1
|
Clairet C, Gay EJ, Porquier A, Blaise F, Marais CL, Balesdent MH, Rouxel T, Soyer JL, Fudal I. Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-player game. THE NEW PHYTOLOGIST 2024; 242:247-261. [PMID: 38358035 DOI: 10.1111/nph.19581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Effector genes, encoding molecules involved in disease establishment, are concertedly expressed throughout the lifecycle of plant-pathogenic fungi. However, little is known about how effector gene expression is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in their regulation was recently investigated, notably establishing that the repressive histone modification H3K9me3, deposited by KMT1, was involved in several fungal species including Leptosphaeria maculans. Nevertheless, previous data suggest that a second regulatory layer, probably involving a specific transcription factor (TF), might be required. In L. maculans, a Dothideomycete causing stem canker of oilseed rape, we identified the ortholog of Pf2, a TF belonging to the Zn2Cys6 fungal-specific family, and described as essential for pathogenicity and effector gene expression. We investigated its role together with KMT1, by inactivating and over-expressing LmPf2 in a wild-type strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis and we found a major effect of LmPf2 on the induction of effector gene expression once KMT1 repression is lifted. Our results show, for the first time, a dual control of effector gene expression.
Collapse
Affiliation(s)
- Colin Clairet
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Antoine Porquier
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| |
Collapse
|
2
|
Nishitani A, Hiramatsu K, Kadooka C, Mori K, Okutsu K, Yoshizaki Y, Takamine K, Tashiro K, Goto M, Tamaki H, Futagami T. Expression of heterochromatin protein 1 affects citric acid production in Aspergillus luchuensis mut. kawachii. J Biosci Bioeng 2023; 136:443-451. [PMID: 37775438 DOI: 10.1016/j.jbiosc.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
A putative methyltransferase, LaeA, controls citric acid production through epigenetic regulation of the citrate exporter gene, cexA, in the white koji fungus Aspergillus luchuensis mut. kawachii. In this study, we investigated the role of another epigenetic regulator, heterochromatin protein 1, HepA, in citric acid production. The ΔhepA strain exhibited reduced citric acid production in liquid culture, although to a lesser extent compared to the ΔlaeA strain. In addition, the ΔlaeA ΔhepA strain showed citric acid production similar to the ΔlaeA strain, indicating that HepA plays a role in citric acid production, albeit with a less-significant regulatory effect than LaeA. RNA-seq analysis revealed that the transcriptomic profiles of the ΔhepA and ΔlaeA strains were similar, and the expression level of cexA was reduced in both strains. These findings suggest that the genes regulated by HepA are similar to those regulated by LaeA in A. luchuensis mut. kawachii. However, the reductions in citric acid production and cexA expression observed in the disruptants were mitigated in rice koji, a solid-state culture. Thus, the mechanism by which citric acid production is regulated differs between liquid and solid cultivation. Further investigation is thus needed to understand the regulatory mechanism in koji.
Collapse
Affiliation(s)
- Atsushi Nishitani
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Center for Advanced Science Research and Promotion, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kentaro Hiramatsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto 860-0082, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kayu Okutsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Kagoshima 890-0065, Japan; Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| |
Collapse
|
3
|
Hao L, Zhang M, Yang C, Pan X, Wu D, Lin H, Ma D, Yao Y, Fu W, Chang J, Yang Y, Zhuang Z. The epigenetic regulator Set9 harmonizes fungal development, secondary metabolism, and colonization capacity of Aspergillus flavus. Int J Food Microbiol 2023; 403:110298. [PMID: 37392609 DOI: 10.1016/j.ijfoodmicro.2023.110298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/17/2023] [Accepted: 06/18/2023] [Indexed: 07/03/2023]
Abstract
As a widely distributed food-borne pathogenic fungus, Aspergillus flavus and its secondary metabolites, mainly aflatoxin B1 (AFB1), pose a great danger to humans. It is urgent to reveal the complex regulatory network of toxigenic and virulence of this fungus. The bio-function of Set9, a SET-domain-containing histone methyltransferase, is still unknown in A. flavus. By genetic engineering means, this study revealed that, through catalyzing H4K20me2 and -me3, Set9 is involved in fungal growth, reproduction, and mycotoxin production via the orthodox regulation pathway, and regulates fungal colonization on crop kernels through adjusting fungal sensitivity reactions to oxidation stress and cell wall integrity stress. Further domain deletion and point mutation inferred that the SET domain is the core element in catalyzing H4K20 methylation, and D200 site of the domain is the key amino acid in the active center of the methyltransferase. Combined with RNA-seq analysis, this study revealed that Set9 regulates the aflatoxin gene cluster by the AflR-like protein (ALP), other than traditional AflR. This study revealed the epigenetic regulation mechanism of fungal morphogenesis, secondary metabolism, and pathogenicity of A. flavus mediated by the H4K20-methyltransferase Set9, which might provide a potential new target for early prevention of contamination of A. flavus and its deadly mycotoxins.
Collapse
Affiliation(s)
- Ling Hao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengjuan Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Key Laboratory of Propagated Sensation along Meridian, Fujian Academy of Chinese Medical Sciences, Fuzhou 350003, China
| | - Dandan Wu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Ma
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanfang Yao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wangzhuo Fu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiarui Chang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanling Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
4
|
Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
Collapse
Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| |
Collapse
|
5
|
Zuo H, Ji L, Pan J, Chen X, Gao C, Liu J, Wei W, Wu J, Song W, Liu L. Engineering growth phenotypes of Aspergillus oryzae for L-malate production. BIORESOUR BIOPROCESS 2023; 10:25. [PMID: 38647943 PMCID: PMC10991988 DOI: 10.1186/s40643-023-00642-7] [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: 12/24/2022] [Accepted: 03/09/2023] [Indexed: 04/09/2023] Open
Abstract
Improving the growth status of Aspergillus oryzae is an efficient way to enhance L-malate production. However, the growth mechanism of filamentous fungi is relatively complex, which limits A. oryzae as a cell factory to produce L-malate industrially. This study determined the relationship between growth status and L-malate production. The optimal ranges of colony diameter, percentage of vegetative mycelia, and pellet number of A. oryzae were determined to be 26-30 mm, 35-40%, and 220-240/mL, respectively. To achieve this optimum range, adaptive evolution was used to obtain the evolved strain Z07 with 132.54 g/L L-malate and a productivity of 1.1 g/L/h. Finally, a combination of transcriptome analysis and morphological characterization was used to identify the relevant pathway genes that affect the growth mechanism of A. oryzae. The strategies used in this study and the growth mechanism provide a good basis for efficient L-malate production by filamentous fungi.
Collapse
Affiliation(s)
- Huiyun Zuo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Lihao Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jingyu Pan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Effect of Water Activity on Conidia Germination in Aspergillus flavus. Microorganisms 2022; 10:microorganisms10091744. [PMID: 36144346 PMCID: PMC9504883 DOI: 10.3390/microorganisms10091744] [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: 07/25/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we explored the mechanism underlying Aspergillus flavus conidia germination inhibited by decreased water activity. The impact of low water activity was analyzed at 4 h, 8 h and 12 h. Additionally, we demonstrated that low water activity affected cell shape and decreased cell sizes. Transcriptomics found numerous differentially expressed genes (DEGs) during the first 12 h of germination, with 654 DEGs observed among 4 h, 8 h and 12 h. In particular, more DEGs were detected at 8 h of germinating. Therefore, proteomics was performed at 8 h, and 209 differentially expressed proteins (DEPs) were speculated, with 94 up-regulated and 115 down-regulated. Combined analysis of KEGG of transcriptomics and proteomics demonstrated that the dominant pathways were nutrient metabolism and translation. We also found several DEGs and DEPs in the Mitogen Activated Protein Kinase (MAPK) pathway. Therefore, we concluded that low water activity inhibited conidia germination, causing unregular morphology. In addition, low water activity influenced expression of creA, TreB in carbohydrate metabolism, Clr4, RmtA in amino acid metabolism and RPL37, RPL3 in translation in Aspergillus flavus.
Collapse
|
8
|
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.
