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4. Enhanced surface colonisation and competition during bacterial adaptation to a fungus

Author

Richter, Anne, Blei, Felix, Hu, Guohai, Schwitalla, Jan W., Lozano-Andrade, Carlos N., Xie, Jiyu, Jarmusch, Scott A., Wibowo, Mario, Kjeldgaard, Bodil, Surabhi, Surabhi, Xu, Xinming, Jautzus, Theresa, Phippen, Christopher B. W., Tyc, Olaf, Arentshorst, Mark, Wang, Yue, Garbeva, Paolina, Larsen, Thomas Ostenfeld, Ram, Arthur F. J., van den Hondel, Cees A. M., Maróti, Gergely, and Kovács, Ákos T.

Published
2024
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5. Compatible solutes determine the heat resistance of conidia

Author

Seekles, Sjoerd J., van den Brule, Tom, Punt, Maarten, Dijksterhuis, Jan, Arentshorst, Mark, Ijadpanahsaravi, Maryam, Roseboom, Winfried, Meuken, Gwendolin, Ongenae, Véronique, Zwerus, Jordy, Ohm, Robin A., Kramer, Gertjan, Wösten, Han A. B., de Winde, Johannes H., and Ram, Arthur F. J.

Published
2023
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6. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.

Author

Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt, Chevret, Didier, Daum, Chris, Mariette, Jérôme, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald, Gathman, Allen, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina, Kües, Ursula, Lilly, Walt, Mäkelä, Miia, Martinez, Angel, Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, Francisco, Record, Eric, Rosso, Marie-Noëlle, Grigoriev, Igor, Lipzen, Anna, and Riley, Robert

Subjects
CAZyme, Class II Peroxidase, lignocellulose, lytic polysaccharide monooxygenase, wood decay, Carbohydrate Dehydrogenases, Cellulose, Fungal Proteins, Genome, Fungal, Lignin, Phylogeny, Pycnoporus, Wood
Abstract

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

Published
2020

9. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

de Vries, Ronald P, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna A, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C, Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, dos Santos, Renato Augusto Corrêa, Damásio, André Ricardo de Lima, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María Laura, Henrissat, Bernard, Hildén, Kristiina S, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F, MacCabe, Andrew, Mäkelä, Miia R, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P, Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur FJ, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S, Samson, Rob A, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M, Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E, van de Wiele, Nathalie, van Rossen-Uffink, Diana, Oliveira, Juliana Velasco de Castro, Vesth, Tammi C, Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, and Andersen, Mikael R

Subjects
Human Genome, Genetics, Biotechnology, Emerging Infectious Diseases, Infectious Diseases, Adaptation, Biological, Aspergillus, Biodiversity, Biomass, Carbon, Computational Biology, Cytochrome P-450 Enzyme System, DNA Methylation, Fungal Proteins, Gene Expression Regulation, Fungal, Gene Regulatory Networks, Genome, Fungal, Genomics, Humans, Metabolic Networks and Pathways, Molecular Sequence Annotation, Multigene Family, Oxidoreductases, Phylogeny, Plants, Secondary Metabolism, Signal Transduction, Stress, Physiological, Genome sequencing, Comparative genomics, Fungal biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Published
2017

12. Protoplast-mediated transformation of Madurella mycetomatis using hygromycin resistance as a selection marker

Author

du Pré, Saskia, Konings, Mickey, Schoorl, Dorenda, Fahal, Ahmed, Arentshorst, Mark, Ram, Arthur, van de Sande, Wendy, du Pré, Saskia, Konings, Mickey, Schoorl, Dorenda, Fahal, Ahmed, Arentshorst, Mark, Ram, Arthur, and van de Sande, Wendy

Abstract

Madurella mycetomatis is the main cause of mycetoma, a chronic granulomatous infection for which currently no adequate therapy is available. To improve therapy, more knowledge on a molecular level is required to understand how M. mycetomatis is able to cause this disease. However, the genetic toolbox for M. mycetomatis is limited. To date, no method is available to genetically modify M. mycetomatis. In this paper, a protoplast-mediated transformation protocol was successfully developed for this fungal species, using hygromycin as a selection marker. Furthermore, using this method, a cytoplasmic-GFP-expressing M. mycetomatis strain was created. The reported methodology will be invaluable to explore the pathogenicity of M. mycetomatis and to develop reporter strains which can be useful in drug discovery as well as in genetic studies.

