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1. Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa.

Author

Arfi Y, Buée M, Marchand C, Levasseur A, and Record E

Subjects
Ascomycota classification, Ascomycota genetics, Ascomycota growth & development, Biodiversity, Ecology, Ecosystem, Fungi genetics, Fungi growth & development, New Caledonia, Avicennia microbiology, Fungi classification, Rhizophoraceae microbiology
Abstract

Fungi are important actors in ecological processes and trophic webs in mangroves. Although saprophytic fungi occurring in the intertidal part of mangrove have been well studied, little is known about the diversity and structure of the fungal communities in this ecosystem or about the importance of functional groups like pathogens and mutualists. Using tag-encoded 454 pyrosequencing of the ITS1, ITS2, nu-ssu-V5 and nu-ssu-V7 regions, we studied and compared the fungal communities found on the marine and aerial parts of Avicennia marina and Rhizophora stylosa trees in a mangrove in New Caledonia. A total of 209,544 reads were analysed, corresponding to several thousand molecular operational taxonomic units (OTU). There is a marked zonation in the species distribution, with most of the OTU being found specifically in one of the microhabitat studied. Ascomycetes are the dominant phylum (82%), Basidiomycetes are very rare (3%), and 15% of the sequences correspond to unknown taxa. Our results indicate that host specificity is a key factor in the distribution of the highly diverse fungal communities, in both the aerial and intertidal parts of the trees. This study also validates the usefulness of multiple markers in tag-encoded pyrosequencing to consolidate and refine the assessment of the taxonomic diversity., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Published
2012
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2. Fungal protein production: design and production of chimeric proteins.

Author

Punt PJ, Levasseur A, Visser H, Wery J, and Record E

Subjects
Biotechnology, Fungal Proteins chemistry, Fungal Proteins genetics, Fungi chemistry, Fungi genetics, Genetic Engineering, Recombinant Proteins chemistry, Recombinant Proteins genetics, Fungal Proteins metabolism, Fungi enzymology, Recombinant Proteins metabolism
Abstract

For more than a century, filamentous fungi have been used for the production of a wide variety of endogenous enzymes of industrial interest. More recently, with the use of genetic engineering tools developed for these organisms, this use has expanded for the production of nonnative heterologous proteins. In this review, an overview is given of examples describing the production of a special class of these proteins, namely chimeric proteins. The production of two types of chimeric proteins have been explored: (a) proteins grafted for a specific substrate-binding domain and (b) fusion proteins containing two separate enzymatic activities. Various application areas for the use of these chimeric proteins are described.

Published
2011
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3. FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.

Author

Levasseur A, Piumi F, Coutinho PM, Rancurel C, Asther M, Delattre M, Henrissat B, Pontarotti P, Asther M, and Record E

Subjects
Fungal Proteins genetics, Oxidoreductases genetics, Sequence Homology, Amino Acid, Databases, Protein, Fungal Proteins classification, Fungal Proteins metabolism, Fungi enzymology, Lignin metabolism, Oxidoreductases classification, Oxidoreductases metabolism
Abstract

The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.

Published
2008
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4. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., and Grigoriev, Igor V.

Published
2014

5. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

Author

DiGuistini, Scott, Wang, Ye, Liao, Nancy Y., Taylor, Greg, Tanguay, Philippe, Feau, Nicolas, Henrissat, Bernard, Chan, Simon K., Hesse-Orce, Uljana, Alamouti, Sepideh Massoumi, Tsui, Clement K. M., Docking, Roderick T., Levasseur, Anthony, Haridas, Sajeet, Robertson, Gordon, Birol, Inanc, Holt, Robert A., Marra, Marco A., Hamelin, Richard C., Hirst, Martin, Jones, Steven J. M., Bohlmann, Jörg, Breuil, Colette, and Croteau, Rodney B.

Published
2011

6. Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution

Author

Devaux, Christian, Pinault, Lucile, Delerce, Jérémy, Raoult, Didier, Levasseur, Anthony, Frutos, Roger, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre National de la Recherche Scientifique (CNRS), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, viruses, fungi, COVID-19, ACE2, COVID-19 vaccines, Review, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, NRP-1, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, variant viruses, mink coronavirus
Abstract

International audience; The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines.

