51
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Fischer J, Müller SY, Netzker T, Jäger N, Gacek-Matthews A, Scherlach K, Stroe MC, García-Altares M, Pezzini F, Schoeler H, Reichelt M, Gershenzon J, Krespach MKC, Shelest E, Schroeckh V, Valiante V, Heinzel T, Hertweck C, Strauss J, Brakhage AA. Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites. eLife 2018; 7:e40969. [PMID: 30311911 PMCID: PMC6234034 DOI: 10.7554/elife.40969] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/11/2018] [Indexed: 12/15/2022] Open
Abstract
The eukaryotic epigenetic machinery can be modified by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. We discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster in the fungus Aspergillus nidulans. Using this model, we aim understanding mechanisms of microbial communication based on bacteria-triggered chromatin modification. Using genome-wide ChIP-seq analysis of acetylated histone H3, we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus and relate changes in the acetylation to that in the fungal transcriptome. Differentially acetylated histones were detected in genes involved in secondary metabolism, in amino acid and nitrogen metabolism, in signaling, and encoding transcription factors. Further molecular analyses identified the Myb-like transcription factor BasR as the regulatory node for transduction of the bacterial signal in the fungus and show its function is conserved in other Aspergillus species.
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Affiliation(s)
- Juliane Fischer
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Institute of MicrobiologyFriedrich Schiller University JenaJenaGermany
| | - Sebastian Y Müller
- Systems Biology and BioinformaticsLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Tina Netzker
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Nils Jäger
- Department of BiochemistryFriedrich Schiller UniversityJenaGermany
| | - Agnieszka Gacek-Matthews
- Department for Applied Genetics and Cell BiologyBOKU University of Natural Resources and Life SciencesViennaAustria
- Institute of MicrobiologyUniversity of Veterinary MedicineViennaAustria
| | - Kirstin Scherlach
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Maria C Stroe
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Institute of MicrobiologyFriedrich Schiller University JenaJenaGermany
| | - María García-Altares
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Francesco Pezzini
- Systems Biology and BioinformaticsLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Hanno Schoeler
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Institute of MicrobiologyFriedrich Schiller University JenaJenaGermany
| | - Michael Reichelt
- Department of BiochemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Jonathan Gershenzon
- Department of BiochemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Mario KC Krespach
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Institute of MicrobiologyFriedrich Schiller University JenaJenaGermany
| | - Ekaterina Shelest
- Systems Biology and BioinformaticsLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Volker Schroeckh
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Vito Valiante
- Leibniz Research Group – Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
| | - Thorsten Heinzel
- Department of BiochemistryFriedrich Schiller UniversityJenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Chair for Natural Product ChemistryFriedrich Schiller UniversityJenaGermany
| | - Joseph Strauss
- Department for Applied Genetics and Cell BiologyBOKU University of Natural Resources and Life SciencesViennaAustria
| | - Axel A Brakhage
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection BiologyJenaGermany
- Institute of MicrobiologyFriedrich Schiller University JenaJenaGermany
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Guzman‐Chavez F, Salo O, Samol M, Ries M, Kuipers J, Bovenberg RAL, Vreeken RJ, Driessen AJM. Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum. Microbiologyopen 2018; 7:e00598. [PMID: 29575742 PMCID: PMC6182556 DOI: 10.1002/mbo3.598] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/08/2018] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
The Pc21 g14570 gene of Penicillium chrysogenum encodes an ortholog of a class 2 histone deacetylase termed HdaA which may play a role in epigenetic regulation of secondary metabolism. Deletion of the hdaA gene induces a significant pleiotropic effect on the expression of a set of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS)-encoding genes. The deletion mutant exhibits a decreased conidial pigmentation that is related to a reduced expression of the PKS gene Pc21 g16000 (pks17) responsible for the production of the pigment precursor naphtha-γ-pyrone. Moreover, the hdaA deletion caused decreased levels of the yellow pigment chrysogine that is associated with the downregulation of the NRPS-encoding gene Pc21 g12630 and associated biosynthetic gene cluster. In contrast, transcriptional activation of the sorbicillinoids biosynthetic gene cluster occurred concomitantly with the overproduction of associated compounds . A new compound was detected in the deletion strain that was observed only under conditions of sorbicillinoids production, suggesting crosstalk between biosynthetic gene clusters. Our present results show that an epigenomic approach can be successfully applied for the activation of secondary metabolism in industrial strains of P. chrysogenum.
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Affiliation(s)
- Fernando Guzman‐Chavez
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Oleksandr Salo
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Marta Samol
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Marco Ries
- Division of Analytical BiosciencesLeiden/Amsterdam Center for Drug ResearchLeidenThe Netherlands
- Netherlands Metabolomics CentreLeiden UniversityLeidenThe Netherlands
| | - Jeroen Kuipers
- Department of Cell biologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Roel A. L. Bovenberg
- Synthetic Biology and Cell EngineeringGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
| | - Rob J. Vreeken
- Division of Analytical BiosciencesLeiden/Amsterdam Center for Drug ResearchLeidenThe Netherlands
- Netherlands Metabolomics CentreLeiden UniversityLeidenThe Netherlands
- Present address:
Rob J. Vreeken, Discovery SciencesJanssen R &DBeerseBelgium
| | - Arnold J. M. Driessen
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
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53
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Pidroni A, Faber B, Brosch G, Bauer I, Graessle S. A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans. Front Microbiol 2018; 9:2212. [PMID: 30283426 PMCID: PMC6156440 DOI: 10.3389/fmicb.2018.02212] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/30/2018] [Indexed: 12/23/2022] Open
Abstract
An outstanding feature of filamentous fungi is their ability to produce a wide variety of small bioactive molecules that contribute to their survival, fitness, and pathogenicity. The vast collection of these so-called secondary metabolites (SMs) includes molecules that play a role in virulence, protect fungi from environmental damage, act as toxins or antibiotics that harm host tissues, or hinder microbial competitors for food sources. Many of these compounds are used in medical treatment; however, biosynthetic genes for the production of these natural products are arranged in compact clusters that are commonly silent under growth conditions routinely used in laboratories. Consequently, a wide arsenal of yet unknown fungal metabolites is waiting to be discovered. Here, we describe the effects of deletion of hosA, one of four classical histone deacetylase (HDAC) genes in Aspergillus nidulans; we show that HosA acts as a major regulator of SMs in Aspergillus with converse regulatory effects depending on the metabolite gene cluster examined. Co-inhibition of all classical enzymes by the pan HDAC inhibitor trichostatin A and the analysis of HDAC double mutants indicate that HosA is able to override known regulatory effects of other HDACs such as the class 2 type enzyme HdaA. Chromatin immunoprecipitation analysis revealed a direct correlation between hosA deletion, the acetylation status of H4 and the regulation of SM cluster genes, whereas H3 hyper-acetylation could not be detected in all the upregulated SM clusters examined. Our data suggest that HosA has inductive effects on SM production in addition to its classical role as a repressor via deacetylation of histones. Moreover, a genome wide transcriptome analysis revealed that in addition to SMs, expression of several other important protein categories such as enzymes of the carbohydrate metabolism or proteins involved in disease, virulence, and defense are significantly affected by the deletion of HosA.
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Affiliation(s)
- Angelo Pidroni
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Birgit Faber
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerald Brosch
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ingo Bauer
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Graessle
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
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54
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Janevska S, Güldener U, Sulyok M, Tudzynski B, Studt L. Set1 and Kdm5 are antagonists for H3K4 methylation and regulators of the major conidiation-specific transcription factor gene ABA1 in Fusarium fujikuroi. Environ Microbiol 2018; 20:3343-3362. [PMID: 30047187 PMCID: PMC6175112 DOI: 10.1111/1462-2920.14339] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/31/2018] [Accepted: 06/22/2018] [Indexed: 12/19/2022]
Abstract
Here we present the identification and characterization of the H3K4‐specific histone methyltransferase Set1 and its counterpart, the Jumonji C demethylase Kdm5, in the rice pathogen Fusarium fujikuroi. While Set1 is responsible for all detectable H3K4me2/me3 in this fungus, Kdm5 antagonizes the H3K4me3 mark. Notably, deletion of both SET1 and KDM5 mainly resulted in the upregulation of genome‐wide transcription, also affecting a large set of secondary metabolite (SM) key genes. Although H3K4 methylation is a hallmark of actively transcribed euchromatin, several SM gene clusters located in subtelomeric regions were affected by Set1 and Kdm5. While the regulation of many of them is likely indirect, H3K4me2 levels at gibberellic acid (GA) genes correlated with GA biosynthesis in the wild type, Δkdm5 and OE::KDM5 under inducing conditions. Whereas Δset1 showed an abolished GA3 production in axenic culture, phytohormone biosynthesis was induced in planta, so that residual amounts of GA3 were detected during rice infection. Accordingly, Δset1 exhibited a strongly attenuated, though not abolished, virulence on rice. Apart from regulating secondary metabolism, Set1 and Kdm5 function as activator and repressor of conidiation respectively. They antagonistically regulate H3K4me3 levels and expression of the major conidiation‐specific transcription factor gene ABA1 in F. fujikuroi.