Published
2024

21. Enhanced niche colonisation and competition during bacterial adaptation to a fungus

Author

Richter, Anne, primary, Blei, Felix, additional, Hu, Guohai, additional, Schwitalla, Jan W, additional, Lozano-Andrade, Carlos, additional, Jarmusch, Scott A, additional, Wibowo, Mario, additional, Kjeldgaard, Bodil, additional, Surabhi, Surabhi, additional, Jautzus, Theresa, additional, Phippen, Christopher B W, additional, Tyc, Olaf, additional, Arentshorst, Mark, additional, Wang, Yue, additional, Garbeva, Paolina, additional, Larsen, Thomas, additional, Ram, Arthur F.J., additional, Hondel, Cees van den, additional, Maróti, Gergely, additional, and Kovács, Ákos T, additional

Published
2023
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22. Growing a circular economy with fungal biotechnology: a white paper

Author

Meyer, Vera, Basenko, Evelina Y., Benz, J. Philipp, Braus, Gerhard H., Caddick, Mark X., Csukai, Michael, de Vries, Ronald P., Endy, Drew, Frisvad, Jens C., Gunde-Cimerman, Nina, Haarmann, Thomas, Hadar, Yitzhak, Hansen, Kim, Johnson, Robert I., Keller, Nancy P., Kraševec, Nada, Mortensen, Uffe H., Perez, Rolando, Ram, Arthur F. J., Record, Eric, Ross, Phil, Shapaval, Volha, Steiniger, Charlotte, van den Brink, Hans, van Munster, Jolanda, Yarden, Oded, and Wösten, Han A. B.

Published
2020
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26. Compatible solutes determine the heat resistance of conidia

Author

Sub Molecular Microbiology, Molecular Microbiology, Seekles, Sjoerd J., van den Brule, Tom, Punt, Maarten, Dijksterhuis, Jan, Arentshorst, Mark, Ijadpanahsaravi, Maryam, Roseboom, Winfried, Meuken, Gwendolin, Ongenae, Véronique, Zwerus, Jordy, Ohm, Robin A., Kramer, Gertjan, Wösten, Han A.B., de Winde, Johannes H., Ram, Arthur F.J., Sub Molecular Microbiology, Molecular Microbiology, Seekles, Sjoerd J., van den Brule, Tom, Punt, Maarten, Dijksterhuis, Jan, Arentshorst, Mark, Ijadpanahsaravi, Maryam, Roseboom, Winfried, Meuken, Gwendolin, Ongenae, Véronique, Zwerus, Jordy, Ohm, Robin A., Kramer, Gertjan, Wösten, Han A.B., de Winde, Johannes H., and Ram, Arthur F.J.

Published
2023

31. Screening for Compounds Exerting Antifungal Activities

Author

Ouedraogo, Jean-Paul, Lagendijk, Ellen L., van den Hondel, Cees A. M. J. J., Ram, Arthur F. J., Meyer, Vera, Gupta, Vijai Kumar, editor, Tuohy, Maria G., editor, Ayyachamy, Manimaran, editor, Turner, Kevin M., editor, and O’Donovan, Anthonia, editor

Published
2013
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32. Utilization of ferulic acid in Aspergillus niger requires the transcription factor FarA and a newly identified Far-like protein (FarD) that lacks the canonical Zn(II)2Cys6 domain

Author

Arentshorst, Mark, primary, Reijngoud, Jos, additional, van Tol, Daan J. C., additional, Reid, Ian D., additional, Arendsen, Yvonne, additional, Pel, Herman J., additional, van Peij, Noël N. M. E., additional, Visser, Jaap, additional, Punt, Peter J., additional, Tsang, Adrian, additional, and Ram, Arthur F. J., additional

Published
2022
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34. Genome sequences of 24 Aspergillus niger sensu stricto strains to study strain diversity, heterokaryon compatibility, and sexual reproduction

Author

Seekles, Sjoerd J, Punt, Maarten, Savelkoel, Niki, Houbraken, Jos, Wösten, Han A B, Ohm, Robin A, Ram, Arthur F J, Sub Molecular Microbiology, Molecular Microbiology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Sub Molecular Microbiology, and Molecular Microbiology

Subjects
Spores, parasexual cycle, Parasexual Cycle, Spores, Fungal/genetics, Aspergillus niger/genetics, sexual cycle, Sclerotia, Genetics, Genetics(clinical), Sexual Cycle, mating type, Molecular Biology, CRISPR/Cas9, Genetics (clinical), Phylogeny, whole genome sequencing, Mating Type, Fungal/genetics, Whole Genome Sequencing, Reproduction, sclerotia, Spores, Fungal, heterokaryon incompatibility, Diploidy, Aspergillus, Heterokaryon Incompatibility, heterozygous diploid, Heterozygous Diploid, Aspergillus niger
Abstract

