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101. Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation of Neurospora Crassa using Maximum Entropy Optimizations and Reinforcement Learning

Author

Cannon, William R., primary, Britton, Samuel R., additional, Banwarth-Kuhn, Mikahl, additional, Alber, Mark, additional, Hurley, Jennifer M., additional, Jankowski, Meaghan S., additional, Zucker, Jeremy D., additional, Baxter, Douglas J., additional, Kumar, Neeraj, additional, Baker, Scott E., additional, and Dunlap, Jay C., additional

Published
2019
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102. High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger

Author

Kowalczyk, Joanna E, Khosravi, Claire, Purvine, Samuel, Dohnalkova, Alice, Chrisler, William B., Orr, Galya, Robinson, Errol, Zink, Erika, Wiebenga, Ad, Peng, Mao, Battaglia, Evy, Baker, Scott E, de Vries, Ronald P., Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Fungal Physiology

Published
2017

103. Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways

Author

Hurley, Jennifer M., primary, Jankowski, Meaghan S., additional, De los Santos, Hannah, additional, Crowell, Alexander M., additional, Fordyce, Samuel B., additional, Zucker, Jeremy D., additional, Kumar, Neeraj, additional, Purvine, Samuel O., additional, Robinson, Errol W., additional, Shukla, Anil, additional, Zink, Erika, additional, Cannon, William R., additional, Baker, Scott E., additional, Loros, Jennifer J., additional, and Dunlap, Jay C., additional

Published
2018
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105. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

Author

Herrera-Estrella Alfredo, Grigoriev Igor, Sun Jibin, Schmoll Monika, Martínez Pedro, Zeilinger Susanne, Koptchinskiy Alexeji, Gruber Sabine, Lindquist Erika, Song Lifu, Seidl Verena, Baker Scott E, and Kubicek Christian P

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Combating the action of plant pathogenic microorganisms by mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since two decades. The fungal genus Trichoderma includes a high number of taxa which are able to recognize, combat and finally besiege and kill their prey. Only fragments of the biochemical processes related to this ability have been uncovered so far, however. Results We analyzed genome-wide gene expression changes during the begin of physical contact between Trichoderma atroviride and two plant pathogens Botrytis cinerea and Rhizoctonia solani, and compared with gene expression patterns of mycelial and conidiating cultures, respectively. About 3000 ESTs, representing about 900 genes, were obtained from each of these three growth conditions. 66 genes, represented by 442 ESTs, were specifically and significantly overexpressed during onset of mycoparasitism, and the expression of a subset thereof was verified by expression analysis. The upregulated genes comprised 18 KOG groups, but were most abundant from the groups representing posttranslational processing, and amino acid metabolism, and included components of the stress response, reaction to nitrogen shortage, signal transduction and lipid catabolism. Metabolic network analysis confirmed the upregulation of the genes for amino acid biosynthesis and of those involved in the catabolism of lipids and aminosugars. Conclusion The analysis of the genes overexpressed during the onset of mycoparasitism in T. atroviride has revealed that the fungus reacts to this condition with several previously undetected physiological reactions. These data enable a new and more comprehensive interpretation of the physiology of mycoparasitism, and will aid in the selection of traits for improvement of biocontrol strains by recombinant techniques.

Published
2009
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106. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

Author

Grigoriev Igor V, Gaskell Simon J, Riba-Garcia Isabel, Francis-McIntyre Sue, Sugden Deana, Wright James C, Baker Scott E, Beynon Robert J, and Hubbard Simon J

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). Results 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. Conclusion This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

Published
2009
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108. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald P. de, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asaollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Diallinas, George, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, 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, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Ngan, Chew Yee, Orejas, Margarita, 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, Robert, Vincent, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sanguinetti, Manuel, Sep?i?, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Shiela E., Wiele, Nathalie van de, Rossen-Uffink, Diana van, Velasco de Castro Oliveira, Juliana, 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, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., and Grigoriev, Igor V.

Subjects
Genome sequencing, Comparative genomics, Fungal biology
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

110. PNNL Fungal Biotechnology Core DOE-OBP Project

Author

Baker, Scott E., primary, Bruno, Kenneth S., additional, Butcher, Mark G., additional, Collett, James R., additional, Culley, David E., additional, Dai, Ziyu, additional, Magnuson, Jon K., additional, and Panisko, Ellen A., additional

Published
2009
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111. What links laminin-5 to the keratin cytoskeleton in epithelial cells?

