15 results on '"Phil Kersten"'
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2. Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood.
- Author
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Chiaki Hori, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima, Hitoshi Suzuki, Emma Master, Patricia Ferreira, Francisco J Ruiz-Dueñas, Benjamin Held, Paulo Canessa, Luis F Larrondo, Monika Schmoll, Irina S Druzhinina, Christian P Kubicek, Jill A Gaskell, Phil Kersten, Franz St John, Jeremy Glasner, Grzegorz Sabat, Sandra Splinter BonDurant, Khajamohiddin Syed, Jagjit Yadav, Anthony C Mgbeahuruike, Andriy Kovalchuk, Fred O Asiegbu, Gerald Lackner, Dirk Hoffmeister, Jorge Rencoret, Ana Gutiérrez, Hui Sun, Erika Lindquist, Kerrie Barry, Robert Riley, Igor V Grigoriev, Bernard Henrissat, Ursula Kües, Randy M Berka, Angel T Martínez, Sarah F Covert, Robert A Blanchette, and Daniel Cullen
- Subjects
Genetics ,QH426-470 - Abstract
Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.
- Published
- 2014
- Full Text
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3. Physical and Mechanical Properties of Cellulose Nanofibril Films from Bleached Eucalyptus Pulp by Endoglucanase Treatment and Microfluidization
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Michael D. Mozuch, Junyong Zhu, Yongcan Jin, Wangxia Wang, Ronald Sabo, and Phil Kersten
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Specific modulus ,Environmental Engineering ,Materials science ,Polymers and Plastics ,biology ,Pulp (paper) ,Cellulase ,engineering.material ,biology.organism_classification ,Eucalyptus ,chemistry.chemical_compound ,Pyrococcus horikoshii ,chemistry ,Ultimate tensile strength ,Materials Chemistry ,engineering ,biology.protein ,Thermal stability ,Cellulose ,Composite material - Abstract
A GH5 hyperthermostable endoglucanase (Ph-GH5) from the archaeon Pyrococcus horikoshii and a commercial endoglucanase (FR) were used to treat bleached eucalyptus pulp (BEP) fibers to produce cellulose nanofibrils (CNF) and subsequently to CNF films. TEM imaging indicated that Ph-GH5 produced longer and more entangled CNF than FR with the same number of microfluidization passes. Physical and mechanical properties of CNF films were characterized. Optical opacity of CNF films from FR (10 mg/g) at 40 passes through the microfluidizer can be as low as 3.7 %, compared with 18.2 % from untreated BEP at the same number of passes. CNF films exhibited similar thermal stability with untreated BEP. Highest specific modulus of CNF films was also obtained from FR (10 mg/g), reaching 56 MNm/kg, approximately 271 % of the CNF films from untreated BEP at 40 passes through the microfluidizer. CNF film from Ph-GH5 (1 mg/g) at 40 passes provided the highest specific maximum tensile strength at 120 kNm/kg.
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- 2015
4. Production of cellulose nanofibrils from bleached eucalyptus fibers by hyperthermostable endoglucanase treatment and subsequent microfluidization
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Phil Kersten, Ronald Sabo, Junyong Zhu, Yongcan Jin, Michael D. Mozuch, and Wangxia Wang
- Subjects
business.product_category ,Materials science ,Polymers and Plastics ,biology ,Pulp (paper) ,Cellulase ,Degree of polymerization ,engineering.material ,biology.organism_classification ,chemistry.chemical_compound ,Pyrococcus horikoshii ,chemistry ,Chemical engineering ,Microfiber ,engineering ,biology.protein ,Cellulose ,Composite material ,business - Abstract
A GH5 hyperthermostable endoglucanase from the archaeon Pyrococcus horikoshii (Ph-GH5) and a commercial endoglucanase FR were used to treat bleached eucalyptus pulp (BEP) fibers to produce cellulose nanofibrils (CNFs) through subsequent microfluidization. Enzymatic treatments facilitated CNF production due to the reduced degree of polymerization (DP) of the fibers. SEM imaging indicated that FR reduced fiber DP drastically and resulted in much shorter fibers than with Ph-GH5, even at very low dosages (1 mg protein/g fiber) of FR treatment compared with a high dosage (10 mg protein/g fiber) of Ph-GH5. The fibers treated with FR were much more uniform in length perhaps due to the presence of exoglucanase and beta-glucosidase saccharifying short microfibers into glucose. TEM imaging indicated that Ph-GH5 produced longer and entangled CNFs than FR with the same number of microfluidization passes. However, the CNF diameters were approximately the same for all CNFs from enzyme-treated fibers using both endoglucanases at two dosages (1 or 10 mg protein/g fiber). CNFs produced from BEP fibers without enzymatic treatment showed larger diameters than those with enzymatic treatment.
