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2. Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity

Author

Venegas, Felipe Andrés, Koutaniemi, Sanna, Langeveld, Sandra M.J., Bellemare, Annie, Chong, Sun-Li, Dilokpimol, Adiphol, Lowden, Michael J., Hilden, Kristiina S., Leyva-Illades, Juan Francisco, Mäkelä, Miia R., My Pham, Thi Thanh, Peng, Mao, Hancock, Mark A., Zheng, Yun, Tsang, Adrian, Tenkanen, Maija, Powlowski, Justin, and de Vries, Ronald P.

Published
2022
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13. Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity

Author

Sub Translational Plant Biology, Translational Plant Biology, Venegas, Felipe Andrés, Koutaniemi, Sanna, Langeveld, Sandra M.J., Bellemare, Annie, Chong, Sun Li, Dilokpimol, Adiphol, Lowden, Michael J., Hilden, Kristiina S., Leyva-Illades, Juan Francisco, Mäkelä, Miia R., My Pham, Thi Thanh, Peng, Mao, Hancock, Mark A., Zheng, Yun, Tsang, Adrian, Tenkanen, Maija, Powlowski, Justin, de Vries, Ronald P., Sub Translational Plant Biology, Translational Plant Biology, Venegas, Felipe Andrés, Koutaniemi, Sanna, Langeveld, Sandra M.J., Bellemare, Annie, Chong, Sun Li, Dilokpimol, Adiphol, Lowden, Michael J., Hilden, Kristiina S., Leyva-Illades, Juan Francisco, Mäkelä, Miia R., My Pham, Thi Thanh, Peng, Mao, Hancock, Mark A., Zheng, Yun, Tsang, Adrian, Tenkanen, Maija, Powlowski, Justin, and de Vries, Ronald P.

Published
2022

15. Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia

Author

Hilden, Kristiina S., Bortfeldt, Ralf, Hofrichter, Martin, Hatakka, Annele, and Lundell, Taina K.

Subjects
Peroxidase -- Physiological aspects, Peroxidase -- Research, Basidiomycota -- Physiological aspects, Basidiomycota -- Identification and classification, Basidiomycota -- Research, Biological sciences
Abstract

The basidiomycete isolate b19, originally identified by morphological characteristics of the fruiting body as Nematoloma frowardii, efficiently produces manganese peroxidase (MNP) and is used for degradation of natural, persistent aromatic polymers (lignin, humic acids and brown coal components). The N. frowardii MNP has shown good activity in conversion of xenobiotic compounds such as polycyclic hydrocarbons and trinitrotoluene. However, this biotechnologically promising fungus has not previously been studied at the molecular biology level. We show here that according to the molecular characterization of its main MNP isozyme, Nf b19 MNP2, and partial sequencing of its MNP3-, three lignin peroxidase- and two laccase-encoding genes, and the gene encoding the ribosomal SSU 18S RNA, that the fungus has a close phylogenetic relationship to the white-rot basidiomycete Phlebia radiata (Fr.). Ribosomal internal transcribed spacer (ITS) sequence (ITS1 +5.8S+ITS2) phylogeny reclassifies Nf b19 as a possible representative of a new species of the genus Phlebia, nearest to the Phlebia acerina clade. The genus Phlebia belongs to a completely different family (Corticiaceae) and order (Aphyllophorales) within the phylum Basidiomycota than the genus Nematoloma, which is classified in the order Agaricales, family Strophariaceae. Our results thus indicate a need for systematic re-identification of the previously named N. frowardii isolate b19.