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Affiliation(s)
- Slavica Janevska
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Ulrich Güldener
- Department of Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Michael Sulyok
- Center for Analytical Chemistry, Department IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Lena Studt
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Department of Applied Genetics and Cell Biology-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
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55
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Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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56
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Baral B, Akhgari A, Metsä-Ketelä M. Activation of microbial secondary metabolic pathways: Avenues and challenges. Synth Syst Biotechnol 2018; 3:163-178. [PMID: 30345402 PMCID: PMC6190515 DOI: 10.1016/j.synbio.2018.09.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial natural products are a tremendous source of new bioactive chemical entities for drug discovery. Next generation sequencing has revealed an unprecedented genomic potential for production of secondary metabolites by diverse micro-organisms found in the environment and in the microbiota. Genome mining has further led to the discovery of numerous uncharacterized 'cryptic' metabolic pathways in the classical producers of natural products such as Actinobacteria and fungi. These biosynthetic gene clusters may code for improved biologically active metabolites, but harnessing the full genetic potential has been hindered by the observation that many of the pathways are 'silent' under laboratory conditions. Here we provide an overview of the various biotechnological methodologies, which can be divided to pleiotropic, biosynthetic gene cluster specific, and targeted genome-wide approaches that have been developed for the awakening of microbial secondary metabolic pathways.
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Affiliation(s)
| | | | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014, Turku, Finland
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57
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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58
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Schmoll M. Regulation of plant cell wall degradation by light in Trichoderma. Fungal Biol Biotechnol 2018; 5:10. [PMID: 29713489 PMCID: PMC5913809 DOI: 10.1186/s40694-018-0052-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022] Open
Abstract
Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme production in T. reesei emerged as an important regulatory mechanism to be tackled for strain improvement. Gene regulation specific for cellulase inducing conditions is different in light and darkness with substantial regulation by photoreceptors. Genes regulated by light are clustered in the genome, with several of the clusters overlapping with CAZyme clusters. Major cellulase transcription factor genes and at least 75% of glycoside hydrolase encoding genes show the potential of light dependent regulation. Accordingly, light dependent protein complex formation occurs within the promoters of cellulases and their regulators. Additionally growth on diverse carbon sources is different between light and darkness and dependent on the presence of photoreceptors in several cases. Thereby, also light intensity plays a regulatory role, with cellulase levels dropping at higher light intensities dependent in the strain background. The heterotrimeric G-protein pathway is the most important nutrient signaling pathway in the connection with light response and triggers posttranscriptional regulation of cellulase expression. All G-protein alpha subunits impact cellulase regulation in a light dependent manner. The downstream cAMP pathway is involved in light dependent regulation as well. Connections between the regulatory pathways are mainly established via the photoreceptor ENV1. The effect of photoreceptors on plant cell wall degradation also occurs in the model filamentous fungus Neurospora crassa. In the currently proposed model, T. reesei senses the presence of plant biomass in its environment by detection of building blocks of cellulose and hemicellulose. Interpretation of the respective signals is subsequently adjusted to the requirements in light and darkness (or on the surface versus within the substrate) by an interconnection of nutrient signaling with light response. This review provides an overview on the importance of light, photoreceptors and related signaling pathways for formation of plant cell wall degrading enzymes in T. reesei. Additionally, the relevance of light dependent gene regulation for industrial fermentations with Trichoderma as well as strategies for exploitation of the observed effects are discussed.
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Affiliation(s)
- Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
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59
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van Geelen L, Meier D, Rehberg N, Kalscheuer R. (Some) current concepts in antibacterial drug discovery. Appl Microbiol Biotechnol 2018; 102:2949-2963. [PMID: 29455386 DOI: 10.1007/s00253-018-8843-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
Abstract
The rise of multidrug resistance in bacteria rendering pathogens unresponsive to many clinical drugs is widely acknowledged and considered a critical global healthcare issue. There is broad consensus that novel antibacterial chemotherapeutic options are extremely urgently needed. However, the development pipeline of new antibacterial drug lead structures is poorly filled and not commensurate with the scale of the problem since the pharmaceutical industry has shown reduced interest in antibiotic development in the past decades due to high economic risks and low profit expectations. Therefore, academic research institutions have a special responsibility in finding novel treatment options for the future. In this mini review, we want to provide a broad overview of the different approaches and concepts that are currently pursued in this research field.
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Affiliation(s)
- Lasse van Geelen
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Dieter Meier
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Nidja Rehberg
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany.
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60
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Chettri P, Dupont PY, Bradshaw RE. Chromatin-level regulation of the fragmented dothistromin gene cluster in the forest pathogen Dothistroma septosporum. Mol Microbiol 2018; 107:508-522. [DOI: 10.1111/mmi.13898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Pranav Chettri
- Bio-Protection Research Centre, Institute of Fundamental Sciences; Massey University; Palmerston North New Zealand
| | - Pierre-Yves Dupont
- Bio-Protection Research Centre, Institute of Fundamental Sciences; Massey University; Palmerston North New Zealand
| | - Rosie E. Bradshaw
- Bio-Protection Research Centre, Institute of Fundamental Sciences; Massey University; Palmerston North New Zealand
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61
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Abstract
Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery. This modular, self-contained nature of MGCs contributes to the metabolic and ecological adaptability of fungi. The phylogenetic and ecological patterns of MGC distribution reflect the broad diversity of fungal life cycles and nutritional modes. While the origins of most gene clusters are enigmatic, MGCs are thought to be born into a genome through gene duplication, relocation, or horizontal transfer, and analyzing the death and decay of gene clusters provides clues about the mechanisms selecting for their assembly. Gene clustering may provide inherent fitness advantages through metabolic efficiency and specialization, but experimental evidence for this is currently limited. The identification and characterization of gene clusters will continue to be powerful tools for elucidating fungal metabolism as well as understanding the physiology and ecology of fungi.
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Affiliation(s)
- Jason C Slot
- The Ohio State University, Columbus, OH, United States.
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62
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Pfannenstiel BT, Zhao X, Wortman J, Wiemann P, Throckmorton K, Spraker JE, Soukup AA, Luo X, Lindner DL, Lim FY, Knox BP, Haas B, Fischer GJ, Choera T, Butchko RAE, Bok JW, Affeldt KJ, Keller NP, Palmer JM. Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus. mBio 2017; 8:e01246-17. [PMID: 28874473 PMCID: PMC5587912 DOI: 10.1128/mbio.01246-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA). The remaining mutants were backcrossed and sequenced using Illumina and Ion Torrent sequencing platforms. All but one mutant contained one or more sequence variants in predicted open reading frames. Deletion of these genes resulted in identification of mutant alleles responsible for the loss of ST production in 12 of the 17 remaining mutants. Eight of these mutations were in genes already known to affect ST synthesis (laeA, mcsA, fluG, and stcA), while the remaining four mutations (in laeB, sntB, and hamI) were in previously uncharacterized genes not known to be involved in ST production. Deletion of laeB, sntB, and hamI in A. flavus results in loss of aflatoxin production, confirming that these regulators are conserved in the aflatoxigenic aspergilli. This report highlights the multifaceted regulatory mechanisms governing secondary metabolism in Aspergillus Additionally, these data contribute to the increasing number of studies showing that forward genetic screens of fungi coupled with whole-genome resequencing is a robust and cost-effective technique.IMPORTANCE In a postgenomic world, reverse genetic approaches have displaced their forward genetic counterparts. The techniques used in forward genetics to identify loci of interest were typically very cumbersome and time-consuming, relying on Mendelian traits in model organisms. The current work was pursued not only to identify alleles involved in regulation of secondary metabolism but also to demonstrate a return to forward genetics to track phenotypes and to discover genetic pathways that could not be predicted through a reverse genetics approach. While identification of mutant alleles from whole-genome sequencing has been done before, here we illustrate the possibility of coupling this strategy with a genetic screen to identify multiple alleles of interest. Sequencing of classically derived mutants revealed several uncharacterized genes, which represent novel pathways to regulate and control the biosynthesis of sterigmatocystin and of aflatoxin, a societally and medically important mycotoxin.
