Browsing by Author "Berka, Randy M."

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    Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
    (2014) Hori, Chiaki; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Suzuki, Hitoshi; Master, Emma; Ferreira, Patricia; Ruiz-Duenas, Francisco J.; Held, Benjamin; Canessa, Paulo; Larrondo, Luis F.; Schmoll, Monika; Druzhinina, Irina S.; Kubicek, Christian P.; Gaskell, Jill A.; Kersten, Phil; St John, Franz; Glasner, Jeremy; Sabat, Grzegorz; BonDurant, Sandra Splinter; Syed, Khajamohiddin; Yadav, Jagjit; Mgbeahuruike, Anthony C.; Kovalchuk, Andriy; Asiegbu, Fred O.; Lackner, Gerald; Hoffmeister, Dirk; Rencoret, Jorge; Gutierrez, Ana; Sun, Hui; Lindquist, Erika; Barry, Kerrie; Riley, Robert; Grigoriev, Igor V.; Henrissat, Bernard; Kuees, Ursula; Berka, Randy M.; Martinez, Angel T.; Covert, Sarah F.; Blanchette, Robert A.; Cullen, Daniel
    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.
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    Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina
    (2008) Martinez, Diego; Berka, Randy M.; Henrissat, Bernard; Saloheimo, Markku; Arvas, Mikko; Baker, Scott E.; Chapman, Jarod; Chertkov, Olga; Coutinho, Pedro M.; Cullen, Dan; Danchin, Etienne G. J.; Grigoriev, Igor V.; Harris, Paul; Jackson, Melissa; Kubicek, Christian P.; Han, Cliff S.; Ho, Isaac; Larrondo, Luis F.; de Leon, Alfredo Lopez; Magnuson, Jon K.; Merino, Sandy; Misra, Monica; Nelson, Beth; Putnam, Nicholas; Robbertse, Barbara; Salamov, Asaf A.; Schmoll, Monika; Terry, Astrid; Thayer, Nina; Westerholm-Parvinen, Ann; Schoch, Conrad L.; Yao, Jian; Barbote, Ravi; Nelson, Mary Anne; Detter, Chris; Bruce, David; Kuske, Cheryl R.; Xie, Gary; Richardson, Paul; Rokhsar, Daniel S.; Lucas, Susan M.; Rubin, Edward M.; Dunn-Coleman, Nigel; Ward, Michael; Brettin, Thomas S.
    Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.