involved in transcriptional regulation of genes necessary for host penetration. The identification of these infection-specific metalloenzymes opens new avenues on the role of wax-derived compounds and the design of oxidase-specific inhibitors for crop protection. Fungal phytopathogens secrete tandem metalloenzymes that catalyze cuticle oxidation and drive plant cell entry This study was supported by the “Agence Nationale de la Recherche” and by the Natural Sciences and Engineering Research Council of Canada through the ANR-NSERC project “FUNTASTIC” (ANR-17-CE07-0047, STPGP 493781-16). We are grateful to MANE & Fils and the “Association Nationale Recherche Technologie” (ANRT) for funding the Ph.D. fellowship of D.R. (grant no. 2017/1169). Work in Japan was supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research—KAKENHI, grant numbers 15H05780 and 20H02989 to Y.K., and 20K15529 to S.K. Peer Reviewed "Article signat per 18 autors/es: Bastien Bissaro and Sayo Kodama and Takumi Nishiuchi and Anna Maria Díaz-Rovira and Hayat Hage and David Ribeaucourt and Mireille Haon and Sacha Grisel and A. Jalila Simaan and Fred Beisson and Stephanie M. Forget and Harry Brumer and Marie-Noëlle Rosso and Victor Guallar and Richard O’Connell and Mickaël Lafond and Yasuyuki Kubo and Jean-Guy Berrin "

Published
2022

7. In vitro Applications of the Terpene Mini‐Path 2.0

Author

Julie Couillaud, Agnès Amouric, Elise Courvoisier‐Dezord, Létitia Leydet, Nicolas Schweitzer, Marie‐Noëlle Rosso, Hayat Hage, Margot Loussouarn‐Yvon, Renaud Vincentelli, Jean‐Louis Petit, Véronique de Berardinis, Mireille Attolini, Marc Maresca, Katia Duquesne, Gilles Iacazio, Chalmers University of Technology [Gothenburg, Sweden], Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and J. C. thanks the Ministère de la Recherche for Ph.D. Grant N° 2021AIXM0188/010ED250.

Subjects
[CHIM.ORGA]Chemical Sciences/Organic chemistry, cyclobutyl terpenoid derivatives, [SDV]Life Sciences [q-bio], Organic Chemistry, (+)-δ-cadinol, farnesyl diphosphate, [CHIM.CATA]Chemical Sciences/Catalysis, MESH: Alkyl and Aryl Transferases, Biochemistry, MESH: Terpenes, MESH: Diphosphates, tryprostatin B, MESH: Transferases, terpene mini-path, Molecular Medicine, [CHIM]Chemical Sciences, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology
Abstract

International audience; In 2019 four groups reported independently the development of a simplified enzymatic access to the diphosphates (IPP and DMAPP) of isopentenol and dimethylallyl alcohol (IOH and DMAOH). The former are the two universal precursors of all terpenes. We report here on an improved version of what we call the terpene mini-path as well as its use in enzymatic cascades in combination with various transferases. The goal of this study is to demonstrate the in vitro utility of the TMP in, i) synthesizing various natural terpenes, ii) revealing the product selectivity of an unknown terpene synthase, or iii) generating unnatural cyclobutylated terpenes.

Published
2022

8. Unravelling the role of alcohol copper radical oxidases in fungal plant pathogens

Author

A Simaan, Hayat Hage, Fred Beisson, Sacha Grisel, Harry Brumer, Marie-Noëlle Rosso, Bastien Bissaro, David Ribeaucourt, Jean-Guy Berrin, Stephanie M. Forget, Richard J. O'Connell, Mickael Lafond, Mireille Haon, Yasuyuki Kubo, and Sayo Kodama

Subjects
chemistry.chemical_compound, Biochemistry, Chemistry, chemistry.chemical_element, Alcohol, Copper
Abstract

Copper radical oxidases (CRO) form a class of enzymes with a longstanding history encompassing diverse substrate specificities. While the biological function of most CROs remains unknown, we observed that CROs active on aliphatic alcohols are found only in fungal plant pathogens. Here, we unveil the role of these CROs and the identity of their natural redox partner, a haem-iron peroxidase. Combining multiscale approaches, we report that Colletotrichum and Magnaporthe appressoria (specialized cells that puncture the plant cuticles) co-secrete this pair of metalloenzymes early during penetration. We show in vivo that mutant appressoria lacking either or both enzymes have impaired penetration ability and pathogenicity. We reveal in vitro a finely-tuned enzyme interplay is responsible for the oxidation of plant cuticular long-chain alcohols into aldehyde products, suggested to act as key molecular signals in the fungal infection machinery. Our results open new avenues to design oxidase-specific inhibitors as anti-penetrants for crop protection.