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Affiliation(s)
| | - Xixi Zhao
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jennifer Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kurt Throckmorton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexandra A Soukup
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xingyu Luo
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel L Lindner
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian Haas
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory J Fischer
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Tsokyi Choera
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert A E Butchko
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
| | - Jin-Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katharyn J Affeldt
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, Wisconsin, USA
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63
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Monroy AA, Stappler E, Schuster A, Sulyok M, Schmoll M. A CRE1- regulated cluster is responsible for light dependent production of dihydrotrichotetronin in Trichoderma reesei. PLoS One 2017; 12:e0182530. [PMID: 28809958 PMCID: PMC5557485 DOI: 10.1371/journal.pone.0182530] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/19/2017] [Indexed: 02/08/2023] Open
Abstract
Changing light conditions, caused by the rotation of earth resulting in day and night or growth on the surface or within a substrate, result in considerably altered physiological processes in fungi. For the biotechnological workhorse Trichoderma reesei, regulation of glycoside hydrolase gene expression, especially cellulase expression was shown to be a target of light dependent gene regulation. Analysis of regulatory targets of the carbon catabolite repressor CRE1 under cellulase inducing conditions revealed a secondary metabolite cluster to be differentially regulated in light and darkness and by photoreceptors. We found that this cluster is involved in production of trichodimerol and that the two polyketide synthases of the cluster are essential for biosynthesis of dihydrotrichotetronine (syn. bislongiquinolide or bisorbibutenolide). Additionally, an indirect influence on production of the peptaibol antibiotic paracelsin was observed. The two polyketide synthetase genes as well as the monooxygenase gene of the cluster were found to be connected at the level of transcription in a positive feedback cycle in darkness, but negative feedback in light, indicating a cellular sensing and response mechanism for the products of these enzymes. The transcription factor TR_102497/YPR2 residing within the cluster regulates the cluster genes in a light dependent manner. Additionally, an interrelationship of this cluster with regulation of cellulase gene expression was detected. Hence the regulatory connection between primary and secondary metabolism appears more widespread than previously assumed, indicating a sophisticated distribution of resources either to degradation of substrate (feed) or to antagonism of competitors (fight), which is influenced by light.
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Affiliation(s)
- Alberto Alonso Monroy
- AIT - Austrian Institute of Technology GmbH, Center for Health & Bioresources, Tulln, Austria
| | - Eva Stappler
- AIT - Austrian Institute of Technology GmbH, Center for Health & Bioresources, Tulln, Austria
| | - Andre Schuster
- TU Wien, Institute of Chemical Engineering, Research Area Molecular Biotechnology, Vienna, Austria
| | - Michael Sulyok
- University of Natural Resources and Life Sciences Vienna, Department for Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, Tulln, Austria
| | - Monika Schmoll
- AIT - Austrian Institute of Technology GmbH, Center for Health & Bioresources, Tulln, Austria
- * E-mail:
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64
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Dubey A, Jeon J. Epigenetic regulation of development and pathogenesis in fungal plant pathogens. MOLECULAR PLANT PATHOLOGY 2017; 18:887-898. [PMID: 27749982 PMCID: PMC6638268 DOI: 10.1111/mpp.12499] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 05/08/2023]
Abstract
Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen-induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis.
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Affiliation(s)
- Akanksha Dubey
- Department of BiotechnologyCollege of Life and Applied Sciences, Yeungnam UniversityGyeongsanGyeongbuk38541South Korea
| | - Junhyun Jeon
- Department of BiotechnologyCollege of Life and Applied Sciences, Yeungnam UniversityGyeongsanGyeongbuk38541South Korea
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65
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Liang L, Liu Y, Yang K, Lin G, Xu Z, Lan H, Wang X, Wang S. The Putative Histone Methyltransferase DOT1 Regulates Aflatoxin and Pathogenicity Attributes in Aspergillus flavus. Toxins (Basel) 2017; 9:toxins9070232. [PMID: 28737735 PMCID: PMC5535179 DOI: 10.3390/toxins9070232] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022] Open
Abstract
Lysine methyltransferases transfer methyl groups in specific lysine sites, which regulates a variety of important biological processes in eukaryotes. In this study, we characterized a novel homolog of the yeast methyltransferase DOT1 in A. flavus, and observed the roles of dot1 in A. flavus. Deletion of dot1 showed a significant decrease in conidiation, but an increase in sclerotia formation. A change in viability to multiple stresses was also found in the Δdot1 mutant. Additionally, aflatoxin (AF) production was found severely impaired in the Δdot1 mutant. Further analysis by qRT-PCR revealed that the transcription of AF structural genes and their regulator gene aflS were prominently suppressed in the Δdot1 mutant. Furthermore, our data revealed that Dot1 is important for colonizing maize seeds in A. flavus. Our research indicates that Dot1 is involved in fungal development, aflatoxin biosynthesis and fungal virulence in A. flavus, which might provide a potential target for controlling A. flavus with new strategies.
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Affiliation(s)
- Linlin Liang
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yinghang Liu
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Kunlong Yang
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guinan Lin
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhangling Xu
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Huahui Lan
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiuna Wang
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shihua Wang
- Fujian Key Laboratory of Pathogenic Fungi and Mycotoxins, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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66
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Guerriero G, Silvestrini L, Legay S, Maixner F, Sulyok M, Hausman JF, Strauss J. Deletion of the celA gene in Aspergillus nidulans triggers overexpression of secondary metabolite biosynthetic genes. Sci Rep 2017; 7:5978. [PMID: 28729615 PMCID: PMC5519750 DOI: 10.1038/s41598-017-05920-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/06/2017] [Indexed: 11/30/2022] Open
Abstract
Although much progress has been made in the study of cell wall biosynthetic genes in the model filamentous fungus Aspergillus nidulans, there are still targets awaiting characterization. An example is the gene celA (ANIA_08444) encoding a putative mixed linkage glucan synthase. To characterize the role of celA, we deleted it in A. nidulans, analyzed the phenotype of the mycelium and performed RNA-Seq. The strain shows a very strong phenotype, namely “balloons” along the hyphae and aberrant conidiophores, as well as an altered susceptibility to cell wall drugs. These data suggest a potential role of the gene in cell wall-related processes. The Gene Ontology term Enrichment analysis shows increased expression of secondary metabolite biosynthetic genes (sterigmatocystin in particular) in the deleted strain. Our results show that the deletion of celA triggers a strong phenotype reminiscent of cell wall-related aberrations and the upregulation of some secondary metabolite gene clusters in A. nidulans.
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Affiliation(s)
- Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg.
| | - Lucia Silvestrini
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, BOKU Campus, Tulln/Donau, A-3430, Austria
| | - Sylvain Legay
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Frank Maixner
- European Academy of Bozen/Bolzano (EURAC), Institute for Mummies and the Iceman, Bolzano, 39100, Italy
| | - Michael Sulyok
- University of Natural Resources and Life Sciences Vienna (BOKU), Department for Agrobiotechnology (IFA-Tulln), A-3430, Tulln, Austria
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Joseph Strauss
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, BOKU Campus, Tulln/Donau, A-3430, Austria.
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67
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Itoh E, Shigemoto R, Oinuma KI, Shimizu M, Masuo S, Takaya N. Sirtuin A regulates secondary metabolite production by Aspergillus nidulans. J GEN APPL MICROBIOL 2017; 63:228-235. [PMID: 28674377 DOI: 10.2323/jgam.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Late-stage cultures of filamentous fungi under nutrient starvation produce valuable secondary metabolites such as pharmaceuticals and pigments, as well as deleterious mycotoxins, all of which have remarkable structural diversity and wide-spectrum bioactivity. The fungal mechanisms regulating the synthesis of many of these compounds are not fully understood, but sirtuin A (SirA) is a key factor that initiates production of the secondary metabolites, sterigmatocystin and penicillin G, by Aspergillus nidulans. Sirtuin is a ubiquitous NAD+-dependent histone deacetylase that converts euchromatin to heterochromatin and silences gene expression. In this study, we have investigated the transcriptome of a sirA gene disruptant (SirAΔ), and found that SirA concomitantly repressed the expression of gene clusters for synthesizing secondary metabolites and activated that of others. Extracts of SirAΔ cultures grown on solid agar and analyzed by HPLC indicated that SirA represses the production of austinol, dehydroaustinol and sterigmatocystin. These results indicated that SirA is a transcriptional regulator of fungal secondary metabolism.
