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

Author

de Vries, Ronald P, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna A, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo C, Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, dos Santos, Renato Augusto Corrêa, Damásio, André Ricardo de Lima, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María Laura, Henrissat, Bernard, Hildén, Kristiina S, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F, MacCabe, Andrew, Mäkelä, 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 FJ, Ramón, 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, van de Wiele, Nathalie, van Rossen-Uffink, Diana, Oliveira, Juliana Velasco de Castro, Vesth, Tammi C, Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, and Andersen, Mikael R

Subjects
Human Genome, Genetics, Biotechnology, Emerging Infectious Diseases, Infectious Diseases, Adaptation, Biological, Aspergillus, Biodiversity, Biomass, Carbon, Computational Biology, Cytochrome P-450 Enzyme System, DNA Methylation, Fungal Proteins, Gene Expression Regulation, Fungal, Gene Regulatory Networks, Genome, Fungal, Genomics, Humans, Metabolic Networks and Pathways, Molecular Sequence Annotation, Multigene Family, Oxidoreductases, Phylogeny, Plants, Secondary Metabolism, Signal Transduction, Stress, Physiological, Genome sequencing, Comparative genomics, Fungal biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsMany 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

2. 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, and Grigoriev, Igor V

Subjects
Microbiology, Biochemistry and Cell Biology, Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Evolution, Molecular, Gene Duplication, Genome, Fungal, Light, Mucor, Multigene Family, Perception, Phycomyces, Signal Transduction, Transcription, Genetic, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
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 [3-6]. 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.

Published
2016

7. Identification of the genes encoding the catalytic steps corresponding to LRA4 (l‐2‐keto‐3‐deoxyrhamnonate aldolase) and l‐lactaldehyde dehydrogenase in Aspergillus nidulans: evidence for involvement of the loci AN9425/lraD and AN0544/aldA in the l‐rhamnose catabolic pathway

Author

MacCabe, Andrew P., Sanmartín, Gemma, Orejas, Margarita, Ministerio de Economía y Competitividad (España), and Generalitat Valenciana

Subjects
Filamentous fungi, Catabolism, L‐rhamnose, Aspergillus nidulans
Abstract

This is the peer reviewed version of the following article: MacCabe, A., Sanmartín, G. and Orejas, M. (2021), Identification of the genes encoding the catalytic steps corresponding to LRA4 (l‐2‐keto‐3‐deoxyrhamnonate aldolase) and l‐lactaldehyde dehydrogenase in Aspergillus nidulans: evidence for involvement of the loci AN9425/lraD and AN0544/aldA in the l‐rhamnose catabolic pathway. Environ Microbiol. https://doi.org/10.1111/1462-2920.15439, which has been published in final form at https://doi.org/10.1111/1462-2920.15439. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions., l‐rhamnose is found in nature mainly as a component of structural plant polysaccharides and can be used as a carbon source by certain microorganisms. Catabolism of this sugar in bacteria, archaea and fungi occurs by two routes involving either phosphorylated or non‐phosphorylated intermediates. Unlike the corresponding pathway in yeasts, the metabolic details of the non‐phosphorylated pathway in filamentous fungi are not fully defined. The first three genes (lraA, lraB and lraC) of the non‐phosphorylated pathway in Aspergillus nidulans have recently been studied revealing dependence on lraA function for growth on l‐rhamnose and α‐l‐rhamnosidase production. In the present work, two genes encoding the subsequent steps catalysed by l‐2‐keto‐3‐deoxyrhamnonate (l‐KDR) aldolase (AN9425) and l‐lactaldehyde dehydrogenase (AN0554) are identified. Loss‐of‐function mutations cause adverse growth effects on l‐rhamnose. Akin to genes lraA‐C and those encoding rhamnosidases (rhaA, rhaE), their expression is induced on l‐rhamnose via the transcriptional activator RhaR. Interestingly, the aldolase belongs to the ftablamily of bacterial l‐KDR aldolases (PF03328/COG3836) and not that of yeasts (PF00701/COG0329). In addition, AN0554 corresponds to the previously characterized aldA gene (encodes aldehyde dehydrogenase involved in ethanol utilization) thus revealing a previously unknown role for this gene in the catabolism of l‐rhamnose., This work was supported by the Spanish Ministerio de Economía y Competitividad/FEDER (grant number AGL2015‐6631‐C2‐2‐R) ‐ which also supported G.S. ‐ and the Generalitat Valenciana‐Conselleria d'Educació PROMETEO/2018/066.