Collapse
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,
| |
Collapse
|
9
|
Yaseen I, White SA, Torres-Garcia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M, Rappsilber J, Pidoux AL, Allshire RC. Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance. Nat Struct Mol Biol 2022; 29:745-758. [PMID: 35879419 PMCID: PMC7613290 DOI: 10.1038/s41594-022-00801-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/06/2022] [Indexed: 12/03/2022]
Abstract
Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism by which Epe1 is regulated in response to stress. Exposure to caffeine or antifungals results in Epe1 ubiquitylation and proteasome-dependent removal of the N-terminal 150 residues from Epe1, generating truncated Epe1 (tEpe1) which accumulates in the cytoplasm. Constitutive tEpe1 expression increases H3K9 methylation over several chromosomal regions, reducing expression of underlying genes and enhancing resistance. Reciprocally, constitutive non-cleavable Epe1 expression decreases resistance. tEpe1-mediated resistance requires a functional JmjC demethylase domain. Moreover, caffeine-induced Epe1-to-tEpe1 cleavage is dependent on an intact cell integrity MAP kinase stress signaling pathway, mutations in which alter resistance. Thus, environmental changes elicit a mechanism that curtails the function of this key epigenetic modifier, allowing heterochromatin to reprogram gene expression, thereby bestowing resistance to some cells within a population. H3K9me-heterochromatin components are conserved in human and crop-plant fungal pathogens for which a limited number of antifungals exist. Our findings reveal how transient heterochromatin-dependent antifungal resistant epimutations develop and thus inform on how they might be countered.
Collapse
Affiliation(s)
- Imtiyaz Yaseen
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- CSIR Indian Institute of Integrative Medicine, Jammu, India
| | - Sharon A White
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sito Torres-Garcia
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Marcel Lafos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Elisabeth Gaberdiel
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rebecca Yeboah
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Meriem El Karoui
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
10
|
Meng S, Huang S, Liu J, Gai Y, Li M, Duan S, Zhang S, Sun X, Yang Q, Wang Y, Xu K, Ma H. Histone Methylation Is Required for Virulence, Conidiation, and Multi-Stress Resistance of Alternaria alternata. Front Microbiol 2022; 13:924476. [PMID: 35783406 PMCID: PMC9245015 DOI: 10.3389/fmicb.2022.924476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Histone methylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs). This study determined the function of 5 HMTs (AaDot1, AaHMT1, AaHnrnp, AaSet1, and AaSet2) and 1 HDMs (AaGhd2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. The vegetative growth, conidiation, and pathogenicity of ∆AaSet1 and ∆AaSet2 were severely inhibited indicating that AaSet1 and AaSet2 play critical roles in cell development in A. alternata. Multiple stresses analysis revealed that both AaSet1 and AaSet2 were involved in the adaptation to cell wall interference agents and osmotic stress. Meanwhile, ∆AaSet1 and ∆AaSet2 displayed serious vegetative growth defects in sole carbon source medium, indicating that AaSet1 and AaSet2 play an important role in carbon source utilization. In addition, ∆AaSet2 colony displayed white in color, while the wild-type colony was dark brown, indicating AaSet2 is an essential gene for melanin biosynthesis in A. alternata. AaSet2 was required for the resistance to oxidative stress. On the other hand, all of ∆AaDot1, ∆AaHMT1, and ∆AaGhd2 mutants displayed wild-type phenotype in vegetative growth, multi-stress resistance, pathogenicity, carbon source utilization, and melanin biosynthesis. To explore the regulatory mechanism of AaSet1 and AaSet2, RNA-seq of these mutants and wild-type strain was performed. Phenotypes mentioned above correlated well with the differentially expressed genes in ∆AaSet1 and ∆AaSet2 according to the KEGG and GO enrichment results. Overall, our study provides genetic evidence that defines the central role of HMTs and HDMs in the pathological and biological functions of A. alternata.
Collapse
Affiliation(s)
- Shuai Meng
- 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, China
| | - Suya Huang
- 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, China
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co., LTD, Hangzhou, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuting Zhang
- 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, 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, China
| | - Qi Yang
- Linyi Inspection and Testing Center, Linyi, China
| | - Yuchun Wang
- 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, China
| | - Kai Xu
- 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, China
| | - Haijie Ma
- 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, China
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Margalit A, Sheehan D, Carolan JC, Kavanagh K. Exposure to the Pseudomonas aeruginosa secretome alters the proteome and secondary metabolite production of Aspergillus fumigatus. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001164. [PMID: 35333152 PMCID: PMC9558348 DOI: 10.1099/mic.0.001164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/16/2022] [Indexed: 01/09/2023]
Abstract
The fungal pathogen Aspergillus fumigatus is frequently cultured from the sputum of cystic fibrosis (CF) patients along with the bacterium Pseudomonas aeruginosa. A. fumigatus secretes a range of secondary metabolites, and one of these, gliotoxin, has inhibitory effects on the host immune response. The effect of P. aeruginosa culture filtrate (CuF) on fungal growth and gliotoxin production was investigated. Exposure of A. fumigatus hyphae to P. aeruginosa cells induced increased production of gliotoxin and a decrease in fungal growth. In contrast, exposure of A. fumigatus hyphae to P. aeruginosa CuF led to increased growth and decreased gliotoxin production. Quantitative proteomic analysis was used to characterize the proteomic response of A. fumigatus upon exposure to P. aeruginosa CuF. Changes in the profile of proteins involved in secondary metabolite biosynthesis (e.g. gliotoxin, fumagillin, pseurotin A), and changes to the abundance of proteins involved in oxidative stress (e.g. formate dehydrogenase) and detoxification (e.g. thioredoxin reductase) were observed, indicating that the bacterial secretome had a profound effect on the fungal proteome. Alterations in the abundance of proteins involved in detoxification and oxidative stress highlight the ability of A. fumigatus to differentially regulate protein synthesis in response to environmental stresses imposed by competitors such as P. aeruginosa. Such responses may ultimately have serious detrimental effects on the host.
Collapse
Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - David Sheehan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - James C. Carolan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| |
Collapse
|
13
|
Colabardini AC, Wang F, Miao Z, Pardeshi L, Valero C, de Castro PA, Akiyama DY, Tan K, Nora LC, Silva-Rocha R, Marcet-Houben M, Gabaldón T, Fill T, Wong KH, Goldman GH. Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genet 2022; 18:e1010001. [PMID: 35007279 PMCID: PMC8782537 DOI: 10.1371/journal.pgen.1010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/21/2022] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Invasive Pulmonary Aspergillosis, which is caused by the filamentous fungus Aspergillus fumigatus, is a life-threatening infection for immunosuppressed patients. Chromatin structure regulation is important for genome stability maintenance and has the potential to drive genome rearrangements and affect virulence and pathogenesis of pathogens. Here, we performed the first A. fumigatus global chromatin profiling of two histone modifications, H3K4me3 and H3K9me3, focusing on the two most investigated A. fumigatus clinical isolates, Af293 and CEA17. In eukaryotes, H3K4me3 is associated with active transcription, while H3K9me3 often marks silent genes, DNA repeats, and transposons. We found that H3K4me3 deposition is similar between the two isolates, while H3K9me3 is more variable and does not always represent transcriptional silencing. Our work uncovered striking differences in the number, locations, and expression of transposable elements between Af293 and CEA17, and the differences are correlated with H3K9me3 modifications and higher genomic variations among strains of Af293 background. Moreover, we further showed that the Af293 strains from different laboratories actually differ in their genome contents and found a frequently lost region in chromosome VIII. For one such Af293 variant, we identified the chromosomal changes and demonstrated their impacts on its secondary metabolites production, growth and virulence. Overall, our findings not only emphasize the influence of genome heterogeneity on A. fumigatus fitness, but also caution about unnoticed chromosomal variations among common laboratory strains.