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- 2014
5. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis
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Elena, Fernandez-Fueyo, Francisco J, Ruiz-Dueñas, Patricia, Ferreira, Dimitrios, Floudas, David S, Hibbett, Paulo, Canessa, Luis F, Larrondo, Tim Y, James, Daniela, Seelenfreund, Sergio, Lobos, Rubén, Polanco, Mario, Tello, Yoichi, Honda, Takahito, Watanabe, Takashi, Watanabe, Jae San, Ryu, Ryu Jae, San, Christian P, Kubicek, Monika, Schmoll, Jill, Gaskell, Kenneth E, Hammel, Franz J, St John, Amber, Vanden Wymelenberg, Grzegorz, Sabat, Sandra, Splinter BonDurant, Khajamohiddin, Syed, Jagjit S, Yadav, Harshavardhan, Doddapaneni, Venkataramanan, Subramanian, José L, Lavín, José A, Oguiza, Gumer, Perez, Antonio G, Pisabarro, Lucia, Ramirez, Francisco, Santoyo, Emma, Master, Pedro M, Coutinho, Bernard, Henrissat, Vincent, Lombard, Jon Karl, Magnuson, Ursula, Kües, Chiaki, Hori, Kiyohiko, Igarashi, Masahiro, Samejima, Benjamin W, Held, Kerrie W, Barry, Kurt M, LaButti, Alla, Lapidus, Erika A, Lindquist, Susan M, Lucas, Robert, Riley, Asaf A, Salamov, Dirk, Hoffmeister, Daniel, Schwenk, Yitzhak, Hadar, Oded, Yarden, Ronald P, de Vries, Ad, Wiebenga, Jan, Stenlid, Daniel, Eastwood, Igor V, Grigoriev, Randy M, Berka, Robert A, Blanchette, Phil, Kersten, Angel T, Martinez, Rafael, Vicuna, Dan, Cullen, Universidad Pública de Navarra. Departamento de Producción Agraria, and Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
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Selective ligninolysis ,Molecular Sequence Data ,Lignin ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Species Specificity ,Manganese peroxidase ,Phylogeny ,030304 developmental biology ,Chrysosporium ,Laccase ,0303 health sciences ,Phanerochaete chrysosporium ,Multidisciplinary ,biology ,030306 microbiology ,Basidiomycota ,Hydrolysis ,Fungal genetics ,Lignin peroxidase ,Genomics ,Biological Sciences ,biology.organism_classification ,3. Good health ,chemistry ,biology.protein ,Phanerochaete ,Ceriporiopsis subvermispora ,Oxidation-Reduction ,Peroxidase - Abstract
Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium . Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium , respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli , the enzymes were shown to oxidize high redox potential substrates, but not Mn 2+ . Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium .
- Published
- 2017
6. Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12
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Kurt LaButti, David S. Hibbett, Igor V. Grigoriev, Matt Nolan, Debbie Yaver, Kerrie Barry, Dan Cullen, Jagjit S. Yadav, Emma R. Master, Anna Lipzen, Cindy Chen, Kathleen Lail, Randy M. Berka, Robert A. Blanchette, Ángel T. Martínez, Paulo Canessa, Diego Martinez, Phil Kersten, Bernard Henrissat, Jon K. Magnuson, Robert Riley, Christian P. Kubicek, Luis F. Larrondo, Jill Gaskell, Andrea Aerts, Monika Schmoll, Pontificia Universidad Católica de Chile (UC), Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Clark University, 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), Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], AMIDEX foundation (MicrobioE project) [ANR-11-IDEX-0001-02], Cullen, Dan, Department of Energy (US), Universidad de Castilla-La Mancha (UCLM), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
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0301 basic medicine ,lcsh:QH426-470 ,030106 microbiology ,Rhodonia placenta ,macromolecular substances ,Biochemistry ,complex mixtures ,Postia placenta ,03 medical and health sciences ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Data in Brief ,Genetics ,Theology ,[SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology ,biology ,technology, industry, and agriculture ,Monokaryon ,food and beverages ,biology.organism_classification ,3. Good health ,lcsh:Genetics ,030104 developmental biology ,Molecular Medicine ,Postia ,Biotechnology - Abstract
3 p.-2 tab. Gaskell, Jill et al., We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin., The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. BH was funded by the AMIDEX foundation (MicrobioE project, grant number ANR-11-IDEX-0001-02).