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Affiliation(s)
- Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | | | - Ken-Ichi Oinuma
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Motoyuki Shimizu
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba
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68
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Sbaraini N, Andreis FC, Thompson CE, Guedes RLM, Junges Â, Campos T, Staats CC, Vainstein MH, Ribeiro de Vasconcelos AT, Schrank A. Genome-Wide Analysis of Secondary Metabolite Gene Clusters in O phiostoma ulmi and Ophiostoma novo-ulmi Reveals a Fujikurin-Like Gene Cluster with a Putative Role in Infection. Front Microbiol 2017; 8:1063. [PMID: 28659888 PMCID: PMC5468452 DOI: 10.3389/fmicb.2017.01063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023] Open
Abstract
The emergence of new microbial pathogens can result in destructive outbreaks, since their hosts have limited resistance and pathogens may be excessively aggressive. Described as the major ecological incident of the twentieth century, Dutch elm disease, caused by ascomycete fungi from the Ophiostoma genus, has caused a significant decline in elm tree populations (Ulmus sp.) in North America and Europe. Genome sequencing of the two main causative agents of Dutch elm disease (Ophiostoma ulmi and Ophiostoma novo-ulmi), along with closely related species with different lifestyles, allows for unique comparisons to be made to identify how pathogens and virulence determinants have emerged. Among several established virulence determinants, secondary metabolites (SMs) have been suggested to play significant roles during phytopathogen infection. Interestingly, the secondary metabolism of Dutch elm pathogens remains almost unexplored, and little is known about how SM biosynthetic genes are organized in these species. To better understand the metabolic potential of O. ulmi and O. novo-ulmi, we performed a deep survey and description of SM biosynthetic gene clusters (BGCs) in these species and assessed their conservation among eight species from the Ophiostomataceae family. Among 19 identified BGCs, a fujikurin-like gene cluster (OpPKS8) was unique to Dutch elm pathogens. Phylogenetic analysis revealed that orthologs for this gene cluster are widespread among phytopathogens and plant-associated fungi, suggesting that OpPKS8 may have been horizontally acquired by the Ophiostoma genus. Moreover, the detailed identification of several BGCs paves the way for future in-depth research and supports the potential impact of secondary metabolism on Ophiostoma genus’ lifestyle.
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Affiliation(s)
- Nicolau Sbaraini
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Fábio C Andreis
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Claudia E Thompson
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Rafael L M Guedes
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Ângela Junges
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Thais Campos
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Charley C Staats
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Marilene H Vainstein
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Ana T Ribeiro de Vasconcelos
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Augusto Schrank
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
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69
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Kim W, Park JJ, Dugan FM, Peever TL, Gang DR, Vandemark G, Chen W. Production of the antibiotic secondary metabolite solanapyrone A by the fungal plant pathogen Ascochyta rabiei during fruiting body formation in saprobic growth. Environ Microbiol 2017; 19:1822-1835. [PMID: 28109049 DOI: 10.1111/1462-2920.13673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/10/2017] [Accepted: 01/14/2017] [Indexed: 11/30/2022]
Abstract
Fungi are noted producers of a diverse array of secondary metabolites, many of which are of pharmacological importance. However, the biological roles of the vast majority of these molecules during the fungal life cycle in nature remain elusive. Solanapyrones are polyketide-derived secondary metabolites produced by diverse fungal species including the plant pathogen Ascochyta rabiei. This molecule was originally thought to function as a phytotoxin facilitating pathogenesis of A. rabiei. Chemical profiling and gene expression studies showed that solanapyrone A was specifically produced during saprobic, but not parasitic growth of A. rabiei. Expression of the gene encoding the final enzymatic step in solanapyrone biosynthesis was specifically associated with development of the asexual fruiting bodies of the fungus on certain substrates. In confrontation assays with saprobic fungi that were commonly found in chickpea debris in fields, A. rabiei effectively suppressed the growth of all competing fungi, such as Alternaria, Epicoccum and Ulocladium species. Solanapyrone A was directly detected in the inhibitory zone using a MALDI-imaging mass spectrometry, and the purified compound showed significant antifungal activities against the potential saprobic competitors. These results suggest that solanapyrone A plays an important role for competition and presumably the survival of the fungus.
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Affiliation(s)
- Wonyong Kim
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Jeong-Jin Park
- Tissue Imaging & Proteomics Laboratory, Washington State University, Pullman, Washington, USA
| | - Frank M Dugan
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Western Regional Plant Introduction Station, Washington State University, Pullman, Washington, USA
| | - Tobin L Peever
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - David R Gang
- Tissue Imaging & Proteomics Laboratory, Washington State University, Pullman, Washington, USA.,Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - George Vandemark
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, Washington, USA
| | - Weidong Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, Washington, USA
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70
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Studt L, Janevska S, Arndt B, Boedi S, Sulyok M, Humpf HU, Tudzynski B, Strauss J. Lack of the COMPASS Component Ccl1 Reduces H3K4 Trimethylation Levels and Affects Transcription of Secondary Metabolite Genes in Two Plant-Pathogenic Fusarium Species. Front Microbiol 2017; 7:2144. [PMID: 28119673 PMCID: PMC5220078 DOI: 10.3389/fmicb.2016.02144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/20/2016] [Indexed: 01/07/2023] Open
Abstract
In the two fungal pathogens Fusarium fujikuroi and Fusarium graminearum, secondary metabolites (SMs) are fitness and virulence factors and there is compelling evidence that the coordination of SM gene expression is under epigenetic control. Here, we characterized Ccl1, a subunit of the COMPASS complex responsible for methylating lysine 4 of histone H3 (H3K4me). We show that Ccl1 is not essential for viability but a regulator of genome-wide trimethylation of H3K4 (H3K4me3). Although, recent work in Fusarium and Aspergillus spp. detected only sporadic H3K4 methylation at the majority of the SM gene clusters, we show here that SM profiles in CCL1 deletion mutants are strongly deviating from the wild type. Cross-complementation experiments indicate high functional conservation of Ccl1 as phenotypes of the respective △ccl1 were rescued in both fungi. Strikingly, biosynthesis of the species-specific virulence factors gibberellic acid and deoxynivalenol produced by F. fujikuroi and F. graminearum, respectively, was reduced in axenic cultures but virulence was not attenuated in these mutants, a phenotype which goes in line with restored virulence factor production levels in planta. This suggests that yet unknown plant-derived signals are able to compensate for Ccl1 function during pathogenesis.
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Affiliation(s)
- Lena Studt
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria,Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany,*Correspondence: Lena Studt, Joseph Strauss,
| | - Slavica Janevska
- Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany
| | - Birgit Arndt
- Institute of Food Chemistry, Westfälische Wilhelms UniversityMünster, Germany
| | - Stefan Boedi
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria
| | - Michael Sulyok
- Center for Analytical Chemistry, Department IFA-Tulln, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms UniversityMünster, Germany
| | - Bettina Tudzynski
- Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany
| | - Joseph Strauss
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria,*Correspondence: Lena Studt, Joseph Strauss,
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71
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Macheleidt J, Mattern DJ, Fischer J, Netzker T, Weber J, Schroeckh V, Valiante V, Brakhage AA. Regulation and Role of Fungal Secondary Metabolites. Annu Rev Genet 2016; 50:371-392. [DOI: 10.1146/annurev-genet-120215-035203] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juliane Macheleidt
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Derek J. Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Vito Valiante
- Research Group Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745 Jena, Germany;
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
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72
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Studt L, Rösler SM, Burkhardt I, Arndt B, Freitag M, Humpf HU, Dickschat JS, Tudzynski B. Knock-down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. Environ Microbiol 2016; 18:4037-4054. [PMID: 27348741 PMCID: PMC5118082 DOI: 10.1111/1462-2920.13427] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/19/2016] [Indexed: 01/07/2023]
Abstract
Filamentous fungi produce a vast array of secondary metabolites (SMs) and some play a role in agriculture or pharmacology. Sequencing of the rice pathogen Fusarium fujikuroi revealed the presence of far more SM-encoding genes than known products. SM production is energy-consuming and thus tightly regulated, leaving the majority of SM gene clusters silent under laboratory conditions. One important regulatory layer in SM biosynthesis involves histone modifications that render the underlying genes either silent or poised for transcription. Here, we show that the majority of the putative SM gene clusters in F. fujikuroi are located within facultative heterochromatin marked by trimethylated lysine 27 on histone 3 (H3K27me3). Kmt6, the methyltransferase responsible for establishing this histone mark, appears to be essential in this fungus, and knock-down of Kmt6 in the KMT6kd strain shows a drastic phenotype affecting fungal growth and development. Transcription of four so far cryptic and otherwise silent putative SM gene clusters was induced in the KMT6kd strain, in which decreased expression of KMT6 is accompanied by reduced H3K27me3 levels at the respective gene loci and accumulation of novel metabolites. One of the four putative SM gene clusters, named STC5, was analysed in more detail thereby revealing a novel sesquiterpene.