Author

Jones, Jonathan C.R., Skalli, Omar, Goldman, Robert D., and Baker, Scott E.

Subjects
Cytoskeleton -- Research, Keratinocytes -- Research, Extracellular matrix -- Research, Laminin -- Research, Cell interaction -- Research, Biological sciences, Research
Abstract

The extracellular matrix plays an important role in tissue morphogenesis. It does so, in part, by interacting with a family of heterodimeric cell surface receptors called integrins. Indeed, the integrins [...]

Published
1998

113. Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels

Author

Tisch, Doris, primary, Pomraning, Kyle R., additional, Collett, James R., additional, Freitag, Michael, additional, Baker, Scott E., additional, Chen, Chia-Ling, additional, Hsu, Paul Wei-Che, additional, Chuang, Yu Chien, additional, Schuster, Andre, additional, Dattenböck, Christoph, additional, Stappler, Eva, additional, Sulyok, Michael, additional, Böhmdorfer, Stefan, additional, Oberlerchner, Josua, additional, Wang, Ting-Fang, additional, and Schmoll, Monika, additional

Published
2017
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114. Ortholog prediction of the Aspergillus genus applicable for synthetic biology

Author

Jane Nybo, Tammi Camilla Vesth, Sebastian Theobald, Jens Frisvad, Grigoriev, Igor V., Baker, Scott E., and Mikael Rørdam Andersen

Abstract

The Aspergillus genus contains leading industrial microorganisms, excelling in producing bioactive compounds and enzymes. Using synthetic biology and bioinformatics, we aim to re-engineer these organisms for applications within human health, pharmaceuticals, environmental engineering, and food production. In this project, we compare the genomes of +300 species from the Aspergillus genus to generate a high-resolution pan-genomic map, representing genetic diversity spanning ~200 million years. We are identifying genes specific to species and clades to allow for guilt-by-association-based mapping of genotype-to-phenotype. To achieve this, we have developed orthologous protein prediction software that utilizes genus-wide genetic diversity. The approach is optimized for large data sets, based on BLASTp considering protein identity and alignment coverage, and clustering using single linkage of bi-directional hits. The result is orthologous protein families describing the genomic and functional features of individual species, clades and the core/pan genome of Aspergillus; and applicable to genotype-to-phenotype analyses in other microbial genera.

Published
2016

115. The Aspergillus Mine - publishing bioinformatics

Author

Vesth, Tammi Camilla, Rasmussen, Jane Lind Nybo, Theobald, Sebastian, Kjærbølling, Inge, Frisvad, Jens Christian, Nielsen, Kristian Fog, Lyhne, Ellen Kirstine, Kogle, Martin Engelhard, Kuo, Alan, Riley, Robert, de Vries, R.P., Grigoriev, Igor V., Mortensen, Uffe Hasbro, Henrissat, Bernard, Baker, Scott E., and Andersen, Mikael Rørdam

Subjects
Bioinformatic, Aspergillus, Comparative genomics, Data publishing, Fungi
Abstract

Genome analysis is no longer a field reserved for specialists and experimental laboratories are doing groundbreaking research using genome sequencing and analysis. In this new era, it is essential that data, analysis and results are shared between scientists. But this can be a challenge, even more so with no computational specialist. Here we present a setup for analysis and publication of genome data of 70 species of Aspergillus fungi. The platform is based on R, Python and uses the RShiny framework to create interactive web‐applications. It allows all participants to create interactive analysis which can be shared with the team and in connection with publications. We present analysis for investigation of genetic diversity, secondary and primary metabolism and general data overview. The platform, the Aspergillus Mine, is a collection of analysis tools based on data from collaboration with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from the web‐app. This resource will be of great benefit to the Aspergillus community which is in a rapid development in regards to genome sequencing and analysis. At the moment, the service includes analysis of more than 70 genomes, and is expected to double in the next 6 months, with the final goal of the project is the analysis of 300 Aspergillus species.