Mating-type distribution within a phylogenetic tree, heterokaryon compatibility, and subsequent diploid formation were studied in 24 Aspergillus niger sensu stricto strains. The genomes of the 24 strains were sequenced and analyzed revealing an average of 6.1 ± 2.0 variants/kb between Aspergillus niger sensu stricto strains. The genome sequences were used together with available genome data to generate a phylogenetic tree revealing 3 distinct clades within Aspergillus niger sensu stricto. The phylogenetic tree revealed that both MAT1-1 and MAT1-2 mating types were present in each of the 3 clades. The phylogenetic differences were used to select for strains to analyze heterokaryon compatibility. Conidial color markers (fwnA and brnA) and auxotrophic markers (pyrG and nicB) were introduced via CRISPR/Cas9-based genome editing in a selection of strains. Twenty-three parasexual crosses using 11 different strains were performed. Only a single parasexual cross between genetically highly similar strains resulted in a successful formation of heterokaryotic mycelium and subsequent diploid formation, indicating widespread heterokaryon incompatibility as well as multiple active heterokaryon incompatibility systems between Aspergillus niger sensu stricto strains. The 2 vegetatively compatible strains were of 2 different mating types and a stable diploid was isolated from this heterokaryon. Sclerotium formation was induced on agar media containing Triton X-100; however, the sclerotia remained sterile and no ascospores were observed. Nevertheless, this is the first report of a diploid Aspergillus niger sensu stricto strain with 2 different mating types, which offers the unique possibility to screen for conditions that might lead to ascospore formation in A. niger.

Published
2022

36. High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster

Author

Punt, Maarten, Seekles, Sjoerd J, van Dam, Jisca L, de Adelhart Toorop, Connor, Martina, Raithel R, Houbraken, Jos, Ram, Arthur F J, Wösten, Han A B, Ohm, Robin A, Sub Molecular Microbiology, Molecular Microbiology, Sub Molecular Microbiology, Molecular Microbiology, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology

Subjects
Cancer Research, Sorbus/genetics, Penicillium/genetics, Fungi, Penicillium, Sorbic Acid, Multigene Family, Genetics, Sorbus, Sorbic Acid/pharmacology, Fungi/genetics, Molecular Biology, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Genome-Wide Association Study
Abstract

Penicillium roquefortiis a major food-spoilage fungus known for its high resistance to the food preservative sorbic acid. Here, we demonstrate that the minimum inhibitory concentration of undissociated sorbic acid (MICu) ranges between 4.2 and 21.2 mM when 34P.roquefortistrains were grown on malt extract broth. A genome-wide association study revealed that the six most resistant strains contained the 180 kbp gene cluster SORBUS, which was absent in the other 28 strains. In addition, a SNP analysis revealed five genes outside the SORBUS cluster that may be linked to sorbic acid resistance. A partial SORBUS knock-out (>100 of 180 kbp) in a resistant strain reduced sorbic acid resistance to similar levels as observed in the sensitive strains. Whole genome transcriptome analysis revealed a small set of genes present in both resistant and sensitiveP.roquefortistrains that were differentially expressed in the presence of the weak acid. These genes could explain whyP.roquefortiis more resistant to sorbic acid when compared to other fungi, even in the absence of the SORBUS cluster. Together, the MICuof 21.2 mM makesP.roquefortiamong the most sorbic acid-resistant fungi, if not the most resistant fungus, which is mediated by the SORBUS gene cluster.