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Affiliation(s)
- Lena Studt
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany,Corresponding author: L. Studt, Division of Microbial Genetics and Pathogen Interaction, Department of Applied Genetics and Cell Biology, Campus-Tulln, BOKU-University of Natural Resources and Life Science, Vienna, Austria, , phone: (+43) 1 / 47654-6722
| | - Sarah M. Rösler
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany,Institute of Food Chemistry, Westfälische Wilhelms-University Münster, 48149 Münster, Germany
| | - Immo Burkhardt
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121 Bonn, Germany
| | - Birgit Arndt
- Institute of Food Chemistry, Westfälische Wilhelms-University Münster, 48149 Münster, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, 97331 Oregon, United States of America
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-University Münster, 48149 Münster, Germany
| | - Jeroen S. Dickschat
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121 Bonn, Germany
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University Münster, 48143 Münster, Germany
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Abstract
Histone deacetylases (HDACs) remove acetyl moieties from lysine residues at histone tails and nuclear regulatory proteins and thus significantly impact chromatin remodeling and transcriptional regulation in eukaryotes. In recent years, HDACs of filamentous fungi were found to be decisive regulators of genes involved in pathogenicity and the production of important fungal metabolites such as antibiotics and toxins. Here we present proof that one of these enzymes, the class 1 type HDAC RpdA, is of vital importance for the opportunistic human pathogen Aspergillus fumigatus Recombinant expression of inactivated RpdA shows that loss of catalytic activity is responsible for the lethal phenotype of Aspergillus RpdA null mutants. Furthermore, we demonstrate that a fungus-specific C-terminal region of only a few acidic amino acids is required for both the nuclear localization and catalytic activity of the enzyme in the model organism Aspergillus nidulans Since strains with single or multiple deletions of other classical HDACs revealed no or only moderate growth deficiencies, it is highly probable that the significant delay of germination and the growth defects observed in strains growing under the HDAC inhibitor trichostatin A are caused primarily by inhibition of catalytic RpdA activity. Indeed, even at low nanomolar concentrations of the inhibitor, the catalytic activity of purified RpdA is considerably diminished. Considering these results, RpdA with its fungus-specific motif represents a promising target for novel HDAC inhibitors that, in addition to their increasing impact as anticancer drugs, might gain in importance as antifungals against life-threatening invasive infections, apart from or in combination with classical antifungal therapy regimes. IMPORTANCE This paper reports on the fungal histone deacetylase RpdA and its importance for the viability of the fungal pathogen Aspergillus fumigatus and other filamentous fungi, a finding that is without precedent in other eukaryotic pathogens. Our data clearly indicate that loss of RpdA activity, as well as depletion of the enzyme in the nucleus, results in lethality of the corresponding Aspergillus mutants. Interestingly, both catalytic activity and proper cellular localization depend on the presence of an acidic motif within the C terminus of RpdA-type enzymes of filamentous fungi that is missing from the homologous proteins of yeasts and higher eukaryotes. The pivotal role, together with the fungus-specific features, turns RpdA into a promising antifungal target of histone deacetylase inhibitors, a class of molecules that is successfully used for the treatment of certain types of cancer. Indeed, some of these inhibitors significantly delay the germination and growth of different filamentous fungi via inhibition of RpdA. Upcoming analyses of clinically approved and novel inhibitors will elucidate their therapeutic potential as new agents for the therapy of invasive fungal infections-an interesting aspect in light of the rising resistance of fungal pathogens to conventional therapies.
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Geisen R, Schmidt-Heydt M. Molecular approaches for monitoring the activation of fungal secondary metabolite biosynthesis in relation to food environmental conditions. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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75
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Okada BK, Seyedsayamdost MR. Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiol Rev 2016; 41:19-33. [PMID: 27576366 DOI: 10.1093/femsre/fuw035] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/03/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022] Open
Abstract
Natural products have traditionally served as a dominant source of therapeutic agents. They are produced by dedicated biosynthetic gene clusters that assemble complex, bioactive molecules from simple precursors. Recent genome sequencing efforts coupled with advances in bioinformatics indicate that the majority of biosynthetic gene clusters are not expressed under normal laboratory conditions. Termed 'silent' or 'cryptic', these gene clusters represent a treasure trove for discovery of novel small molecules, their regulatory circuits and their biosynthetic pathways. In this review, we assess the capacity of exogenous small molecules in activating silent secondary metabolite gene clusters. Several approaches that have been developed are presented, including coculture techniques, ribosome engineering, chromatin remodeling and high-throughput elicitor screens. The rationale, applications and mechanisms attendant to each are discussed. Some general conclusions can be drawn from our analysis: exogenous small molecules comprise a productive avenue for the discovery of cryptic metabolites. Specifically, growth-inhibitory molecules, in some cases clinically used antibiotics, serve as effective inducers of silent biosynthetic gene clusters, suggesting that old antibiotics may be used to find new ones. The involvement of natural antibiotics in modulating secondary metabolism at subinhibitory concentrations suggests that they represent part of the microbial vocabulary through which inter- and intraspecies interactions are mediated.
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Affiliation(s)
- Bethany K Okada
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA .,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans. PLoS Genet 2016; 12:e1006222. [PMID: 27548260 PMCID: PMC4993369 DOI: 10.1371/journal.pgen.1006222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production. In this work we monitored by proteomic analysis and ChIP-seq the genome-wide distribution of several key modifications on histone H3 in the model fungus Aspergillus nidulans cultivated either under optimal physiological conditions (active growth) or less favourable conditions which are known to promote the production of secondary metabolites (SM). When we correlated the chromatin status to transcriptional activities in actively growing cells we found that the silenced SM gene clusters are flanked by heterochromatic domains presumably contributing to silencing but that the bodies of the clusters only carry background levels of any of the investigated marks. In nutrient-depleted conditions, activating marks were invading some, but by far not all transcribed clusters, leaving open the question how activation of these regions occurs at the chromatin level. Surprisingly, a large number of these gene clusters actually depend on KdmB for normal activation and it will be interesting to see in future how this protein thought to mainly act as repressor by removing positive H3K4m3 marks switches gears to activate transcription directly or indirectly.
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77
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Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability. J Genet Genomics 2016; 43:503-11. [DOI: 10.1016/j.jgg.2016.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 02/01/2023]
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Boedi S, Berger H, Sieber C, Münsterkötter M, Maloku I, Warth B, Sulyok M, Lemmens M, Schuhmacher R, Güldener U, Strauss J. Comparison of Fusarium graminearum Transcriptomes on Living or Dead Wheat Differentiates Substrate-Responsive and Defense-Responsive Genes. Front Microbiol 2016; 7:1113. [PMID: 27507961 PMCID: PMC4960244 DOI: 10.3389/fmicb.2016.01113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/04/2016] [Indexed: 11/28/2022] Open
Abstract
Fusarium graminearum is an opportunistic pathogen of cereals where it causes severe yield losses and concomitant mycotoxin contamination of the grains. The pathogen has mixed biotrophic and necrotrophic (saprophytic) growth phases during infection and the regulatory networks associated with these phases have so far always been analyzed together. In this study we compared the transcriptomes of fungal cells infecting a living, actively defending plant representing the mixed live style (pathogenic growth on living flowering wheat heads) to the response of the fungus infecting identical, but dead plant tissues (cold-killed flowering wheat heads) representing strictly saprophytic conditions. We found that the living plant actively suppressed fungal growth and promoted much higher toxin production in comparison to the identical plant tissue without metabolism suggesting that molecules signaling secondary metabolite induction are not pre-existing or not stable in the plant in sufficient amounts before infection. Differential gene expression analysis was used to define gene sets responding to the active or the passive plant as main impact factor and driver for gene expression. We correlated our results to the published F. graminearum transcriptomes, proteomes, and secretomes and found that only a limited number of in planta- expressed genes require the living plant for induction but the majority uses simply the plant tissue as signal. Many secondary metabolite (SM) gene clusters show a heterogeneous expression pattern within the cluster indicating that different genetic or epigenetic signals govern the expression of individual genes within a physically linked cluster. Our bioinformatic approach also identified fungal genes which were actively repressed by signals derived from the active plant and may thus represent direct targets of the plant defense against the invading pathogen.