Published
2016

116. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

Author

Corrochano, Luis M, Kuo, Alan, Marcet-Houben, Marina, Polaino, Silvia, Salamov, Asaf, Villalobos-Escobedo, José M, Grimwood, Jane, Álvarez, M Isabel, Avalos, Javier, Bauer, Diane, Benito, Ernesto P, Benoit, Isabelle, Burger, Gertraud, Camino, Lola P, Cánovas, David, Cerdá-Olmedo, Enrique, Cheng, Jan-Fang, Domínguez, Angel, Eliáš, Marek, Eslava, Arturo P, Glaser, Fabian, Gutiérrez, Gabriel, Heitman, Joseph, Henrissat, Bernard, Iturriaga, Enrique A, Lang, B Franz, Lavín, José L, Lee, Soo Chan, Li, Wenjun, Lindquist, Erika, López-García, Sergio, Luque, Eva M, Marcos, Ana T, Martin, Joel, McCluskey, Kevin, Medina, Humberto R, Miralles-Durán, Alejandro, Miyazaki, Atsushi, Muñoz-Torres, Elisa, Oguiza, José A, Ohm, Robin A, Olmedo, María, Orejas, Margarita, Ortiz-Castellanos, Lucila, Pisabarro, Antonio G, Rodríguez-Romero, Julio, Ruiz-Herrera, José, Ruiz-Vázquez, Rosa, Sanz, Catalina, Schackwitz, Wendy, Shahriari, Mahdi, Shelest, Ekaterina, Silva-Franco, Fátima, Soanes, Darren, Syed, Khajamohiddin, Tagua, Víctor G, Talbot, Nicholas J, Thon, Michael R, Tice, Hope, de Vries, Ronald P, Wiebenga, Ad, Yadav, Jagjit S, Braun, Edward L, Baker, Scott E, Garre, Victoriano, Schmutz, Jeremy, Horwitz, Benjamin A, Torres-Martínez, Santiago, Idnurm, Alexander, Herrera-Estrella, Alfredo, Gabaldón, Toni, Grigoriev, Igor V, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Molecular Plant Physiology, 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), Universidad de Sevilla. Departamento de Genética, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Molecular Plant Physiology, Universidad Pública de Navarra. Departamento de Producción Agraria, Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Light, Transcription, Genetic, Mutant, Genome, Medical and Health Sciences, Phycomyces, Gene Duplication, Gene duplication, ComputingMilieux_MISCELLANEOUS, Genetics, Agricultural and Biological Sciences(all), [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Fungal, Mucor, Multigene Family, Signal transduction, Genome, Fungal, General Agricultural and Biological Sciences, Transcription, Biotechnology, Signal Transduction, Evolution, 1.1 Normal biological development and functioning, 030106 microbiology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Genetic, Underpinning research, Gene family, Gene, Biochemistry, Genetics and Molecular Biology(all), Psychology and Cognitive Sciences, Fungi, Neurosciences, Molecular, biology.organism_classification, 030104 developmental biology, Genome duplication, Perception, Phycomyces blakesleeanus, Generic health relevance, Developmental Biology
Abstract

Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3, 4, 5, 6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes. The work by the US 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 project was supported by European funds (European Regional Development Fund, ERDF), the Spanish Ministerio de Economía y Competitividad (BIO2005-25029-E, BIO2015-67148-R), and the Regional Government (Junta de Andalucía, P06-CVI-01650) to L.M.C.; Conacyt (Mexico) (FORDECYT-2012-02-193512) to A.H.-E.; the US National Science Foundation (MCB-0920581) to A.I.; and the Czech Science Foundation (13-33039S) to M.E.

Published
2015

117. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction

Author

Ivanova, Christa, primary, Ramoni, Jonas, additional, Aouam, Thiziri, additional, Frischmann, Alexa, additional, Seiboth, Bernhard, additional, Baker, Scott E., additional, Le Crom, Stéphane, additional, Lemoine, Sophie, additional, Margeot, Antoine, additional, and Bidard, Frédérique, additional

Published
2017
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125. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Published
2017
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132. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Author

