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Shao W, Wang J, Zhang Y, Zhang C, Chen J, Chen Y, Fei Z, Ma Z, Sun X, Jiao C. The jet-like chromatin structure defines active secondary metabolism in fungi. Nucleic Acids Res 2024; 52:4906-4921. [PMID: 38407438 PMCID: PMC11109943 DOI: 10.1093/nar/gkae131] [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: 09/06/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.
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Affiliation(s)
- Wenyong Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jingrui Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yueqi Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chaofan Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Jie Chen
- National Joint Engineering Laboratory of Biopesticide Preparation, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Chen Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
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2
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Zhao P, Cao S, Wang J, Lin J, Zhang Y, Liu C, Liu H, Zhang Q, Wang M, Meng Y, Yin X, Qi J, Zhang L, Xia X. Activation of secondary metabolite gene clusters in Chaetomium olivaceum via the deletion of a histone deacetylase. Appl Microbiol Biotechnol 2024; 108:332. [PMID: 38734756 PMCID: PMC11088548 DOI: 10.1007/s00253-024-13173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Histone acetylation modifications in filamentous fungi play a crucial role in epigenetic gene regulation and are closely linked to the transcription of secondary metabolite (SM) biosynthetic gene clusters (BGCs). Histone deacetylases (HDACs) play a pivotal role in determining the extent of histone acetylation modifications and act as triggers for the expression activity of target BGCs. The genus Chaetomium is widely recognized as a rich source of novel and bioactive SMs. Deletion of a class I HDAC gene of Chaetomium olivaceum SD-80A, g7489, induces a substantial pleiotropic effect on the expression of SM BGCs. The C. olivaceum SD-80A ∆g7489 strain exhibited significant changes in morphology, sporulation ability, and secondary metabolic profile, resulting in the emergence of new compound peaks. Notably, three polyketides (A1-A3) and one asterriquinone (A4) were isolated from this mutant strain. Furthermore, our study explored the BGCs of A1-A4, confirming the function of two polyketide synthases (PKSs). Collectively, our findings highlight the promising potential of molecular epigenetic approaches for the elucidation of novel active compounds and their biosynthetic elements in Chaetomium species. This finding holds great significance for the exploration and utilization of Chaetomium resources. KEY POINTS: • Deletion of a class I histone deacetylase activated secondary metabolite gene clusters. • Three polyketides and one asterriquinone were isolated from HDAC deleted strain. • Two different PKSs were reported in C. olivaceum SD-80A.
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Affiliation(s)
- Peipei Zhao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Shengling Cao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jiahui Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jiaying Lin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Yunzeng Zhang
- Department of Thoracic Surgery, Shandong Public Health Clinical Center, Jinan, 250013, Shandong, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Hairong Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Qingqing Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Mengmeng Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Yiwei Meng
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Xin Yin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jun Qi
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Lixin Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Xuekui Xia
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China.