Collapse
Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Yuri Akiyama
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Luisa Czamanski Nora
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Silva-Rocha
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR of China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR of China
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
14
|
Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021. [PMID: 34728591 PMCID: PMC8550911 DOI: 10.1007/s12038-021-00215-w] [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] [Indexed: 10/31/2022]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
Collapse
|
15
|
Atanasoff-Kardjalieff AK, Lünne F, Kalinina S, Strauss J, Humpf HU, Studt L. Biosynthesis of Fusapyrone Depends on the H3K9 Methyltransferase, FmKmt1, in Fusarium mangiferae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:671796. [PMID: 37744112 PMCID: PMC10512364 DOI: 10.3389/ffunb.2021.671796] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/09/2021] [Indexed: 09/26/2023]
Abstract
The phytopathogenic fungus Fusarium mangiferae belongs to the Fusarium fujikuroi species complex (FFSC). Members of this group cause a wide spectrum of devastating diseases on diverse agricultural crops. F. mangiferae is the causal agent of the mango malformation disease (MMD) and as such detrimental for agriculture in the southern hemisphere. During plant infection, the fungus produces a plethora of bioactive secondary metabolites (SMs), which most often lead to severe adverse defects on plants health. Changes in chromatin structure achieved by posttranslational modifications (PTM) of histones play a key role in regulation of fungal SM biosynthesis. Posttranslational tri-methylation of histone 3 lysine 9 (H3K9me3) is considered a hallmark of heterochromatin and established by the SET-domain protein Kmt1. Here, we show that FmKmt1 is involved in H3K9me3 in F. mangiferae. Loss of FmKmt1 only slightly though significantly affected fungal hyphal growth and stress response and is required for wild type-like conidiation. While FmKmt1 is largely dispensable for the biosynthesis of most known SMs, removal of FmKMT1 resulted in an almost complete loss of fusapyrone and deoxyfusapyrone, γ-pyrones previously only known from Fusarium semitectum. Here, we identified the polyketide synthase (PKS) FmPKS40 to be involved in fusapyrone biosynthesis, delineate putative cluster borders by co-expression studies and provide insights into its regulation.
Collapse
Affiliation(s)
- Anna K. Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Friederike Lünne
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Svetlana Kalinina
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| |
Collapse
|
16
|
Carlier F, Li M, Maroc L, Debuchy R, Souaid C, Noordermeer D, Grognet P, Malagnac F. Loss of EZH2-like or SU(VAR)3-9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina. Epigenetics Chromatin 2021; 14:22. [PMID: 33962663 PMCID: PMC8105982 DOI: 10.1186/s13072-021-00395-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Selective gene silencing is key to development. It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. Conversely, H3K9me3-enriched heterochromatin prevents differentiation but constitutes protection against transposable elements. We exploited the fungus Podospora anserina, a valuable alternative to higher eukaryote models, to question the biological relevance and functional interplay of these two distinct heterochromatin conformations. RESULTS We established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. Indeed, removal of the PaKmt6 EZH2-like enzyme resulted not only in loss of H3K27me3 but also in significant H3K9me3 reduction. Similarly, removal of PaKmt1 SU(VAR)3-9-like enzyme caused loss of H3K9me3 and substantial decrease of H3K27me3. Removal of the H3K9me binding protein PaHP1 provided further support to the notion that each type of heterochromatin requires the presence of the other. We also established that P. anserina developmental programs require H3K27me3-mediated silencing, since loss of the PaKmt6 EZH2-like enzyme caused severe defects in most aspects of the life cycle including growth, differentiation processes and sexual reproduction, whereas loss of the PaKmt1 SU(VAR)3-9-like enzyme resulted only in marginal defects, similar to loss of PaHP1. CONCLUSIONS Our findings support a conserved function of the PRC2 complex in fungal development. However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin.
Collapse
Affiliation(s)
- F Carlier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris, France
| | - M Li
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - L Maroc
- Génétique Quantitative et Évolution-Le Moulon, INRA-Université Paris-Saclay-CNRS-AgroParisTech, Batiment 400, UFR Des Sciences, 91405, Orsay CEDEX, France
| | - R Debuchy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - C Souaid
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, Aix-Marseille University, 13288, Marseille, France
| | - D Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - P Grognet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - F Malagnac
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| |
Collapse
|
17
|
Retanal C, Ball B, Geddes-McAlister J. Post-Translational Modifications Drive Success and Failure of Fungal-Host Interactions. J Fungi (Basel) 2021; 7:jof7020124. [PMID: 33572187 PMCID: PMC7914884 DOI: 10.3390/jof7020124] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) change the structure and function of proteins and regulate a diverse array of biological processes. Fungal pathogens rely on PTMs to modulate protein production and activity during infection, manipulate the host response, and ultimately, promote fungal survival. Given the high mortality rates of fungal infections on a global scale, along with the emergence of antifungal-resistant species, identifying new treatment options is critical. In this review, we focus on the role of PTMs (e.g., phosphorylation, acetylation, ubiquitination, glycosylation, and methylation) among the highly prevalent and medically relevant fungal pathogens, Candida spp., Aspergillus spp., and Cryptococcus spp. We explore the role of PTMs in fungal stress response and host adaptation, the use of PTMs to manipulate host cells and the immune system upon fungal invasion, and the importance of PTMs in conferring antifungal resistance. We also provide a critical view on the current knowledgebase, pose questions key to our understanding of the intricate roles of PTMs within fungal pathogens, and provide research opportunities to uncover new therapeutic strategies.
Collapse
|
18
|
Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021; 46:94. [PMID: 34728591 PMCID: PMC8550911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
Collapse
Affiliation(s)
- Ramisetti Rajeev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ambey Prasad Dwivedi
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anunay Sinha
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.502122.60000 0004 1774 5631Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Viplove Agarwaal
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Rachana Roshan Dev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Anjana Kar
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sanjeev Khosla
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.417641.10000 0004 0504 3165Institute of Microbial Technology (IMTech), Chandigarh, India
| |
Collapse
|
19
|
Lukito Y, Lee K, Noorifar N, Green KA, Winter DJ, Ram A, Hale TK, Chujo T, Cox MP, Johnson LJ, Scott B. Regulation of host-infection ability in the grass-symbiotic fungus Epichloë festucae by histone H3K9 and H3K36 methyltransferases. Environ Microbiol 2020; 23:2116-2131. [PMID: 33350014 DOI: 10.1111/1462-2920.15370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/02/2020] [Accepted: 12/19/2020] [Indexed: 01/30/2023]
Abstract
Recent studies have identified key genes that control the symbiotic interaction between Epichloë festucae and Lolium perenne. Here we report on the identification of specific E. festucae genes that control host infection. Deletion of setB, which encodes a homologue of the H3K36 histone methyltransferase Set2/KMT3, reduced histone H3K36 trimethylation and led to severe defects in colony growth and hyphal development. The E. festucae ΔclrD mutant, which lacks the gene encoding the homologue of the H3K9 methyltransferase KMT1, displays similar developmental defects. Both mutants are completely defective in their ability to infect L. perenne. Alleles that complement the culture and plant phenotypes of both mutants also complement the histone methylation defects. Co-inoculation of either ΔsetB or ΔclrD with the wild-type strain enables these mutants to colonize the host. However, successful colonization by the mutants resulted in death or stunting of the host plant. Transcriptome analysis at the early infection stage identified four fungal candidate genes, three of which encode small-secreted proteins, that are differentially regulated in these mutants compared to wild type. Deletion of crbA, which encodes a putative carbohydrate binding protein, resulted in significantly reduced host infection rates by E. festucae.