Schmoll, Monika, primary, Dattenböck, Christoph, additional, Carreras-Villaseñor, Nohemí, additional, Mendoza-Mendoza, Artemio, additional, Tisch, Doris, additional, Alemán, Mario Ivan, additional, Baker, Scott E., additional, Brown, Christopher, additional, Cervantes-Badillo, Mayte Guadalupe, additional, Cetz-Chel, José, additional, Cristobal-Mondragon, Gema Rosa, additional, Delaye, Luis, additional, Esquivel-Naranjo, Edgardo Ulises, additional, Frischmann, Alexa, additional, Gallardo-Negrete, Jose de Jesus, additional, García-Esquivel, Monica, additional, Gomez-Rodriguez, Elida Yazmin, additional, Greenwood, David R., additional, Hernández-Oñate, Miguel, additional, Kruszewska, Joanna S., additional, Lawry, Robert, additional, Mora-Montes, Hector M., additional, Muñoz-Centeno, Tania, additional, Nieto-Jacobo, Maria Fernanda, additional, Nogueira Lopez, Guillermo, additional, Olmedo-Monfil, Vianey, additional, Osorio-Concepcion, Macario, additional, Piłsyk, Sebastian, additional, Pomraning, Kyle R., additional, Rodriguez-Iglesias, Aroa, additional, Rosales-Saavedra, Maria Teresa, additional, Sánchez-Arreguín, J. Alejandro, additional, Seidl-Seiboth, Verena, additional, Stewart, Alison, additional, Uresti-Rivera, Edith Elena, additional, Wang, Chih-Li, additional, Wang, Ting-Fang, additional, Zeilinger, Susanne, additional, Casas-Flores, Sergio, additional, and Herrera-Estrella, Alfredo, additional

Published
2016
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134. Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites

Author

Niu, Jing, primary, Arentshorst, Mark, additional, Nair, P Deepa S, additional, Dai, Ziyu, additional, Baker, Scott E, additional, Frisvad, Jens C, additional, Nielsen, Kristian F, additional, Punt, Peter J, additional, and Ram, Arthur F J, additional

Published
2016
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137. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in <italic>Aspergillus niger</italic>.

Author

Reilly, Morgann C., Kim, Joonhoon, Lynn, Jed, Simmons, Blake A., Gladden, John M., Magnuson, Jon K., and Baker, Scott E.

Subjects
ASPERGILLUS niger, FUNGAL genetics, FUNGAL enzymes, NUCLEOTIDE sequencing, PLANT biomass, MUTAGENESIS
Abstract

Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter. [ABSTRACT FROM AUTHOR]

Published
2018
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138. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillussection Nigri

Author

Vesth, Tammi C., Nybo, Jane L., Theobald, Sebastian, Frisvad, Jens C., Larsen, Thomas O., Nielsen, Kristian F., Hoof, Jakob B., Brandl, Julian, Salamov, Asaf, Riley, Robert, Gladden, John M., Phatale, Pallavi, Nielsen, Morten T., Lyhne, Ellen K., Kogle, Martin E., Strasser, Kimchi, McDonnell, Erin, Barry, Kerrie, Clum, Alicia, Chen, Cindy, LaButti, Kurt, Haridas, Sajeet, Nolan, Matt, Sandor, Laura, Kuo, Alan, Lipzen, Anna, Hainaut, Matthieu, Drula, Elodie, Tsang, Adrian, Magnuson, Jon K., Henrissat, Bernard, Wiebenga, Ad, Simmons, Blake A., Mäkelä, Miia R., de Vries, Ronald P., Grigoriev, Igor V., Mortensen, Uffe H., Baker, Scott E., and Andersen, Mikael R.

Abstract

Aspergillussection Nigricomprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus nigerisolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillusspecies.

Published
2018
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139. The plant cell wall decomposing machinery underlies the functional diversity of forest fungi

Author

Kauserud, H&#228, Lavin, Jos&#233, Oguiza, Jos&#233, K&#252, H&#246, Eastwood, Daniel C., Floudas, Dimitrios, Binder, Manfred, Majcherczyk, Andrzej, Schneider, Patrick, Aerts, Andrea, Asiegbu, Fred O., Baker, Scott E., Barry, Kerrie, Bendiksby, Mika, Blumentritt, Melanie, Coutinho, Pedro M., Cullen, Dan, Vries, Ronald P. de, Gathman, Allen, Goodell, Barry, Henrissat, Bernard, Ihrmark, Katarina, Kohler, Annegret, LaButti, Kurt, Lapidus, Alla, Lee, Yong-Hwan, Lindquist, Erika, Lilly, Walt, Lucas, Susan, Morin, Emmanuelle, Murat, Claude, Park, Jongsun, Pisabarro, Antonio G., Riley, Robert, Rosling, Anna, Salamov, Asaf, Schmidt, Olaf, Schmutz, Jeremy, Skrede, Inger, Stenlid, Jan, Wiebenga, Ad, Xie, Xinfeng, Hibbett, David S., Hoffmeister, Dirk, Martin, Francis, Grigoriev, Igor V., and Watkinson, Sarah C.