Published
2021

7. Additional file 9: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
fungi
Abstract

Figure S5. Multiple alignments of seven MITEs involved in HTs between viruses and its cellular hosts or species related to their hosts. (PDF 5206Â kb)

Published
2018
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8. Additional file 7: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

Author

Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiong, Xiao-Min, Luchetti, Andrea, Raoult, Didier, Levasseur, Anthony, Santini, Sebastien, Abergel, Chantal, Legendre, Matthieu, Jean-Michel Drezen, BĂŠliveau, Catherine, Cusson, Michel, Jiang, Shen-Hua, Bao, Hai-Ou, Sun, Cheng, Bureau, Thomas, Cheng, Peng-Fei, Min-Jin Han, Zhang, Ze, Xiao-Gu Zhang, and Fang-Yin Dai

Subjects
endocrine system, integumentary system, fungi
Abstract

Figure S4. Determination of the boundary and TSD of seven MITEs identified in viral hosts or species related to their hosts. A Multiple alignments of full-length copies as well as the flanking sequences of each MITE. TSD is shown using red color and the boundary is indicated usingi black shading. B Empty paralogous sites of five MITEs identified in viral cellular hosts. (PDF 2219Â kb)

Published
2018
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9. Additional file 8: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, inorganic chemicals, nervous system, fungi
Abstract

Effect of SHAM and KCN on fungal growth and sporulation. (PDF 252 kb)

Published
2017
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10. Additional file 6: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, animal structures, nervous system, fungi
Abstract

Overview of number of putative orthologs/paralogs in the compared fungal species related to primary carbon metabolism. (PDF 237 kb)

Published
2017
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11. Additional file 5: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, behavior and behavior mechanisms, reproductive and urinary physiology
Abstract

Expression of mating and pheromone-signalling pathway genes in representative asexual aspergilli. (PDF 488 kb)

Published
2017
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12. Comparative Genome Analysis of Basidiomycete Fungi Reveals the Genetic Signatures of Wood Degraders

Author

Riley, Robert, Salamov, Asaf, Morin, Emmanuelle, Nagy, Laszlo, Manning, Gerard, Baker, Scott, Brown, Daren, Henrissat, Bernard, Levasseur, Anthony, Hibbett, David, Martin, Francis, and Grigoriev, Igor

Subjects
fungi, technology, industry, and agriculture, food and beverages, complex mixtures
Abstract

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum between the white rot and brown rot modes of wood decay. Patterns of protein kinases, secondary metabolic enzymes, and secreted proteins shed additional light on the broad array of phenotypes found in the basidiomycetes. We suggest that the lignocellulose gene content of an organism can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

Published
2012

13. Comparative Genome Analysis of Basidiomycete Fungi

Author

Riley, Robert, Salamov, Asaf, Morin, Emmanuelle, Nagy, Laszlo, Manning, Gerard, Baker, Scott, Brown, Daren, Henrissat, Bernard, Levasseur, Anthony, Hibbett, David, Martin, Francis, and Grigoriev, Igor

Subjects
fungi, technology, industry, and agriculture, food and beverages, complex mixtures
Abstract

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

Published
2012

14. Fungal Strategies for Lignin Degradation

Author

Sigoillot, Jean-Claude, Berrin, Jean-Guy, Bey, Mathieu, Lesage-Meessen, Laurence, Levasseur, Anthony, Lomascolo, Anne, Record, Eric, Boukhris-uzan, Eva, Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
ERYNGII VERSATILE PEROXIDASE, MANGANESE PEROXIDASE, PLEUROTUS-ERYNGII, [SDV]Life Sciences [q-bio], fungi, technology, industry, and agriculture, food and beverages, macromolecular substances, FLAVOCYTOCHROME CELLOBIOSE DEHYDROGENASE, BROWN-ROT, complex mixtures, BASIDIOMYCETE PHANEROCHAETE-CHRYSOSPORIUM, MULTIPLE SEQUENCE ALIGNMENT, ARYL-ALCOHOL OXIDASE, SITE-DIRECTED MUTAGENESIS, WHITE-ROT FUNGUS
Abstract

Document Type : Book Chapter; A number of microorganisms, bacteria and filamentous fungi, are able to degrade lignocellulosic components to various extents. However, only a few ones can degrade lignins, among which wood-rotting fungi. White-rot fungi, the most frequent ones, mineralize cell wall components (cellulose, hemicelluloses and lignins) and extensively degrade lignins, which results in a bleached aspect of decayed wood. Fungal lignin degradation involves secreted heme-peroxidases and laccases that use oxidants as electron acceptors (H2O2 and O-2). The three main heme-peroxidases are lignin peroxidases, manganese peroxidases and versatile peroxidases. Lignin and versatile peroxidases are able to oxidize non-phenolic lignin units. By contrast, manganese peroxidase needs diffusible Mn-chelated ions and mainly degrades lignin units with free phenolic groups. Other peroxidases have been recently found, such as dye peroxidases with potential applications in bioremediation and other industrial processes. Peroxidases need the cooperation of other oxidases such as glyoxal or aryl-alcohol oxidases to produce hydrogen peroxide. The recent availability of complete fungal genomes opens innovative opportunities to annotate lignocellulolytic gene families. Phylogenetic approaches are unique tools to comparatively analyse these data and predict or infer gene function. The increasing number of putative lignin-degrading enzymes emerging from genome analyses requires the development of high-throughput expression systems to meet the demands of industries. Several expression systems have been developed to produce more efficient recombinant 'ligninases' and auxiliary enzymes. Fungi and yeasts are useful hosts for the production of recombinant enzymes, but only a few ones are devoted to ligninase production. In this review, we give a survey of the main fungal and enzymatic actors of lignin degradation before discussing the phylogenetic inference strategy used to predict lignocellulolytic enzymes and reviewing the recombinant production of these enzymes in fungal hosts.