Published
2008

16. Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

Author

Daly, Paul, Lopez, Sara Casado, Peng, Mao, Lancefield, Christopher S., Purvine, Samuel O., Kim, Young-Mo, Zink, Erika M., Dohnalkova, Alice, Singan, Vasanth R., Lipzen, Anna, Dilworth, David, Wang, Mei, Ng, Vivian, Robinson, Errol, Orr, Galya, Baker, Scott E., Bruijnincx, Pieter C. A., Hilden, Kristiina S., Grigoriev, Igor V., Maekelae, Miia R., de Vries, Ronald P., Sub Biomol.Mass Spectrometry & Proteom., Sub Inorganic Chemistry and Catalysis, Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Molecular Plant Physiology, University of St Andrews. School of Chemistry, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Sub Biomol.Mass Spectrometry & Proteom., Sub Inorganic Chemistry and Catalysis, Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Molecular Plant Physiology, Department of Microbiology, Helsinki Institute of Sustainability Science (HELSUS), and Fungal Genetics and Biotechnology

Subjects
0301 basic medicine, Softwood, ASPERGILLUS-NIGER, Biology, WHITE-ROT FUNGI, Lignin, complex mixtures, Microbiology, Polyporaceae, Mannans, Fungal Proteins, 03 medical and health sciences, chemistry.chemical_compound, Hardwood, QD, Food science, Picea, 1183 Plant biology, microbiology, virology, Betula, Ecology, Evolution, Behavior and Systematics, GENE-EXPRESSION, Mannan, Laccase, Evolutionary Biology, Basidiomycota, fungi, technology, industry, and agriculture, DAS, PHANEROCHAETE-CHRYSOSPORIUM, QR Microbiology, DEGRADATION, 15. Life on land, QD Chemistry, Solid wood, Wood, Xylan, QR, ACCURATE MASS, 030104 developmental biology, Peroxidases, chemistry, AROMATIC-COMPOUNDS, Composition (visual arts), LIQUID-CHROMATOGRAPHY, PLANT BIOMASS
Abstract

PD was supported by a grant of the Netherlands Scientific Organization NWO 824.15.023 to RPdV. The Academy of Finland grant no. 308284 to MRM is acknowledged. Part of the research was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research, located at the Pacific Northwest National Laboratory in Richland, WA, USA. The work conducted by the U.S. Department of Energy Joint Genome Institute (JGI), was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE‐AC02‐05CH11231. CSL was supported by the CatchBio program. White‐rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed‐wood forests containing both soft‐ and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi‐natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D‐NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G‐lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment. Publisher PDF

Published
2018
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17. 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, Francois, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Mariette, Jerome, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald P., Gathman, Allen C., Hainaut, Matthieu, Henrissat, Bernard, Hilden, Kristiina S., Kuees, Ursula, Lilly, Walt, Lipzen, Anna, Makela, Miia R., Martinez, Angel T., Morel-Rouhier, Melanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur F. J., Wosten, Han A. B., Ruiz-Duenas, Francisco J., Riley, Robert, Record, Eric, Grigoriev, Igor, V, Rosso, Marie-Noelle, Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, Francois, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Mariette, Jerome, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald P., Gathman, Allen C., Hainaut, Matthieu, Henrissat, Bernard, Hilden, Kristiina S., Kuees, Ursula, Lilly, Walt, Lipzen, Anna, Makela, Miia R., Martinez, Angel T., Morel-Rouhier, Melanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur F. J., Wosten, Han A. B., Ruiz-Duenas, Francisco J., Riley, Robert, Record, Eric, Grigoriev, Igor, V, and Rosso, Marie-Noelle

Published
2020

18. Draft Genome Sequences of Three Monokaryotic Isolates o the White-Rot Basidiomycete Fungus Dichomitus squalens

Author

Lopez, Sara Casado, Peng, Mao, Daly, Paul, Andreopoulos, Bill, Pangilinan, Jasmyn, Lipzen, Anna, Riley, Robert, Ahrendt, Steven, Ng, Vivian, Barry, Kerrie, Daum, Chris, Grigoriev, Igor, V, Hilden, Kristiina S., Makela, Miia R., de Vries, Ronald P., Lopez, Sara Casado, Peng, Mao, Daly, Paul, Andreopoulos, Bill, Pangilinan, Jasmyn, Lipzen, Anna, Riley, Robert, Ahrendt, Steven, Ng, Vivian, Barry, Kerrie, Daum, Chris, Grigoriev, Igor, V, Hilden, Kristiina S., Makela, Miia R., and de Vries, Ronald P.

