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Karahoda B, Pfannenstiel BT, Sarikaya-Bayram Ö, Dong Z, Ho Wong K, Fleming AB, Keller NP, Bayram Ö. The KdmB-EcoA-RpdA-SntB (KERS) chromatin regulatory complex controls development, secondary metabolism and pathogenicity in Aspergillus flavus. Fungal Genet Biol 2023; 169:103836. [PMID: 37666447 PMCID: PMC10841535 DOI: 10.1016/j.fgb.2023.103836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The filamentous fungus Aspergillus flavus is a plant and human pathogen predominantly found in the soil as spores or sclerotia and is capable of producing various secondary metabolites (SM) such as the carcinogenic mycotoxin aflatoxin. Recently, we have discovered a novel nuclear chromatin binding complex (KERS) that contains the JARID1-type histone demethylase KdmB, a putative cohesion acetyl transferase EcoA, a class I type histone deacetylase RpdA and the PHD ring finger reader protein SntB in the model filamentous fungus Aspergillus nidulans. Here, we show the presence of the KERS complex in A. flavus by immunoprecipitation-coupled mass spectrometry and constructed kdmBΔ and rpdAΔ strains to study their roles in fungal development, SM production and histone post-translational modifications (HPTMs). We found that KdmB and RpdA couple the regulation of SM gene clusters with fungal light-responses and HPTMs. KdmB and RpdA have opposing roles in light-induced asexual conidiation, while both factors are positive regulators of sclerotia development through the nsdC and nsdD pathway. KdmB and RpdA are essential for the productions of aflatoxin (similar to findings for SntB) as well as cyclopiazonic acid, ditryptophenaline and leporin B through controlling the respective SM biosynthetic gene clusters. We further show that both KdmB and RpdA regulate H3K4me3 and H3K9me3 levels, while RpdA also acts on H3K14ac levels in nuclear extracts. Therefore, the chromatin modifiers KdmB and RpdA of the KERS complex are key regulators for fungal development and SM metabolism in A. flavus.
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Affiliation(s)
- Betim Karahoda
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Brandon T Pfannenstiel
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | | | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau; Institute of Translational Medicine, University of Macau, Macau; Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | - Özgür Bayram
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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2
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Verma A, Tiwari H, Singh S, Gupta P, Rai N, Kumar Singh S, Singh BP, Rao S, Gautam V. Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions. Mycology 2023; 14:275-291. [PMID: 38187885 PMCID: PMC10769123 DOI: 10.1080/21501203.2023.2241486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/21/2023] [Indexed: 01/09/2024] Open
Abstract
Fungal endophytes have emerged as a promising source of secondary metabolites with significant potential for various applications in the field of biomedicine. The biosynthetic gene clusters of endophytic fungi are responsible for encoding several enzymes and transcriptional factors that are involved in the biosynthesis of secondary metabolites. The investigation of fungal metabolic potential at genetic level faces certain challenges, including the synthesis of appropriate amounts of chemicals, and loss of the ability of fungal endophytes to produce secondary metabolites in an artificial culture medium. Therefore, there is a need to delve deeper into the field of fungal genomics and transcriptomics to explore the potential of fungal endophytes in generating secondary metabolites governed by biosynthetic gene clusters. The silent biosynthetic gene clusters can be activated by modulating the chromatin structure using chemical compounds. Epigenetic modification plays a significant role by inducing cryptic gene responsible for the production of secondary metabolites using DNA methyl transferase and histone deacetylase. CRISPR-Cas9-based genome editing emerges an effective tool to enhance the production of desired metabolites by modulating gene expression. This review primarily focuses on the significance of epigenetic elicitors and their capacity to boost the production of secondary metabolites from endophytes. This article holds the potential to rejuvenate the drug discovery pipeline by introducing new chemical compounds.
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Affiliation(s)
- Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harshita Tiwari
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Swati Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Bhim Pratap Singh
- Department of Agriculture & Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Sonepat, India
| | - Sombir Rao
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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3
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Zhang X, Noberini R, Vai A, Bonaldi T, Seidl MF, Collemare J. Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genet Biol 2023; 167:103800. [PMID: 37146898 DOI: 10.1016/j.fgb.2023.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
In eukaryotes, the combination of different histone post-translational modifications (PTMs) - the histone code - impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy.