- Published
- 2017
7. Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporiopsis subvermispora during Growth on Aspen Wood Reveal This Organism's Strategy for Degrading Lignocellulose
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Michael D. Mozuch, Kiyohiko Igarashi, Jill Gaskell, Masahiro Samejima, Dan Cullen, Chiaki Hori, and Phil Kersten
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Cellobiose dehydrogenase ,Time Factors ,Proteome ,Cellulase ,Polysaccharide ,Lignin ,Applied Microbiology and Biotechnology ,Mass Spectrometry ,Fungal Proteins ,Cell wall ,chemistry.chemical_compound ,Glycoside hydrolase ,Cellulose ,Biotransformation ,chemistry.chemical_classification ,Ecology ,biology ,Gene Expression Profiling ,technology, industry, and agriculture ,biology.organism_classification ,Wood ,Enzymes ,chemistry ,Biochemistry ,Biodegradation ,biology.protein ,Coriolaceae ,Ceriporiopsis ,Chromatography, Liquid ,Food Science ,Biotechnology - Abstract
The white-rot basidiomycetes efficiently degrade all wood cell wall polymers. Generally, these fungi simultaneously degrade cellulose and lignin, but certain organisms, such as Ceriporiopsis subvermispora , selectively remove lignin in advance of cellulose degradation. However, relatively little is known about the mechanism of selective ligninolysis. To address this issue, C. subvermispora was grown in liquid medium containing ball-milled aspen, and nano-liquid chromatography-tandem mass spectrometry was used to identify and estimate extracellular protein abundance over time. Several manganese peroxidases and an aryl alcohol oxidase, both associated with lignin degradation, were identified after 3 days of incubation. A glycoside hydrolase (GH) family 51 arabinofuranosidase was also identified after 3 days but then successively decreased in later samples. Several enzymes related to cellulose and xylan degradation, such as GH10 endoxylanase, GH5_5 endoglucanase, and GH7 cellobiohydrolase, were detected after 5 days. Peptides corresponding to potential cellulose-degrading enzymes GH12, GH45, lytic polysaccharide monooxygenase, and cellobiose dehydrogenase were most abundant after 7 days. This sequential production of enzymes provides a mechanism consistent with selective ligninolysis by C. subvermispora .
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- 2014
8. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium
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Phil Kersten and Dan Cullen
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biology ,Phanerochaete ,biology.organism_classification ,Lignin ,Microbiology ,Cell wall ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Oxidative enzyme ,Genetics ,Extracellular ,Hemicellulose ,Cellulose ,Oxidoreductases ,Chrysosporium - Abstract
The US Department of Energy has assembled a high quality draft genome of Phanerochaete chrysosporium, a white rot Basidiomycete capable of completely degrading all major components of plant cell walls including cellulose, hemicellulose and lignin. Hundreds of sequences are predicted to encode extracellular enzymes including an impressive number of oxidative enzymes potentially involved in lignocellulose degradation. Herein, we summarize the number, organization, and expression of genes encoding peroxidases, copper radical oxidases, FAD-dependent oxidases, and multicopper oxidases. Possibly relevant to extracellular oxidative systems are genes involved in posttranslational processes and a large number of hypothetical proteins.