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3
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Wang Y, Fan J, Zhou Z, Goldman GH, Lu L, Zhang Y. Histone acetyltransferase Sas3 contributes to fungal development, cell wall integrity, and virulence in Aspergillus fumigatus. Appl Environ Microbiol 2024; 90:e0188523. [PMID: 38451077 PMCID: PMC11022558 DOI: 10.1128/aem.01885-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Histone acetyltransferase (HAT)-mediated epigenetic modification is essential for diverse cellular processes in eukaryotes. However, the functions of HATs in the human pathogen Aspergillus fumigatus remain poorly understood. In this study, we characterized the functions of MOZ, Ybf2/Sas3, Sas2, and Tip60 (MYST)-family histone acetyltransferase something about silencing (Sas3) in A. fumigatus. Phenotypic analysis revealed that loss of Sas3 results in significant impairments in colony growth, conidiation, and virulence in the Galleria mellonella model. Subcellular localization and Western blot analysis demonstrated that Sas3 localizes to nuclei and is capable of acetylating lysine 9 and 14 of histone H3 in vivo. Importantly, we found that Sas3 is critical for the cell wall integrity (CWI) pathway in A. fumigatus as evidenced by hypersensitivity to cell wall-perturbing agents, altered cell wall thickness, and abnormal phosphorylation levels of CWI protein kinase MpkA. Furthermore, site-directed mutagenesis studies revealed that the conserved glycine residues G641 and G643 and glutamate residue E664 are crucial for the acetylation activity of Sas3. Unexpectedly, only triple mutations of Sas3 (G641A/G643A/E664A) displayed defective phenotypes similar to the Δsas3 mutant, while double or single mutations did not. This result implies that the role of Sas3 may extend beyond histone acetylation. Collectively, our findings demonstrate that MYST-family HAT Sas3 plays an important role in the fungal development, virulence, and cell wall integrity in A. fumigatus. IMPORTANCE Epigenetic modification governed by HATs is indispensable for various cellular processes in eukaryotes. Nonetheless, the precise functions of HATs in the human pathogen Aspergillus fumigatus remain elusive. In this study, we unveil the roles of MYST-family HAT Sas3 in colony growth, conidiation, virulence, and cell wall stress response in A. fumigatus. Particularly, our findings demonstrate that Sas3 can function through mechanisms unrelated to histone acetylation, as evidenced by site-directed mutagenesis experiments. Overall, this study broadens our understanding of the regulatory mechanism of HATs in fungal pathogens.
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Affiliation(s)
- Yamei Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jialu Fan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhengyu Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuanwei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Speckbacher V, Flatschacher D, Martini-Lösch N, Ulbrich L, Baldin C, Bauer I, Ruzsanyi V, Zeilinger S. The histone deacetylase Hda1 affects oxidative and osmotic stress response as well as mycoparasitic activity and secondary metabolite biosynthesis in Trichoderma atroviride. Microbiol Spectr 2024; 12:e0309723. [PMID: 38334386 PMCID: PMC10913545 DOI: 10.1128/spectrum.03097-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
The mycoparasitic fungus Trichoderma atroviride is applied in agriculture as a biostimulant and biologic control agent against fungal pathogens that infest crop plants. Secondary metabolites are among the main agents determining the strength and progress of the mycoparasitic attack. However, expression of most secondary metabolism-associated genes requires specific cues, as they are silent under routine laboratory conditions due to their maintenance in an inactive heterochromatin state. Therefore, histone modifications are crucial for the regulation of secondary metabolism. Here, we functionally investigated the role of the class II histone deacetylase encoding gene hda1 of T. atroviride by targeted gene deletion, phenotypic characterization, and multi-omics approaches. Deletion of hda1 did not result in obvious phenotypic alterations but led to an enhanced inhibitory activity of secreted metabolites and reduced mycoparasitic abilities of T. atroviride against the plant-pathogenic fungi Botrytis cinerea and Rhizoctonia solani. The ∆hda1 mutants emitted altered amounts of four volatile organic compounds along their development, produced different metabolite profiles upon growth in liquid culture, and showed a higher susceptibility to oxidative and osmotic stress. Moreover, hda1 deletion affected the expression of several notable gene categories such as polyketide synthases, transcription factors, and genes involved in the HOG MAPK pathway.IMPORTANCEHistone deacetylases play crucial roles in regulating chromatin structure and gene transcription. To date, classical-Zn2+ dependent-fungal histone deacetylases are divided into two classes, of which each comprises orthologues of the two sub-groups Rpd3 and Hos2 and Hda1 and Hos3 of yeast, respectively. However, the role of these chromatin remodelers in mycoparasitic fungi is poorly understood. In this study, we provide evidence that Hda1, the class II histone deacetylases of the mycoparasitic fungus Trichoderma atroviride, regulates its mycoparasitic activity, secondary metabolite biosynthesis, and osmotic and oxidative stress tolerance. The function of Hda1 in regulating bioactive metabolite production and mycoparasitism reveals the importance of chromatin-dependent regulation in the ability of T. atroviride to successfully control fungal plant pathogens.
