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5. Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.

Author

Selbmann, Laura, Benkő, Zsigmond, Coleine, Claudia, de Hoog, Sybren, Donati, Claudio, Druzhinina, Irina, Emri, Tamás, Ettinger, Cassie L, Gladfelter, Amy S, Gorbushina, Anna A, Grigoriev, Igor V, Grube, Martin, Gunde-Cimerman, Nina, Karányi, Zsolt Ákos, Kocsis, Beatrix, Kubressoian, Tania, Miklós, Ida, Miskei, Márton, Muggia, Lucia, Northen, Trent, Novak-Babič, Monika, Pennacchio, Christa, Pfliegler, Walter P, Pòcsi, Istvàn, Prigione, Valeria, Riquelme, Meritxell, Segata, Nicola, Schumacher, Julia, Shelest, Ekaterina, Sterflinger, Katja, Tesei, Donatella, U'Ren, Jana M, Varese, Giovanna C, Vázquez-Campos, Xabier, Vicente, Vania A, Souza, Emanuel M, Zalar, Polona, Walker, Allison K, and Stajich, Jason E

Subjects
Dothideomycetes, Eurotiomycetes, adaptation, black fungi, extremophiles, genomics, metabolomics, secondary metabolites, stress conditions, transcriptomics
Abstract

The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the "Shed light in The daRk lineagES of the fungal tree of life" (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.

Published
2020

10. 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

27. The Negative Effect of Protein Phosphatase Z1 Deletion on the Oxidative Stress Tolerance of Candida albicans Is Synergistic with Betamethasone Exposure

Author

Jakab, Ágnes, Emri, Tamás, Csillag, Kinga, Szabó, Anita, Nagy, Fruzsina, Baranyai, Edina, Sajtos, Zsófi, Géczi, Dóra, Antal, Károly, Kovács, Renátó, Szabó, Krisztina, Dombrádi, Viktor, and Pócsi, István

Subjects
antifungal therapy, Candida albicans, transcriptome analysis, QH301-705.5, combinatorial stress, oxidative stress, glucocorticoid, stress response, Biology (General), protein phosphatase Z1, hormones, hormone substitutes, and hormone antagonists, menadione
Abstract

The glucocorticoid betamethasone (BM) has potent anti-inflammatory and immunosuppressive effects, however, it increases the susceptibility of patients to superficial Candida infections. Previously we found that this disadvantageous side effect can be counteracted by menadione sodium bisulfite (MSB) induced oxidative stress treatment. The fungus specific protein phosphatase Z1 (CaPpz1) has a pivotal role in oxidative stress response of Candida albicans and was proposed as a potential antifungal drug target. The aim of this study was to investigate the combined effects of CaPPZ1 gene deletion and MSB treatment in BM pre-treated C. albicans cultures. We found that the combined treatment increased redox imbalance, enhanced the specific activities of antioxidant enzymes, and reduced the growth in cappz1 mutant (KO) strain. RNASeq data demonstrated that the presence of BM markedly elevated the number of differentially expressed genes in the MSB treated KO cultures. Accumulation of reactive oxygen species, increased iron content and fatty acid oxidation, as well as the inhibiting ergosterol biosynthesis and RNA metabolic processes explain, at least in part, the fungistatic effect caused by the combined stress exposure. We suggest that the synergism between MSB treatment and CaPpz1 inhibition could be considered in developing of a novel combinatorial antifungal strategy accompanying steroid therapy.

Published
2021

31. Physiological background of the remarkably high Cd2+ tolerance of the Aspergillus fumigatus Af293 strain

Author

Kurucz, Vivien, Kiss, Beáta, Szigeti, Zsuzsa M, Nagy, Gábor, Orosz, Erzsébet, Hargitai, Zoltán, Harangi, Sándor, Wiebenga, Ad, de Vries, Ronald P, Pócsi, István, Emri, Tamás, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, and Molecular Plant Physiology