Published
2021
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8. Transcriptional analysis of the lichenase-like gene cel12A of the filamentous fungus Stachybotrys atra BP-A and its relevance for lignocellulose depolymerization

Author

Generalitat Valenciana, Ministerio de Economía y Competitividad (España), Picart, Pere, Pastor, F. I. Javier, Orejas, Margarita, Generalitat Valenciana, Ministerio de Economía y Competitividad (España), Picart, Pere, Pastor, F. I. Javier, and Orejas, Margarita

Abstract

To rationally optimize the production of industrial enzymes by molecular means requires previous knowledge of the regulatory circuits controlling the expression of the corresponding genes. The genus Stachybotrys is an outstanding producer of cellulose-degrading enzymes. Previous studies isolated and characterized the lichenase-like/non-typical cellulase Cel12A of S. atra (AKA S. chartarum) belonging to glycosyl hydrolase family 12 (GH12). In this study, we used RT-qPCR to determine the pattern of expression of cel12A under different carbon sources and initial ambient pH. Among the carbon sources examined, rice straw triggered a greater increase in the expression of cel12A than 1% lactose or 0.1% glucose, indicating specific induction by rice straw. In contrast, cel12A was repressed in the presence of glucose even when combined with this inducer. The proximity of 2 adjacent 5′-CTGGGGTCTGGGG-3′ CreA consensus target sites to the translational start site of cel12A strongly suggests that the carbon catabolite repression observed is directly mediated by CreA. Ambient pH did not have a significant effect on cel12A expression. These findings present new knowledge on transcriptional regulatory networks in Stachybotrys associated with cellulose/hemicellulose depolymerization. Rational engineering of CreA to remove CCR could constitute a novel strategy for improving the production of Cel12A.

Published
2021

9. Additional file 1 of Catabolism of l-rhamnose in A. nidulans proceeds via the non-phosphorylated pathway and is glucose repressed by a CreA-independent mechanism

Author

MacCabe, Andrew P., Ninou, Elpinickie I., Pardo, Ester, and Orejas, Margarita

Abstract

Additional file 1: Figure S1. Schemes of microbial l-rhamnose catabolic pathways. (A) Catabolic pathways for l-rhamnose and (B) organisation of the genes encoding the corresponding activities in E. coli and various fungi. Homologous genes are indicated using the same colour code. Chr: chromosome number.

Published
2020
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10. The wide-domain carbon catabolite repressor CreA indirectly controls expression of the Aspergillus nidulans xlnB gene, encoding the acidic endo-beta-(1,4)-xylanase X(sub)24

Author

Orejas, Margarita, MacCabe, Andrew P., Perez-Gonzalez, Jose Antonio, Kumar, Sudeep, and Ramon, Daniel

Subjects
Aspergillus -- Genetic aspects, Microbial metabolism -- Genetic aspects, Gene expression -- Analysis, Sugar -- Microbiology, Biological sciences
Abstract

Results show that although mutation in the wide-domain repressor CreA gene leads to an elevated levels of xlnB mRNA, none of the CreA consensus target sites are localized in the xlnB gene. Data suggest that the catabolite repression of the xlnB encoded xylanase is exerted in an indirect manner.

Published
2001

11. Agrobacterium tumefaciens-Mediated Transformation of NHEJ Mutant Aspergillus nidulans Conidia: An Efficient Tool for Targeted Gene Recombination Using Selectable Nutritional Markers.