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jérȏme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina. J Fungi (Basel) 2022; 9:jof9010009. [PMID: 36675830 PMCID: PMC9864250 DOI: 10.3390/jof9010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The coprophilous ascomycete Podospora anserina is known to have a high potential to synthesize a wide array of secondary metabolites (SMs). However, to date, the characterization of SMs in this species, as in other filamentous fungal species, is far less than expected by the functional prediction through genome mining, likely due to the inactivity of most SMs biosynthesis gene clusters (BGCs) under standard conditions. In this work, our main objective was to compare the global strategies usually used to deregulate SM gene clusters in P. anserina, including the variation of culture conditions and the modification of the chromatin state either by genetic manipulation or by chemical treatment, and to show the complementarity of the approaches between them. In this way, we showed that the metabolomics-driven comparative analysis unveils the unexpected diversity of metabolic changes in P. anserina and that the integrated strategies have a mutual complementary effect on the expression of the fungal metabolome. Then, our results demonstrate that metabolite production is significantly influenced by varied cultivation states and epigenetic modifications. We believe that the strategy described in this study will facilitate the discovery of fungal metabolites of interest and will improve the ability to prioritize the production of specific fungal SMs with an optimized treatment.
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5
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Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses. Microb Genom 2022; 8. [PMID: 36129736 PMCID: PMC9676040 DOI: 10.1099/mgen.0.000856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.,Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy
| | - Jerome Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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6
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Li Y, Song Z, Wang E, Dong L, Bai J, Wang D, Zhu J, Zhang C. Potential antifungal targets based on histones post-translational modifications against invasive aspergillosis. Front Microbiol 2022; 13:980615. [PMID: 36016791 PMCID: PMC9395700 DOI: 10.3389/fmicb.2022.980615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
As a primary cause of death in patients with hematological malignancies and transplant recipients, invasive aspergillosis (IA) is a condition that warrants attention. IA infections have been increasing, which remains a significant cause of morbidity and mortality in immunocompromised patients. During the past decade, antifungal drug resistance has emerged, which is especially concerning for management given the limited options for treating azole-resistant infections and the possibility of failure of prophylaxis in those high-risk patients. Histone posttranslational modifications (HPTMs), mainly including acetylation, methylation, ubiquitination and phosphorylation, are crucial epigenetic mechanisms regulating various biological events, which could modify the conformation of histone and influence chromatin-associated nuclear processes to regulate development, cellular responsiveness, and biological phenotype without affecting the underlying genetic sequence. In recent years, fungi have become important model organisms for studying epigenetic regulation. HPTMs involves in growth and development, secondary metabolite biosynthesis and virulence in Aspergillus. This review mainly aims at summarizing the acetylation, deacetylation, methylation, demethylation, and sumoylation of histones in IA and connect this knowledge to possible HPTMs-based antifungal drugs. We hope this research could provide a reference for exploring new drug targets and developing low-toxic and high-efficiency antifungal strategies.
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Affiliation(s)
- Yiman Li
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhihui Song
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ente Wang
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Liming Dong
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jie Bai
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Dong Wang
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jinyan Zhu
- Department of Hematology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chao Zhang
- Department of Pharmacy, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chao Zhang,
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7
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The Lysine Demethylases KdmA and KdmB Differently Regulate Asexual Development, Stress Response, and Virulence in Aspergillus fumigatus. J Fungi (Basel) 2022; 8:jof8060590. [PMID: 35736073 PMCID: PMC9225160 DOI: 10.3390/jof8060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Histone demethylases govern diverse cellular processes, including growth, development, and secondary metabolism. In the present study, we investigated the functions of two lysine demethylases, KdmA and KdmB, in the opportunistic human pathogenic fungus Aspergillus fumigatus. Experiments with mutants harboring deletions of genes encoding KdmA (ΔkdmA) and KdmB (ΔkdmB) showed that KdmA is necessary for normal growth and proper conidiation, whereas KdmB negatively regulates vegetative growth and conidiation. In both mutant strains, tolerance to H2O2 was significantly decreased, and the activities of both conidia-specific catalase (CatA) and mycelia-specific catalase (Cat1) were decreased. Both mutants had significantly increased sensitivity to the guanine nucleotide synthesis inhibitor 6-azauracil (6AU). The ΔkdmA mutant produced more gliotoxin (GT), but the virulence was not changed significantly in immunocompromised mice. In contrast, the production of GT and virulence were markedly reduced by the loss of kdmB. Comparative transcriptomic analyses revealed that the expression levels of developmental process-related genes and antioxidant activity-related genes were downregulated in both mutants. Taken together, we concluded that KdmA and KdmB have opposite roles in vegetative growth, asexual sporulation, and GT production. However, the two proteins were equally important for the development of resistance to 6AU.