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- 2007
9. Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
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Ursula Kües, Kiyohiko Igarashi, Gerald Lackner, Paulo Canessa, Luis F. Larrondo, Patricia Ferreira, Christian P. Kubicek, Robert Riley, Ángel T. Martínez, Hui Sun, Jorge Rencoret, Monika Schmoll, Igor V. Grigoriev, Dirk Hoffmeister, Grzegorz Sabat, Khajamohiddin Syed, Randy M. Berka, Sarah F. Covert, Chiaki Hori, Jill Gaskell, Emma R. Master, Irina S. Druzhinina, Masahiro Samejima, Franz J. St John, Ana Gutiérrez, Sandra Splinter BonDurant, Benjamin W. Held, Jagjit S. Yadav, Erika Lindquist, Daniel Cullen, Robert A. Blanchette, Bernard Henrissat, Andriy Kovalchuk, Hitoshi Suzuki, Francisco J. Ruiz-Dueñas, Anthony C. Mgbeahuruike, Fred O. Asiegbu, Phil Kersten, Jeremy D. Glasner, Kerrie Barry, Takuya Ishida, Department of Forest Sciences, Viikki Plant Science Centre (ViPS), Forest Ecology and Management, and Ministerio de Economía y Competitividad (España)
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Proteomics ,Cancer Research ,ALCOHOL-DEHYDROGENASE ,Fungal genetics ,Fungal genomics ,Fungi ,Gene expression ,Multiple alignment calculation ,Peroxidases ,Phylogenetic analysis ,Sequence alignment ,Applied Microbiology ,Gene Identification and Analysis ,CELLOBIOSE DEHYDROGENASE ,Gene Expression ,Genome ,Biochemistry ,Lignin ,Transcriptome ,Cell Wall ,Gene Expression Regulation, Fungal ,Genome Sequencing ,Fungal Biochemistry ,Genetics (clinical) ,2. Zero hunger ,4112 Forestry ,biology ,Proteomic Databases ,Genomics ,Wood ,Functional Genomics ,1181 Ecology, evolutionary biology ,Biodegradation ,Genome, Fungal ,Transcriptome Analysis ,Research Article ,Biotechnology ,lcsh:QH426-470 ,LIGNIN MODEL COMPOUNDS ,education ,Mycology ,BROWN-ROT ,Microbiology ,Agaricomycetes ,Cell wall ,Molecular Genetics ,Fungal Proteins ,BASIDIOMYCETE PHANEROCHAETE-CHRYSOSPORIUM ,Environmental Biotechnology ,Botany ,Genetics ,Gene Regulation ,Molecular Biology Techniques ,Sequencing Techniques ,Cellulose ,Gene ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,PENIOPHORA-GIGANTEA ,MULTICOPPER OXIDASE ,Basidiomycota ,Organisms ,Gigantea ,Biology and Life Sciences ,Computational Biology ,Molecular Sequence Annotation ,15. Life on land ,biology.organism_classification ,Genome Analysis ,MOLECULAR EVOLUTION ,Transformation (genetics) ,lcsh:Genetics ,WHITE-ROT FUNGUS ,COPRINOPSIS-CINEREA ,Genome Expression Analysis ,Function (biology) - Abstract
20 p.-3 tab.-9 fig., Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on freshcut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes., The major portions of this work were performed under US Department of Agriculture Cooperative State, Research, Education, and Extension Service Grant 2007-35504-18257 (to DC and RAB). The US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231. This work was also supported by the HIPOP (BIO2011-26694) project of the Spanish Ministry of Economy and Competitiveness (MINECO) (to FJRD), the PEROXICATS (KBBE-2010-4-265397) and INDOX (KBBE-2013-.3.3-04-613549) European projects (to ATM), and the Chilean National Fund for Scientific and Technological Development Grant 1131030 (to LFL).
- Published
- 2014
10. Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes
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Phil Kersten and Dan Cullen
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Models, Molecular ,Free Radicals ,Protein Conformation ,Sequence Homology ,Oxidative phosphorylation ,Microbiology ,Agaricomycetes ,chemistry.chemical_compound ,Polypore ,Catalytic Domain ,Genetics ,Extracellular ,Lignin ,Gene ,Conserved Sequence ,Phylogeny ,chemistry.chemical_classification ,biology ,Basidiomycota ,Lignin peroxidase ,biology.organism_classification ,Enzyme ,chemistry ,Biochemistry ,Oxidoreductases ,Oxidation-Reduction ,Copper - Abstract
Extracellular peroxide generation, a key component of oxidative lignocellulose degradation, has been attributed to various enzymes including the copper radical oxidases. Encoded by a family of structurally related sequences, the genes are widely distributed among wood decay fungi including three recently completed polypore genomes. In all cases, core catalytic residues are conserved, but five subfamilies are recognized. Glyoxal oxidase, the most intensively studied representative, has been shown physiologically connected to lignin peroxidase. Relatively little is known about structure–function relationships among more recently discovered copper radical oxidases. Nevertheless, differences in substrate preferences have been observed in one case and the proteins have been detected in filtrates of various wood-grown cultures. Such diversity may reflect adaptations to host cell wall composition and changing environmental conditions.