Author

Castillo, Virginia Casado-del, MacCabe, Andrew P., and Orejas, Margarita

Subjects
AGROBACTERIUM tumefaciens, ASPERGILLUS nidulans, CONIDIA, RECOMBINANT DNA, TRANSGENE expression
Abstract

Protoplast transformation for the introduction of recombinant DNA into Aspergillus nidulans is technically demanding and dependant on the availability and batch variability of commercial enzyme preparations. Given the success of Agrobacterium tumefaciens-mediated transformation (ATMT) in diverse pathogenic fungi, we have adapted this method to facilitate transformation of A. nidulans. Using suitably engineered binary vectors, gene-targeted ATMT of A. nidulans non-homologous end-joining (NHEJ) mutant conidia has been carried out for the first time by complementation of a nutritional requirement (uridine/uracil auxotrophy). Site-specific integration in the DnkuA host genome occurred at high efficiency. Unlike other transformation techniques, however, cross-feeding of certain nutritional requirements from the bacterium to the fungus was found to occur, thus limiting the choice of auxotrophies available for ATMT. In complementation tests and also for comparative purposes, integration of recombinant cassettes at a specific locus could provide a means to reduce the influence of position effects (chromatin structure) on transgene expression. In this regard, targeted disruption of the wA locus permitted visual identification of transformants carrying site-specific integration events by conidial colour (white), even when auxotrophy selection was compromised due to cross-feeding. The protocol described offers an attractive alternative to the protoplast procedure for obtaining locus-targeted A. nidulans transformants. [ABSTRACT FROM AUTHOR]

Published
2021
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14. L-Rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake

Author

Tamayo-Ramos Juan A, Flipphi Michel, Pardo Ester, Manzanares Paloma, and Orejas Margarita

Subjects
Aspergillus nidulans, Carbon catabolite repression, CreA-independent, Inducer exclusion, α-L-rhamnosidase, Transcriptional regulation, Microbiology, QR1-502
Abstract

Abstract Background Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Results Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. Conclusions The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR.

Published
2012
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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, 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

16. Additional file 8: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Subjects
body regions, inorganic chemicals, nervous system, fungi
Abstract

Effect of SHAM and KCN on fungal growth and sporulation. (PDF 252 kb)

Published
2017
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17. Additional file 27: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Abstract

Maximum likelihood rooted phylogeny of the FCY-like transporters of the aspergilli and some penicillia. (PDF 324 kb)

Published
2017
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18. Additional file 7: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Abstract

Comparative growth profiling of the aspergilli and selected other fungi. (PDF 8.65 kb)

Published
2017
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19. Additional file 6: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Subjects
body regions, animal structures, nervous system, fungi
Abstract

Overview of number of putative orthologs/paralogs in the compared fungal species related to primary carbon metabolism. (PDF 237 kb)

Published
2017
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20. Additional file 5: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Subjects
body regions, nervous system, fungi, behavior and behavior mechanisms, reproductive and urinary physiology
Abstract

Expression of mating and pheromone-signalling pathway genes in representative asexual aspergilli. (PDF 488 kb)

Published
2017
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21. Additional file 15: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Abstract

Extended analysis of stress tolerance of the aspergilli. (PDF 706 kb)

Published
2017
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22. Additional file 35: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Abstract

Maximal likelihood phylogeny of MASC1/RID1 orthologs. (PDF 115 kb)

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

Author

European Commission, Ministerio de Economía y Competitividad (España), Vries, Ronald P. de, Grigoriev, Igor V., MacCabe, Andrew P., Orejas, Margarita, European Commission, Ministerio de Economía y Competitividad (España), Vries, Ronald P. de, Grigoriev, Igor V., MacCabe, Andrew P., and Orejas, Margarita

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

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

Author

de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, 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, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, 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, Roehrig, 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, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, 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 R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, Grigoriev, Igor V, de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, 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, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, 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, Roehrig, 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, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, 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 R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, and Grigoriev, Igor V

Published
2017

25. 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

26. Enhanced production of a plant monoterpene by overexpression of the 3-hydroxy-3-methylglutaryl coenzyme A reductase catalytic domain in Saccharomyces cerevisiae

Author

Rico, Juan, Pardo, Ester, and Orejas, Margarita

Subjects
Brewer's yeast -- Genetic aspects, Brewer's yeast -- Physiological aspects, Gene expression -- Analysis, Biological sciences
Abstract

Linalool production is analyzed in different Saccharomyces cerevisiae strains expressing the Clarkia breweri linalool synthase gene (LIS). The performance of the wine strain [T.sub.73] is enhanced by manipulating the endogenous mevalonate (MVA) pathway, deregulated overexpression of the rate-limiting 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA redustace) doubled linalool production.