Published
2022

40. Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

Author

Agence Nationale de la Recherche (France), Department of Energy (US), Ministerio de Ciencia, Innovación y Universidades (España), Miyauchi, Shingo [0000-0002-0620-5547], Hage, Hayat [0000-0003-4118-1816], Drula, Elodie [0000-0002-9168-5214], Lesage-Meessen, Laurence [0000-0003-2275-2978], Berrin, Jean-Guy [0000-0001-7570-3745], Navarro, David [0000-0002-3266-8270], Favel, Anne [0000-0003-2255-3637], Haon, Mireille [0000-0002-5669-5177], Levasseur, Anthony [0000-0003-2989-7539], Lomascolo, Anne [0000-0003-3829-8503], Ahrendt, Steven [0000-0002-3029-2126], LaButti, Kurt M. [0000-0002-5838-1972], Chevret, Didier [0000-0001-9531-7657], Daum, Chris [0000-0003-3895-5892], Klopp, Christophe [0000-0001-7126-5477], Vries, Ronald P. de [0000-0002-4363-1123], Hainaut, Matthieu [0000-0002-7567-657X], Henrissat, Bernard [0000-0002-3434-8588], Hildén, Kristiina S. [0000-0002-0126-8186], Kües, Ursula [0000-0001-9180-4079], Lipzen, Anna [0000-0003-2293-9329], Mäkelä, Miia [0000-0003-0771-2329], Martínez, Ángel T. [0000-0002-1584-2863], Morel-Rouhier, Mélanie [0000-0001-5149-0474], Morin, Emmanuelle [0000-0002-7268-972X], Ram, Arthur [0000-0002-2487-8016], Wösten, Han [0000-0002-0399-3648], Ruiz-Dueñas, F. J. [0000-0002-9837-5665], Record, Éric [0000-0002-7545-9997], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Mariette, Jér̂ome, Klopp, Christophe, Cullen, Dan, Vries, Ronald P. de, Gathman, Allen C., Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S., Kües, Ursula, Lilly, Walt, Lipzen, Anna, Mäkelä, Miia, Martínez, Ángel T., Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, F. J., Riley, Robert, Record, Éric, Grigoriev, Igor V., Rosso, Marie-Noëlle, Agence Nationale de la Recherche (France), Department of Energy (US), Ministerio de Ciencia, Innovación y Universidades (España), Miyauchi, Shingo [0000-0002-0620-5547], Hage, Hayat [0000-0003-4118-1816], Drula, Elodie [0000-0002-9168-5214], Lesage-Meessen, Laurence [0000-0003-2275-2978], Berrin, Jean-Guy [0000-0001-7570-3745], Navarro, David [0000-0002-3266-8270], Favel, Anne [0000-0003-2255-3637], Haon, Mireille [0000-0002-5669-5177], Levasseur, Anthony [0000-0003-2989-7539], Lomascolo, Anne [0000-0003-3829-8503], Ahrendt, Steven [0000-0002-3029-2126], LaButti, Kurt M. [0000-0002-5838-1972], Chevret, Didier [0000-0001-9531-7657], Daum, Chris [0000-0003-3895-5892], Klopp, Christophe [0000-0001-7126-5477], Vries, Ronald P. de [0000-0002-4363-1123], Hainaut, Matthieu [0000-0002-7567-657X], Henrissat, Bernard [0000-0002-3434-8588], Hildén, Kristiina S. [0000-0002-0126-8186], Kües, Ursula [0000-0001-9180-4079], Lipzen, Anna [0000-0003-2293-9329], Mäkelä, Miia [0000-0003-0771-2329], Martínez, Ángel T. [0000-0002-1584-2863], Morel-Rouhier, Mélanie [0000-0001-5149-0474], Morin, Emmanuelle [0000-0002-7268-972X], Ram, Arthur [0000-0002-2487-8016], Wösten, Han [0000-0002-0399-3648], Ruiz-Dueñas, F. J. [0000-0002-9837-5665], Record, Éric [0000-0002-7545-9997], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Mariette, Jér̂ome, Klopp, Christophe, Cullen, Dan, Vries, Ronald P. de, Gathman, Allen C., Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S., Kües, Ursula, Lilly, Walt, Lipzen, Anna, Mäkelä, Miia, Martínez, Ángel T., Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, F. J., Riley, Robert, Record, Éric, Grigoriev, Igor V., and Rosso, Marie-Noëlle

Abstract

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics,transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date,despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin.The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process.