Collapse
Affiliation(s)
- Yonathan Lukito
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Kate Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Nazanin Noorifar
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Kimberly A Green
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - David J Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Arvina Ram
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tracy K Hale
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tetsuya Chujo
- Research and Development Center, Mayekawa Mfg. Co., Ltd, Tokyo, Japan
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Linda J Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| |
Collapse
|
20
|
Liu Y, Xin J, Liu L, Song A, Liao Y, Guan Z, Fang W, Chen F. Ubiquitin E3 Ligase AaBre1 Responsible for H2B Monoubiquitination Is Involved in Hyphal Growth, Conidiation and Pathogenicity in Alternaria alternata. Genes (Basel) 2020; 11:genes11020229. [PMID: 32098172 PMCID: PMC7074354 DOI: 10.3390/genes11020229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 11/16/2022] Open
Abstract
Ubiquitination is one of several post-transcriptional modifications of histone 2B (H2B) which affect the chromatin structure and, hence, influence gene transcription. This study focuses on Alternaria alternata, a fungal pathogen responsible for leaf spot in many plant species. The experiments show that the product of AaBRE1, a gene which encodes H2B monoubiquitination E3 ligase, regulates hyphal growth, conidial formation and pathogenicity. Knockout of AaBRE1 by the homologous recombination strategy leads to the loss of H2B monoubiquitination (H2Bub1), as well as a remarkable decrease in the enrichment of trimethylated lysine 4 on histone 3 (H3K4me3). RNA sequencing assays elucidated that the transcription of genes encoding certain C2H2 zinc-finger family transcription factors, cell wall-degrading enzymes and chitin-binding proteins was suppressed in the AaBRE1 knockout cells. GO enrichment analysis showed that these proteins encoded by the set of genes differentially transcribed between the deletion mutant and wild type were enriched in the functional categories “macramolecular complex”, “cellular metabolic process”, etc. A major conclusion was that the AaBRE1 product, through its effect on histone 2B monoubiquitination and histone 3 lysine 4 trimethylation, makes an important contribution to the fungus’s hyphal growth, conidial formation and pathogenicity.
Collapse
|
21
|
Chronic Mild Stress Modified Epigenetic Mechanisms Leading to Accelerated Senescence and Impaired Cognitive Performance in Mice. Int J Mol Sci 2020; 21:ijms21031154. [PMID: 32050516 PMCID: PMC7037343 DOI: 10.3390/ijms21031154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cognitive and behavioural disturbances are a growing public healthcare issue for the modern society, as stressful lifestyle is becoming more and more common. Besides, several pieces of evidence state that environment is crucial in the development of several diseases as well as compromising healthy aging. Therefore, it is important to study the effects of stress on cognition and its relationship with aging. To address these queries, Chronic Mild Stress (CMS) paradigm was used in the senescence-accelerated mouse prone 8 (SAMP8) and resistant 1 (SAMR1). On one hand, we determined the changes produced in the three main epigenetic marks after 4 weeks of CMS treatment, such as a reduction in histone posttranslational modifications and DNA methylation, and up-regulation or down-regulation of several miRNA involved in different cellular processes in mice. In addition, CMS treatment induced reactive oxygen species (ROS) damage accumulation and loss of antioxidant defence mechanisms, as well as inflammatory signalling activation through NF-κB pathway and astrogliosis markers, like Gfap. Remarkably, CMS altered mTORC1 signalling in both strains, decreasing autophagy only in SAMR1 mice. We found a decrease in glycogen synthase kinase 3 β (GSK-3β) inactivation, hyperphosphorylation of Tau and an increase in sAPPβ protein levels in mice under CMS. Moreover, reduction in the non-amyloidogenic secretase ADAM10 protein levels was found in SAMR1 CMS group. Consequently, detrimental effects on behaviour and cognitive performance were detected in CMS treated mice, affecting mainly SAMR1 mice, promoting a turning to SAMP8 phenotype. In conclusion, CMS is a feasible intervention to understand the influence of stress on epigenetic mechanisms underlying cognition and accelerating senescence.
Collapse
|
22
|
Buscaino A. Chromatin-Mediated Regulation of Genome Plasticity in Human Fungal Pathogens. Genes (Basel) 2019; 10:E855. [PMID: 31661931 PMCID: PMC6896017 DOI: 10.3390/genes10110855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 12/20/2022] Open
Abstract
Human fungal pathogens, such as Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, are a public health problem, causing millions of infections and killing almost half a million people annually. The ability of these pathogens to colonise almost every organ in the human body and cause life-threating infections relies on their capacity to adapt and thrive in diverse hostile host-niche environments. Stress-induced genome instability is a key adaptive strategy used by human fungal pathogens as it increases genetic diversity, thereby allowing selection of genotype(s) better adapted to a new environment. Heterochromatin represses gene expression and deleterious recombination and could play a key role in modulating genome stability in response to environmental changes. However, very little is known about heterochromatin structure and function in human fungal pathogens. In this review, I use our knowledge of heterochromatin structure and function in fungal model systems as a road map to review the role of heterochromatin in regulating genome plasticity in the most common human fungal pathogens: Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans.
Collapse
Affiliation(s)
- Alessia Buscaino
- University of Kent, School of Biosciences, Kent Fungal Group, Canterbury Kent CT2 7NJ, UK.
| |
Collapse
|
23
|
GPCR-mediated glucose sensing system regulates light-dependent fungal development and mycotoxin production. PLoS Genet 2019; 15:e1008419. [PMID: 31609971 PMCID: PMC6812930 DOI: 10.1371/journal.pgen.1008419] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 10/24/2019] [Accepted: 09/13/2019] [Indexed: 01/09/2023] Open
Abstract
Microorganisms sense environmental fluctuations in nutrients and light, coordinating their growth and development accordingly. Despite their critical roles in fungi, only a few G-protein coupled receptors (GPCRs) have been characterized. The Aspergillus nidulans genome encodes 86 putative GPCRs. Here, we characterise a carbon starvation-induced GPCR-mediated glucose sensing mechanism in A. nidulans. This includes two class V (gprH and gprI) and one class VII (gprM) GPCRs, which in response to glucose promote cAMP signalling, germination and hyphal growth, while negatively regulating sexual development in a light-dependent manner. We demonstrate that GprH regulates sexual development via influencing VeA activity, a key light-dependent regulator of fungal morphogenesis and secondary metabolism. We show that GprH and GprM are light-independent negative regulators of sterigmatocystin biosynthesis. Additionally, we reveal the epistatic interactions between the three GPCRs in regulating sexual development and sterigmatocystin production. In conclusion, GprH, GprM and GprI constitute a novel carbon starvation-induced glucose sensing mechanism that functions upstream of cAMP-PKA signalling to regulate fungal development and mycotoxin production.
Collapse
|
24
|
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]
|
25
|
Pfannenstiel BT, Greco C, Sukowaty AT, Keller NP. The epigenetic reader SntB regulates secondary metabolism, development and global histone modifications in Aspergillus flavus. Fungal Genet Biol 2018; 120:9-18. [PMID: 30130575 PMCID: PMC6215504 DOI: 10.1016/j.fgb.2018.08.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/22/2022]
Abstract
Due to the role, both beneficial and harmful, that fungal secondary metabolites play in society, the study of their regulation is of great importance. Genes for any one secondary metabolite are contiguously arranged in a biosynthetic gene cluster (BGC) and subject to regulation through the remodeling of chromatin. Histone modifying enzymes can place or remove post translational modifications (PTM) on histone tails which influences how tight or relaxed the chromatin is, impacting transcription of BGCs. In a recent forward genetic screen, the epigenetic reader SntB was identified as a transcriptional regulator of the sterigmatocystin BGC in A. nidulans, and regulated the related metabolite aflatoxin in A. flavus. In this study we investigate the role of SntB in the plant pathogen A. flavus by analyzing both ΔsntB and overexpression sntB genetic mutants. Deletion of sntB increased global levels of H3K9K14 acetylation and impaired several developmental processes including sclerotia formation, heterokaryon compatibility, secondary metabolite synthesis, and ability to colonize host seeds; in contrast the overexpression strain displayed fewer phenotypes. ΔsntB developmental phenotypes were linked with SntB regulation of NosA, a transcription factor regulating the A. flavus cell fusion cascade.