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Affiliation(s)
| | | | | | - Laura Ulbrich
- Umweltmonitoring und Forensische Chemie, Hochschule Hamm-Lippstadt, Hamm, Germany
| | - Clara Baldin
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Susanne Zeilinger
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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5
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Bühring S, Brunner A, Heeb K, Mergard MP, Schmauck G, Jacob S. An array of signal-specific MoYpd1 isoforms determines full virulence in the pathogenic fungus Magnaporthe oryzae. Commun Biol 2024; 7:265. [PMID: 38438487 PMCID: PMC10912366 DOI: 10.1038/s42003-024-05941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Magnaporthe oryzae is placed first on a list of the world's top ten plant pathogens with the highest scientific and economic importance. The locus MGG_07173 occurs only once in the genome of M. oryzae and encodes the phosphotransfer protein MoYpd1p, which plays an important role in the high osmolarity glycerol (HOG) signaling pathway for osmoregulation. Originating from this locus, at least three MoYPD1 isoforms are produced in a signal-specific manner. The transcript levels of these MoYPD1-isoforms were individually affected by external stress. Salt (KCI) stress raised MoYPD1_T0 abundance, whereas osmotic stress by sorbitol elevates MoYPD1_T1 levels. In line with this, signal-specific nuclear translocation of green fluorescent protein-fused MoYpd1p isoforms in response to stress was observed. Mutant strains that produce only one of the MoYpd1p isoforms are less virulent, suggesting a combination thereof is required to invade the host successfully. In summary, we demonstrate signal-specific production of MoYpd1p isoforms that individually increase signal diversity and orchestrate virulence in M. oryzae.
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Affiliation(s)
- Sri Bühring
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Antonia Brunner
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Klemens Heeb
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Marius-Peter Mergard
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Greta Schmauck
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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Wei Z, Shu D, Hou X, Li T, Li Z, Luo D, Yang J, Tan H. Normal distribution of H3K9me3 occupancy co-mediated by histone methyltransferase BcDIM5 and histone deacetylase BcHda1 maintains stable ABA synthesis in Botrytis cinerea TB-31. Front Microbiol 2024; 15:1339576. [PMID: 38500582 PMCID: PMC10944950 DOI: 10.3389/fmicb.2024.1339576] [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: 11/21/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024] Open
Abstract
Abscisic acid (ABA) is a conserved and important "sesquiterpene signaling molecule" widely distributed in different organisms with unique biological functions. ABA coordinates reciprocity and competition between microorganisms and their hosts. In addition, ABA also regulates immune and stress responses in plants and animals. Therefore, ABA has a wide range of applications in agriculture, medicine and related fields. The plant pathogenic ascomycete B. cinerea has been extensively studied as a model strain for ABA production. Nevertheless, there is a relative dearth of research regarding the regulatory mechanism governing ABA biosynthesis in B. cinerea. Here, we discovered that H3K9 methyltransferase BcDIM5 is physically associated with the H3K14 deacetylase BcHda1. Deletion of Bcdim5 and Bchda1 in the high ABA-producing B. cinerea TB-31 led to severe impairment of ABA synthesis. The combined analysis of RNA-seq and ChIP-seq has revealed that the absence of BcDIM5 and BcHda1 has resulted in significant global deficiencies in the normal distribution and level of H3K9me3 modification. In addition, we found that the cause of the decreased ABA production in the ΔBcdim5 and ΔBchda1 mutants was due to cluster gene repression caused by the emergence of hyper-H3K9me3 in the ABA gene cluster. We concluded that the ABA gene cluster is co-regulated by BcDIM5 and BcHda1, which are essential for the normal distribution of the B. cinerea TB-31 ABA gene cluster H3K9me3. This work expands our understanding of the complex regulatory network of ABA biosynthesis and provides a theoretical basis for genetic improvement of high-yielding ABA strains.