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8
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Yang K, Tian J, Keller NP. Post-translational modifications drive secondary metabolite biosynthesis in Aspergillus: a review. Environ Microbiol 2022; 24:2857-2881. [PMID: 35645150 PMCID: PMC9545273 DOI: 10.1111/1462-2920.16034] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 12/26/2022]
Abstract
Post‐translational modifications (PTMs) are important for protein function and regulate multiple cellular processes and secondary metabolites (SMs) in fungi. Aspergillus species belong to a genus renown for an abundance of bioactive secondary metabolites, many important as toxins, pharmaceuticals and in industrial production. The genes required for secondary metabolites are typically co‐localized in biosynthetic gene clusters (BGCs), which often localize in heterochromatic regions of genome and are ‘turned off’ under laboratory condition. Efforts have been made to ‘turn on’ these BGCs by genetic manipulation of histone modifications, which could convert the heterochromatic structure to euchromatin. Additionally, non‐histone PTMs also play critical roles in the regulation of secondary metabolism. In this review, we collate the known roles of epigenetic and PTMs on Aspergillus SM production. We also summarize the proteomics approaches and bioinformatics tools for PTM identification and prediction and provide future perspectives on the emerging roles of PTM on regulation of SM biosynthesis in Aspergillus and other fungi.
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Affiliation(s)
- Kunlong Yang
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China.,Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, 53705, USA
| | - Jun Tian
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, 53705, USA
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9
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Fungal Lysine Deacetylases in Virulence, Resistance, and Production of Small Bioactive Compounds. Genes (Basel) 2021; 12:genes12101470. [PMID: 34680865 PMCID: PMC8535771 DOI: 10.3390/genes12101470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
The growing number of immunocompromised patients begs for efficient therapy strategies against invasive fungal infections. As conventional antifungal treatment is increasingly hampered by resistance to commonly used antifungals, development of novel therapy regimens is required. On the other hand, numerous fungal species are industrially exploited as cell factories of enzymes and chemicals or as producers of medically relevant pharmaceuticals. Consequently, there is immense interest in tapping the almost inexhaustible fungal portfolio of natural products for potential medical and industrial applications. Both the pathogenicity and production of those small metabolites are significantly dependent on the acetylation status of distinct regulatory proteins. Thus, classical lysine deacetylases (KDACs) are crucial virulence determinants and important regulators of natural products of fungi. In this review, we present an overview of the members of classical KDACs and their complexes in filamentous fungi. Further, we discuss the impact of the genetic manipulation of KDACs on the pathogenicity and production of bioactive molecules. Special consideration is given to inhibitors of these enzymes and their role as potential new antifungals and emerging tools for the discovery of novel pharmaceutical drugs and antibiotics in fungal producer strains.
