Search

Your search keyword '"Baker, Scott E."' showing total 20 results
Start Over Author "Baker, Scott E." Publisher biomed central
20 results on '"Baker, Scott E."'

1. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicilliumbiforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Published
2023
Full Text
View/download PDF

4. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Author

Kubicek, Christian P, Herrera-Estrella, Alfredo, Seidl-Seiboth, Verena, Martinez, Diego A, Druzhinina, Irina S, Thon, Michael, Zeilinger, Susanne, Casas-Flores, Sergio, Horwitz, Benjamin A, Mukherjee, Prasun K, Mukherjee, Mala, Kredics, László, Alcaraz, Luis D, Aerts, Andrea, Antal, Zsuzsanna, Atanasova, Lea, Cervantes-Badillo, Mayte G, Challacombe, Jean, Chertkov, Olga, McCluskey, Kevin, Coulpier, Fanny, Deshpande, Nandan, von Döhren, Hans, Ebbole, Daniel J, Esquivel-Naranjo, Edgardo U, Fekete, Erzsébet, Flipphi, Michel, Glaser, Fabian, Gómez-Rodríguez, Elida Y, Gruber, Sabine, Han, Cliff, Henrissat, Bernard, Hermosa, Rosa, Hernández-Oñate, Miguel, Karaffa, Levente, Kosti, Idit, Le Crom, Stéphane, Lindquist, Erika, Lucas, Susan, Lübeck, Mette, Lübeck, Peter S, Margeot, Antoine, Metz, Benjamin, Misra, Monica, Nevalainen, Helena, Omann, Markus, Packer, Nicolle, Perrone, Giancarlo, Uresti-Rivera, Edith E, Salamov, Asaf, Schmoll, Monika, Seiboth, Bernhard, Shapiro, Harris, Sukno, Serenella, Tamayo-Ramos, Juan Antonio, Tisch, Doris, Wiest, Aric, Wilkinson, Heather H, Zhang, Michael, Coutinho, Pedro M, Kenerley, Charles M, Monte, Enrique, Baker, Scott E, and Grigoriev, Igor V

Published
2011
Full Text
View/download PDF

5. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., de Vries, Ronald P., Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young Mo, Baker, Scott E., and de Vries, Ronald P.

Published
2018

6. 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

7. A molecular genetic toolbox for Yarrowia lipolytica.

Author

Bredeweg, Erin L., Pomraning, Kyle R., Ziyu Dai, Nielsen, Jens, Kerkhoven, Eduard J., and Baker, Scott E.

Subjects
MOLECULAR genetics, LIPIDS, INDUSTRIAL engineering, NUCLEOTIDE sequencing, PLASMIDS
Abstract

Background: Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. Results: We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. Conclusions: These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

8. Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica.

Author

Pomraning, Kyle R., Young-Mo Kim, Nicora, Carrie D., Chu, Rosalie K., Bredeweg, Erin L., Purvine, Samuel O., Dehong Hu, Metz, Thomas O., and Baker, Scott E.

Subjects
NITROGEN analysis, LIPID synthesis, PHOSPHORYLATION, DNA analysis, ENZYME analysis
Abstract

Background: Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to characterize the response to nitrogen limitation at system-wide levels, including the proteome, phosphoproteome and metabolome, to better understand how this organism regulates and controls lipid metabolism and to identify targets that may be manipulated to improve lipid yield. Results: We found that ribosome structural genes are down-regulated under nitrogen limitation, during which nitrogen containing compounds (alanine, putrescine, spermidine and urea) are depleted and sugar alcohols and TCA cycle intermediates accumulate (citrate, fumarate and malate). We identified 1219 novel phosphorylation sites in Y. lipolytica, 133 of which change in their abundance during nitrogen limitation. Regulatory proteins, including kinases and DNA binding proteins, are particularly enriched for phosphorylation. Within lipid synthesis pathways, we found that ATP-citrate lyase, acetyl-CoA carboxylase and lecithin cholesterol acyl transferase are phosphorylated during nitrogen limitation while many of the proteins involved in β-oxidation are down-regulated, suggesting that storage lipid accumulation may be regulated by phosphorylation of key enzymes. Further, we identified short DNA elements that associate specific transcription factor families with up- and down-regulated genes. Conclusions: Integration of metabolome, proteome and phosphoproteome data identifies lipid accumulation in response to nitrogen limitation as a two-fold result of increased production of acetyl-CoA from excess citrate and decreased capacity for β-oxidation. [ABSTRACT FROM AUTHOR]

Published
2016
Full Text
View/download PDF

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

Subjects
TRICHODERMA reesei, REGULATOR genes, CELLULASE, BIOMASS, HYDROLYSIS, BIOMASS energy, MUTAGENESIS, PROGENITOR cells
Abstract

Background: Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a. Results: In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level. Conclusion: The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