Published
2010

27. 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

29. Construction of a genetically modified wine yeast strain expressing the Aspergillus aculeatus rhaA gene, encoding an alpha-L-Rhamnosidase of enological interest

Author

Orejas, Margarita, Manzanares, Paloma, and Gil, Jose Vincente

Subjects
Genetic code -- Research, Yeast fungi -- Genetic aspects, Aspergillus -- Genetic aspects, Biological sciences
Abstract

The expression of the gene encoding A. aculeatus RhaA in a commercial wine yeast strain was investigated. The data indicate the biotechnological feasibility of the combination of wine yeast strains producing alpha- L-rhamnosidase of enological relevance.

Published
2003

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

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Microbiology, Molecular Plant Physiology, 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, 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, and Grigoriev, Igor V

Published
2016

32. Enhanced glycosyl hydrolase production in Aspergillus nidulans using transcription factor engineering approaches

Author

Tamayo-Ramos, Juan Antonio, Orejas, Margarita, Tamayo-Ramos, Juan Antonio, and Orejas, Margarita

Abstract

Background: Engineered fungi are attractive platforms for the production of plant cell wall hydrolytic enzymes which, among other biotechnological applications, are required for the efficient conversion of biomass to glucose and other fermentable sugars. As a fungal model system, Aspergillus nidulans provides genetic tools that are of relevance in this context and potentially applicable to industrially important filamentous fungi. The goal of this study is to assess the utility of A. nidulans as a host for recombinant protein production. Results: We have successfully applied a transcription factor engineering approach to improve the efficiency of the A. nidulans xylanolytic XlnR-xln p expression system. Specifically, endo-1,4-β-xylanases and an -L-rhamnosidase were chosen as representatives of endogenous and heterologous glycosyl hydrolases involved in plant cell wall deconstruction. By deregulating the expression of the xylanolytic transcriptional activator XlnR and modulating the activity of the pH regulator PacC we improved protein production and reduced production times. Xylanase activity was about 200-fold greater in gpdA p::xlnR strains compared to controls 4 hours after transfer to inducing conditions, and 10-fold greater after 24 hours. Remarkably, 75% of the xylanase activity was present in the engineered strains within 4 hours. Engineering XlnR expression also had a considerable impact on foreign protein production, especially when the promoter of the 'acidic' xlnB gene was used to express the transgene. -L-rhamnosidase activity in xlnB p::rhaA, gpdA p::xlnR strains was about 19-fold greater than that of controls 72 hours after transfer to xylan (about 85% of the total activity produced), and 10-fold greater at later times (120 hours). The performance of these strains was further enhanced by impeding the proteolytic activation of PacC; introduction of the palA1 allele in xlnB p::rhaA, gpdA p

Published
2014

33. La nueva Biotecnología apuesta por la vinificación

Author

Manzanares, Paloma and Orejas, Margarita

Subjects
Vinificación, Biotecnología, ADN recombinante, Fermentación, Saccharomyces cerevisiae, Ingeniería genética
Abstract