Collapse
Affiliation(s)
| | - Claudio Greco
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew T Sukowaty
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
26
|
Jain S, Sekonyela R, Knox BP, Palmer JM, Huttenlocher A, Kabbage M, Keller NP. Selenate sensitivity of a laeA mutant is restored by overexpression of the bZIP protein MetR in Aspergillus fumigatus. Fungal Genet Biol 2018; 117:1-10. [PMID: 29753128 PMCID: PMC6064392 DOI: 10.1016/j.fgb.2018.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023]
Abstract
LaeA is a conserved global regulator of secondary metabolism and development in filamentous fungi. Examination of Aspergillus fumigatus transcriptome data of laeA deletion mutants have been fruitful in identifying genes and molecules contributing to the laeA mutant phenotype. One of the genes significantly down regulated in A. fumigatus ΔlaeA is metR, encoding a bZIP DNA binding protein required for sulfur and methionine metabolism in fungi. LaeA and MetR deletion mutants exhibit several similarities including down regulation of sulfur assimilation and methionine metabolism genes and ability to grow on the toxic sulfur analog, sodium selenate. However, unlike ΔmetR, ΔlaeA strains are able to grow on sulfur, sulfite, and cysteine. To examine if any parameter of the ΔlaeA phenotype is due to decreased metR expression, an over-expression allele (OE::metR) was placed in a ΔlaeA background. The OE::metR allele could not significantly restore expression of MetR regulated genes in ΔlaeA but did restore sensitivity to sodium selenate. In A. nidulans a second bZIP protein, MetZ, also regulates sulfur and methionine metabolism genes. However, addition of an OE::metZ construct to the A. fumigatus ΔlaeA OE::metR strain still was unable to rescue the ΔlaeA phenotype to wildtype with regards gliotoxin synthesis and virulence in a zebrafish aspergillosis model.
Collapse
Affiliation(s)
- Sachin Jain
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Relebohile Sekonyela
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Jonathan M Palmer
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, United States.
| |
Collapse
|
27
|
Jain S, Wiemann P, Thill E, Williams B, Keller NP, Kabbage M. A Bcl-2 Associated Athanogene ( bagA) Modulates Sexual Development and Secondary Metabolism in the Filamentous Fungus Aspergillus nidulans. Front Microbiol 2018; 9:1316. [PMID: 29963036 PMCID: PMC6013550 DOI: 10.3389/fmicb.2018.01316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023] Open
Abstract
The Bcl-2 associated athanogene (Bag) family is a multifunctional group of proteins distinguished by a conserved region known as the Bag domain (BD). Herein, we discuss the discovery and characterization of a Bag protein in the model genetic fungus Aspergillus nidulans, we designated BagA. BagA shares striking similarities in 3D structure, domain organization, amino acid properties, and Hsp70 binding surfaces to animal and plant Bags. While Hsp70 binding is a common feature of Bag proteins, our experimental evidence shows that BagA does not cooperate with A. nidulans Hsp70s, suggesting this association may not be a universal feature of Bag proteins. Gene expression of bagA was strongly induced during sexual development suggesting a role in developmental processes. Accordingly, the deletion of bagA (ΔbagA) negatively impacted sexual development, while its overexpression resulted in constitutive induction of sexual fruiting bodies and spores. Asexual and sexual development was linked to secondary metabolism in A. nidulans. Our data show that the deletion of bagA also provoked an altered secondary metabolite (SM) profile in both sexual and vegetative growth phases. Indeed, LC-MS analysis showed a significant enrichment of SMs in ΔbagA, including novel metabolites not produced by wild type strain. Enrichment of SMs in ΔbagA strain is particularly intriguing and suggest that altering cellular homeostasis can be used as a provocative strategy to activate cryptic metabolites and uncover novel bioactive compounds. Overall, our results indicate that Bag proteins in filamentous fungi share developmental regulatory roles with their animal and plant counterparts. We also show a potentially unique role for BagA in modulating secondary metabolism in A. nidulans. To our knowledge, this study provides a first insight into Bag function in filamentous fungi.
Collapse
Affiliation(s)
- Sachin Jain
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Elizabeth Thill
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Wiemann P, Soukup AA, Folz JS, Wang PM, Noack A, Keller NP. CoIN: co-inducible nitrate expression system for secondary metabolites in Aspergillus nidulans. Fungal Biol Biotechnol 2018; 5:6. [PMID: 29564145 PMCID: PMC5851313 DOI: 10.1186/s40694-018-0049-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequencing of fungal species has demonstrated the existence of thousands of putative secondary metabolite gene clusters, the majority of them harboring a unique set of genes thought to participate in production of distinct small molecules. Despite the ready identification of key enzymes and potential cluster genes by bioinformatics techniques in sequenced genomes, the expression and identification of fungal secondary metabolites in the native host is often hampered as the genes might not be expressed under laboratory conditions and the species might not be amenable to genetic manipulation. To overcome these restrictions, we developed an inducible expression system in the genetic model Aspergillus nidulans. RESULTS We genetically engineered a strain of A. nidulans devoid of producing eight of the most abundant endogenous secondary metabolites to express the sterigmatocystin Zn(II)2Cys6 transcription factor-encoding gene aflR and its cofactor aflS under control of the nitrate inducible niiA/niaD promoter. Furthermore, we identified a subset of promoters from the sterigmatocystin gene cluster that are under nitrate-inducible AflR/S control in our production strain in order to yield coordinated expression without the risks from reusing a single inducible promoter. As proof of concept, we used this system to produce β-carotene from the carotenoid gene cluster of Fusarium fujikuroi. CONCLUSION Utilizing one-step yeast recombinational cloning, we developed an inducible expression system in the genetic model A. nidulans and show that it can be successfully used to produce commercially valuable metabolites.
Collapse
Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Hexagon Bio, Menlo Park, CA 94025 USA
| | - Alexandra A. Soukup
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705 USA
| | - Jacob S. Folz
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Davis Genome Center – Metabolomics, University of California, 451 Health Science Drive, Davis, CA 95616 USA
| | - Pin-Mei Wang
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Ocean College, Zhejiang University, Hangzhou, 310058 Zhejiang Province People’s Republic of China
| | - Andreas Noack
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
| |
Collapse
|
30
|
Lind AL, Lim FY, Soukup AA, Keller NP, Rokas A. An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus. mSphere 2018; 3:e00050-18. [PMID: 29564395 PMCID: PMC5853485 DOI: 10.1128/msphere.00050-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
Biosynthesis of many ecologically important secondary metabolites (SMs) in filamentous fungi is controlled by several global transcriptional regulators, like the chromatin modifier LaeA, and tied to both development and vegetative growth. In Aspergillus molds, asexual development is regulated by the BrlA > AbaA > WetA transcriptional cascade. To elucidate BrlA pathway involvement in SM regulation, we examined the transcriptional and metabolic profiles of ΔbrlA, ΔabaA, and ΔwetA mutant and wild-type strains of the human pathogen Aspergillus fumigatus. We find that BrlA, in addition to regulating production of developmental SMs, regulates vegetative SMs and the SrbA-regulated hypoxia stress response in a concordant fashion to LaeA. We further show that the transcriptional and metabolic equivalence of the ΔbrlA and ΔlaeA mutations is mediated by an LaeA requirement preventing heterochromatic marks in the brlA promoter. These results provide a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen. IMPORTANCE Filamentous fungi produce a spectacular variety of small molecules, commonly known as secondary or specialized metabolites (SMs), which are critical to their ecologies and lifestyles (e.g., penicillin, cyclosporine, and aflatoxin). Elucidation of the regulatory network that governs SM production is a major question of both fundamental and applied research relevance. To shed light on the relationship between regulation of development and regulation of secondary metabolism in filamentous fungi, we performed global transcriptomic and metabolomic analyses on mutant and wild-type strains of the human pathogen Aspergillus fumigatus under conditions previously shown to induce the production of both vegetative growth-specific and asexual development-specific SMs. We find that the gene brlA, previously known as a master regulator of asexual development, is also a master regulator of secondary metabolism and other cellular processes. We further show that brlA regulation of SM is mediated by laeA, one of the master regulators of SM, providing a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen.