10. A versatile toolkit for high throughput functional genomics with Trichoderma reesei.

Author

Schuster, André, Bruno, Kenneth S., Collett, James R., Baker, Scott E., Seiboth, Bernhard, Kubicek, Christian P., and Schmoll, Monika

Subjects
FUNCTIONAL genomics, TRICHODERMA reesei, ASCOMYCETES, CELLULASE, MUTAGENESIS, BIOTECHNOLOGY, ELECTROPORATION, DELETION mutation
Abstract

Background: The ascomycete fungus, Trichoderma reesei (anamorph of Hypocrea jecorina), represents a biotechnological workhorse and is currently one of the most proficient cellulase producers. While strain improvement was traditionally accomplished by random mutagenesis, a detailed understanding of cellulase regulation can only be gained using recombinant technologies. Results: Aiming at high efficiency and high throughput methods, we present here a construction kit for gene knock out in T. reesei. We provide a primer database for gene deletion using the pyr4, amdS and hph selection markers. For high throughput generation of gene knock outs, we constructed vectors using yeast mediated recombination and then transformed a T. reesei strain deficient in non-homologous end joining (NHEJ) by spore electroporation. This NHEJ-defect was subsequently removed by crossing of mutants with a sexually competent strain derived from the parental strain, QM9414. Conclusions: Using this strategy and the materials provided, high throughput gene deletion in T. reesei becomes feasible. Moreover, with the application of sexual development, the NHEJ-defect can be removed efficiently and without the need for additional selection markers. The same advantages apply for the construction of multiple mutants by crossing of strains with different gene deletions, which is now possible with considerably less hands-on time and minimal screening effort compared to a transformation approach. Consequently this toolkit can considerably boost research towards efficient exploitation of the resources of T. reesei for cellulase expression and hence second generation biofuel production. [ABSTRACT FROM AUTHOR]

Published
2012
Full Text
View/download PDF

11. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey.

Author

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

Subjects
TRICHODERMA, PATHOGENIC microorganisms, GENE expression, MYCOPARASITISM, AMINO acids
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. [ABSTRACT FROM AUTHOR]

Published
2009
Full Text
View/download PDF

12. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.

Author

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

Subjects
PROTEOMICS, MASS spectrometry, PRIMA facie evidence, GEL electrophoresis, NUCLEOTIDE sequence
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. [ABSTRACT FROM AUTHOR]

Published
2009
Full Text
View/download PDF

13. 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, 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.

Full Text
View/download PDF

14. 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, 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.

Full Text
View/download PDF

15. 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, 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.

Full Text
View/download PDF

16. 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., 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, Cánovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Corrêa dos Santos, Renato Augusto, Lima Damásio, André Ricardo de, Diallinas, George, Emri, Tamás, Fekete, Erzébet, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hildén, 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, Mäkela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos P., Mulé, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsébet, 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, Riaño-Pachón, Diego Mauricio, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, 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, Pócsi, István, 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.

Full Text
View/download PDF

17. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in <italic>Aspergillus nidulans</italic>.

Author

Khosravi, Claire, Battaglia, Evy, Kun, Roland S., Dalhuijsen, Sacha, Visser, Jaap, Aguilar-Pontes, María Victoria, Zhou, Miaomiao, Heyman, Heino M., Kim, Young-Mo, Baker, Scott E., and de Vries, Ronald P.

Subjects
PENTOSE metabolism, HEXOSES, GLYCOLYSIS, PLANT biomass, ASPERGILLUS nidulans, AGRICULTURAL wastes, BIOACCUMULATION
Abstract

Background: Plant biomass is the most abundant carbon source for many fungal species. In the biobased industry fungi, are used to produce lignocellulolytic enzymes to degrade agricultural waste biomass. Here we evaluated if it would be possible to create an Aspergillus nidulans strain that releases, but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were impaired in glycolysis, by using hexokinase (hxkA) and glucokinase (glkA) negative strains. To prevent repression of enzyme production due to the hexose accumulation, strains were generated that combined these mutations with a deletion in creA, the repressor involved in regulating preferential use of different carbon catabolic pathways. Results: Phenotypic analysis revealed reduced growth for the hxkA1 glkA4 mutant on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. The creAΔ4 mutation in combination with preventing initial phosphorylation in glycolysis resulted in better growth than the hxkA/glkA mutant and an increased expression of pentose catabolic and pentose phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources created a shift towards the pentose fraction of wheat bran as a major carbon source to support growth. Conclusion: Blocking the direct entry of hexoses to glycolysis activates alternative metabolic conversion of these sugars in A. nidulans during growth on plant biomass, but also upregulates conversion of other sugars, such as pentoses. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

18. 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 C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, and Bidard F

Abstract

Background: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei , the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype., Results: Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1 , and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions., Conclusion: We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei , as in Neurospora crassa , vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results