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- 2014
11. Recent Advances on the Genomics of Litter- and Soil-Inhabiting Agaricomycetes
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Phil Kersten and Dan Cullen
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biology ,Ecology ,Genomics ,biology.organism_classification ,Proteomics ,complex mixtures ,Genome ,Agaricomycetes ,Cell wall ,chemistry.chemical_compound ,chemistry ,Botany ,White rot ,Litter ,Lignin - Abstract
Fungi, particularly the Agaricomycetes, play a pivotal role cycling nutrients in forest soils. Although these filamentous fungi are clearly responsible for lignocellulose decomposition, the underlying mechanisms remain uncertain. This article reviews current understanding of Agaricomycete physiology as it relates to lignocellulose conversions. Fresh insights into the mechanisms of plant cell wall degradation have been made possible by recently available genome sequences. For efficient lignin degradation, the repertoire of genes and expression analyses support an important role for high oxidation potential peroxidases working in conjunction with peroxide-generating oxidases. Generally associated with dead wood, some of these “white rot” fungi are also tree pathogens and litter-inhabiting saprophytes. In contrast, certain wood-decay fungi are unable to remove lignin but have adapted to rapidly depolymerize cellulose. Such decay patterns are typically classified as brown rot, and evidence suggests the involvement of small molecular oxidants such as hydroxyl radical. Uncertainty remains in part due to the dearth of experimental tools, but progress in transcriptomics, proteomics, and genetic transformation offers opportunities for rapid advances.
- Published
- 2013
12. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
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László Nagy, Luis F. Larrondo, Daniel C. Eastwood, Ad Wiebenga, Ángel T. Martínez, Darcy Young, Isabelle Benoit, Chiaki Hori, Robert Riley, Erika Lindquist, Ronald P. de Vries, Grzegorz Sabat, Rachael Martin, Robin A. Ohm, Kurt LaButti, Dan Cullen, Pedro M. Coutinho, Susan Lucas, Alan Kuo, Vincent Lombard, Joel A. Jurgens, Jill Gaskell, Andrea Aerts, Jan Stenlid, Alexis Carlson, David S. Hibbett, Hui Sun, Brian Foster, Robert Otillar, Francisco J. Ruiz-Dueñas, Manfred Binder, Dylan Glotzer, Patricia Ferreira, Ingo Morgenstern, Francis Martin, Jason C. Slot, T. K. Arun Kumar, Matthew J Nolan, Taina Lundell, Phil Kersten, Aleksandrina Patyshakuliyeva, Khajamohiddin Syed, Antonis Rokas, Jagjit S. Yadav, Robert A. Blanchette, Franz J. St John, Jeremy Schmutz, Joseph W. Spatafora, Igor V. Grigoriev, Antonio G. Pisabarro, Emanuelle Morin, Sheng Sun, Albee Y. Ling, Bernard Henrissat, Adrian Tsang, Annegret Kohler, Dimitrios Floudas, Masahiro Samejima, Cedar N. Hesse, Alexander Boyd, Keisha Findley, Nathan M Kallen, Kerrie Barry, Kiyohiko Igarashi, Paweł Górecki, Claude Murat, Ursula Kües, Joseph Heitman, Asaf Salamov, Alex Copeland, David J. McLaughlin, Biology Department, Clark University, Joint Genome Institute, United States Department of Energy, Department of Plant Pathology, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, 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), Centro de investigaciones biológicas, Spanish National Research Council (CSIC), Department of Botany and Plant Pathology, Oregon State University (OSU), College of Medicine, Department of Environmental Health, Environmental Genetics and Molecular Toxicology Division, University of Cincinnati (UC), Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University [Utrecht], CBS-KNAW Fungal Biodiversity Centre, Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Medical Center, Department of Molecular Genetics and Microbiology, Duke University [Durham], Forest Products Laboratory, United States Department of Agriculture, Institute of Informatics, University of Warsaw (UW), Graduate School of Agricultural and Life Sciences, Department of Biomaterial Sciences, The University of Tokyo, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Université Henri Poincaré - Nancy 1 (UHP), Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University [Göttingen], Department of Plant Biology, Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile (UC), Viikki Plant Science Centre (ViPS), Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki-University of Helsinki, Centre for Structural and Functional Genomics, Concordia University [Montreal], Department of Biological Sciences, Vanderbilt University [Nashville], Biotechnology Center, University of Wisconsin, Hudson Alpha Institute for Biotechnology, Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences (SLU), Genetics and Microbiology Research Group, Public University of Navarre, College of Science, Swansea University, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], Assembling the Fungal Tree of Life (AFTOL) project under NSF [DEB-0732968, DEB-0732993, DEB-0732550], University of Minnesota [Twin Cities] (UMN), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institute of Informatics [Warsaw], Faculty of Mathematics, Informatics, and Mechanics [Warsaw] (MIMUW), University of Warsaw (UW)-University of Warsaw (UW), Graduate School of Agricultural and Life Sciences [UTokyo] (GSALS), The University of Tokyo (UTokyo), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), University of Wisconsin-Madison, Department of Forest Mycology and Plant Pathology, College of Science [Swansea], Georg-August-University = Georg-August-Universität Göttingen, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA)
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Indoles ,[SDV]Life Sciences [q-bio] ,Lineage (evolution) ,macromolecular substances ,Fungus ,Lignin ,complex mixtures ,Agaricomycetes ,Evolution, Molecular ,03 medical and health sciences ,chemistry.chemical_compound ,Mycology ,Agaricomycotina ,Botany ,Polyporales ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,biology ,030306 microbiology ,Basidiomycota ,fungi ,technology, industry, and agriculture ,food and beverages ,Bayes Theorem ,biology.organism_classification ,Wood ,Peroxidases ,chemistry ,Genome, Fungal - Abstract
5 páginas, 1 figura, 1 tabla, 22 figuras suplementarias, 16 tablas suplementarias -- PAGS nros. 1715-1719 et al., Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period, The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. Also supported by the Assembling the Fungal Tree of Life (AFTOL) project under NSF awards DEB-0732968 (D.S.H.), DEB-0732993 (J.W.S.), and DEB-0732550 (D.J.M.).
- Published
- 2012
13. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion
- Author
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Randy M. Berka, Daniel S. Rokhsar, Patrik J. Hoegger, Pedro M. Coutinho, José Luis Lavín, Paulo Canessa, Francisco J. Ruiz-Dueñas, Martin Pospíšek, Timothy Y. James, Erika Lindquist, Luis F. Larrondo, Jill Gaskell, Antonio G. Pisabarro, Amber Vanden Wymelenberg, Phil Kersten, Sarah Teter, David S. Hibbett, Grzegorz Sabat, Susan Lucas, Dan Cullen, Patricia Ferreira, Bernard Henrissat, Ángel T. Martínez, Jagjit S. Yadav, José A. Oguiza, Kenneth E. Hammel, Preethi Ramaiya, William Kenealy, Sandra Splinter BonDurant, Harshavardhan Doddapaneni, Christian P. Kubicek, Jean F. Challacombe, Scott E. Baker, Hank Tu, Asaf Salamov, Monika Schmoll, Martin Mokrejs, Kenneth S. Bruno, Ingo Morgenstern, Igor V. Grigoriev, Ursula Kües, Rafael Vicuña, Diego Martinez, Monica Misra, Paul Harris, Emma R. Master, Harris Shapiro, Jon K. Magnuson, Debbie Yaver, Gary Xie, Thomas Brettin, Christine L. Chee, Venkataramanan Subramanian, Universidad Pública de Navarra. Departamento de Producción Agraria, and Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
- Subjects
Fenton ,Glycoside Hydrolases ,Molecular Sequence Data ,Cellulase ,Genome ,Lignin ,Transcriptome ,Postia placenta ,03 medical and health sciences ,chemistry.chemical_compound ,Cellulases ,Glycoside hydrolase ,Cellulose ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,Multidisciplinary ,Base Sequence ,biology ,030306 microbiology ,Gene Expression Profiling ,Biological Sciences ,15. Life on land ,biology.organism_classification ,Biological Evolution ,Wood ,Enzymes ,Wood-decay fungus ,Brown-Rot ,chemistry ,Biochemistry ,biology.protein ,Phanerochaete ,Genome, Fungal ,Oxidoreductases ,Polyporales ,Metabolic Networks and Pathways - Abstract
Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative β -1–4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also upregulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H2O2. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H2O2 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. This work was supported by the U.S. Department of Energy’s Office of Science, Biological and Environmental Research Program, and University of California, Lawrence Berkeley National Laboratory Contract DE-AC02–05CH11231; Lawrence Livermore National Laboratory Contract DE-AC52–07NA27344; Los Alamos National Laboratory Contract DE-AC02–06NA25396; University of Wisconsin Grant DE-FG02–87ER13712; Forest Products Laboratory, U.S. Department of Agriculture, Cooperative State Research, Education, and Extension Services Grant 2007–35504-18257; National Institutes of Health Grant GM060201 (to University of New Mexico); Centro de Investigaciones Biológicas (Madrid) EUproject NMP2–2006-026456; Ministry of Education Czech Republic Grant LC06066.
- Published
- 2009
- Full Text
- View/download PDF
14. Rapid analysis of abietanes in conifers
- Author
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Barbara L. Illman, Kenneth F. Raffa, Brian J. Kopper, and Phil Kersten
- Subjects
Chromatography ,Time Factors ,Plant Extracts ,fungi ,Carboxylic Acids ,Immunity ,General Medicine ,Biology ,Phloem ,Plants ,Biochemistry ,High-performance liquid chromatography ,chemistry.chemical_compound ,Tracheophyta ,Uv spectra ,chemistry ,Abietanes ,Dehydroabietic acid ,Oleoresin ,Diterpene ,Abietic acid ,Ecology, Evolution, Behavior and Systematics ,Levopimaric acid ,Chromatography, High Pressure Liquid - Abstract
Diterpene resin acids are major constituents of conifer oleoresin and play important roles in tree defense against insects and microbial pathogens. The tricyclic C-20 carboxylic acids are generally classified into two groups, the abietanes and the pimaranes. The abietanes have conjugated double bonds and exhibit characteristic UV spectra. Here, we report the analysis of abietanes by reversed-phase high-performance liquid chromatography using multiwavelength detection to optimize quantification of underivatized abietic, neoabietic, palustric, levopimaric, and dehydroabietic acids. The utility of the method is demonstrated with methanol extracts of white spruce (Picea glauca) phloem, and representative concentrations are reported.
- Published
- 2006
15. Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins
- Author
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Patrick Minges, Nik Putnam, Jill Gaskell, Dan Cullen, Igor V. Grigoriev, Phil Kersten, Paula Belinky, Harris Shapiro, Amber Vanden Wymelenberg, Carlos G. Dosoretz, Grzegorz Sabat, Andrea Aerts, Diego Martinez, and Asaf Salamov
- Subjects
Glycoside Hydrolases ,Hypothetical protein ,Phanerochaete ,Microbiology ,Mass Spectrometry ,Fungal Proteins ,Gene cluster ,Genetics ,Gene family ,Glycoside hydrolase ,Gene ,biology ,Sequence Homology, Amino Acid ,Computational Biology ,Lignin peroxidase ,Lipase ,biology.organism_classification ,Phosphoric Monoester Hydrolases ,Culture Media ,Protein Transport ,Biochemistry ,Peroxidases ,Proteome ,Genome, Fungal ,Databases, Nucleic Acid ,Carboxylic Ester Hydrolases ,Peptide Hydrolases - Abstract
The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identiWed in the earlier database (v1.0). Within the v2.1 ‘computational secretome,’ 43% showed no signiWcant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed signiWcant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identiWed in culture Wltrates by mass spectrometry (LS–MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identiWed in carbon-starved cultures. Beyond proteases and M6Pase, 28 speciWc gene products were identiWed including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium’s extracellular enzyme systems. Published by Elsevier Inc.
- Published
- 2005
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