Collapse
Affiliation(s)
- Abigail L. Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Fang Yun Lim
- Department of Medical Microbiology & Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra A. Soukup
- Department of Genetics, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Nancy P. Keller
- Department of Medical Microbiology & Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Antonis Rokas
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
31
|
Wiemann P, Perevitsky A, Lim FY, Shadkchan Y, Knox BP, Landero Figueora JA, Choera T, Niu M, Steinberger AJ, Wüthrich M, Idol RA, Klein BS, Dinauer MC, Huttenlocher A, Osherov N, Keller NP. Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense. Cell Rep 2018; 19:1008-1021. [PMID: 28467895 DOI: 10.1016/j.celrep.2017.04.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 03/13/2017] [Accepted: 04/06/2017] [Indexed: 12/23/2022] Open
Abstract
The Fenton-chemistry-generating properties of copper ions are considered a potent phagolysosome defense against pathogenic microbes, yet our understanding of underlying host/microbe dynamics remains unclear. We address this issue in invasive aspergillosis and demonstrate that host and fungal responses inextricably connect copper and reactive oxygen intermediate (ROI) mechanisms. Loss of the copper-binding transcription factor AceA yields an Aspergillus fumigatus strain displaying increased sensitivity to copper and ROI in vitro, increased intracellular copper concentrations, decreased survival in challenge with murine alveolar macrophages (AMΦs), and reduced virulence in a non-neutropenic murine model. ΔaceA survival is remediated by dampening of host ROI (chemically or genetically) or enhancement of copper-exporting activity (CrpA) in A. fumigatus. Our study exposes a complex host/microbe multifactorial interplay that highlights the importance of host immune status and reveals key targetable A. fumigatus counter-defenses.
Collapse
Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA
| | - Adi Perevitsky
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA
| | - Yana Shadkchan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Benjamin P Knox
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA
| | - Julio A Landero Figueora
- University of Cincinnati/Agilent Technologies Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Tsokyi Choera
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA
| | - Mengyao Niu
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA
| | | | - Marcel Wüthrich
- Department of Pediatrics, University of Wisconsin, Madison, WI 53706, USA
| | - Rachel A Idol
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Bruce S Klein
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin, Madison, WI 53706, USA; Department of Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Mary C Dinauer
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin, Madison, WI 53706, USA
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
| |
Collapse
|
32
|
Zhang S, Chen Y, Ma Z, Chen Q, Ostapska H, Gravelat FN, Lu L, Sheppard DC. PtaB, a lim-domain binding protein in Aspergillus fumigatus regulates biofilm formation and conidiation through distinct pathways. Cell Microbiol 2017; 20. [PMID: 29114981 DOI: 10.1111/cmi.12799] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/18/2022]
Abstract
The exopolysaccharide galactosaminogalactan (GAG) plays an important role in mediating adhesion, biofilm formation, and virulence in the pathogenic fungus Aspergillus fumigatus. The developmental modifiers MedA, StuA, and SomA regulate GAG biosynthesis, but the mechanisms underlying this regulation are poorly understood. PtaB is a lim-domain binding protein that interacts with the transcription factor SomA and is required for normal conidiation and biofilm formation. Disruption of ptaB resulted in impaired GAG production and conidiation in association with a markedly reduced expression of GAG biosynthetic genes (uge3 and agd3), developmental regulators (medA and stuA), and genes involved in the core conidiation pathway. Overexpression of medA and dual overexpression of uge3 and agd3 in the ΔptaB mutant increased biofilm formation but not conidiation, whereas overexpression of core conidiation genes rescued conidiation but not biofilm formation. Overexpression of stuA modestly increased both conidiation and biofilm formation. Analysis of ptaB truncation mutants revealed that overexpression of the lim-domain binding region restored conidiation but not biofilm formation, suggesting that ptaB may govern these processes by interacting with different partners. These studies establish that PtaB governs GAG biosynthesis at the level of substrate availability and polymer deacetylation and that PtaB-mediated biofilm formation and conidiation are largely independent pathways.
Collapse
Affiliation(s)
- Shizhu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Departments of Medicine and of Microbiology and Immunology, McGill University, Montreal, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Yuan Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhihua Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuyi Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hanna Ostapska
- Departments of Medicine and of Microbiology and Immunology, McGill University, Montreal, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Fabrice N Gravelat
- Departments of Medicine and of Microbiology and Immunology, McGill University, Montreal, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Donald C Sheppard
- Departments of Medicine and of Microbiology and Immunology, McGill University, Montreal, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Canada
| |
Collapse
|
33
|
Maeda K, Izawa M, Nakajima Y, Jin Q, Hirose T, Nakamura T, Koshino H, Kanamaru K, Ohsato S, Kamakura T, Kobayashi T, Yoshida M, Kimura M. Increased metabolite production by deletion of an HDA1-type histone deacetylase in the phytopathogenic fungi, Magnaporthe oryzae (Pyricularia oryzae) and Fusarium asiaticum. Lett Appl Microbiol 2017; 65:446-452. [PMID: 28862744 DOI: 10.1111/lam.12797] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/10/2017] [Accepted: 08/27/2017] [Indexed: 11/29/2022]
Abstract
Histone deacetylases (HDACs) play an important role in the regulation of chromatin structure and gene expression. We found that dark pigmentation of Magnaporthe oryzae (anamorph Pyricularia oryzae) ΔMohda1, a mutant strain in which an orthologue of the yeast HDA1 was disrupted by double cross-over homologous recombination, was significantly stimulated in liquid culture. Analysis of metabolites in a ΔMohda1 mutant culture revealed that the accumulation of shunt products of the 1,8-dihydroxynaphthalene melanin and ergosterol pathways were significantly enhanced compared to the wild-type strain. Northern blot analysis of the ΔMohda1 mutant revealed transcriptional activation of three melanin genes that are dispersed throughout the genome of M. oryzae. The effect of deletion of the yeast HDA1 orthologue was also observed in Fusarium asiaticum from the Fusarium graminearum species complex; the HDF2 deletion mutant produced increased levels of nivalenol-type trichothecenes. These results suggest that histone modification via HDA1-type HDAC regulates the production of natural products in filamentous fungi. SIGNIFICANCE AND IMPACT OF THE STUDY Natural products of fungi have significant impacts on human welfare, in both detrimental and beneficial ways. Although HDA1-type histone deacetylase is not essential for vegetative growth, deletion of the gene affects the expression of clustered secondary metabolite genes in some fungi. Here, we report that such phenomena are also observed in physically unlinked genes required for melanin biosynthesis in the rice blast fungus. In addition, production of Fusarium trichothecenes, previously reported to be unaffected by HDA1 deletion, was significantly upregulated in another Fusarium species. Thus, the HDA1-inactivation strategy may be regarded as a general approach for overproduction and/or discovery of fungal metabolites.
Collapse
Affiliation(s)
- K Maeda
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan.,Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan.,Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - M Izawa
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan.,Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Y Nakajima
- Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Q Jin
- Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - T Hirose
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan.,Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - T Nakamura
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), Wako, Saitama, Japan
| | - H Koshino
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), Wako, Saitama, Japan
| | - K Kanamaru
- Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - S Ohsato
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - T Kamakura
- Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - T Kobayashi
- Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - M Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan
| | - M Kimura
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan.,Department of Biological Mechanisms and Function, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| |
Collapse
|
34
|
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
| |
Collapse
|
35
|
Zhou H, Liu Q, Shi T, Yu Y, Lu H. Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation. Yeast 2015; 32:643-55. [DOI: 10.1002/yea.3085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Qi Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing Technology; Shanghai 200237 People's Republic of China
| |
Collapse
|
36
|
Netzker T, Fischer J, Weber J, Mattern DJ, König CC, Valiante V, Schroeckh V, Brakhage AA. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front Microbiol 2015; 6:299. [PMID: 25941517 PMCID: PMC4403501 DOI: 10.3389/fmicb.2015.00299] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/26/2015] [Indexed: 11/22/2022] Open
Abstract
Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.