Published
2019

21. The synthetic potential of fungal feruloyl esterases

Author

Antonopoulou, Io, Dilokpimol, Adiphol, Iancu, Laura, Makela, Miia R., Varriale, Simona, Cerullo, Gabriella, Huttner, Silvia, Uthoff, Stefan, Juetten, Peter, Piechot, Alexander, Steinbuechel, Alexander, Olsson, Lisbeth, Faraco, Vincenza, Hilden, Kristiina S., de Vries, Ronald P., Rova, Ulrika, Christakopoulos, Paul, Sub Molecular Plant Physiology, Molecular Plant Physiology, Antonopoulou, I., Dilokpimol, A., Iancu, L., Mäkelä, M. R., Varriale, S., Cerullo, G., Hüttner, S., Uthoff, S., Jütten, P., Piechot, A., Steinbüchel, A., Olsson, L., Faraco, V., Hildén, K. S., de Vries, R. P., Rova, U. and Christakopoulos P., Department of Microbiology, Fungal Genetics and Biotechnology, Helsinki Institute of Sustainability Science (HELSUS), Doctoral Programme in Microbiology and Biotechnology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Sub Molecular Plant Physiology, and Molecular Plant Physiology

Subjects
0106 biological sciences, 0301 basic medicine, sugar esters, antioxidant, ENZYMATIC-SYNTHESIS, 116 Chemical sciences, Glyceryl ferulate, Alcohol, l<%2Fspan>-arabinose+ferulate%22">l-arabinose ferulate, lcsh:Chemical technology, 01 natural sciences, Antioxidants, lcsh:Chemistry, chemistry.chemical_compound, Feruloyl esterase, CRYSTAL-STRUCTURE, lcsh:TP1-1185, L-arabinose ferulate, Prenyl caffeate, 1183 Plant biology, microbiology, virology, chemistry.chemical_classification, Butyl ferulate, biology, Prenyl ferulate, Sugar esters, FAMILY, OLIGOSACCHARIDES, Biocatalysis and Enzyme Technology, antioxidants, prenyl ferulate, ESTERIFICATION, Stereochemistry, Phylogenetic classification, butyl ferulate, ASPERGILLUS-NIGER, FUSARIUM-OXYSPORUM, Catalysis, 03 medical and health sciences, l-arabinose+ferulate%22">">l-arabinose ferulate, Prenylation, 010608 biotechnology, phylogenetic classification, feruloyl esterase, Homology modeling, Physical and Theoretical Chemistry, OPTIMIZATION, Bioprocess Technology, glyceryl ferulate, prenyl caffeate, l-arabinose ferulate, Aspergillus niger, Organic Chemistry, Transesterification, biology.organism_classification, Xylan, transesterification, 030104 developmental biology, Enzyme, chemistry, lcsh:QD1-999, ACID ESTERASES, CATALYZED SYNTHESIS
Abstract

Twenty-eight fungal feruloyl esterases (FAEs) were evaluated for their synthetic abilities in a ternary system of n-hexane: t-butanol: 100 mM MOPS-NaOH pH 6.0 forming detergentless microemulsions. Five main derivatives were synthesized, namely prenyl ferulate, prenyl caffeate, butyl ferulate, glyceryl ferulate, and l-arabinose ferulate, offering, in general, higher yields when more hydrophilic alcohol substitutions were used. Acetyl xylan esterase-related FAEs belonging to phylogenetic subfamilies (SF) 5 and 6 showed increased synthetic yields among tested enzymes. In particular, it was shown that FAEs belonging to SF6 generally transesterified aliphatic alcohols more efficiently while SF5 members preferred bulkier l-arabinose. Predicted surface properties and structural characteristics were correlated with the synthetic potential of selected tannase-related, acetyl-xylan-related, and lipase-related FAEs (SF1-2, -6, -7 members) based on homology modeling and small molecular docking simulations.