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10
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Kim W, Jeong MH, Yun SH, Hur JS. Transcriptome Analysis Identifies a Gene Cluster for the Biosynthesis of Biruloquinone, a Rare Phenanthraquinone, in a Lichen-Forming Fungus Cladonia macilenta. J Fungi (Basel) 2021; 7:398. [PMID: 34065383 PMCID: PMC8161216 DOI: 10.3390/jof7050398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022] Open
Abstract
Lichens are prolific producers of natural products of polyketide origin. We previously described a culture of lichen-forming fungus (LFF) Cladonia macilenta that produces biruloquinone, a purple pigment that is a phenanthraquinone rarely found in nature. However, there was no genetic information on the biosynthesis of biruloquinone. To identify a biosynthetic gene cluster for biruloquinone, we mined polyketide synthase (PKS) genes from the genome sequence of a LFF isolated from thalli of C. macilenta. The 38 PKS in C. macilenta are highly diverse, many of which form phylogenetic clades with PKS previously characterized in non-lichenized fungi. We compared transcriptional profiles of the 38 PKS genes in two chemotypic variants, one producing biruloquinone and the other producing no appreciable metabolite in vitro. We identified a PKS gene (hereafter PKS21) that was highly upregulated in the LFF that produces biruloquinone. The boundaries of a putative biruloquinone gene cluster were demarcated by co-expression patterns of six clustered genes, including the PKS21. Biruloquinone gene clusters exhibited a high degree of synteny between related species. In this study we identified a novel PKS family responsible for the biosynthesis of biruloquinone through whole-transcriptome analysis.
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Affiliation(s)
- Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
| | - Min-Hye Jeong
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
| | - Sung-Hwan Yun
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea;
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
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11
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Lyu HN, Liu HW, Keller NP, Yin WB. Harnessing diverse transcriptional regulators for natural product discovery in fungi. Nat Prod Rep 2020; 37:6-16. [DOI: 10.1039/c8np00027a] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers diverse transcriptional regulators for the activation of secondary metabolism and novel natural product discovery in fungi.
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Affiliation(s)
- Hai-Ning Lyu
- State Key Laboratory of Mycology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
| | - Hong-Wei Liu
- State Key Laboratory of Mycology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology and Bacteriology
- University of Wisconsin–Madison
- Madison
- USA
| | - Wen-Bing Yin
- State Key Laboratory of Mycology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
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12
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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13
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Lukito Y, Chujo T, Hale TK, Mace W, Johnson LJ, Scott B. Regulation of subtelomeric fungal secondary metabolite genes by H3K4me3 regulators CclA and KdmB. Mol Microbiol 2019; 112:837-853. [DOI: 10.1111/mmi.14320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Yonathan Lukito
- Institute of Fundamental Sciences Massey University Palmerston North New Zealand
- Grasslands Research Centre AgResearch Limited Palmerston North New Zealand
| | - Tetsuya Chujo
- Institute of Fundamental Sciences Massey University Palmerston North New Zealand
| | - Tracy K. Hale
- Institute of Fundamental Sciences Massey University Palmerston North New Zealand
| | - Wade Mace
- Grasslands Research Centre AgResearch Limited Palmerston North New Zealand
| | - Linda J. Johnson
- Grasslands Research Centre AgResearch Limited Palmerston North New Zealand
| | - Barry Scott
- Institute of Fundamental Sciences Massey University Palmerston North New Zealand
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14
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Dallery J, Adelin É, Le Goff G, Pigné S, Auger A, Ouazzani J, O'Connell RJ. H3K4 trimethylation by CclA regulates pathogenicity and the production of three families of terpenoid secondary metabolites in Colletotrichum higginsianum. MOLECULAR PLANT PATHOLOGY 2019; 20:831-842. [PMID: 30924614 PMCID: PMC6637877 DOI: 10.1111/mpp.12795] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The role of histone 3 lysine 4 (H3K4) methylation is poorly understood in plant pathogenic fungi. Here, we analysed the function of CclA, a subunit of the COMPASS complex mediating H3K4 methylation, in the brassica anthracnose pathogen Colletotrichum higginsianum. We show that CclA is required for full genome-wide H3K4 trimethylation. The deletion of cclA strongly reduced mycelial growth, asexual sporulation and spore germination but did not impair the morphogenesis of specialized infection structures (appressoria and biotrophic hyphae). Virulence of the ΔcclA mutant on plants was strongly attenuated, associated with a marked reduction in appressorial penetration ability on both plants and inert cellophane membranes. The secondary metabolite profile of the ΔcclA mutant was greatly enriched compared to that of the wild type, with three different families of terpenoid compounds being overproduced by the mutant, namely the colletochlorins, higginsianins and sclerosporide. These included five novel molecules that were produced exclusively by the ΔcclA mutant: colletorin D, colletorin D acid, higginsianin C, 13-epi-higginsianin C and sclerosporide. Taken together, our findings indicate that H3K4 trimethylation plays a critical role in regulating fungal growth, development, pathogenicity and secondary metabolism in C. higginsianum.
