1. The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown
- Author
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Levasseur, Anthony, Lomascolo, Anne, Chabrol, Olivier, Ruiz-Dueñas, Francisco J, Boukhris-Uzan, Eva, Piumi, François, Kües, Ursula, Ram, Arthur F J, Murat, Claude, Haon, Mireille, Benoit, Isabelle, Arfi, Yonathan, Chevret, Didier, Drula, Elodie, Kwon, Min Jin, Gouret, Philippe, Lesage-Meessen, Laurence, Lombard, Vincent, Mariette, Jérôme, Noirot, Céline, Park, Joohae, Patyshakuliyeva, Aleksandrina, Sigoillot, Jean Claude, Wiebenga, Ad, Wösten, Han A B, Martin, Francis, Coutinho, Pedro M, de Vries, Ronald P, Martínez, Angel T, Klopp, Christophe, Pontarotti, Pierre, Henrissat, Bernard, Record, Eric, Wosten, Han, Molecular Microbiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigaciones Biológicas (CIB), Institut des Sciences Moléculaires de Marseille (ISM2), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Molecular Wood Biotechnology and Technical Mycology, Georg-August-University [Göttingen], Department of Molecular Microbiology and Biotechnology, Universiteit Leiden [Leiden], Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Faculty of Biological Chemistry, Weizmann Institute of Science, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Department of Microbiology, Kluyver Cenre for Genomics of Industrial Fermentation, Utrecht University [Utrecht], Molecular Microbiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Georg-August-University = Georg-August-Universität Göttingen, Universiteit Leiden, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Weizmann Institute of Science [Rehovot, Israël], Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), European Commission, and Ministerio de Economía y Competitividad (España)
- Subjects
CAZy ,Glycosylation ,Proteome ,Auxiliary activities ,[SDV]Life Sciences [q-bio] ,7. Clean energy ,Lignin ,Fungal Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Manganese peroxidase ,Botany ,Genetics ,Versatile peroxidase ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,Fungal protein ,biology ,030306 microbiology ,Molecular Sequence Annotation ,Lignin peroxidase ,Pycnoporus cinnabarinus ,Sequence Analysis, DNA ,biology.organism_classification ,Wood ,Pycnoporus ,White-rot fungi ,chemistry ,Peroxidases ,Genetic Loci ,Oxidoreductase ,Genome, Fungal ,Protein Processing, Post-Translational ,Lignocellulose ,Biotechnology ,Research Article ,Genome annotation - Abstract
24 p.-8 fig.-4 tab.-- Levasseur, Anthony et al., [Background] Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology., [Results] The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases., [Conclusions] With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass., This work was funded by the Commission of the European Communities through the BIORENEW project (NMP2-CT-2006-026456 “White Biotechnology for added-value products from re newable plant polymers: Design of tailor-made biocatalysts and new industrial bioprocesses”) and the PEROXICATS project (KBBE-2010-4-265397 “Novel and more robust fungal peroxidases as industrial biocatalysts.”), and by the Spanish Ministerio de Economía y Competitividad (MINECO) through the HIPOP project (BIO2011-26694, “Screening and engineering of new high-redox-potential peroxidases”).
- Published
- 2014
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