Published
2018
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22. Basidiomycete Genomics

Author

de Vries, Ronald P., Makela, Miia R., Hilden, Kristiina S., Kamper, Jorg, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Fungal Physiology

Subjects
0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, Basidiomycota, Genetics, Genomics, Genome, Fungal, Microbiology, 030217 neurology & neurosurgery, 030304 developmental biology
Published
2018

23. The Synthetic Potential of Fungal Feruloyl Esterases: A Correlation with Current Classification Systems and Predicted Structural Properties

Author

Antonopoulou, Io, Dilokpimol, Adiphol, Iancu, Laura, Makela, Miia R., Varriale, Simona, Cerullo, Gabriella, Huttner, Silvia, Uthoff, Stefan, Juetten, Peter, Piechot, Alexander, Steinbuechel, Alexander, Olsson, Lisbeth, Faraco, Vincenza, Hilden, Kristiina S., de Vries, Ronald P., Rova, Ulrika, Christakopoulos, Paul, Antonopoulou, Io, Dilokpimol, Adiphol, Iancu, Laura, Makela, Miia R., Varriale, Simona, Cerullo, Gabriella, Huttner, Silvia, Uthoff, Stefan, Juetten, Peter, Piechot, Alexander, Steinbuechel, Alexander, Olsson, Lisbeth, Faraco, Vincenza, Hilden, Kristiina S., de Vries, Ronald P., Rova, Ulrika, and Christakopoulos, Paul

Abstract

Twenty-eight fungal feruloyl esterases (FAEs) were evaluated for their synthetic abilities in a ternary system of n-hexane: t-butanol: 100 mM MOPS-NaOH pH 6.0 forming detergentless microemulsions. Five main derivatives were synthesized, namely prenyl ferulate, prenyl caffeate, butyl ferulate, glyceryl ferulate, and l-arabinose ferulate, offering, in general, higher yields when more hydrophilic alcohol substitutions were used. Acetyl xylan esterase-related FAEs belonging to phylogenetic subfamilies (SF) 5 and 6 showed increased synthetic yields among tested enzymes. In particular, it was shown that FAEs belonging to SF6 generally transesterified aliphatic alcohols more efficiently while SF5 members preferred bulkier l-arabinose. Predicted surface properties and structural characteristics were correlated with the synthetic potential of selected tannase-related, acetyl-xylan-related, and lipase-related FAEs (SF1-2, -6, -7 members) based on homology modeling and small molecular docking simulations.

Published
2018

24. The Synthetic Potential of Fungal Feruloyl Esterases: A Correlation with Current Classification Systems and Predicted Structural Properties

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Antonopoulou, Io, Dilokpimol, Adiphol, Iancu, Laura, Makela, Miia R., Varriale, Simona, Cerullo, Gabriella, Huttner, Silvia, Uthoff, Stefan, Juetten, Peter, Piechot, Alexander, Steinbuechel, Alexander, Olsson, Lisbeth, Faraco, Vincenza, Hilden, Kristiina S., de Vries, Ronald P., Rova, Ulrika, Christakopoulos, Paul, Sub Molecular Plant Physiology, Molecular Plant Physiology, Antonopoulou, Io, Dilokpimol, Adiphol, Iancu, Laura, Makela, Miia R., Varriale, Simona, Cerullo, Gabriella, Huttner, Silvia, Uthoff, Stefan, Juetten, Peter, Piechot, Alexander, Steinbuechel, Alexander, Olsson, Lisbeth, Faraco, Vincenza, Hilden, Kristiina S., de Vries, Ronald P., Rova, Ulrika, and Christakopoulos, Paul