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Affiliation(s)
- Zhao Wei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dan Shu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaonan Hou
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Tianfu Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhemin Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Di Luo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jie Yang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Xu M, Sun Z, Shi H, Yue J, Xiong X, Wu Z, Kou Y, Tao Z. Two H3K36 methyltransferases differentially associate with transcriptional activity and enrichment of facultative heterochromatin in rice blast fungus. ABIOTECH 2024; 5:1-16. [PMID: 38576437 PMCID: PMC10987451 DOI: 10.1007/s42994-023-00127-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/17/2023] [Indexed: 04/06/2024]
Abstract
Di- and tri-methylation of lysine 36 on histone H3 (H3K36me2/3) is catalysed by histone methyltransferase Set2, which plays an essential role in transcriptional regulation. Although there is a single H3K36 methyltransferase in yeast and higher eukaryotes, two H3K36 methyltransferases, Ash1 and Set2, were present in many filamentous fungi. However, their roles in H3K36 methylation and transcriptional regulation remained unclear. Combined with methods of RNA-seq and ChIP-seq, we revealed that both Ash1 and Set2 are redundantly required for the full H3K36me2/3 activity in Magnaporthe oryzae, which causes the devastating worldwide rice blast disease. Ash1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription, respectively. Furthermore, Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin, and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied genes. With the different roles of Ash1 and Set2, in H3K36me2/3 enrichment and transcriptional regulation on the stress-responsive genes, they differentially respond to various stresses in M. oryzae. Overall, we reveal a novel mechanism by which two H3K36 methyltransferases catalyze H3K36me2/3 that differentially associate with transcriptional activities and contribute to enrichment of facultative heterochromatin in eukaryotes. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00127-3.
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Affiliation(s)
- Mengting Xu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Ziyue Sun
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Huanbin Shi
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310021 China
| | - Jiangnan Yue
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Xiaohui Xiong
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Zhongling Wu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yanjun Kou
- State Key Lab of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310021 China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
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Xue M, Zhao S, Gu G, Xu D, Zhang X, Hou X, Miao J, Dong H, Hu D, Lai D, Zhou L. A Genome-Wide Comparison of Rice False Smut Fungus Villosiclava virens Albino Strain LN02 Reveals the Genetic Diversity of Secondary Metabolites and the Cause of Albinism. Int J Mol Sci 2023; 24:15196. [PMID: 37894876 PMCID: PMC10607355 DOI: 10.3390/ijms242015196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Rice false smut (RFS) caused by Villosiclava virens (anamorph: Ustilaginoidea virens) has become one of the most destructive fungal diseases to decrease the yield and quality of rice grains. An albino strain LN02 was isolated from the white RFS balls collected in the Liaoning Province of China in 2019. The strain LN02 was considered as a natural albino mutant of V. virens by analyzing its phenotypes, internal transcribed spacer (ITS) conserved sequence, and biosynthesis gene clusters (BGCs) for secondary metabolites. The total assembled genome of strain LN02 was 38.81 Mb, which was comprised of seven nuclear chromosomes and one mitochondrial genome with an N50 value of 6,326,845 bp and 9339 protein-encoding genes. In addition, the genome of strain LN02 encoded 19 gene clusters for biosynthesis of secondary metabolites mainly including polyketides, terpenoids and non-ribosomal peptides (NRPs). Four sorbicillinoid metabolites were isolated from the cultures of strain LN02. It was found that the polyketide synthase (PKS)-encoding gene uspks1 for ustilaginoidin biosynthesis in strain LN02 was inactivated due to the deletion of four bases in the promoter sequence of uvpks1. The normal uvpks1 complementary mutant of strain LN02 could restore the ability to synthesize ustilaginoidins. It demonstrated that deficiency of ustilaginoidin biosynthesis is the cause of albinism for RFS albino strain LN02, and V. virens should be a non-melanin-producing fungus. This study further confirmed strain LN02 as a white phenotype mutant of V. virens. The albino strain LN02 will have a great potential in the development and application of secondary metabolites. The physiological and ecological functions of ustilaginoidins in RFS fungus are needed for further investigation.