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Affiliation(s)
- Jean‐Félix Dallery
- UMR BIOGER, INRA, AgroParisTechUniversité Paris‐Saclay78850Thiverval‐GrignonFrance
- Centre National de la Recherche ScientifiqueInstitut de Chimie des Substances Naturelles ICSNAvenue de la Terrasse91198Gif‐sur‐Yvette, cedexFrance
| | - Émilie Adelin
- Centre National de la Recherche ScientifiqueInstitut de Chimie des Substances Naturelles ICSNAvenue de la Terrasse91198Gif‐sur‐Yvette, cedexFrance
| | - Géraldine Le Goff
- Centre National de la Recherche ScientifiqueInstitut de Chimie des Substances Naturelles ICSNAvenue de la Terrasse91198Gif‐sur‐Yvette, cedexFrance
| | - Sandrine Pigné
- UMR BIOGER, INRA, AgroParisTechUniversité Paris‐Saclay78850Thiverval‐GrignonFrance
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTechUniversité Paris‐Saclay78850Thiverval‐GrignonFrance
| | - Jamal Ouazzani
- Centre National de la Recherche ScientifiqueInstitut de Chimie des Substances Naturelles ICSNAvenue de la Terrasse91198Gif‐sur‐Yvette, cedexFrance
| | - Richard J. O'Connell
- UMR BIOGER, INRA, AgroParisTechUniversité Paris‐Saclay78850Thiverval‐GrignonFrance
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15
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Bauer I, Lechner L, Pidroni A, Petrone AM, Merschak P, Lindner H, Kremser L, Graessle S, Golderer G, Allipour S, Brosch G. Type I and II PRMTs regulate catabolic as well as detoxifying processes in Aspergillus nidulans. Fungal Genet Biol 2019; 129:86-100. [PMID: 31145992 DOI: 10.1016/j.fgb.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 11/28/2022]
Abstract
In filamentous fungi, arginine methylation has been implicated in morphogenesis, mycotoxin biosynthesis, pathogenicity, and stress response although the exact role of this posttranslational modification in these processes remains obscure. Here, we present the first genome-wide transcriptome analysis in filamentous fungi that compared expression levels of genes regulated by type I and type II protein arginine methyltransferases (PRMTs). In Aspergillus nidulans, three conserved type I and II PRMTs are present that catalyze asymmetric or symmetric dimethylation of arginines. We generated a double type I mutant (ΔrmtA/rmtB) and a combined type I and type II mutant (ΔrmtB/rmtC) to perform genome-wide comparison of their effects on gene expression, but also to monitor putative overlapping activities and reciprocal regulations of type I and type II PRMTs in Aspergillus. Our study demonstrates, that rmtA and rmtC as type I and type II representatives act together as repressors of proteins that are secreted into the extracellular region as the majority of up-regulated genes are mainly involved in catabolic pathways that constitute the secretome of Aspergillus. In addition to a strong up-regulation of secretory genes we found a significant enrichment of down-regulated genes involved in processes related to oxidation-reduction, transmembrane transport and secondary metabolite biosynthesis. Strikingly, nearly 50% of down-regulated genes in both double mutants correspond to redox reaction/oxidoreductase processes, a remarkable finding in light of our recently observed oxidative stress phenotypes of ΔrmtA and ΔrmtC. Finally, analysis of nuclear and cytoplasmic extracts for mono-methylated proteins revealed the presence of both, common and specific substrates of RmtA and RmtC. Thus, our data indicate that type I and II PRMTs in Aspergillus seem to co-regulate the same biological processes but also specifically affect other pathways in a non-redundant fashion.