Published
2018

26. Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga

Author

Makela, Miia R., Peng, Mao, Granchi, Zoraide, Chin-A-Woeng, Thomas, Hegi, Rosa, van Pelt, Sake, I, Ahrendt, Steven, Riley, Robert, Hainaut, Matthieu, Henrissat, Bernard, Grigoriev, Igor, V, de Vries, Ronald P., Hilden, Kristiina S., Makela, Miia R., Peng, Mao, Granchi, Zoraide, Chin-A-Woeng, Thomas, Hegi, Rosa, van Pelt, Sake, I, Ahrendt, Steven, Riley, Robert, Hainaut, Matthieu, Henrissat, Bernard, Grigoriev, Igor, V, de Vries, Ronald P., and Hilden, Kristiina S.

Published
2018

27. Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization

Author

Sub Molecular Plant Physiology, Molecular Plant Physiology, Dilokpimol, Adiphol, Mäkelä, Miia R, Cerullo, Gabriella, Zhou, Miaomiao, Varriale, Simona, Gidijala, Loknath, Brás, Joana L A, Jütten, Peter, Piechot, Alexander, Verhaert, Raymond, Faraco, Vincenza, Hilden, Kristiina S, de Vries, Ronald P, Sub Molecular Plant Physiology, Molecular Plant Physiology, Dilokpimol, Adiphol, Mäkelä, Miia R, Cerullo, Gabriella, Zhou, Miaomiao, Varriale, Simona, Gidijala, Loknath, Brás, Joana L A, Jütten, Peter, Piechot, Alexander, Verhaert, Raymond, Faraco, Vincenza, Hilden, Kristiina S, and de Vries, Ronald P

Published
2018

28. Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

Author

Sub Biomol.Mass Spectrometry & Proteom., Sub Inorganic Chemistry and Catalysis, Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Molecular Plant Physiology, Daly, Paul, Lopez, Sara Casado, Peng, Mao, Lancefield, Christopher S., Purvine, Samuel O., Kim, Young-Mo, Zink, Erika M., Dohnalkova, Alice, Singan, Vasanth R., Lipzen, Anna, Dilworth, David, Wang, Mei, Ng, Vivian, Robinson, Errol, Orr, Galya, Baker, Scott E., Bruijnincx, Pieter C. A., Hilden, Kristiina S., Grigoriev, Igor V., Maekelae, Miia R., de Vries, Ronald P., Sub Biomol.Mass Spectrometry & Proteom., Sub Inorganic Chemistry and Catalysis, Sub Organic Chemistry and Catalysis, Sub Molecular Plant Physiology, Molecular Plant Physiology, Daly, Paul, Lopez, Sara Casado, Peng, Mao, Lancefield, Christopher S., Purvine, Samuel O., Kim, Young-Mo, Zink, Erika M., Dohnalkova, Alice, Singan, Vasanth R., Lipzen, Anna, Dilworth, David, Wang, Mei, Ng, Vivian, Robinson, Errol, Orr, Galya, Baker, Scott E., Bruijnincx, Pieter C. A., Hilden, Kristiina S., Grigoriev, Igor V., Maekelae, Miia R., and de Vries, Ronald P.

Published
2018

30. The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi

Author

Peng, Mao, Dilokpirnol, Adiphol, Makela, Miia R., Hilden, Kristiina S., Bervoets, Sander, Riley, Robert, Grigoriev, Igor V, Hainaut, Matthieu, Henrissat, Bernard, de Vries, Ronald P., Granchi, Zoraide, Peng, Mao, Dilokpirnol, Adiphol, Makela, Miia R., Hilden, Kristiina S., Bervoets, Sander, Riley, Robert, Grigoriev, Igor V, Hainaut, Matthieu, Henrissat, Bernard, de Vries, Ronald P., and Granchi, Zoraide

Published
2017

31. 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 W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, Grigoriev, Igor V, de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, and Grigoriev, Igor V

Published
2017

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

Author

de Vries, Ronald, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Rohrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Sheila E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, Velasco de Castro Oliveria, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miamiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., de Vries, Ronald, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Rohrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Sheila E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, Velasco de Castro Oliveria, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miamiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., and Grigoriev, Igor V.