Subjects
inorganic chemicals, 0301 basic medicine, Male, pca1 efflux pump, Siderophore, Transcription, Genetic, 030106 microbiology, Oxidative Stress/drug effects, Virulence, chemistry.chemical_element, Aspergillus fumigatus/drug effects, Applied Microbiology and Biotechnology, Aspergillus fumigatus, Microbiology, Ferrous, 03 medical and health sciences, chemistry.chemical_compound, Mice, Genetic, Animals, oxidative stress, siderophore production, iron metabolism, cadmium toxicity, Inbred BALB C, Cadmium, Mice, Inbred BALB C, biology, Chemistry, Adenosine Triphosphatases/genetics, Cation Transport Proteins/genetics, General Medicine, biology.organism_classification, 030104 developmental biology, Fungal Proteins/biosynthesis, Siderophores/biosynthesis, Female, Heterologous expression, Efflux, Transcription, Cadmium/metabolism, Iron/metabolism, PCAA
Abstract

The physiological background of the unusually high cadmium tolerance (MIC50 > 2 mM) of Aspergillus fumigatus Af293 was investigated. The cadmium tolerance of the tested environmental and clinical A. fumigatus strains varied over a wide range (0.25 mM 2 mM, and this phenotype was accompanied by increased in vivo virulence in mice. A strong correlation was found between the cadmium tolerance and the transcription of the pcaA gene, which encodes a putative cadmium efflux pump. The cadmium tolerance also correlated with the iron tolerance and the extracellular siderophore production of the strains. In addition to these findings, Af293 did not show the synergism between iron toxicity and cadmium toxicity that was detected in the other strains. Based on these results, we suggest that the primary function of PcaA should be acting as a ferrous iron pump and protecting cells from iron overload. Nevertheless, the heterologous expression of pcaA may represent an attractive strain improvement strategy to construct fungal strains for use in biosorption or biomining processes or to prevent accumulation of this toxic metal in crops.

Published
2018

44. FvmnSOD is involved in oxidative stress defence, mitochondrial stability and apoptosis prevention in Fusarium verticillioides

Author

Szabó, Zsuzsa, primary, Pákozdi, Klaudia, additional, Murvai, Katalin, additional, Kecskeméti, Ádám, additional, Oláh, Viktor, additional, Logrieco, Antonio F., additional, Madar, Anett, additional, Dienes, Beatrix, additional, Csernoch, László, additional, Emri, Tamás, additional, Hornok, László, additional, Pócsi, István, additional, and Leiter, Éva, additional

Published
2020
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45. FvatfA regulates growth, stress tolerance as well as mycotoxin and pigment productions in Fusarium verticillioides

Author

Szabó, Zsuzsa, primary, Pákozdi, Klaudia, additional, Murvai, Katalin, additional, Pusztahelyi, Tünde, additional, Kecskeméti, Ádám, additional, Gáspár, Attila, additional, Logrieco, Antonio F., additional, Emri, Tamás, additional, Ádám, Attila L., additional, Leiter, Éva, additional, Hornok, László, additional, and Pócsi, István, additional

Published
2020
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47. Increased Cd2+biosorption capability ofAspergillus nidulanselicited bycrpAdeletion

Author

Boczonádi, Imre, primary, Török, Zsófia, additional, Jakab, Ágnes, additional, Kónya, Gábor, additional, Gyurcsó, Klaudia, additional, Baranyai, Edina, additional, Szoboszlai, Zoltán, additional, Döncző, Boglárka, additional, Fábián, István, additional, Leiter, Éva, additional, Lee, Mi-Kyung, additional, Csernoch, László, additional, Yu, Jae-Hyuk, additional, Kertész, Zsófia, additional, Emri, Tamás, additional, and Pócsi, István, additional

Published
2020
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49. Rare earth element sequestration by Aspergillus oryzae biomass

Author

Boczonádi, Imre, primary, Jakab, Ágnes, additional, Baranyai, Edina, additional, Tóth, Csilla Noémi, additional, Daróczi, Lajos, additional, Csernoch, László, additional, Kis, Gréta, additional, Antal, Miklós, additional, Pusztahelyi, Tünde, additional, Grawunder, Anja, additional, Merten, Dirk, additional, Emri, Tamás, additional, Fábián, István, additional, Kothe, Erika, additional, and Pócsi, István, additional

Published
2020
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