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Affiliation(s)
- Mengyao Xue
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Siji Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Gan Gu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Dan Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Xuping Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Xuwen Hou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Jiankun Miao
- Institute of Plant Protection, Liaoning Academy of Agricultural Science, Shenyang 110161, China; (J.M.); (H.D.)
| | - Hai Dong
- Institute of Plant Protection, Liaoning Academy of Agricultural Science, Shenyang 110161, China; (J.M.); (H.D.)
| | - Dongwei Hu
- Biotechnology Institute, Zhejiang University, Hangzhou 310058, China;
| | - Daowan Lai
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
| | - Ligang Zhou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (S.Z.); (G.G.); (D.X.); (X.Z.); (X.H.); (D.L.)
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Liu Q, Zheng Y, Liu B, Tang F, Shao Y. Histone deacetylase MrHos3 negatively regulates the production of citrinin and pigments in Monascus ruber. J Basic Microbiol 2023; 63:1128-1138. [PMID: 37236161 DOI: 10.1002/jobm.202300138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
Monascus spp. can produce a variety of beneficial metabolites widely used in food and pharmaceutical industries. However, some Monascus species contain the complete gene cluster responsible for citrinin biosynthesis, which raises our concerns about the safety of their fermented products. In this study, the gene Mrhos3, encoding histone deacetylase (HDAC), was deleted to evaluate its effects on the production of mycotoxin (citrinin) and the edible pigments as well as the developmental process of Monascus ruber M7. The results showed that absence of Mrhos3 caused an enhancement of citrinin content by 105.1%, 82.4%, 111.9%, and 95.7% at the 5th, 7th, 9th, and 11th day, respectively. Furthermore, deletion of Mrhos3 increased the relative expression of citrinin biosynthetic pathway genes including pksCT, mrl1, mrl2, mrl4, mrl6, and mrl7. In addition, deletion of Mrhos3 led to an increase in total pigment content and six classic pigment components. Western blot results revealed that deletion of Mrhos3 could significantly elevate the acetylation level of H3K9, H4K12, H3K18, and total protein. This study provides an important insight into the effects of hos3 gene on the secondary metabolites production in filamentous fungi.
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Affiliation(s)
- Qianrui Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunfan Zheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Baixue Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fufang Tang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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Chen A, Zhou Y, Ren Y, Liu C, Han X, Wang J, Ma Z, Chen Y. Ubiquitination of acetyltransferase Gcn5 contributes to fungal virulence in Fusarium graminearum. mBio 2023; 14:e0149923. [PMID: 37504517 PMCID: PMC10470610 DOI: 10.1128/mbio.01499-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023] Open
Abstract
The histone acetyltransferase general control non-depressible 5 (Gcn5) plays a critical role in the epigenetic landscape and chromatin modification for regulating a wide variety of biological events. However, the post-translational regulation of Gcn5 itself is poorly understood. Here, we found that Gcn5 was ubiquitinated and deubiquitinated by E3 ligase Tom1 and deubiquitinating enzyme Ubp14, respectively, in the important plant pathogenic fungus Fusarium graminearum. Tom1 interacted with Gcn5 in the nucleus and subsequently ubiquitinated Gcn5 mainly at K252 to accelerate protein degradation. Conversely, Ubp14 deubiquitinated Gcn5 and enhanced its stability. In the deletion mutant Δubp14, protein level of Gcn5 was significantly reduced and resulted in attenuated virulence in the fungus by affecting the mycotoxin production, autophagy process, and the penetration ability. Our findings indicate that Tom1 and Ubp14 show antagonistic functions in the control of the protein stability of Gcn5 via post-translational modification and highlight the importance of Tom1-Gcn5-Ubp14 circuit in the fungal virulence. IMPORTANCE Post-translational modification (PTM) enzymes have been reported to be involved in regulating numerous cellular processes. However, the modification of these PTM enzymes themselves is largely unknown. In this study, we found that the E3 ligase Tom1 and deubiquitinating enzyme Ubp14 contributed to the regulation of ubiquitination and deubiquitination of acetyltransferase Gcn5, respectively, in Fusarium graminearum, the causal agent of Fusarium head blight of cereals. Our findings provide deep insights into the modification of acetyltransferase Gcn5 and its dynamic regulation via ubiquitination and deubiquitination. To our knowledge, this work is the most comprehensive analysis of a regulatory network of ubiquitination that impinges on acetyltransferase in filamentous pathogens. Moreover, our findings are important because we present the novel roles of the Tom1-Gcn5-Ubp14 circuit in fungal virulence, providing novel possibilities and targets to control fungal diseases.