La OTRI del Centro Tecnológico Nacional de la Conserva y Alimentación junto con la OTT del Consejo Superior de Investigaciones Científicas, colaboran en el Proyecto AGROCSIC, el cual fue aprobado por el Ministerio de Ciencia y Tecnología y financiado por el Ministerio de Educación y Ciencia. El objetivo principal de esta nueva actuación es estudiar las distintas líneas de trabajo de los Centros del CSIC relacionadas con la alimentación, para transferir sus resultados al sector industrial., Desde el punto de vista microbiológico, la transformación del mosto de uva en vino o vinificación es un proceso complejo en el que intervienen distintos microorganismos, y donde las levaduras, principalmente Saccharomyces cerevisiae, juegan el papel más destacado. Durante la vinificación las levaduras utilizan los azúcares y otros componentes del mosto para su crecimiento, produciendo etanol, anhídrido carbónico, y en menor medida otros compuestos responsables de la composición química y las cualidades sensoriales del vino. Desde un punto de vista bioquímico, el vino puede considerarse como un producto de la transformación enzimática del mosto de uva., En las últimas décadas, coincidiendo con el avance de la Biotecnología, se han desarrollado nuevas técnicas de vinificación, que incluyen, entre otras, la utilización de cepas seleccionadas de S. cerevisiae (para normalizar la microbiota inicial y dar lugar a fermentaciones homogéneas año tras año), y el empleo de enzimas (para solucionar problemas puntuales del proceso y mejorar la calidad del producto final). El uso de levaduras seleccionadas, capaces de conducir la fermentación alcohólica e imponerse al resto de levaduras presentes, abre la posibilidad de aplicar técnicas de ingeniería genética a la levadura vínica para obtener nuevas cepas capaces de producir, a lo largo de la fermentación, las enzimas de interés en enología cuya adición se realiza de forma regular. Asimismo, las técnicas de ADN recombinante se están aplicando a la vid, donde se están produciendo importantes avances (como por ejemplo la producción de plantas resistentes a ciertas enfermedades víricas y fúngicas) y a los microorganismos productores de los preparados enzimáticos comerciales de uso en enología (por ejemplo para conseguir mayores rendimientos y preparados más específicos)., La información que las autoras aportan a esta revisión es fruto del desarrollo de varios proyectos financiados por la Comisión Interministerial de Ciencia y Tecnología (CICYT) entre los que se incluyen los proyectos en curso AGL2002-01906, AGL2003-01295/ALI y AGL2004-00978/ALI.

Published
2005

37. Construction of a Genetically Modified Wine Yeast Strain Expressing the Aspergillus aculeatus rhaA Gene, Encoding an {alpha}-L-Rhamnosidase of Enological Interest

Author

Manzanares, Paloma, Orejas, Margarita, Gil, José Vicente, Graaff, Leo H. de, Visser, Jaap, and Ramón, Daniel

Subjects
Aromatic compounds, Microvinification, Alpha-L-rhamnosidase, food and beverages, Linalool
Abstract

The Aspergillus aculeatus rhaA gene encoding an {alpha}-L-rhamnosidase has been expressed in both laboratory and industrial wine yeast strains. Wines produced in microvinifications, conducted using a combination of the genetically modified industrial strain expressing rhaA and another strain expressing a ß-glucosidase, show increased content mainly of the aromatic compound linalool., Ramón Areces grant and also by the CICYT AGL2002-01906 project (Spanish Ministry of Science and Technology-FEDER)

Published
2003

38. Evaluación de nuevas xilanasas fúngicas para el desarrollo de alimentos funcionales derivados de cereales

Author

Haros, Claudia Monika, Orejas, Margarita, Gavara Clemente, Rafael José, Universitat Politècnica de València. Escuela Técnica Superior del Medio Rural y Enología - Escola Tècnica Superior del Medi Rural i Enologia, Obando Garzón, Catalina, Haros, Claudia Monika, Orejas, Margarita, Gavara Clemente, Rafael José, Universitat Politècnica de València. Escuela Técnica Superior del Medio Rural y Enología - Escola Tècnica Superior del Medi Rural i Enologia, and Obando Garzón, Catalina