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Affiliation(s)
- Stefan Boedi
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU University, University and Research Centre TullnTulln, Austria
| | - Harald Berger
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU University, University and Research Centre TullnTulln, Austria
- Bioresources, Austrian Institute of Technology GmbHTulln, Austria
| | - Christian Sieber
- Department of Earth and Planetary Sciences, University of California, BerkeleyBerkeley, CA, USA
| | - Martin Münsterkötter
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und UmweltNeuherberg, Germany
| | - Imer Maloku
- Department for Agrobiotechnology (IFA-Tulln), BOKU UniversityTulln, Austria
| | - Benedikt Warth
- Department for Agrobiotechnology (IFA-Tulln), BOKU UniversityTulln, Austria
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), BOKU UniversityTulln, Austria
| | - Marc Lemmens
- Department for Agrobiotechnology (IFA-Tulln), BOKU UniversityTulln, Austria
| | - Rainer Schuhmacher
- Department for Agrobiotechnology (IFA-Tulln), BOKU UniversityTulln, Austria
| | - Ulrich Güldener
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität MünchenMünchen, Germany
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU University, University and Research Centre TullnTulln, Austria
- Bioresources, Austrian Institute of Technology GmbHTulln, Austria
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79
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Insights into microbial cryptic gene activation and strain improvement: principle, application and technical aspects. J Antibiot (Tokyo) 2016; 70:25-40. [PMID: 27381522 DOI: 10.1038/ja.2016.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/22/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022]
Abstract
As bacteria and fungi have been found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often silent under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. This review addresses current progress in the activation of these pathways, describing methods for activating silent genes. It especially focuses on genetic manipulation of transcription and translation (ribosome engineering), the utilization of elicitors, metabolism remodeling and co-cultivation. In particular, the principles and technical points of ribosome engineering and the significance of S-adenosylmethionine in bacterial physiology, especially secondary metabolism, are described in detail.
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80
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The Post-genomic Era of Trichoderma reesei: What's Next? Trends Biotechnol 2016; 34:970-982. [PMID: 27394390 DOI: 10.1016/j.tibtech.2016.06.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 11/21/2022]
Abstract
The ascomycete Trichoderma reesei is one of the most well studied cellulolytic microorganisms. This fungus is widely used in the biotechnology industry, mainly in the production of biofuels. Due to its importance, its genome was sequenced in 2008, opening new avenues to study this microorganism. In this 'post-genomic' era, a transcriptomic and proteomic era has emerged. Here, we present an overview of new findings in the gene expression regulation network of T. reesei. We also discuss new rational strategies to obtain mutants that produce hydrolytic enzymes with a higher yield, using metabolic engineering. Finally, we present how synthetic biology strategies can be used to create engineered promoters to efficiently synthesize enzymes for biomass degradation to produce bioethanol.
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81
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Zutz C, Bacher M, Parich A, Kluger B, Gacek-Matthews A, Schuhmacher R, Wagner M, Rychli K, Strauss J. Valproic Acid Induces Antimicrobial Compound Production in Doratomyces microspores. Front Microbiol 2016; 7:510. [PMID: 27148199 PMCID: PMC4829596 DOI: 10.3389/fmicb.2016.00510] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/29/2016] [Indexed: 01/01/2023] Open
Abstract
One of the biggest challenges in public health is the rising number of antibiotic resistant pathogens and the lack of novel antibiotics. In recent years there is a rising focus on fungi as sources of antimicrobial compounds due to their ability to produce a large variety of bioactive compounds and the observation that virtually every fungus may still contain yet unknown so called “cryptic,” often silenced, compounds. These putative metabolites could include novel bioactive compounds. Considerable effort is spent on methods to induce production of these “cryptic” metabolites. One approach is the use of small molecule effectors, potentially influencing chromatin landscape in fungi. We observed that the supernatant of the fungus Doratomyces (D.) microsporus treated with valproic acid (VPA) displayed antimicrobial activity against Staphylococcus (S.) aureus and two methicillin resistant clinical S. aureus isolates. VPA treatment resulted in enhanced production of seven antimicrobial compounds: cyclo-(L-proline-L-methionine) (cPM), p-hydroxybenzaldehyde, cyclo-(phenylalanine-proline) (cFP), indole-3-carboxylic acid, phenylacetic acid (PAA) and indole-3-acetic acid. The production of the antimicrobial compound phenyllactic acid was exclusively detectable after VPA treatment. Furthermore three compounds, cPM, cFP, and PAA, were able to boost the antimicrobial activity of other antimicrobial compounds. cPM, for the first time isolated from fungi, and to a lesser extent PAA, are even able to decrease the minimal inhibitory concentration of ampicillin in MRSA strains. In conclusion we could show in this study that VPA treatment is a potent tool for induction of “cryptic” antimicrobial compound production in fungi, and that the induced compounds are not exclusively linked to the secondary metabolism. Furthermore this is the first discovery of the rare diketopiperazine cPM in fungi. Additionally we could demonstrate that cPM and PAA boost antibiotic activity against antibiotic resistant strains, suggesting a possible application in combinatorial antibiotic treatment against resistant pathogens.
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Affiliation(s)
- Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine ViennaVienna, Austria; Research Platform Bioactive Microbial Metabolites, Bioresources and Technologies Campus in TullnTulln an der Donau, Austria
| | - Markus Bacher
- Division of Chemistry of Renewables, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna Tulln an der Donau, Austria
| | - Alexandra Parich
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna Tulln an der Donau, Austria
| | - Bernhard Kluger
- Research Platform Bioactive Microbial Metabolites, Bioresources and Technologies Campus in TullnTulln an der Donau, Austria; Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, ViennaTulln an der Donau, Austria
| | - Agnieszka Gacek-Matthews
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna Tulln an der Donau, Austria
| | - Rainer Schuhmacher
- Center for Analytical Chemistry, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna Tulln an der Donau, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna Vienna, Austria
| | - Kathrin Rychli
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna Vienna, Austria
| | - Joseph Strauss
- Research Platform Bioactive Microbial Metabolites, Bioresources and Technologies Campus in TullnTulln an der Donau, Austria; Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, ViennaTulln an der Donau, Austria; Health and Environment Department, Bioresources, Austrian Institute of Technology GmbH, University and Research Campus TullnTulln an der Donau, Austria
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82
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Yu N, Nützmann HW, MacDonald JT, Moore B, Field B, Berriri S, Trick M, Rosser SJ, Kumar SV, Freemont PS, Osbourn A. Delineation of metabolic gene clusters in plant genomes by chromatin signatures. Nucleic Acids Res 2016; 44:2255-65. [PMID: 26895889 PMCID: PMC4797310 DOI: 10.1093/nar/gkw100] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 12/26/2022] Open
Abstract
Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi.
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Affiliation(s)
- Nan Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Ben Moore
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Ben Field
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Souha Berriri
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh, EH9 3JR, UK
| | - S Vinod Kumar
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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84
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85
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Fischer MJC, Rustenhloz C, Leh-Louis V, Perrière G. Molecular and functional evolution of the fungal diterpene synthase genes. BMC Microbiol 2015; 15:221. [PMID: 26483054 PMCID: PMC4617483 DOI: 10.1186/s12866-015-0564-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 10/12/2015] [Indexed: 11/24/2022] Open
Abstract
Background Terpenes represent one of the largest and most diversified families of natural compounds and are used in numerous industrial applications. Terpene synthase (TPS) genes originated in bacteria as diterpene synthase (di-TPS) genes. They are also found in plant and fungal genomes. The recent availability of a large number of fungal genomes represents an opportunity to investigate how genes involved in diterpene synthesis were acquired by fungi, and to assess the consequences of this process on the fungal metabolism. Results In order to investigate the origin of fungal di-TPS, we implemented a search for potential fungal di-TPS genes and identified their presence in several unrelated Ascomycota and Basidiomycota species. The fungal di-TPS phylogenetic tree is function-related but is not associated with the phylogeny based on housekeeping genes. The lack of agreement between fungal and di-TPS-based phylogenies suggests the presence of Horizontal Gene Transfer (HGTs) events. Further evidence for HGT was provided by conservation of synteny of di-TPS and neighbouring genes in distantly related fungi. Conclusions The results obtained here suggest that fungal di-TPSs originated from an ancient HGT event of a single di-TPS gene from a plant to a fungus in Ascomycota. In fungi, these di-TPSs allowed for the formation of clusters consisting in di-TPS, GGPPS and P450 genes to create functional clusters that were transferred between fungal species, producing diterpenes acting as hormones or toxins, thus affecting fungal development and pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0564-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc J C Fischer
- Université de Strasbourg, INRA, Inst Natl Recherche Agron, Métab Second Vigne, Unit Mixte Recherche Santé Vigne & Qual Vins, 28 rue de Herrlisheim, F-68021, Colmar, France.
| | - Camille Rustenhloz
- Université de Strasbourg, INRA, Inst Natl Recherche Agron, Métab Second Vigne, Unit Mixte Recherche Santé Vigne & Qual Vins, 28 rue de Herrlisheim, F-68021, Colmar, France.
| | - Véronique Leh-Louis
- Université de Strasbourg, CNRS, FRE 2326, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Guy Perrière
- Universite Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, F-69622, Villeurbanne, France.