Published
2021

9. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

Author

Lionel Tarrago, Hayat Hage, Marie-Noëlle Rosso, Biodiversité et Biotechnologie Fongiques (BBF), and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0301 basic medicine, thiol oxidoreductase, [SDV]Life Sciences [q-bio], Reductase, Protein oxidation, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, methionine sulfoxide, Methionine, 0302 clinical medicine, Physiology (medical), protein oxidation, genome, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, Methionine sulfoxide, Eukaryota, Sulfoxide, 15. Life on land, biology.organism_classification, 030104 developmental biology, chemistry, Methionine Sulfoxide Reductases, Horizontal gene transfer, methionine sulfoxide reductase, Methionine sulfoxide reductase, horizontal gene transfer, fungi, Oxidation-Reduction, 030217 neurology & neurosurgery, Bacteria, MSRA
Abstract

Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.HighlightsFree and protein-bound methionine can be oxidized into methionine sulfoxide (MetO).Methionine sulfoxide reductases (Msr) reduce MetO in most organisms.Sequence characterization and phylogenomics revealed strong conservation of Msr in fungi.fRMsr is widely conserved in unicellular and multicellular fungi.Some msr genes were acquired from bacteria via horizontal gene transfers.

Published
2021

10. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

Author

Hayat, Hage, Shingo, Miyauchi, Máté, Virágh, Elodie, Drula, Byoungnam, Min, Delphine, Chaduli, David, Navarro, Anne, Favel, Manon, Norest, Laurence, Lesage-Meessen, Balázs, Bálint, Zsolt, Merényi, Laura, de Eugenio, Emmanuelle, Morin, Angel T, Martínez, Petr, Baldrian, Martina, Štursová, María Jesús, Martínez, Cenek, Novotny, Jon K, Magnuson, Joey W, Spatafora, Sundy, Maurice, Jasmyn, Pangilinan, Willian, Andreopoulos, Kurt, LaButti, Hope, Hundley, Hyunsoo, Na, Alan, Kuo, Kerrie, Barry, Anna, Lipzen, Bernard, Henrissat, Robert, Riley, Steven, Ahrendt, László G, Nagy, Igor V, Grigoriev, Francis, Martin, Marie-Noëlle, Rosso, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Biological Research Centre [Szeged] (BRC), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), US Department of Energy Joint Genome Institute, University of California, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Centro de Investigaciones Biológicas Margarita Salas, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Microbiology of the ASCR, v. v. i. [Prague, Czech Republic], Technical University of Ostrava [Ostrava] (VSB), Pacific Northwest National Laboratory (PNNL), Department of Botany and Plant Pathology, Oregon State University (OSU), University of Oslo (UiO), King Abdulaziz University, Institute of Biology [Budapest], Faculty of Sciences [Budapest], Eötvös Loránd University (ELTE)-Eötvös Loránd University (ELTE), United States Department of Energy (DOE) DE-AC02-05CH11231DE-SC0019427Institut Carnot 3BCARRegion Provence-Alpes-Cote d'AzurGroupement de Recherche Genomique EnvironnementaleRegion Grand-EstEuropean CommissionHungarian Academy of Sciences' Momentum Program LP2019-13/2019Spanish Ministry of Economy, Industry and Competitiveness BIO2017-86559-RConsejo Superior de Investigaciones Cientificas PIE-201620E081Agencia Estatal de InvestigacionMinistry of Science, Innovation and Universities RTI2018-093683-B-I00Grant Agency of the Czech Republic 17-20110SFrench National Research Institute for Agriculture, Food and Environment, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), University of California (UC), Joint Genome Institute (US), Institut Carnot Pasteur MS, l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (France), Conseil Régional Provence-Alpes-Côte d'Azur, Centre National de la Recherche Scientifique (France), Labex ARBRE, Conseil Régional de Lorraine, European Commission, Hungarian Academy of Sciences, Ministerio de Economía, Industria y Competitividad (España), Consejo Superior de Investigaciones Científicas (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Czech Science Foundation, Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Favel, Anne, Lesage-Meessen, Laurence, Merényi, Z., Eugenio, Laura I. de, Morin, Emmanuelle, Martínez, Ángel T., Baldrian, Petr, Stursová, Martina, Martínez, María Jesús, Novotny, Cenek, Maurice, Sundy, Andreopoulos, William, LaButti, Kurt M., Na, Hyunsoo, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Ahrendt, Steven, Grigoriev, Igor V., Rosso, Marie-Noëlle, Hage, Hayat [0000-0003-4118-1816], Miyauchi, Shingo [0000-0002-0620-5547], Virágh, Máté [0000-0002-2278-1288], Drula, Elodie [0000-0002-9168-5214], Min, Byoungnam [0000-0002-7469-088X], Favel, Anne [0000-0003-2255-3637], Lesage-Meessen, Laurence [0000-0003-2275-2978], Merényi, Z. [0000-0003-1114-3739], Eugenio, Laura I. de [0000-0002-0496-8663], Morin, Emmanuelle [0000-0002-7268-972X], Martínez, Ángel T. [0000-0002-1584-2863], Baldrian, Petr [0000-0002-8983-2721], Stursová, Martina [0000-0003-1387-6426], Martínez, María Jesús [0000-0003-2166-1097], Novotny, Cenek [0000-0003-3274-471X], Maurice, Sundy [0000-0002-5376-0981], Andreopoulos, William [0000-0001-9097-1123], LaButti, Kurt M. [0000-0002-5838-1972], Na, Hyunsoo [0000-0002-4386-017X], Barry, Kerrie [0000-0002-8999-6785], Lipzen, Anna [0000-0003-2293-9329], Henrissat, Bernard [0000-0002-3434-8588], Ahrendt, Steven [0000-0002-3029-2126], Grigoriev, Igor V. [0000-0002-3136-8903], and Rosso, Marie-Noëlle [0000-0001-8317-7220]

