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Two histone deacetylases, FfHda1 and FfHda2, are important for Fusarium fujikuroi secondary metabolism and virulence. Appl Environ Microbiol 2013; 79:7719-34. [PMID: 24096420 PMCID: PMC3837819 DOI: 10.1128/aem.01557-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Histone modifications are crucial for the regulation of secondary metabolism in various filamentous fungi. Here we studied the involvement of histone deacetylases (HDACs) in secondary metabolism in the phytopathogenic fungus Fusarium fujikuroi, a known producer of several secondary metabolites, including phytohormones, pigments, and mycotoxins. Deletion of three Zn(2+)-dependent HDAC-encoding genes, ffhda1, ffhda2, and ffhda4, indicated that FfHda1 and FfHda2 regulate secondary metabolism, whereas FfHda4 is involved in developmental processes but is dispensable for secondary-metabolite production in F. fujikuroi. Single deletions of ffhda1 and ffhda2 resulted not only in an increase or decrease but also in derepression of metabolite biosynthesis under normally repressing conditions. Moreover, double deletion of both the ffhda1 and ffhda2 genes showed additive but also distinct phenotypes with regard to secondary-metabolite biosynthesis, and both genes are required for gibberellic acid (GA)-induced bakanae disease on the preferred host plant rice, as Δffhda1 Δffhda2 mutants resemble the uninfected control plant. Microarray analysis with a Δffhda1 mutant that has lost the major HDAC revealed differential expression of secondary-metabolite gene clusters, which was subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are involved not only in gene silencing but also in the activation of some genes. Chromatin immunoprecipitation with the Δffhda1 mutant revealed significant alterations in the acetylation state of secondary-metabolite gene clusters compared to the wild type, thereby providing insights into the regulatory mechanism at the chromatin level. Altogether, manipulation of HDAC-encoding genes constitutes a powerful tool to control secondary metabolism in filamentous fungi.
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103
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Zutz C, Gacek A, Sulyok M, Wagner M, Strauss J, Rychli K. Small chemical chromatin effectors alter secondary metabolite production in Aspergillus clavatus. Toxins (Basel) 2013; 5:1723-41. [PMID: 24105402 PMCID: PMC3813908 DOI: 10.3390/toxins5101723] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/29/2013] [Accepted: 09/16/2013] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Aspergillus clavatus is known to produce a variety of secondary metabolites (SM) such as patulin, pseurotin A, and cytochalasin E. In fungi, the production of most SM is strongly influenced by environmental factors and nutrients. Furthermore, it has been shown that the regulation of SM gene clusters is largely based on modulation of a chromatin structure. Communication between fungi and bacteria also triggers chromatin-based induction of silent SM gene clusters. Consequently, chemical chromatin effectors known to inhibit histone deacetylases (HDACs) and DNA-methyltransferases (DNMTs) influence the SM profile of several fungi. In this study, we tested the effect of five different chemicals, which are known to affect chromatin structure, on SM production in A. clavatus using two growth media with a different organic nitrogen source. We found that production of patulin was completely inhibited and cytochalasin E levels strongly reduced, whereas growing A. clavatus in media containing soya-derived peptone led to substantially higher pseurotin A levels. The HDAC inhibitors valproic acid, trichostatin A and butyrate, as well as the DNMT inhibitor 5-azacytidine (AZA) and N-acetyl-d-glucosamine, which was used as a proxy for bacterial fungal co-cultivation, had profound influence on SM accumulation and transcription of the corresponding biosynthetic genes. However, the repressing effect of the soya-based nitrogen source on patulin production could not be bypassed by any of the small chemical chromatin effectors. Interestingly, AZA influenced some SM cluster genes and SM production although no Aspergillus species has yet been shown to carry detectable DNA methylation.
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Affiliation(s)
- Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Veterinaerplatz1, Vienna 1210, Austria; E-Mails: (C.Z.); (M.W.)
| | - Agnieszka Gacek
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Konrad Lorenz-Straße 24/II, Tulln/Donau 3430, Austria; E-Mails: (A.G.); (J.S.)
| | - Michael Sulyok
- Center for Analytical Chemistry, Department for Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, Tulln/Donau 3430, Austria; E-Mail:
| | - Martin Wagner
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Veterinaerplatz1, Vienna 1210, Austria; E-Mails: (C.Z.); (M.W.)