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86
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Mao XM, Xu W, Li D, Yin WB, Chooi YH, Li YQ, Tang Y, Hu Y. Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products. Angew Chem Int Ed Engl 2015; 54:7592-6. [PMID: 26013262 DOI: 10.1002/anie.201502452] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/13/2022]
Abstract
The small-molecule biosynthetic potential of most filamentous fungi has remained largely unexplored and represents an attractive source for the discovery of new compounds. Genome sequencing of Calcarisporium arbuscula, a mushroom-endophytic fungus, revealed 68 core genes that are involved in natural product biosynthesis. This is in sharp contrast to the predominant production of the ATPase inhibitors aurovertin B and D in the wild-type fungus. Inactivation of a histone H3 deacetylase led to pleiotropic activation and overexpression of more than 75 % of the biosynthetic genes. Sampling of the overproduced compounds led to the isolation of ten compounds of which four contained new structures, including the cyclic peptides arbumycin and arbumelin, the diterpenoid arbuscullic acid A, and the meroterpenoid arbuscullic acid B. Such epigenetic modifications therefore provide a rapid and global approach to mine the chemical diversity of endophytic fungi.
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Affiliation(s)
- Xu-Ming Mao
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).,College of Life Sciences, Zhejiang University, Hangzhou 310058 (China)
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Dehai Li
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 (China)
| | - Wen-Bing Yin
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).,Current address: State Key Laboratory of Mycology, The Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)
| | - Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).,Current address: Research School of Biology, Australian National University, Canberra, ACT 0200 (Australia)
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058 (China)
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).
| | - Youcai Hu
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA). .,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050 (China).
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87
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Mao XM, Xu W, Li D, Yin WB, Chooi YH, Li YQ, Tang Y, Hu Y. Epigenetic Genome Mining of an Endophytic Fungus Leads to the Pleiotropic Biosynthesis of Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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88
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Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:180-93. [PMID: 25804821 PMCID: PMC4937988 DOI: 10.1016/j.plantsci.2015.02.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/05/2023]
Abstract
The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna (BOKU), University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria; Health and Environment Department, Austrian Institute of Technology GmbH - AIT, University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Khawar Sohail Siddiqui
- Biology Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia.
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89
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Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 2015; 6:299. [PMID: 25941517 PMCID: PMC4403501 DOI: 10.3389/fmicb.2015.00299] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/26/2015] [Indexed: 11/22/2022] Open
Abstract
Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.
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Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Claudia C König
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
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90
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Eidem HR, McGary KL, Rokas A. Shared Selective Pressures on Fungal and Human Metabolic Pathways Lead to Divergent yet Analogous Genetic Responses. Mol Biol Evol 2015; 32:1449-55. [DOI: 10.1093/molbev/msv034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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91
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Spencer S, Gugliotta A, Koenitzer J, Hauser H, Wirth D. Stability of single copy transgene expression in CHOK1 cells is affected by histone modifications but not by DNA methylation. J Biotechnol 2015; 195:15-29. [DOI: 10.1016/j.jbiotec.2014.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/22/2022]
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92
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Sarikaya-Bayram Ö, Palmer JM, Keller N, Braus GH, Bayram Ö. One Juliet and four Romeos: VeA and its methyltransferases. Front Microbiol 2015; 6:1. [PMID: 25653648 PMCID: PMC4299510 DOI: 10.3389/fmicb.2015.00001] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/01/2015] [Indexed: 11/19/2022] Open
Abstract
Fungal secondary metabolism has become an important research topic with great biomedical and biotechnological value. In the postgenomic era, understanding the diversity and the molecular control of secondary metabolites (SMs) are two challenging tasks addressed by the research community. Discovery of the LaeA methyltransferase 10 years ago opened up a new horizon on the control of SM research when it was found that expression of many SM gene clusters is controlled by LaeA. While the molecular function of LaeA remains an enigma, discovery of the velvet family proteins as interaction partners further extended the role of the LaeA beyond secondary metabolism. The heterotrimeric VelB–VeA–LaeA complex plays important roles in development, sporulation, secondary metabolism, and pathogenicity. Recently, three other methyltransferases have been found to associate with the velvet complex, the LaeA-like methyltransferase F and the methyltransferase heterodimers VipC–VapB. Interaction of VeA with at least four methyltransferase proteins indicates a molecular hub function for VeA that questions: Is there a VeA supercomplex or is VeA part of a highly dynamic cellular control network with many different partners?
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Affiliation(s)
- Özlem Sarikaya-Bayram
- Department of Biology, Maynooth University, National University of Ireland , Maynooth, Ireland
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, United States Forest Service , Madison, WI, USA
| | - Nancy Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin at Madison , Madison, WI, USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Georg-August Universität Göttingen , Göttingen, Germany
| | - Özgür Bayram
- Department of Biology, Maynooth University, National University of Ireland , Maynooth, Ireland
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93
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A modified recombineering protocol for the genetic manipulation of gene clusters in Aspergillus fumigatus. PLoS One 2014; 9:e111875. [PMID: 25372385 PMCID: PMC4221250 DOI: 10.1371/journal.pone.0111875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/02/2014] [Indexed: 01/07/2023] Open
Abstract
Genomic analyses of fungal genome structure have revealed the presence of physically-linked groups of genes, termed gene clusters, where collective functionality of encoded gene products serves a common biosynthetic purpose. In multiple fungal pathogens of humans and plants gene clusters have been shown to encode pathways for biosynthesis of secondary metabolites including metabolites required for pathogenicity. In the major mould pathogen of humans Aspergillus fumigatus, multiple clusters of co-ordinately upregulated genes were identified as having heightened transcript abundances, relative to laboratory cultured equivalents, during the early stages of murine infection. The aim of this study was to develop and optimise a methodology for manipulation of gene cluster architecture, thereby providing the means to assess their relevance to fungal pathogenicity. To this end we adapted a recombineering methodology which exploits lambda phage-mediated recombination of DNA in bacteria, for the generation of gene cluster deletion cassettes. By exploiting a pre-existing bacterial artificial chromosome (BAC) library of A. fumigatus genomic clones we were able to implement single or multiple intra-cluster gene replacement events at both subtelomeric and telomere distal chromosomal locations, in both wild type and highly recombinogenic A. fumigatus isolates. We then applied the methodology to address the boundaries of a gene cluster producing a nematocidal secondary metabolite, pseurotin A, and to address the role of this secondary metabolite in insect and mammalian responses to A. fumigatus challenge.
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94
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Scazzocchio C. Fungal biology in the post-genomic era. Fungal Biol Biotechnol 2014; 1:7. [PMID: 28955449 PMCID: PMC5611559 DOI: 10.1186/s40694-014-0007-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/15/2014] [Indexed: 12/12/2022] Open
Abstract
In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick’s central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The “next generation” sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.
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Affiliation(s)
- Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK.,Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, Orsay, 91405 France
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95
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Restraint of the G2/M transition by the SR/RRM family mRNA shuttling binding protein SNXAHRB1 in Aspergillus nidulans. Genetics 2014; 198:617-33. [PMID: 25104516 DOI: 10.1534/genetics.114.167445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Control of the eukaryotic G2/M transition by CDC2/CYCLINB is tightly regulated by protein-protein interactions, protein phosphorylations, and nuclear localization of CDC2/CYCLINB. We previously reported a screen, in Aspergillus nidulans, for extragenic suppressors of nimX2(cdc2) that resulted in the identification of the cold-sensitive snxA1 mutation. We demonstrate here that snxA1 suppresses defects in regulators of the CDK1 mitotic induction pathway, including nimX2(cdc) (2), nimE6(cyclinB), and nimT23(cdc) (25), but does not suppress G2-arresting nimA1/nimA5 mutations, the S-arresting nimE10(cyclinB) mutation, or three other G1/S phase mutations. snxA encodes the A. nidulans homolog of Saccharomyces cerevisiae Hrb1/Gbp2; nonessential shuttling messenger RNA (mRNA)-binding proteins belonging to the serine-arginine-rich (SR) and RNA recognition motif (RRM) protein family; and human heterogeneous ribonucleoprotein-M, a spliceosomal component involved in pre-mRNA processing and alternative splicing. snxA(Hrb) (1) is nonessential, its deletion phenocopies the snxA1 mutation, and its overexpression rescues snxA1 and ΔsnxA mutant phenotypes. snxA1 and a second allele isolated in this study, snxA2, are hypomorphic mutations that result from decreased transcript and protein levels, suggesting that snxA acts normally to restrain cell cycle progression. SNXA(HRB1) is predominantly nuclear, but is not retained in the nucleus during the partially closed mitosis of A. nidulans. We show that the snxA1 mutation does not suppress nimX2 by altering NIMX2(CDC2)/NIME(CYCLINB) kinase activity and that snxA1 or ΔsnxA alter localization patterns of NIME(CYCLINB) at the restrictive temperatures for snxA1 and nimX2. Together, these findings suggest a novel and previously unreported role of an SR/RRM family protein in cell cycle regulation, specifically in control of the CDK1 mitotic induction pathway.