Abstract

[ES] Las endo-1,4-xilanasas (xilanasas; E.C. 3.2.1.8) son enzimas hidrolíticas que catalizan la degradación de los xilanos, rompiendo al azar los enlaces glicosídicos ß-(1-4) de las cadenas de xilosa presentes en la hemicelulosa de la pared celular vegetal, produciendo oligosacáridos (solubles e insolubles) de diferentes tamaños. Estas enzimas son extensamente utilizadas como coadyuvantes tecnológicos en la industria panadera por sus beneficios tecnológicos, como son el incremento del volumen de la pieza panaria, la mayor durabilidad del producto y la mejora de la calidad de la miga. El objetivo de este trabajo fue estudiar la utilidad de nuevas xilanasas de origen fúngico con el fin de incrementar el contenido de fibra soluble en productos de panadería, y por consiguiente su valor nutricional y funcional. Los ensayos se realizaron con tres formulaciones diferentes de pan: 100% harina de trigo (F-100), 50% harina de trigo + 50% harina de trigo integral (WWF-50) y 100% harina de trigo integral (WWF-100). Las enzimas estudiadas fueron dos xilanasas de Aspergillus nidulans (XlnA/X22 y XlnC/X34) expresadas en un organismo genéticamente modificado (Pichia pastoris) y una enzima comercial procedente de Thermomyces lanuginosus y expresada en Aspergillus oryzae (XlnPP), como referencia positiva. Cada formulación fue adicionada durante la etapa de amasado con las enzimas en estudio y éstas fueron comparadas con una muestra control sin la adición enzimática. En términos de volumen específico no se encontraron diferencias significativas entre el control y las muestras tratadas con enzimas, si bien se observó una tendencia positiva en las formulaciones con xilanasa comercial y XlnC/X34. Por otra parte, la aplicación de xilanasas ocasionó incrementos significativos en la cantidad de fibra soluble del pan. Estas diferencias fueron significativas entre el control y las muestras adicionadas con las enzimas XlnA/X22 y XlnPP, aumentando la fibra soluble un 7% y un 27% respectivamente, [EN] Xylanases are hemicellulolytic enzymes, which catalyze the degradation of xylan -the major polysaccharide constituent of hemicellulose- producing oligosaccharides (soluble or insoluble) of different sizes. These enzymes are widely used as food processing aids in baking for technological benefits such as increased volume, bread durability and improved crumb quality. The aim of this work was to test new fungal endoxylanases in order to enhance the production of soluble fibre in bakery products. The assays were performed using three different bread formulations: 100% wheat flour (F-100), 50% wheat flour + 50% whole wheat flour (WWF-50) and 100% whole wheat flour (WWF-100). The enzymes added during mixing were two Aspergillus nidulans endoxylanases (XlnA/X22 and XlnC/X34) overexpressed in genetically modified organisms (Pichia pastoris) and a commercial enzyme from Thermomyces lanuginosus and expressed in Aspergillus oryzae (XlnPP), as positive reference and samples were compared against control ones without enzymes. In terms of specific volume, no significant differences were found between control and samples treated with enzymes; however a tendency towards increasing was observed using either commercial xylanase or XlnC/X34. Application of endoxylanases resulted to be useful increasing the soluble fibre amount in breads. Significant differences were found between control samples and XlnA/X22 (7% increase) or the commercial endoxylanase (27%) in WWF-50 formulations. Remarkably, about 35% increase was observed when applying XlnA/X22 in whole wheat bread formulations. The F-100 bread showed a significant increase when the XlnC/X34 enzyme was added comparing to the control sample without enzyme. These results illustrate that in addition to their current technological applications, endoxylanases from A. nidulas showed themselves capable of developing bakery products with functional properties., [CA] Les xilanasas són enzims hidrolíticas les quals catalitzen la degradació del xilano, trencant els enllaços 1-4 de les cadenes de xilosa presents en l'hemicelulosa de la paret cellular, produint oligosacàrids (solubles i insolubles) de diferents grandàries." Estos enzims són extensament utilitzades com coadyuvants tecnològics en la indústria fornera pels seus beneficis tecnològics, com són l'increment del volum de la peça panaria, la major durabilitat del producte i millora de la qualitat de la molla. L'objectiu d'este treball va ser estudiar la utilitat de noves endoxilanasas d'origen fúngic a fi d'incrementar el contingut de fibra soluble en productes de forn i per consegüent el seu valor nutricional i funcional. Els assajos es van realitzar amb tres formulacions diferents de pa: 100% farina de blat (F-100), 50% farina de blat + 50% farina de blat integral (WWF-50) i 100% farina de blat integral (WWF-100) . Els enzims, les quals van ser addiciones durant l'etapa de pastat, van ser dos endoxilanasas d'Aspergillus nidulans (XlnA/X22 i XlnC/X34) expressades en un organisme genèticament modificat (Pichia pastoris) i un enzim comercial procedent de Thermomyces lanuginosus i expressada en Aspergillus oryzae (XlnPP), com a referència positiva. Les mostres van ser addicionades amb enzims i van ser comparades amb una mostra control sense enzims. En termes de volum especifique no es van trobar diferències significatives entre el control i les mostres tractades amb enzims, observant-se una tendència a incrementar-se en les formulacions amb xilanasa comercial i XlnC/X34. D'altra banda, l'aplicació de les endoxilanasas va mostrar un increment significatiu en la quantitat de fibra soluble en el producte final. Estes diferències van ser significatives entre el control i les mostres addicionades amb els enzims XlnA/X22 i XlnPP, augmentant un 7% i 27%, respectivament en la formulació WWF-50. En la formulació de pa integral es va observar un increment del 35% quan es va addicio