Subjects
Special Issue Articles, [SDV]Life Sciences [q-bio], Wood decay, Microbiology, Fungal Proteins, Genetics, Plant cell wall, Fungal ecology, Phylogeny, Evolutionary Biology, Genome, Basidiomycota, Human Genome, Special Issue Article, Phylogenomics, Biodiversity, Wood, Climate Action, Fungal, Genome, Fungal, Polyporales, Transcriptome, Lignocellulose, CAZymes, Biotechnology
Abstract

17 p.-7 fig., Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete., We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources.The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signaling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and Lytic Polysaccharide Monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition.Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay., This work was supported by the U.S. Department of Energy Joint Genome Institute, a Department of Energy Office of Science User Facility (grant # DE-AC02-05CH11231, DESC0019427 to I.V.G. and B.M.); Institut Carnot 3BCAR, the French National Research Institute for Agriculture, Food and Environment, The Region Provence Alpes Côte d’Azur and the Groupement de Recherche Génomique Environnementale to H.H.; the Laboratory of Excellence ARBRE (grant # ANR-11-LABX-0002-01 to F.M.); the Region Lorraine and the European Regional Development Fund to F.M.; the Hungarian Academy of Sciences’ Momentum Program (grant # LP2019-13/2019 to L.G.N.); the Spanish Ministry of Economy, Industry and Competitiveness (grant # BIO2017-86559-R to A.T.M.); the Consejo Superior de Investigaciones Científicas (grant # PIE-201620E081 to A.T.M.); the Agencia Estatal de Investigación, the European Regional Development Fund and the Ministry of Science, Innovation and Universities (grant # RTI2018-093683-B-I00 to L.D.E. and M.J.M.) and the Czech Science Foundation (grant# 17-20110S to P.B. and M.Š.).

Published
2021

11. Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass

Author

Junyan Lin, Anaïs Rancon, Delphine Chaduli, Sana Raouche, Marie-Noëlle Rosso, Bernard Henrissat, Anna Lipzen, Isabelle Herpoël-Gimbert, Didier Chevret, Matthieu Hainaut, Hayat Hage, Elodie Drula, Igor V. Grigoriev, David Navarro, Shingo Miyauchi, Francisco J. Ruiz-Dueñas, Mei Wang, Laurence Lesage-Meessen, Sacha Grisel, Robert Riley, Jasmyn Pangilinan, Anne Favel, Simeng Zhou, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, Centro de Investigaciones Biológicas (CIB), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Department of Plant and Microbial Biology, University of California, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), ANR-12-BIME-0009 ANR-14-CE06-0020-01, ANR-10-EQPX-29-01Office of Science of the U.S. Department of Energy, DE-AC02-05CH11231, Spanish Ministry of Economy, Industry and Competitiveness BIO2017-86559-R, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC), Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Department of Energy (US), Ministerio de Economía, Industria y Competitividad (España), University of California (UC), and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Polyporus brumalis, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Biomass, Applied Microbiology and Biotechnology, 7. Clean energy, chemistry.chemical_compound, Solid-state fermentation, Lignin, Polyporales, 0303 health sciences, Plant biomass transformation, biology, Lignin degradation, food and beverages, Chemical Engineering, approche omique, lignine, Polyporus, General Energy, amélioration des champignons, procédé biotechnologique, Biotechnology, lcsh:Biotechnology, 030106 microbiology, Lignocellulosic biomass, lignin, Biotechnologies, Fungus, Management, Monitoring, Policy and Law, complex mixtures, lcsh:Fuel, Industrial Biotechnology, 03 medical and health sciences, Affordable and Clean Energy, lcsh:TP315-360, lcsh:TP248.13-248.65, Botany, Oxidative enzyme, Genetics, Cellulose, 030304 developmental biology, biomasse végétale, Renewable Energy, Sustainability and the Environment, 030306 microbiology, fungi, technology, industry, and agriculture, enzyme oxydative, 15. Life on land, biology.organism_classification, 030104 developmental biology, fermentation à l'état solide, chemistry, Fermentation, polyporus
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., This work was supported by The French National Agency for Research (ANR-12-BIME-0009, ANR-14-CE06-0020-01). The work by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The work by CSIC was supported by the Spanish Ministry of Economy, Industry and Competitiveness (BIO2017-86559-R). The HPC resources of Aix-Marseille Université was supported by The French National Agency for Research (ANR-10-EQPX-29-01).

Published
2018

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