Abstract

Background The 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. Results We 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. Conclusions Many 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

34. Fungal Ligninolytic Enzymes and Their Applications

Author

Makela, Miia R., Bredeweg, Erin L., Magnuson, Jon K., Baker, Scott E, De Vries, Ronald P., Hilden, Kristiina S., Makela, Miia R., Bredeweg, Erin L., Magnuson, Jon K., Baker, Scott E, De Vries, Ronald P., and Hilden, Kristiina S.

Published
2016

35. Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

Author

Benoit, Isabelle, Culleton, Helena, Zhou, Miaomiao, DiFalco, Marcos, Aguilar-Osorio, Guillermo, Battaglia, Evy, Bouzid, Ourdia, Brouwer, Carlo P. J. M., El-Bushari, Hala B. O., Coutinho, Pedro M., Gruben, Birgit S., Hilden, Kristiina S., Houbraken, Jos, Barboza, Luis Alexis Jimenez, Levasseur, Anthony, Majoor, Eline, Makela, Miia R., Narang, Hari-Mander, Trejo-Aguilar, Blanca, van den Brink, Joost, vanKuyk, Patricia A., Wiebenga, Ad, McKie, Vincent, McCleary, Barry, Tsang, Adrian, Henrissat, Bernard, de Vries, Ronald P., Benoit, Isabelle, Culleton, Helena, Zhou, Miaomiao, DiFalco, Marcos, Aguilar-Osorio, Guillermo, Battaglia, Evy, Bouzid, Ourdia, Brouwer, Carlo P. J. M., El-Bushari, Hala B. O., Coutinho, Pedro M., Gruben, Birgit S., Hilden, Kristiina S., Houbraken, Jos, Barboza, Luis Alexis Jimenez, Levasseur, Anthony, Majoor, Eline, Makela, Miia R., Narang, Hari-Mander, Trejo-Aguilar, Blanca, van den Brink, Joost, vanKuyk, Patricia A., Wiebenga, Ad, McKie, Vincent, McCleary, Barry, Tsang, Adrian, Henrissat, Bernard, and de Vries, Ronald P.

Published
2015

36. Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga

Author

Steven R. Ahrendt, Zoraide Granchi, Thomas Chin-A-Woeng, Igor V. Grigoriev, Matthieu Hainaut, Mao Peng, Bernard Henrissat, Robert Riley, Sake van Pelt, Ronald P. de Vries, Kristiina Hildén, Rosa Hegi, Miia R. Mäkelä, University of Helsinki, Utrecht University [Utrecht], GenomeScan B.V., GenomeScan BV, Leiden University, DOE Joint Genome Institute [Walnut Creek], Joint Genome Institute, United States Department of Energy, 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), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Westerdijk Fungal Biodiversity Center [Utrecht], European Project: 613868,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,OPTIBIOCAT(2013), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universiteit Leiden, Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Hilden, Kristiina S., Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Fungal Physiology

Subjects
0301 basic medicine, Whole genome sequencing, Phlebia centrifuga, biology, Eukaryotes, Strain (biology), fungi, technology, industry, and agriculture, lignin, food and beverages, Picea abies, Fungus, biology.organism_classification, Genome, complex mixtures, 03 medical and health sciences, 030104 developmental biology, rna, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, White rot fungus, Molecular Biology, Gene
Abstract

Here, we report the genome sequence of wood-decaying white-rot fungus Phlebia centrifuga strain FBCC195, isolated from Norway spruce ( Picea abies ) in Finnish Lapland. The 34.66-Mb genome containing 13,785 gene models is similar to the genome length reported for other saprobic white-rot species.

Published
2018
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