Published
2013

42. Activation of the Aspergillus PacC transcription factor in response to alkaline ambient pH requires proteolysis of the carboxy-terminal moiety

Author

Orejas, Margarita, Espeso, Eduardo A., Tilburn, Joan, Sarkar, Sovan, Arst, Herbert Nathan Jr., Peñalva, Miguel Ángel, Orejas, Margarita, Espeso, Eduardo A., Tilburn, Joan, Sarkar, Sovan, Arst, Herbert Nathan Jr., and Peñalva, Miguel Ángel

Abstract

Extremes of pH are an occupational hazard for many microorganisms. In addition to efficient pH homeostasis, survival effectively requires a regulatory system tailoring the syntheses of molecules functioning beyond the cell boundaries (permeases, secreted enzymes, and exported metabolites) to the pH of the growth environment. Our previous work established that the zinc finger PacC transcription factor mediates such pH regulation in the fungus Aspergillus nidulans in response to a signal provided by the products of the six pal genes at alkaline ambient pH. In the presence of this signal, PacC becomes functional, activating transcription of genes expressed at alkaline pH and preventing transcription of genes expressed at acidic pH. Here we detect two forms of PacC in extracts, both forming specific retardation complexes with a PacC-binding site. Under acidic growth conditions or in acidity-mimicking pal mutants (defective in ambient pH signal transduction), the full-length form of PacC predominates. Under alkaline growth conditions or in alkalinity-mimicking pacC(c) mutants (independent of the ambient pH signal), a proteolysed version containing the amino-terminal ~40% of the protein predominates. This specifically cleaved shorter version is clearly functional, both as an activator for alkaline-expressed genes and as a repressor for acid-expressed genes, but the full-length form of PacC must be inactive. Thus, PacC proteolysis is an essential and pH-sensitive step in the regulation of gene expression by ambient pH. Carboxy-terminal truncations, resulting in a gain-of-function (pacC(c)) phenotype, bypass the requirement for the pal signal transduction pathway for conversion of the full-length to the proteolyzed functional form.

Published
1995

43. Specificity Determinants of Proteolytic Processing of Aspergillus PacC Transcription Factor Are Remote from the Processing Site, and Processing Occurs in Yeast If pH Signalling Is Bypassed

Author

Mingot, José-Manuel, primary, Tilburn, Joan, additional, Diez, Eliecer, additional, Bignell, Elaine, additional, Orejas, Margarita, additional, Widdick, David A., additional, Sarkar, Sovan, additional, Brown, Christopher V., additional, Caddick, Mark X., additional, Espeso, Eduardo A., additional, Arst, Herbert N., additional, and Peñalva, Miguel A., additional

Published
1999
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47. Construction of a Genetically Modified Wine Yeast Strain Expressing the Aspergillus aculeatus rhaA Gene, Encoding an α-L-Rhamnosidase of Enological Interest.