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Affiliation(s)
- Ingo Bauer
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Lechner
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Angelo Pidroni
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Maria Petrone
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Petra Merschak
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Graessle
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Georg Golderer
- Division of Biological Chemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Shadab Allipour
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Gerald Brosch
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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16
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Abstract
One of the exciting movements in microbial sciences has been a refocusing and revitalization of efforts to mine the fungal secondary metabolome. The magnitude of biosynthetic gene clusters (BGCs) in a single filamentous fungal genome combined with the historic number of sequenced genomes suggests that the secondary metabolite wealth of filamentous fungi is largely untapped. Mining algorithms and scalable expression platforms have greatly expanded access to the chemical repertoire of fungal-derived secondary metabolites. In this Review, I discuss new insights into the transcriptional and epigenetic regulation of BGCs and the ecological roles of fungal secondary metabolites in warfare, defence and development. I also explore avenues for the identification of new fungal metabolites and the challenges in harvesting fungal-derived secondary metabolites.
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17
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Pfannenstiel BT, Keller NP. On top of biosynthetic gene clusters: How epigenetic machinery influences secondary metabolism in fungi. Biotechnol Adv 2019; 37:107345. [PMID: 30738111 DOI: 10.1016/j.biotechadv.2019.02.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/10/2019] [Accepted: 02/05/2019] [Indexed: 02/07/2023]
Abstract
Fungi produce an abundance of bioactive secondary metabolites which can be utilized as antibiotics and pharmaceutical drugs. The genes encoding secondary metabolites are contiguously arranged in biosynthetic gene clusters (BGCs), which supports co-regulation of all genes required for any one metabolite. However, an ongoing challenge to harvest this fungal wealth is the finding that many of the BGCs are 'silent' in laboratory settings and lie in heterochromatic regions of the genome. Successful approaches allowing access to these regions - in essence converting the heterochromatin covering BGCs to euchromatin - include use of epigenetic stimulants and genetic manipulation of histone modifying proteins. This review provides a comprehensive look at the chromatin remodeling proteins which have been shown to regulate secondary metabolism, the use of chemical inhibitors used to induce BGCs, and provides future perspectives on expansion of epigenetic tools and concepts to mine the fungal metabolome.
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Affiliation(s)
- Brandon T Pfannenstiel
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Nancy P Keller
- Department of Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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18
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Cao PL, Kumagai N, Inoue T, Agata K, Makino T. JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration. Genome Biol Evol 2019; 11:552-564. [PMID: 30698705 PMCID: PMC6390904 DOI: 10.1093/gbe/evz021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low regeneration group during evolution. Ninety-six percent of them were JmjC domain-encoding genes. We denoted the candidate genes as high regenerative species-specific JmjC domain-encoding genes (HRJDs). We observed losses of HRJDs in Helobdella robusta, which lost its high regeneration ability during evolution based on phylogenetic analysis. By RNA sequencing analyses, we observed that HRJD orthologs were differentially expressed during regeneration in two Cnidarians, as well as Platyhelminthes and Urochordata, which are highly regenerative species. Furthermore, >50% of the head and tail parts of amputated planarians (Dugesia japonica) died during regeneration after RNA interference of HRJD orthologs. These results indicate that HRJD are strongly associated with a high regeneration ability in metazoans. HRJD paralogs regulate gene expression by histone demethylation; thus, HRJD may be related to epigenetic regulation controlling stem cell renewal and stem cell differentiation during regeneration. We propose that HRJD play a central role in epigenetic regulation during regeneration.