Collapse
Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Claudia C König
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| | - Vito Valiante
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena , Jena, Germany
| |
Collapse
|
37
|
Wiemann P, Lechner BE, Baccile JA, Velk TA, Yin WB, Bok JW, Pakala S, Losada L, Nierman WC, Schroeder FC, Haas H, Keller NP. Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus. Front Microbiol 2014; 5:530. [PMID: 25386169 PMCID: PMC4208449 DOI: 10.3389/fmicb.2014.00530] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/23/2014] [Indexed: 11/13/2022] Open
Abstract
Iron plays a critical role in survival and virulence of the opportunistic pathogen Aspergillus fumigatus. Two transcription factors, the GATA-factor SreA and the bZip-factor HapX oppositely monitor iron homeostasis with HapX activating iron acquisition pathways (e.g., siderophores) and shutting down iron consumptive pathways (and SreA) during iron starvation conditions whereas SreA negatively regulates HapX and corresponding pathways during iron sufficiency. Recently the non-ribosomal peptide, hexadehydroastechrome (HAS; a tryptophan-derived iron (III)-complex), has been found important in A. fumigatus virulence. We found that HAS overproduction caused an iron starvation phenotype, from alteration of siderophore pools to regulation of iron homeostasis gene expression including sreA. Moreover, we uncovered an iron dependent secondary metabolism network where both SreA and HapX oppositely regulate multiple other secondary metabolites including HAS. This circuitry links iron-acquisition and consumption pathways with secondary metabolism-thus placing HAS as part of a metabolic feedback circuitry designed to balance iron pools in the fungus and presenting iron availability as one environmental trigger of secondary metabolism.
Collapse
Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Beatrix E Lechner
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Thomas A Velk
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Wen-Bing Yin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Suman Pakala
- The J. Craig Venter Institute Rockville, MD, USA
| | | | | | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY, USA
| | - Hubertus Haas
- Division of Molecular Biology/Biocenter, Innsbruck Medical University Innsbruck, Austria
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| |
Collapse
|
38
|
Sarikaya-Bayram O, Bayram O, Feussner K, Kim JH, Kim HS, Kaever A, Feussner I, Chae KS, Han DM, Han KH, Braus GH. Membrane-bound methyltransferase complex VapA-VipC-VapB guides epigenetic control of fungal development. Dev Cell 2014; 29:406-20. [PMID: 24871947 DOI: 10.1016/j.devcel.2014.03.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 02/26/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022]
Abstract
Epigenetic and transcriptional control of gene expression must be coordinated in response to external signals to promote alternative multicellular developmental programs. The membrane-associated trimeric complex VapA-VipC-VapB controls a signal transduction pathway for fungal differentiation. The VipC-VapB methyltransferases are tethered to the membrane by the FYVE-like zinc finger protein VapA, allowing the nuclear VelB-VeA-LaeA complex to activate transcription for sexual development. Once the release from VapA is triggered, VipC-VapB is transported into the nucleus. VipC-VapB physically interacts with VeA and reduces its nuclear import and protein stability, thereby reducing the nuclear VelB-VeA-LaeA complex. Nuclear VapB methyltransferase diminishes the establishment of facultative heterochromatin by decreasing histone 3 lysine 9 trimethylation (H3K9me3). This favors activation of the regulatory genes brlA and abaA, which promote the asexual program. The VapA-VipC-VapB methyltransferase pathway combines control of nuclear import and stability of transcription factors with histone modification to foster appropriate differentiation responses.
Collapse
Affiliation(s)
- Ozlem Sarikaya-Bayram
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany
| | - Ozgür Bayram
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, Georg August University, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany
| | - Jong-Hwa Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea
| | - Hee-Seo Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea; Department of Molecular Biology, Chonbuk National University, Jeonju 561-756, Korea
| | - Alexander Kaever
- Department of Bioinformatics, Georg August University, Goldschmidtstrasse 1, Göttingen 37077, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Georg August University, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany
| | - Keon-Sang Chae
- Department of Molecular Biology, Chonbuk National University, Jeonju 561-756, Korea
| | - Dong-Min Han
- Division of Life Sciences, Wonkwang University, Iksan 570-749, Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany.
| |
Collapse
|
39
|
The histone acetyltransferase GcnE (GCN5) plays a central role in the regulation of Aspergillus asexual development. Genetics 2014; 197:1175-89. [PMID: 24907261 DOI: 10.1534/genetics.114.165688] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Acetylation of histones is a key regulatory mechanism of gene expression in eukaryotes. GcnE is an acetyltransferase of Aspergillus nidulans involved in the acetylation of histone H3 at lysine 9 and lysine 14. Previous works have demonstrated that deletion of gcnE results in defects in primary and secondary metabolism. Here we unveil the role of GcnE in development and show that a ∆gcnE mutant strain has minor growth defects but is impaired in normal conidiophore development. No signs of conidiation were found after 3 days of incubation, and immature and aberrant conidiophores were found after 1 week of incubation. Centroid linkage clustering and principal component (PC) analysis of transcriptomic data suggest that GcnE occupies a central position in Aspergillus developmental regulation and that it is essential for inducing conidiation genes. GcnE function was found to be required for the acetylation of histone H3K9/K14 at the promoter of the master regulator of conidiation, brlA, as well as at the promoters of the upstream developmental regulators of conidiation flbA, flbB, flbC, and flbD (fluffy genes). However, analysis of the gene expression of brlA and the fluffy genes revealed that the lack of conidiation originated in a complete absence of brlA expression in the ∆gcnE strain. Ectopic induction of brlA from a heterologous alcA promoter did not remediate the conidiation defects in the ∆gcnE strain, suggesting that additional GcnE-mediated mechanisms must operate. Therefore, we conclude that GcnE is the only nonessential histone modifier with a strong role in fungal development found so far.
Collapse
|
40
|
Epigenetic control of effector gene expression in the plant pathogenic fungus Leptosphaeria maculans. PLoS Genet 2014; 10:e1004227. [PMID: 24603691 PMCID: PMC3945186 DOI: 10.1371/journal.pgen.1004227] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/22/2014] [Indexed: 01/07/2023] Open
Abstract
Plant pathogens secrete an arsenal of small secreted proteins (SSPs) acting as effectors that modulate host immunity to facilitate infection. SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression at diverse stages of plant infection. To date, little is known about the regulation of their expression. The genome of the Ascomycete Leptosphaeria maculans comprises alternating gene-rich GC-isochores and gene-poor AT-isochores. The AT-isochores harbor mosaics of transposable elements, encompassing one-third of the genome, and are enriched in putative effector genes that present similar expression patterns, namely no expression or low-level expression during axenic cultures compared to strong induction of expression during primary infection of oilseed rape (Brassica napus). Here, we investigated the involvement of one specific histone modification, histone H3 lysine 9 methylation (H3K9me3), in epigenetic regulation of concerted effector gene expression in L. maculans. For this purpose, we silenced the expression of two key players in heterochromatin assembly and maintenance, HP1 and DIM-5 by RNAi. By using HP1-GFP as a heterochromatin marker, we observed that almost no chromatin condensation is visible in strains in which LmDIM5 was silenced by RNAi. By whole genome oligoarrays we observed overexpression of 369 or 390 genes, respectively, in the silenced-LmHP1 and -LmDIM5 transformants during growth in axenic culture, clearly favouring expression of SSP-encoding genes within AT-isochores. The ectopic integration of four effector genes in GC-isochores led to their overexpression during growth in axenic culture. These data strongly suggest that epigenetic control, mediated by HP1 and DIM-5, represses the expression of at least part of the effector genes located in AT-isochores during growth in axenic culture. Our hypothesis is that changes of lifestyle and a switch toward pathogenesis lift chromatin-mediated repression, allowing a rapid response to new environmental conditions.