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Konrad Lorenz-Straße 24/II, Tulln/Donau 3430, Austria; E-Mails: (A.G.); (J.S.)
- AIT-Austrian Institute of Technology GmbH, Health and Environment Department, University and Research Campus Tulln, Konrad Lorenz-Straße 24/II, Tulln/Donau 3430, Austria
| | - Kathrin Rychli
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Veterinaerplatz1, Vienna 1210, Austria; E-Mails: (C.Z.); (M.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +43-1-25077-3510; Fax: +43-1-25077-3590
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Glass NL, Schmoll M, Cate JH, Coradetti S. Plant Cell Wall Deconstruction by Ascomycete Fungi. Annu Rev Microbiol 2013; 67:477-98. [DOI: 10.1146/annurev-micro-092611-150044] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Monika Schmoll
- Austrian Institute of Technology GmbH (AIT), Health and Environment, Bioresources, 3430 Tulln, Austria
| | - Jamie H.D. Cate
- Molecular and Cellular Biology Department, and
- Chemistry Department, University of California, Berkeley, California 94720;
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105
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Niehaus EM, Kleigrewe K, Wiemann P, Studt L, Sieber CMK, Connolly LR, Freitag M, Güldener U, Tudzynski B, Humpf HU. Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway. ACTA ACUST UNITED AC 2013; 20:1055-66. [PMID: 23932525 DOI: 10.1016/j.chembiol.2013.07.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
In this work, the biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunoprecipitation revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. We provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with nuclear magnetic resonance and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, we indicate that PKS/NRPS releases its product with an open ring structure, probably as an alcohol. Our data indicate that 2-pyrrolidone ring closure, oxidation at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, respectively.
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Affiliation(s)
- Eva-Maria Niehaus
- Institute for Biology and Biotechnology of Plants, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, Münster 48143, Germany
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Distinct amino acids of histone H3 control secondary metabolism in Aspergillus nidulans. Appl Environ Microbiol 2013; 79:6102-9. [PMID: 23892751 DOI: 10.1128/aem.01578-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Chromatin remodelling events play an important role in the secondary metabolism of filamentous fungi. Previously, we showed that a bacterium, Streptomyces rapamycinicus, is able to reprogram the histone-modifying Spt-Ada-Gcn5-acetyltransferase/ADA (SAGA/ADA) complex of the model fungus Aspergillus nidulans. Consequently, the histone H3 amino acids lysine 9 and lysine 14 at distinct secondary metabolism genes were specifically acetylated during the bacterial fungal interaction, which, furthermore, was associated with the activation of the otherwise silent orsellinic acid gene cluster. To investigate the importance of the histone modifications for distinct gene expression profiles in fungal secondary metabolism, we exchanged several amino acids of histone H3 of A. nidulans. These amino acids included lysine residues 9, 14, 18, and 23 as well as serine 10 and threonine 11. Lysine residues were replaced by arginine or glutamine residues, and serine/threonine residues were replaced by alanine. All generated mutant strains were viable, allowing direct analysis of the consequences of missing posttranslational histone modifications. In the mutant strains, major changes in the expression patterns at both the transcriptional and metabolite levels of the penicillin, sterigmatocystin, and orsellinic acid biosynthesis gene clusters were detected. These effects were due mainly to the substitution of the acetylatable lysine 14 of histone H3 and were enhanced in a lysine 14/lysine 9 double mutant of histone H3. Taken together, our findings show a causal linkage between the acetylation of lysine residue 14 of histone H3 and the transcription and product formation of secondary metabolite gene clusters.