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Affiliation(s)
- Ping-Lin Cao
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Nobuyoshi Kumagai
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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19
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Schumacher J, Studt L, Tudzynski P. The putative H3K36 demethylase BcKDM1 affects virulence, stress responses and photomorphogenesis in Botrytis cinerea. Fungal Genet Biol 2019; 123:14-24. [DOI: 10.1016/j.fgb.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/04/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022]
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20
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Lv Y, Lv A, Zhai H, Zhang S, Li L, Cai J, Hu Y. Insight into the global regulation of laeA in Aspergillus flavus based on proteomic profiling. Int J Food Microbiol 2018; 284:11-21. [DOI: 10.1016/j.ijfoodmicro.2018.06.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/15/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
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21
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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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22
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Nie X, Li B, Wang S. Epigenetic and Posttranslational Modifications in Regulating the Biology of Aspergillus Species. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:191-226. [PMID: 30342722 DOI: 10.1016/bs.aambs.2018.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Epigenetic and posttranslational modifications have been proved to participate in multiple cellular processes and suggested to be an important regulatory mechanism on transcription of genes in eukaryotes. However, our knowledge about epigenetic and posttranslational modifications mainly comes from the studies of yeasts, plants, and animals. Recently, epigenetic and posttranslational modifications have also raised concern for the relevance of regulating fungal biology in Aspergillus. Emerging evidence indicates that these modifications could be a connection between genetic elements and environmental factors, and their combined effects may finally lead to fungal phenotypical changes. This article describes the advances in typical DNA and protein modifications in the genus Aspergillus, focusing on methylation, acetylation, phosphorylation, ubiquitination, sumoylation, and neddylation.
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Affiliation(s)
- Xinyi Nie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bowen Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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23
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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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24
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Elucidation of the Two H3K36me3 Histone Methyltransferases Set2 and Ash1 in Fusarium fujikuroi Unravels Their Different Chromosomal Targets and a Major Impact of Ash1 on Genome Stability. Genetics 2017; 208:153-171. [PMID: 29146582 DOI: 10.1534/genetics.117.1119] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/12/2017] [Indexed: 12/31/2022] Open
Abstract
In this work, we present a comprehensive analysis of the H3K36 histone methyltransferases Set2 and Ash1 in the filamentous ascomycete Fusarium fujikuroi In Saccharomyces cerevisiae, one single methyltransferase, Set2, confers all H3K36 methylation, while there are two members of the Set2 family in filamentous fungi, and even more H3K36 methyltransferases in higher eukaryotes. Whereas the yeast Set2 homolog has been analyzed in fungi previously, the second member of the Set2 family, designated Ash1, has not been described for any filamentous fungus. Western blot and ChIP-Seq analyses confirmed that F. fujikuroi Set2 and Ash1 are H3K36-specific histone methyltransferases that deposit H3K36me3 at specific loci: Set2 is most likely responsible for H3K36 methylation of euchromatic regions of the genome, while Ash1 methylates H3K36 at the subtelomeric regions (facultative heterochromatin) of all chromosomes, including the accessory chromosome XII. Our data indicate that H3K36me3 cannot be considered a hallmark of euchromatin in F. fujikuroi, and likely also other filamentous fungi, making them different to what is known about nuclear characteristics in yeast and higher eukaryotes. We suggest that the H3K36 methylation mark exerts specific functions when deposited at euchromatic or subtelomeric regions by Set2 or Ash1, respectively. We found an enhanced level of H3K27me3, an increased instability of subtelomeric regions and losses of the accessory chromosome XII over time in Δash1 mutants, indicating an involvement of Ash1 in DNA repair processes. Further phenotypic analyses revealed a role of H3K36 methylation in vegetative growth, sporulation, secondary metabolite biosynthesis, and virulence in F. fujikuroi.
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25
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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26
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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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27
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Pfannmüller A, Leufken J, Studt L, Michielse CB, Sieber CMK, Güldener U, Hawat S, Hippler M, Fufezan C, Tudzynski B. Comparative transcriptome and proteome analysis reveals a global impact of the nitrogen regulators AreA and AreB on secondary metabolism in Fusarium fujikuroi. PLoS One 2017; 12:e0176194. [PMID: 28441411 PMCID: PMC5404775 DOI: 10.1371/journal.pone.0176194] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/06/2017] [Indexed: 11/18/2022] Open
Abstract
The biosynthesis of multiple secondary metabolites in the phytopathogenic ascomycete Fusarium fujikuroi is strongly affected by nitrogen availability. Here, we present the first genome-wide transcriptome and proteome analysis that compared the wild type and deletion mutants of the two major nitrogen regulators AreA and AreB. We show that AreB acts not simply as an antagonist of AreA counteracting the expression of AreA target genes as suggested based on the yeast model. Both GATA transcription factors affect a large and diverse set of common as well as specific target genes and proteins, acting as activators and repressors. We demonstrate that AreA and AreB are not only involved in fungal nitrogen metabolism, but also in the control of several complex cellular processes like carbon metabolism, transport and secondary metabolism. We show that both GATA transcription factors can be considered as master regulators of secondary metabolism as they affect the expression of more than half of the 47 putative secondary metabolite clusters identified in the genome of F. fujikuroi. While AreA acts as a positive regulator of many clusters under nitrogen-limiting conditions, AreB is able to activate and repress gene clusters (e.g. bikaverin) under nitrogen limitation and sufficiency. In addition, ChIP analyses revealed that loss of AreA or AreB causes histone modifications at some of the regulated gene clusters.
