Browsing by Author "Salamov, Asaf"

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    Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion
    (2009) Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo; Hibbett, David; Schmoll, Monika; Kubicek, Christian P.; Ferreira, Patricia; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Kersten, Phil; Hammel, Kenneth E.; Wymelenberg, Amber Vanden; Gaskell, Jill; Lindquist, Erika; Sabat, Grzegorz; BonDurant, Sandra Splinter; Larrondo, Luis F.; Canessa, Paulo; Vicuna, Rafael; Yadav, Jagjit; Doddapaneni, Harshavardhan; Subramanian, Venkataramanan; Pisabarro, Antonio G.; Lavin, Jose L.; Oguiza, Jose A.; Master, Emma; Henrissat, Bernard; Coutinho, Pedro M.; Harris, Paul; Magnuson, Jon Karl; Baker, Scott E.; Bruno, Kenneth; Kenealy, William; Hoegger, Patrik J.; Kuees, Ursula; Ramaiya, Preethi; Lucash, Susan; Salamov, Asaf; Shapiro, Harris; Tu, Hank; Chee, Christine L.; Misra, Monica; Xie, Gary; Teter, Sarah; Yaver, Debbie; James, Tim; Mokrejs, Martin; Pospisek, Martin; Grigoriev, Igor V.; Brettin, Thomas; Rokhsar, Dan; Berka, Randy; Cullen, Dan
    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 exo-cellobiohydrolases 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 beta-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 up-regulated 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.
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    Pan genome of the phytoplankton Emiliania underpins its global distribution
    (2013) Read, Betsy A.; Kegel, Jessica; Klute, Mary J.; Kuo, Alan; Lefebvre, Stephane C.; Maumus, Florian; Mayer, Christoph; Miller, John; Monier, Adam; Salamov, Asaf; Young, Jeremy; Aguilar, Maria; Claverie, Jean-Michel; Frickenhaus, Stephan; Gonzalez, Karina; Herman, Emily K.; Lin, Yao-Cheng; Napier, Johnathan; Ogata, Hiroyuki; Sarno, Analissa F.; Shmutz, Jeremy; Schroeder, Declan; de Vargas, Colomban; Verret, Frederic; von Dassow, Peter; Valentin, Klaus; Van de Peer, Yves; Wheeler, Glen; Dacks, Joel B.; Delwiche, Charles F.; Dyhrman, Sonya T.; Gloeckner, Gernot; John, Uwe; Richards, Thomas; Worden, Alexandra Z.; Zhang, Xiaoyu; Grigoriev, Igor V.; Allen, Andrew E.; Bidle, Kay; Borodovsky, M.; Bowler, C.; Brownlee, Colin; Cock, J. Mark; Elias, Marek; Gladyshev, Vadim N.; Groth, Marco; Guda, Chittibabu; Hadaegh, Ahmad; Iglesias-Rodriguez, Maria Debora; Jenkins, J.; Jones, Bethan M.; Lawson, Tracy; Leese, Florian; Lindquist, Erika; Lobanov, Alexei; Lomsadze, Alexandre; Malik, Shehre-Banoo; Marsh, Mary E.; Mackinder, Luke; Mock, Thomas; Mueller-Roeber, Bernd; Pagarete, Antonio; Parker, Micaela; Probert, Ian; Quesneville, Hadi; Raines, Christine; Rensing, Stefan A.; Riano-Pachon, Diego Mauricio; Richier, Sophie; Rokitta, Sebastian; Shiraiwa, Yoshihiro; Soanes, Darren M.; van der Giezen, Mark; Wahlund, Thomas M.; Williams, Bryony; Wilson, Willie; Wolfe, Gordon; Wurch, Louie L.
    Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.