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108
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Arnold C, Stadler PF, Prohaska SJ. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol 2013; 336:61-74. [PMID: 23880640 DOI: 10.1016/j.jtbi.2013.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/02/2013] [Accepted: 07/15/2013] [Indexed: 01/19/2023]
Abstract
Eukaryotic histones carry a diverse set of specific chemical modifications that accumulate over the life-time of a cell and have a crucial impact on the cell state in general and the transcriptional program in particular. Replication constitutes a dramatic disruption of the chromatin states that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of "recomputing" the desired parental modification patterns on the basis of the partial information contained in that half of the nucleosomes that predate replication. To test whether such a mechanism is theoretically feasible, we have developed a flexible stochastic simulation system (available at http://www.bioinf.uni-leipzig.de/Software/StoChDyn) for studying the dynamics of histone modification states. The implementation is based on Gillespie's approach, i.e., it models the master equation of a detailed chemical model. It is efficient enough to use an evolutionary algorithm to find patterns across multiple cell divisions with high accuracy. We found that it is easy to evolve a system of enzymes that can maintain a particular chromatin state roughly stable, even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors, such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and chemical parameters such as enzymatic binding and dissociation rates. All these factors also influence the accumulation of errors in the wake of cell divisions.
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Affiliation(s)
- Christian Arnold
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Harvard University, Department of Human Evolutionary Biology, 11 Divinity Avenue, Cambridge, MA 02138, USA.
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109
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Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW. The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet 2013; 9:e1003496. [PMID: 23818858 PMCID: PMC3688495 DOI: 10.1371/journal.pgen.1003496] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/20/2013] [Indexed: 01/07/2023] Open
Abstract
The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology.
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Affiliation(s)
- Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Rajani Raja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Jason S. Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mariko Nonogaki
- College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Alexander E. Boyd
- Center for Genome Research & Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - C. Alisha Owensby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brian J. Knaus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Daniel Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Yanming Di
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Kerry L. McPhail
- College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
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Asai T, Yamamoto T, Shirata N, Taniguchi T, Monde K, Fujii I, Gomi K, Oshima Y. Structurally diverse chaetophenol productions induced by chemically mediated epigenetic manipulation of fungal gene expression. Org Lett 2013; 15:3346-9. [PMID: 23767797 DOI: 10.1021/ol401386w] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Epigenetic manipulation of gene expression in Chaetomium indicum using a HDAC inhibitor led to the isolation of structurally diverse chaetophenols, and 3, 4 and 5 bear unprecedented polycyclic skeletons. The expression of two silent genes (pksCH-1 and pksCH-2) for nonreducing PKSs involved in chaetophenol biosynthesis was associated with an increase of histone acetylation level. The heterologous gene expression study in Aspergillus oryzae revealed pksCH-2 to be the NR-PKS gene for 8.
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Affiliation(s)
- Teigo Asai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-yama, Aoba-ku, Sendai 980-8578, Japan.
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Fungus-specific sirtuin HstD coordinates secondary metabolism and development through control of LaeA. EUKARYOTIC CELL 2013; 12:1087-96. [PMID: 23729383 DOI: 10.1128/ec.00003-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sirtuins are members of the NAD(+)-dependent histone deacetylase family that contribute to various cellular functions that affect aging, disease, and cancer development in metazoans. However, the physiological roles of the fungus-specific sirtuin family are still poorly understood. Here, we determined a novel function of the fungus-specific sirtuin HstD/Aspergillus oryzae Hst4 (AoHst4), which is a homolog of Hst4 in A. oryzae yeast. The deletion of all histone deacetylases in A. oryzae demonstrated that the fungus-specific sirtuin HstD/AoHst4 is required for the coordination of fungal development and secondary metabolite production. We also show that the expression of the laeA gene, which is the most studied fungus-specific coordinator for the regulation of secondary metabolism and fungal development, was induced in a ΔhstD strain. Genetic interaction analysis of hstD/Aohst4 and laeA clearly indicated that HstD/AoHst4 works upstream of LaeA to coordinate secondary metabolism and fungal development. The hstD/Aohst4 and laeA genes are fungus specific but conserved in the vast family of filamentous fungi. Thus, we conclude that the fungus-specific sirtuin HstD/AoHst4 coordinates fungal development and secondary metabolism via the regulation of LaeA in filamentous fungi.
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