Published
2012

15. Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune

Author

Ohm, Robin A., Jong, Jan F. de, Lugones, Luis G., Aerts, Andrea, Kothe, Erika, Stajich, Jason E., Vries, Ronald P. de, Record, Eric, Levasseur, Anthony, Baker, Scott E., Bartholomew, Kirk A., Coutinho, Pedro M., Erdmann, Susann, Fowler, Thomas J., Gathman, Allen C., Lombard, Vincent, Henrissat, Bernard, Knabe, Nicole, Kues, Ursula, Lilly, Walt W., Lindquist, Erika, Lucas, Susan, Magnuson, Jon K., Piumi, Francois, Raudaskoski, Marjatta, Salamov, Asaf, Schmutz, Jeremy, Schwarze, Francis W.M.R., Kuyk, Patricia A. van, Horton, J. Stephen, Grigoriev, Igor V., and Wosten, Han A.B.

Subjects
gene expression analysis, fungi, S. commune, food and beverages
Abstract

The wood degrading fungus Schizophyllum commune is a model system for mushroom development. Here, we describe the 38.5 Mb assembled genome of this basidiomycete and application of whole genome expression analysis to study the 13,210 predicted genes. Comparative analyses of the S. commune genome revealed unique wood degrading machinery and mating type loci with the highest number of reported genes. Gene expression analyses revealed that one third of the 471 identified transcription factor genes were differentially expressed during sexual development. Two of these transcription factor genes were deleted. Inactivation of fst4 resulted in the inability to form mushrooms, whereas inactivation of fst3 resulted in more but smaller mushrooms than wild-type. These data illustrate that mechanisms underlying mushroom formation can be dissected using S. commune as a model. This will impact commercial production of mushrooms and the industrial use of these fruiting bodies to produce enzymes and pharmaceuticals

Published
2010

16. Differential Gene Expression in Pycnoporus coccineus during Interspecific Mycelial Interactions with Different Competitors.

Author

Arfi, Yonathan, Levasseur, Anthony, and Record, Eric

Subjects
*GENE expression, *COMPETITION (Biology), *FUNGI, *POLYMERASE chain reaction, *METABOLITES, *METABOLIC detoxification
Abstract

Fungi compete against each other for environmental resources. These interspecific combative interactions encompass a wide range of mechanisms. In this study, we highlight the ability of the white-rot fungus Pycnoporus coccineus to quickly overgrow or replace a wide range of competitor fungi, including the gray-mold fungus Botrytis cinerea and the brown-rot fungus Coniophora puteana. To gain a better understanding of the mechanisms deployed by P. coccineus to compete against other fungi and to assess whether common pathways are used to interact with different competitors, differential gene expression in P. coccineus during cocultivation was assessed by transcriptome sequencing and confirmed by quantitative reverse transcription-PCR analysis of a set of 15 representative genes. Compared with the pure culture, 1,343 transcripts were differentially expressed in the interaction with C. puteana and 4,253 were differentially expressed in the interaction with B. cinerea, but only 197 transcripts were overexpressed in both interactions. Overall, the results suggest that a broad array of functions is necessary for P. coccineus to replace its competitors and that different responses are elicited by the two competitors, although a portion of the mechanism is common to both. However, the functions elicited by the expression of specific transcripts appear to converge toward a limited set of roles, including detoxification of secondary metabolites. [ABSTRACT FROM AUTHOR]

Published
2013
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17. Genome sequence of the model mushroom Schizophyllum commune.

Author

Ohm, Robin A., De Jong, Jan F., Lugones, Luis G., Aerts, Andrea, Kothe, Erika, Stajich, Jason E., De Vries, Ronald P., Record, Eric, Levasseur, Anthony, Baker, Scott E., Bartholomew, Kirk A., Coutinho, Pedro M., Erdmann, Susann, Fowler, Thomas J., Gathman, Allen C., Lombard, Vincent, Henrissat, Bernard, Knabe, Nicole, Kües, Ursula, and Lilly, Walt W.