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Affiliation(s)
- Andreas Pfannmüller
- Institute of Biology and Biotechnology of Plants, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Johannes Leufken
- Institute of Biology and Biotechnology of Plants, Computational Biology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Lena Studt
- Institute of Biology and Biotechnology of Plants, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-University Münster, Münster, Germany
- 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
| | - Caroline B. Michielse
- Institute of Biology and Biotechnology of Plants, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Christian M. K. Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Susan Hawat
- Institute of Biology and Biotechnology of Plants, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Michael Hippler
- Institute of Biology and Biotechnology of Plants, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Christian Fufezan
- Institute of Biology and Biotechnology of Plants, Computational Biology, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Bettina Tudzynski
- Institute of Biology and Biotechnology of Plants, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-University Münster, Münster, Germany
- * E-mail:
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28
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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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Rösler SM, Kramer K, Finkemeier I, Humpf HU, Tudzynski B. The SAGA complex in the rice pathogenFusarium fujikuroi: structure and functional characterization. Mol Microbiol 2016; 102:951-974. [DOI: 10.1111/mmi.13528] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah M. Rösler
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster; Corrensstraße 45 Münster 48149 Germany
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
| | - Katharina Kramer
- Max Planck Institute for Plant Breeding Research, Plant Proteomics Group; Carl-von-Linne-Weg 10 Cologne 50829 Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
- Max Planck Institute for Plant Breeding Research, Plant Proteomics Group; Carl-von-Linne-Weg 10 Cologne 50829 Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster; Corrensstraße 45 Münster 48149 Germany
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster; Schlossplatz 7/8 Münster 48143 Germany
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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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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. Mol Microbiol 2015. [PMID: 26213895 DOI: 10.1111/mmi.13125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hedtke M, Rauscher S, Röhrig J, Rodríguez-Romero J, Yu Z, Fischer R. Light-dependent gene activation inAspergillus nidulansis strictly dependent on phytochrome and involves the interplay of phytochrome and white collar-regulated histone H3 acetylation. Mol Microbiol 2015; 97:733-45. [DOI: 10.1111/mmi.13062] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Maren Hedtke
- Department of Microbiology; Karlsruhe Institute of Technology; Institute for Applied Biosciences; Hertzstrasse 16 D-76187 Karlsruhe Germany
| | - Stefan Rauscher
- Department of Microbiology; Karlsruhe Institute of Technology; Institute for Applied Biosciences; Hertzstrasse 16 D-76187 Karlsruhe Germany
| | - Julian Röhrig
- Department of Microbiology; Karlsruhe Institute of Technology; Institute for Applied Biosciences; Hertzstrasse 16 D-76187 Karlsruhe Germany
| | - Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP) U.P.M. - I.N.I.A.; Campus de Montegancedo; Autopista M-40 (Km 38) 28223 Pozuelo de Alarcón, Madrid Spain
| | - Zhenzhong Yu
- Department of Microbiology; Karlsruhe Institute of Technology; Institute for Applied Biosciences; Hertzstrasse 16 D-76187 Karlsruhe Germany
| | - Reinhard Fischer
- Department of Microbiology; Karlsruhe Institute of Technology; Institute for Applied Biosciences; Hertzstrasse 16 D-76187 Karlsruhe Germany
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