Published
2020

41. Running Title: Cross-species multi-omics and conserved gene regulations

Author

Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M, Chevret, Didier, Daum, Chris, Mariette, Jérôme, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald P, Gathman, Allen C, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S, Kües, Ursula, Lilly, Walt, Lipzen, Anna, Mäkelä, Miia R, Martinez, Angel T, Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur F J, Wösten, Han A B, Ruiz-Dueñas, Francisco J, Riley, Robert, Record, Eric, Grigoriev, Igor V, Rosso, Marie-Noëlle, Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Department of Microbiology, Department of Food and Nutrition, Fungal Genetics and Biotechnology, Helsinki Institute of Sustainability Science (HELSUS), Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute, 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), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), 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), U.S. Department of Energy [Washington] (DOE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), USDA Forest Service Rocky Mountain Forest and Range Experiment Station, United States Department of Agriculture (USDA), Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Missouri Southern State University (MSSU), 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), Department of Molecular Cell Biology [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), DOE Joint Genome Institute [Walnut Creek], Department of Molecular Microbiology and Biotechnology, Tel Aviv University (TAU), Utrecht University [Utrecht], Department of Plant Pathology & Microbiology [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R), ANR-14-CE06-0020,FUNTUNE,Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale(2014), Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), University of Helsinki, Tel Aviv University [Tel Aviv], University of California [Riverside] (UCR), University of California-University of California, COMBE, Isabelle, Appel à projets générique - Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale - - FUNTUNE2014 - ANR-14-CE06-0020 - Appel à projets générique - VALID, Agence Nationale de la Recherche (France), Department of Energy (US), Ministerio de Ciencia, Innovación y Universidades (España), Miyauchi, Shingo [0000-0002-0620-5547], Hage, Hayat [0000-0003-4118-1816], Drula, Elodie [0000-0002-9168-5214], Lesage-Meessen, Laurence [0000-0003-2275-2978], Berrin, Jean-Guy [0000-0001-7570-3745], Navarro, David [0000-0002-3266-8270], Favel, Anne [0000-0003-2255-3637], Haon, Mireille [0000-0002-5669-5177], Levasseur, Anthony [0000-0003-2989-7539], Lomascolo, Anne [0000-0003-3829-8503], Ahrendt, Steven [0000-0002-3029-2126], LaButti, Kurt M. [0000-0002-5838-1972], Chevret, Didier [0000-0001-9531-7657], Daum, Chris [0000-0003-3895-5892], Klopp, Christophe [0000-0001-7126-5477], Vries, Ronald P. de [0000-0002-4363-1123], Hainaut, Matthieu [0000-0002-7567-657X], Henrissat, Bernard [0000-0002-3434-8588], Hildén, Kristiina S. [0000-0002-0126-8186], Kües, Ursula [0000-0001-9180-4079], Lipzen, Anna [0000-0003-2293-9329], Mäkelä, Miia [0000-0003-0771-2329], Martínez, Ángel T. [0000-0002-1584-2863], Morel-Rouhier, Mélanie [0000-0001-5149-0474], Morin, Emmanuelle [0000-0002-7268-972X], Ram, Arthur [0000-0002-2487-8016], Wösten, Han [0000-0002-0399-3648], Ruiz-Dueñas, F. J. [0000-0002-9837-5665], Record, Éric [0000-0002-7545-9997], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Haon, Mireille, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Klopp, Christophe, Vries, Ronald P. de, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S., Kües, Ursula, Lipzen, Anna, Mäkelä, Miia, Martínez, Ángel T., Morel-Rouhier, Mélanie, Morin, Emmanuelle, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, F. J., Record, Éric, Grigoriev, Igor V., and Rosso, Marie-Noëlle

Subjects
AcademicSubjects/SCI01140, SELECTION, Cellobiose, Lignin, ANNOTATION, chemistry.chemical_compound, lignocellulose, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 11832 Microbiology and virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Genome, Full Paper, Basidiomycota, General Medicine, PHANEROCHAETE-CHRYSOSPORIUM, Wood, Pycnoporus, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, GENOME, Fungal, Biochemistry, CAZyme, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lytic polysaccharide monooxygenase, Genome, Fungal, ENZYMES, CAZymes, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Biotechnology, DATABASE, 1.1 Normal biological development and functioning, Plant Biology & Botany, AcademicSubjects/MED00774, Biology, CLASSIFICATION, Fungal Proteins, CERIPORIOPSIS-SUBVERMISPORA, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Underpinning research, Oxidative enzyme, Genetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Cellulose, Molecular Biology, Gene, 030304 developmental biology, Lytic Polysaccharide Monooxygenase (LPMO), Comparative genomics, Lytic Polysaccharide Monooxygenase, 030306 microbiology, 15. Life on land, DEGRADATION, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, Class II Peroxidase, wood decay, Carbohydrate Dehydrogenases, SECRETOME, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

14 p.-8 fig.-1 tab., White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics,transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date,despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin.The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process., This work was supported by The French National Agency for Research (ANR-14-CE06-0020). The work conducted 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 Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R).