Subjects
FUNGI, FOOD, METABOLITES, ENZYMES, LIGNOCELLULOSE, BIOMASS, TRANSCRIPTION factors, DRUGS
Abstract

Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals. [ABSTRACT FROM AUTHOR]

Published
2010
Full Text
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18. Production of a chimeric enzyme tool associating the Trichoderma reesei swollenin with the Aspergillus niger feruloyl esterase A for release of ferulic acid.

Author

Levasseur, Anthony, Saloheimo, Markku, Navarro, David, Andberg, Martina, Monot, Frédéric, Nakari-Setälä, Tiina, Asther, Marcel, and Record, Eric

Subjects
*TRICHODERMA reesei, *BIOTECHNOLOGY, *ASPERGILLUS niger, *FUNGI, *PROTEINS, *ENZYMES
Abstract

The main goals of this work were to produce the fusion protein of the Trichoderma reesei swollenin I (SWOI) and Aspergillus niger feruloyl esterase A (FAEA) and to study the effect of the physical association of the fusion partners on the efficiency of the enzyme. The fusion protein was produced up to 25 mg l−1 in the T. reesei strains Rut-C30 and CL847. In parallel, FAEA alone was produced for use as a control protein in application tests. Recombinant FAEA and SWOI–FAEA were purified to homogeneity and characterized. The biochemical and kinetic characteristics of the two recombinant proteins were found to be similar to those of native FAEA, except for the temperature stability and specific activity of the SWOI–FAEA. Finally, the SWOI–FAEA protein was tested for release of ferulic acid from wheat bran. A period of 24 h of enzymatic hydrolysis with the SWOI–FAEA improved the efficiency of ferulic acid release by 50% compared with the results obtained using the free FAEA and SWOI. Ferulic acid is used as an antioxidant and flavor precursor in the food and pharmaceutical industries. This is the first report of a potential application of the SWOI protein fused with an enzyme of industrial interest. [ABSTRACT FROM AUTHOR]

Published
2006
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19. Additional file 24: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, 3. Good health
Abstract

Phylogenetic relationships of UreA homologs. (PDF 108 kb)

20. Additional file 28: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, humanities, 3. Good health
Abstract

Number of flavohemoglobins and protein IDs found in the genome sequences of the Aspergillus species. (PDF 79 kb)

21. Additional file 33: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, 3. Good health
Abstract

Kinases presented in at least one yeast species and with no orthologous genes in other eurotiomycetes. (PDF 117 kb)

22. Additional file 28: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, humanities, 3. Good health
Abstract

Number of flavohemoglobins and protein IDs found in the genome sequences of the Aspergillus species. (PDF 79 kb)

23. Additional file 24: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, 3. Good health
Abstract

Phylogenetic relationships of UreA homologs. (PDF 108 kb)

24. Additional file 33: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, 3. Good health
Abstract

Kinases presented in at least one yeast species and with no orthologous genes in other eurotiomycetes. (PDF 117 kb)

25. Trichoderma reesei Dehydrogenase, a Pyrroloquinoline Quinone-Dependent Member of Auxiliary Activity Family 12 of the Carbohydrate-Active Enzymes Database: Functional and Structural Characterization.

Author

Turbe-Doan, Annick, Record, Eric, Lombard, Vincent, Kumar, Rajender, Levasseur, Anthony, Henrissat, Bernard, and Garron, Marie-Line

Subjects
*TRICHODERMA reesei, *COFACTORS (Biochemistry), *PQQ (Biochemistry), *ENZYMES, *BINDING sites
Abstract

Pyrroloquinoline quinone (PQQ) is an ortho-quinone cofactor of several prokaryotic oxidases. Widely available in the diet and necessary for the correct growth of mice, PQQ has been suspected to be a vitamin for eukaryotes. However, no PQQ-dependent eukaryotic enzyme had been identified to use the PQQ until 2014, when a basidiomycete enzyme catalyzing saccharide dehydrogenation using PQQ as a cofactor was characterized and served to define auxiliary activity family 12 (AA12). Here we report the biochemical characterization of the AA12 enzyme encoded by the genome of the ascomycete Trichoderma reesei (TrAA12). Surprisingly, only weak activity against uncommon carbohydrates like L-fucose or D-arabinose was measured. The three-dimensional structure of TrAA12 reveals important similarities with bacterial soluble glucose dehydrogenases (sGDH). The enzymatic characterization and the structure solved in the presence of calcium confirm the importance of this ion in catalysis, as observed for sGDH. The structural characterization of TrAA12 was completed by modeling PQQ and L-fucose in the enzyme active site. Based on these results, the AA12 family of enzymes is likely to have a catalytic mechanism close to that of bacterial sGDH. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
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