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Affiliation(s)
- Ahai Chen
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yifan Zhou
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiyi Ren
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xingmin Han
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jing Wang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Liu R, Chen X, Zhao F, Jiang Y, Lu Z, Ji H, Feng Y, Li J, Zhang H, Zheng J, Zhang J, Zhao Y. The COMPASS Complex Regulates Fungal Development and Virulence through Histone Crosstalk in the Fungal Pathogen Cryptococcus neoformans. J Fungi (Basel) 2023; 9:672. [PMID: 37367608 DOI: 10.3390/jof9060672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Complex of Proteins Associated with Set1 (COMPASS) methylates lysine K4 on histone H3 (H3K4) and is conserved from yeast to humans. Its subunits and regulatory roles in the meningitis-causing fungal pathogen Cryptococcus neoformans remain unknown. Here we identified the core subunits of the COMPASS complex in C. neoformans and C. deneoformans and confirmed their conserved roles in H3K4 methylation. Through AlphaFold modeling, we found that Set1, Bre2, Swd1, and Swd3 form the catalytic core of the COMPASS complex and regulate the cryptococcal yeast-to-hypha transition, thermal tolerance, and virulence. The COMPASS complex-mediated histone H3K4 methylation requires H2B mono-ubiquitination by Rad6/Bre1 and the Paf1 complex in order to activate the expression of genes specific for the yeast-to-hypha transition in C. deneoformans. Taken together, our findings demonstrate that putative COMPASS subunits function as a unified complex, contributing to cryptococcal development and virulence.
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Affiliation(s)
- Ruoyan Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoyu Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fujie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixuan Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhenguo Lu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Heng Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
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Navarrete B, Ibeas JI, Barrales RR. Systematic characterization of Ustilago maydis sirtuins shows Sir2 as a modulator of pathogenic gene expression. Front Microbiol 2023; 14:1157990. [PMID: 37113216 PMCID: PMC10126416 DOI: 10.3389/fmicb.2023.1157990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 04/29/2023] Open
Abstract
Phytopathogenic fungi must adapt to the different environmental conditions found during infection and avoid the immune response of the plant. For these adaptations, fungi must tightly control gene expression, allowing sequential changes in transcriptional programs. In addition to transcription factors, chromatin modification is used by eukaryotic cells as a different layer of transcriptional control. Specifically, the acetylation of histones is one of the chromatin modifications with a strong impact on gene expression. Hyperacetylated regions usually correlate with high transcription and hypoacetylated areas with low transcription. Thus, histone deacetylases (HDACs) commonly act as repressors of transcription. One member of the family of HDACs is represented by sirtuins, which are deacetylases dependent on NAD+, and, thus, their activity is considered to be related to the physiological stage of the cells. This property makes sirtuins good regulators during environmental changes. However, only a few examples exist, and with differences in the extent of the implication of the role of sirtuins during fungal phytopathogenesis. In this work, we have performed a systematic study of sirtuins in the maize pathogen Ustilago maydis, finding Sir2 to be involved in the dimorphic switch from yeast cell to filament and pathogenic development. Specifically, the deletion of sir2 promotes filamentation, whereas its overexpression highly reduces tumor formation in the plant. Moreover, transcriptomic analysis revealed that Sir2 represses genes that are expressed during biotrophism development. Interestingly, our results suggest that this repressive effect is not through histone deacetylation, indicating a different target of Sir2 in this fungus.
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