Published
2020

42. LaeA-dependent production of small molecules of Aspergillus niger that compete with specific antibodies that bind to human immune receptors

Author

Escobar, Natalia, Keizer, Esther, Neer, Jacq van, Arentshorst, Mark, Strijp, Jos van, Haas, Pieter-Jan, Ram, Arthur, Punt, Peter, Wosten, Han, Cock, Hans de, Escobar, Natalia, Keizer, Esther, Neer, Jacq van, Arentshorst, Mark, Strijp, Jos van, Haas, Pieter-Jan, Ram, Arthur, Punt, Peter, Wosten, Han, and Cock, Hans de

Abstract

Microorganisms secrete a variety of compounds into their environment such as proteins, carbohydrates, and secondary metabolites. These molecules play diverse roles in the interaction of microbes with their abiotic and biotic environment. Little is known about secreted fungal molecules mediating immune evasion. Here we screened culture media of three Aspergilli to assess whether these fungi secrete molecules that can compete with specific antibodies that bind to human immune receptors. Culture media of Aspergillus fumigatus Af293, Aspergillus tubingensis CBS 133792 and the non-acidifying mutant strain Aspergillus niger D15#26 contained components that showed competition for binding to a total of 13 receptors, of which PSGL-1, CXCR1, and CXCR2, were shared between the three species. Filtration experiments showed that most, if not all, interacting components were [≤] 3 kDa. Production of the components that competed with antibodies to bind to CD88 and CXCR2 was shown to be regulated by LaeA. The component(s) that competed for binding to CXCR1 was not only produced in the non-acidifying strain Aspergillus niger D15#26 but also in the non-acidifying oahA deletion strain of Aspergillus niger. Together, these data show that Aspergillus species might produce small molecules that interact with human immune receptors.

Published
2022

43. High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster

Author

Sub Molecular Microbiology, Molecular Microbiology, Punt, Maarten, Seekles, Sjoerd J, van Dam, Jisca L, de Adelhart Toorop, Connor, Martina, Raithel R, Houbraken, Jos, Ram, Arthur F J, Wösten, Han A B, Ohm, Robin A, Sub Molecular Microbiology, Molecular Microbiology, Punt, Maarten, Seekles, Sjoerd J, van Dam, Jisca L, de Adelhart Toorop, Connor, Martina, Raithel R, Houbraken, Jos, Ram, Arthur F J, Wösten, Han A B, and Ohm, Robin A

Published
2022

44. Intraspecific variability in heat resistance of fungal conidia

Author

Sub Molecular Microbiology, Molecular Microbiology, van den Brule, Tom, Punt, Maarten, Seekles, Sjoerd J., Segers, Frank J.J., Houbraken, Jos, Hazeleger, Wilma C., Ram, Arthur F.J., Wösten, Han A.B., Zwietering, Marcel H., Dijksterhuis, Jan, den Besten, Heidy M.W., Sub Molecular Microbiology, Molecular Microbiology, van den Brule, Tom, Punt, Maarten, Seekles, Sjoerd J., Segers, Frank J.J., Houbraken, Jos, Hazeleger, Wilma C., Ram, Arthur F.J., Wösten, Han A.B., Zwietering, Marcel H., Dijksterhuis, Jan, and den Besten, Heidy M.W.

Published
2022

45. Genome sequences of 24 Aspergillus niger sensu stricto strains to study strain diversity, heterokaryon compatibility and sexual reproduction

Author

Sub Molecular Microbiology, Molecular Microbiology, Seekles, Sjoerd J, Punt, Maarten, Savelkoel, Niki, Houbraken, Jos, Wösten, Han A B, Ohm, Robin A, Ram, Arthur F J, Sub Molecular Microbiology, Molecular Microbiology, Seekles, Sjoerd J, Punt, Maarten, Savelkoel, Niki, Houbraken, Jos, Wösten, Han A B, Ohm, Robin A, and Ram, Arthur F J

Published
2022

46. LaeA-dependent production of small molecules of Aspergillus niger that compete with specific antibodies that bind to human immune receptors

Author

Sub Molecular Microbiology, Molecular Microbiology, Escobar, Natalia, Keizer, Esther, Neer, Jacq van, Arentshorst, Mark, Strijp, Jos van, Haas, Pieter-Jan, Ram, Arthur, Punt, Peter, Wosten, Han, Cock, Hans de, Sub Molecular Microbiology, Molecular Microbiology, Escobar, Natalia, Keizer, Esther, Neer, Jacq van, Arentshorst, Mark, Strijp, Jos van, Haas, Pieter-Jan, Ram, Arthur, Punt, Peter, Wosten, Han, and Cock, Hans de

Published
2022

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