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96
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Lv Y, Xiao J, Pan L. Type III polyketide synthase is involved in the biosynthesis of protocatechuic acid in Aspergillus niger. Biotechnol Lett 2014; 36:2303-10. [PMID: 25048233 DOI: 10.1007/s10529-014-1609-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/03/2014] [Indexed: 12/20/2022]
Abstract
Genomic studies have shown that not only plants but also filamentous fungi contain type III polyketide synthases. To study the function of type III polyketide synthase (AnPKSIII) in Aspergillus niger, a deletion strain (delAnPKSIII) and an overexpression strain (oeAnPKSIII) were constructed in A. niger MA169.4, a derivative of the wild-type (WT) A. niger ATCC 9029 that produces large quantities of gluconic acid. Alterations in the metabolites were analyzed by HPLC when the extract of the overexpression strain was compared with extracts of the WT and deletion strains. Protocatechuic acid (PCA; 3,4-dihydroxybenzoic acid, 3.2 mg/l) was isolated and identified as the main product of AnPKSIII when inductively expressed in A. niger MA169.4. The molecular weight of PCA was 154.1 (m/z 153.1 [M-H](-)), was detected by ESI-MS in the negative ionization mode, and (1)H and (13)C NMR data confirmed its structure.
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Affiliation(s)
- Yangyong Lv
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, People's Republic of China
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97
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Fungi treated with small chemicals exhibit increased antimicrobial activity against facultative bacterial and yeast pathogens. BIOMED RESEARCH INTERNATIONAL 2014; 2014:540292. [PMID: 25121102 PMCID: PMC4119895 DOI: 10.1155/2014/540292] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 11/21/2022]
Abstract
For decades, fungi have been the main source for the discovery of novel antimicrobial drugs. Recent sequencing efforts revealed a still high number of so far unknown “cryptic” secondary metabolites. The production of these metabolites is presumably epigenetically silenced under standard laboratory conditions. In this study, we investigated the effect of six small mass chemicals, of which some are known to act as epigenetic modulators, on the production of antimicrobial compounds in 54 spore forming fungi. The antimicrobial effect of fungal samples was tested against clinically facultative pathogens and multiresistant clinical isolates. In total, 30 samples of treated fungi belonging to six different genera reduced significantly growth of different test organisms compared to the untreated fungal sample (growth log reduction 0.3–4.3). For instance, the pellet of Penicillium restrictum grown in the presence of butyrate revealed significant higher antimicrobial activity against Staphylococcus (S.) aureus and multiresistant S. aureus strains and displayed no cytotoxicity against human cells, thus making it an ideal candidate for antimicrobial compound discovery. Our study shows that every presumable fungus, even well described fungi, has the potential to produce novel antimicrobial compounds and that our approach is capable of rapidly filling the pipeline for yet undiscovered antimicrobial substances.
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98
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The histone acetyltransferase GcnE (GCN5) plays a central role in the regulation of Aspergillus asexual development. Genetics 2014; 197:1175-89. [PMID: 24907261 DOI: 10.1534/genetics.114.165688] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Acetylation of histones is a key regulatory mechanism of gene expression in eukaryotes. GcnE is an acetyltransferase of Aspergillus nidulans involved in the acetylation of histone H3 at lysine 9 and lysine 14. Previous works have demonstrated that deletion of gcnE results in defects in primary and secondary metabolism. Here we unveil the role of GcnE in development and show that a ∆gcnE mutant strain has minor growth defects but is impaired in normal conidiophore development. No signs of conidiation were found after 3 days of incubation, and immature and aberrant conidiophores were found after 1 week of incubation. Centroid linkage clustering and principal component (PC) analysis of transcriptomic data suggest that GcnE occupies a central position in Aspergillus developmental regulation and that it is essential for inducing conidiation genes. GcnE function was found to be required for the acetylation of histone H3K9/K14 at the promoter of the master regulator of conidiation, brlA, as well as at the promoters of the upstream developmental regulators of conidiation flbA, flbB, flbC, and flbD (fluffy genes). However, analysis of the gene expression of brlA and the fluffy genes revealed that the lack of conidiation originated in a complete absence of brlA expression in the ∆gcnE strain. Ectopic induction of brlA from a heterologous alcA promoter did not remediate the conidiation defects in the ∆gcnE strain, suggesting that additional GcnE-mediated mechanisms must operate. Therefore, we conclude that GcnE is the only nonessential histone modifier with a strong role in fungal development found so far.
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99
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Kawauchi M, Iwashita K. Functional analysis of histone deacetylase and its role in stress response, drug resistance and solid-state cultivation in Aspergillus oryzae. J Biosci Bioeng 2014; 118:172-6. [PMID: 24613105 DOI: 10.1016/j.jbiosc.2014.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 01/17/2014] [Accepted: 02/03/2014] [Indexed: 01/03/2023]
Abstract
In the eukaryotic cell, histone deacetylases (HDACs) play key roles in the regulation of fundamental cellular process such as development regulation, stress response, secondary metabolism and genome integrity. Here, we provide a comprehensive phenotypic analysis using HDAC disruptants in Aspergillus oryzae. Our study revealed that four HDACs, hdaA/Aohda1, hdaB/Aorpd3, hdaD/Aohos2 and hst4/AohstD were involved in stress response, cell wall synthesis and chromatin integrity in A. oryzae. Osmotic stress sensitivity of HDAC disruptants differed between plate cultures and liquid cultures, suggesting that HDACs adapt to the difference environmental conditions. Using a common A. oryzae fermentation medium, rice-koji, we also characterized HDACs related to growth and enzyme production to investigate which HDACs will be required for adaptation to environmental conditions and stress resistances. Because HDACs are widely conserved, our study has broad applications and may inform work with filamentous fungi and other eukaryote.
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Affiliation(s)
- Moriyuki Kawauchi
- Department of Molecular Biotechnology, Graduate School of Advanced Science of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-8530, Japan; National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Kazuhiro Iwashita
- Department of Molecular Biotechnology, Graduate School of Advanced Science of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-8530, Japan; National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan.
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100
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Leitão AL, Enguita FJ. Fungal extrolites as a new source for therapeutic compounds and as building blocks for applications in synthetic biology. Microbiol Res 2014; 169:652-65. [PMID: 24636745 DOI: 10.1016/j.micres.2014.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 02/15/2014] [Accepted: 02/16/2014] [Indexed: 01/07/2023]
Abstract
Secondary metabolic pathways of fungal origin provide an almost unlimited resource of new compounds for medical applications, which can fulfill some of the, currently unmet, needs for therapeutic alternatives for the treatment of a number of diseases. Secondary metabolites secreted to the extracellular medium (extrolites) belong to diverse chemical and structural families, but the majority of them are synthesized by the condensation of a limited number of precursor building blocks including amino acids, sugars, lipids and low molecular weight compounds also employed in anabolic processes. In fungi, genes related to secondary metabolic pathways are frequently clustered together and show a modular organization within fungal genomes. The majority of fungal gene clusters responsible for the biosynthesis of secondary metabolites contain genes encoding a high molecular weight condensing enzyme which is responsible for the assembly of the precursor units of the metabolite. They also contain other auxiliary genes which encode enzymes involved in subsequent chemical modification of the metabolite core. Synthetic biology is a branch of molecular biology whose main objective is the manipulation of cellular components and processes in order to perform logically connected metabolic functions. In synthetic biology applications, biosynthetic modules from secondary metabolic processes can be rationally engineered and combined to produce either new compounds, or to improve the activities and/or the bioavailability of the already known ones. Recently, advanced genome editing techniques based on guided DNA endonucleases have shown potential for the manipulation of eukaryotic and bacterial genomes. This review discusses the potential application of genetic engineering and genome editing tools in the rational design of fungal secondary metabolite pathways by taking advantage of the increasing availability of genomic and biochemical data.
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Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica 2829-516, Portugal.
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal.
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