Author

Manzanares, Paloma, Orejas, Margarita, Gil, José Vicente, de Graaff, Leo H., Visser, Jaap, and Ramón, Daniel

Subjects
*ASPERGILLUS, *YEAST, *WINES
Abstract

The Aspergillus aculeatus rhaA gene encoding an α-L-rhamnosidase has been expressed in both laboratory and industrial wine yeast strains. Wines produced in microvinifications, conducted using a combination of the genetically modified industrial strain expressing rhaA and another strain expressing a β-glucosidase, show increased content mainly of the aromatic compound linalool. [ABSTRACT FROM AUTHOR]

Published
2003
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48. Specificity Determinants of Proteolytic Processing of AspergillusPacC Transcription Factor Are Remote from the Processing Site, and Processing Occurs in Yeast If pH Signalling Is Bypassed

Author

Mingot, Jose´-Manuel, Tilburn, Joan, Diez, Eliecer, Bignell, Elaine, Orejas, Margarita, Widdick, David A., Sarkar, Sovan, Brown, Christopher V., Caddick, Mark X., Espeso, Eduardo A., Arst, Herbert N., and alva

Abstract

ABSTRACTThe Aspergillus nidulanstranscription factor PacC, which mediates pH regulation, is proteolytically processed to a functional form in response to ambient alkaline pH. The full-length PacC form is unstable in the presence of an operational pH signal transduction pathway, due to processing to the relatively stable short functional form. We have characterized and used an extensive collection of pacCmutations, including a novel class of “neutrality-mimicking” pacCmutations having aspects of both acidity- and alkalinity-mimicking phenotypes, to investigate a number of important features of PacC processing. Analysis of mutant proteins lacking the major translation initiation residue or truncated at various distances from the C terminus showed that PacC processing does not remove N-terminal residues, indicated that processing yields slightly heterogeneous products, and delimited the most upstream processing site to residues ~252 to 254. Faithful processing of three mutant proteins having deletions of a region including the predicted processing site(s) and of a fourth having 55 frameshifted residues following residue 238 indicated that specificity determinants reside at sequences or structural features located upstream of residue 235. Thus, the PacC protease cuts a peptide bond(s) remote from these determinants, possibly thereby resembling type I endonucleases. Downstream of the cleavage site, residues 407 to 678 are not essential for processing, but truncation at or before residue 333 largely prevents it. Ambient pH apparently regulates the accessibility of PacC to proteolytic processing. Alkalinity-mimicking mutations L259R, L266F, and L340S favor the protease-accessible conformation, whereas a protein with residues 465 to 540 deleted retains a protease-inaccessible conformation, leading to acidity mimicry. Finally, not only does processing constitute a crucial form of modulation for PacC, but there is evidence for its conservation during fungal evolution. Transgenic expression of a truncated PacC protein, which was processed in a pH-independent manner, showed that appropriate processing can occur inSaccharomyces cerevisiae.

Published
1999
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49. Signaling of Ambient pH in AspergillusInvolves a Cysteine Protease (*)

Author

Denison, Steven H., Orejas, Margarita, and Arst, Herbert N.

Abstract

In Aspergillus nidulans, the regulation of gene expression in response to changes in ambient pH is mediated by the PacC zinc finger transcriptional regulator. At alkaline ambient pH, PacC is proteolytically processed to a functional form serving as an activator of alkaline-expressed genes and a repressor of acid-expressed genes. This activation of PacC occurs in response to a signal mediated by the products of the palgenes. Thus, the products of the palA, -B, -C, -F, -H, and -Igenes constitute an alkaline ambient pH signal transduction pathway. How the palsignal transduction pathway senses ambient pH and transduces a signal to trigger PacC processing is a fascinating unresolved problem. We have cloned and sequenced the palBgene. The predicted palBgene product has similarity to the catalytic domain of the calpain family of calcium-activated cysteine proteases. We have shown, however, that the PalB protein does not catalyze the final step of proteolytic processing of PacC.

Published
1995
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50. Additional file 39: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

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

Subjects
3. Good health
Abstract

Phylogeny of the Methallophos domain in A. nidulans. (PDF 96 kb)

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