Subjects
dry rot fungus, technology, industry, and agriculture, food and beverages, lignin, s.lacrymans, macromolecular substances, hemicellulose, saprotrophy, Transcriptome, complex mixtures, brown rot decay
Abstract

Brown rot decay removes cellulose and hemicellulose from wood?residual lignin contributing up to 30percent of forest soil carbon?and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the ?dry rot? fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota

Published
2011

140. Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype

Author

Lichius, Alexander, primary, Bidard, Frédérique, additional, Buchholz, Franziska, additional, Le Crom, Stéphane, additional, Martin, Joel, additional, Schackwitz, Wendy, additional, Austerlitz, Tina, additional, Grigoriev, Igor V., additional, Baker, Scott E., additional, Margeot, Antoine, additional, Seiboth, Bernhard, additional, and Kubicek, Christian P., additional

Published
2015
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141. Genome Sequence and Annotation of Trichoderma parareesei , the Ancestor of the Cellulase Producer Trichoderma reesei

Author

Yang, Dongqing, primary, Pomraning, Kyle, additional, Kopchinskiy, Alexey, additional, Karimi Aghcheh, Razieh, additional, Atanasova, Lea, additional, Chenthamara, Komal, additional, Baker, Scott E., additional, Zhang, Ruifu, additional, Shen, Qirong, additional, Freitag, Michael, additional, Kubicek, Christian P., additional, and Druzhinina, Irina S., additional

Published
2015
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142. Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

Author

Pomraning, Kyle R., primary, Wei, Siwei, additional, Karagiosis, Sue A., additional, Kim, Young-Mo, additional, Dohnalkova, Alice C., additional, Arey, Bruce W., additional, Bredeweg, Erin L., additional, Orr, Galya, additional, Metz, Thomas O., additional, and Baker, Scott E., additional

Published
2015
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143. Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection

Author

Qu, Yi, primary, Feng, Ju, additional, Deng, Shuang, additional, Cao, Li, additional, Zhang, Qibin, additional, Zhao, Rui, additional, Zhang, Zhaorui, additional, Jiang, Yuxuan, additional, Zink, Erika M., additional, Baker, Scott E., additional, Lipton, Mary S., additional, Paša-Tolić, Ljiljana, additional, Hu, Jian Zhi, additional, and Wu, Si, additional

Published
2014
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144. Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms.

Author

Tao Geng, Smallwood, Chuck R., Bredeweg, Erin L., Pomraning, Kyle R., Plymale, Andrew E., Baker, Scott E., Evans, James E., and Kelly, Ryan T.

Subjects
MICROFLUIDIC devices, CELL culture, CELL imaging, CELL growth, CELL analysis
Abstract

Modern live-cell imaging approaches permit real-time visualization of biological processes, yet limitations exist for unicellular organism isolation, culturing, and long-term imaging that preclude fully understanding how cells sense and respond to environmental perturbations and the link between single-cell variability and whole-population dynamics. Here, we present a microfluidic platform that provides fine control over the local environment with the capacity to replace media components at any experimental time point, and provides both perfused and compartmentalized cultivation conditions depending on the valve configuration. The functionality and flexibility of the platform were validated using both bacteria and yeast having different sizes, motility, and growth media. The demonstrated ability to track the growth and dynamics of both motile and non-motile prokaryotic and eukaryotic organisms emphasizes the versatility of the devices, which should enable studies in bioenergy and environmental research. [ABSTRACT FROM AUTHOR]

Published
2017
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145. Genomes to Proteomes

Author

Panisko, Ellen A., primary, Grigoriev, Igor, additional, Daly, Don S., additional, Webb-Robertson, Bobbie-Jo, additional, and Baker, Scott E., additional

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149. Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger

Author

Dai, Ziyu, primary, Aryal, Uma K., additional, Shukla, Anil, additional, Qian, Wei-Jun, additional, Smith, Richard D., additional, Magnuson, Jon K., additional, Adney, William S., additional, Beckham, Gregg T., additional, Brunecky, Roman, additional, Himmel, Michael E., additional, Decker, Stephen R., additional, Ju, Xiaohui, additional, Zhang, Xiao, additional, and Baker, Scott E., additional

Published
2013
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