Collapse
|
41
|
Connolly LR, Smith KM, Freitag M. The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet 2013; 9:e1003916. [PMID: 24204317 PMCID: PMC3814326 DOI: 10.1371/journal.pgen.1003916] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/10/2013] [Indexed: 12/16/2022] Open
Abstract
The cereal pathogen Fusarium graminearum produces secondary metabolites toxic to humans and animals, yet coordinated transcriptional regulation of gene clusters remains largely a mystery. By chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq) we found that regions with secondary metabolite clusters are enriched for trimethylated histone H3 lysine 27 (H3K27me3), a histone modification associated with gene silencing. H3K27me3 was found predominantly in regions that lack synteny with other Fusarium species, generally subtelomeric regions. Di- or trimethylated H3K4 (H3K4me2/3), two modifications associated with gene activity, and H3K27me3 are predominantly found in mutually exclusive regions of the genome. To find functions for H3K27me3, we deleted the gene for the putative H3K27 methyltransferase, KMT6, a homolog of Drosophila Enhancer of zeste, E(z). The kmt6 mutant lacks H3K27me3, as shown by western blot and ChIP-seq, displays growth defects, is sterile, and constitutively expresses genes for mycotoxins, pigments and other secondary metabolites. Transcriptome analyses showed that 75% of 4,449 silent genes are enriched for H3K27me3. A subset of genes that were enriched for H3K27me3 in WT gained H3K4me2/3 in kmt6. A largely overlapping set of genes showed increased expression in kmt6. Almost 95% of the remaining 2,720 annotated silent genes showed no enrichment for either H3K27me3 or H3K4me2/3 in kmt6. In these cases mere absence of H3K27me3 was insufficient for expression, which suggests that additional changes are required to activate genes. Taken together, we show that absence of H3K27me3 allowed expression of an additional 14% of the genome, resulting in derepression of genes predominantly involved in secondary metabolite pathways and other species-specific functions, including putative secreted pathogenicity factors. Results from this study provide the framework for novel targeted strategies to control the “cryptic genome”, specifically secondary metabolite expression. Changes in chromatin structure are required for time- and tissue-specific gene regulation. How exactly these changes are mediated is under intense scrutiny. The interplay between activating histone modifications, e.g. H3K4me, and the silencing H3K27me3 mark has been recognized as critical to orchestrate differentiation and development in plants and animals. Here we show that filamentous fungi, exemplified by the cereal pathogen Fusarium graminearum, can use H3K27 methylation to generate silenced, facultative heterochromatin, covering more than a third of the genome, much more than the 5–8% of Neurospora or metazoan genomes. Removal of the silencing mark by mutation of the methyltransferase subunit of the PRC2 silencing complex resulted in activation of more than 1,500 genes, 14% of the genome. We show that generation of facultative heterochromatin by H3K27 methylation is an ancestral process that has been lost in certain lineages (e.g. at least some hemiascomycetes, the genus Aspergillus and some basidiomycetes). Our studies will open the door to future precise “epigenetic engineering” of gene clusters that generate bioactive compounds, e.g. putative mycotoxins, antibiotics and industrial feedstocks. Availability of tractable fungal model systems for studies of the control and function of H3K27 methylation may accelerate mechanistic research.
Collapse
Affiliation(s)
- Lanelle R. Connolly
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Kristina M. Smith
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
42
|
Strategies for mining fungal natural products. J Ind Microbiol Biotechnol 2013; 41:301-13. [PMID: 24146366 DOI: 10.1007/s10295-013-1366-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/05/2013] [Indexed: 10/26/2022]
Abstract
Fungi are well known for their ability to produce a multitude of natural products. On the one hand their potential to provide beneficial antibiotics and immunosuppressants has been maximized by the pharmaceutical industry to service the market with cost-efficient drugs. On the other hand identification of trace amounts of known mycotoxins in food and feed samples is of major importance to ensure consumer health and safety. Although several fungal natural products, their biosynthesis and regulation are known today, recent genome sequences of hundreds of fungal species illustrate that the secondary metabolite potential of fungi has been substantially underestimated. Since expression of genes and subsequent production of the encoded metabolites are frequently cryptic or silent under standard laboratory conditions, strategies for activating these hidden new compounds are essential. This review will cover the latest advances in fungal genome mining undertaken to unlock novel products.
Collapse
|
43
|
Patananan AN, Palmer JM, Garvey GS, Keller NP, Clarke SG. A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine. J Biol Chem 2013; 288:14032-14045. [PMID: 23532849 PMCID: PMC3656261 DOI: 10.1074/jbc.m113.465765] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungi in the genus Aspergillus are opportunistic plant and animal pathogens that can adapt to their environment by producing various secondary metabolites, including lovastatin, penicillin, and aflatoxin. The synthesis of these small molecules is dependent on gene clusters that are globally regulated by the LaeA protein. Null mutants of LaeA in all pathogenic fungi examined to date show decreased virulence coupled with reduced secondary metabolism. Although the amino acid sequence of LaeA contains the motifs characteristic of seven-β-strand methyltransferases, a methyl-accepting substrate of LaeA has not been identified. In this work we did not find a methyl-accepting substrate in Aspergillus nidulans with various assays, including in vivo S-adenosyl-[methyl-(3)H]methionine labeling, targeted in vitro methylation experiments using putative protein substrates, or in vitro methylation assays using whole cell extracts grown under different conditions. However, in each experiment LaeA was shown to self-methylate. Amino acid hydrolysis of radioactively labeled LaeA followed by cation exchange and reverse phase chromatography identified methionine as the modified residue. Point mutations show that the major site of modification of LaeA is on methionine 207. However, in vivo complementation showed that methionine 207 is not required for the biological function of LaeA. LaeA is the first protein to exhibit automethylation at a methionine residue. These findings not only indicate LaeA may perform novel chemistry with S-adenosylmethionine but also provide new insights into the physiological function of LaeA.
Collapse
Affiliation(s)
- Alexander N. Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | | | | | - Nancy P. Keller
- the Departments of Medical Microbiology and Immunology and ,Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - Steven G. Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095 and , To whom correspondence should be addressed: Dept. of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, 607 Charles E. Young Dr. East, Los Angeles, CA. Tel.: 310-825-8754; Fax: 310-825-1968; E-mail:
| |
Collapse
|
44
|
RsmA regulates Aspergillus fumigatus gliotoxin cluster metabolites including cyclo(L-Phe-L-Ser), a potential new diagnostic marker for invasive aspergillosis. PLoS One 2013; 8:e62591. [PMID: 23671611 PMCID: PMC3646020 DOI: 10.1371/journal.pone.0062591] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/26/2013] [Indexed: 11/19/2022] Open
Abstract
Dimeric basic leucine zipper (bZIP) proteins are conserved transcriptional enhancers found in all eukaryotes. A recently reported and novel function for bZIPs is association of these proteins with secondary metabolite production in filamentous fungi. In particular a Yap-like bZIP termed RsmA (restorer of secondary metabolism A) was identified in Aspergillus nidulans that positively regulates the carcinogen sterigmatocystin. To assess for conserved function for RsmA, we examined a role of this protein in secondary metabolism in the pathogen A. fumigatus. RsmA was found to positively regulate gliotoxin where overexpression (OE) of rsmA led to 2–100 fold increases of twelve gli cluster metabolites in culture medium including the newly identified gli metabolite cyclo(L-Phe-L-Ser). Lungs from both wild type and OErsmA infected mice contained gliotoxin (2.3 fold higher in OErsmA treatment) as well as the gliotoxin precursor cyclo(L-Phe-L-Ser) (3.2 fold higher in OErsmA treatment). The data here presents a conserved role for RsmA in secondary metabolite cluster activation and suggests cyclo(L-Phe-L-Ser) may serve as an alternative marker for diagnosis of invasive aspergillosis.
Collapse
|
45
|
Palmer JM, Bok JW, Lee S, Dagenais TRT, Andes DR, Kontoyiannis DP, Keller NP. Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus. PeerJ 2013; 1:e4. [PMID: 23638376 PMCID: PMC3629006 DOI: 10.7717/peerj.4] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/04/2012] [Indexed: 12/13/2022] Open
Abstract
Secondary metabolite (SM) production in filamentous fungi is mechanistically associated with chromatin remodeling of specific SM clusters. One locus recently shown to be involved in SM suppression in Aspergillus nidulans was CclA, a member of the histone 3 lysine 4 methylating COMPASS complex. Here we examine loss of CclA and a putative H3K4 demethylase, HdmA, in the human pathogen Aspergillus fumigatus. Although deletion of hdmA showed no phenotype under the conditions tested, the cclA deletant was deficient in tri- and di-methylation of H3K4 and yielded a slowly growing strain that was rich in the production of several SMs, including gliotoxin. Similar to deletion of other chromatin modifying enzymes, ΔcclA was sensitive to 6-azauracil indicating a defect in transcriptional elongation. Despite the poor growth, the ΔcclA mutant had wild-type pathogenicity in a murine model and the Toll-deficient Drosophila model of invasive aspergillosis. These data indicate that tri- and di-methylation of H3K4 is involved in the regulation of several secondary metabolites in A. fumigatus, however does not contribute to pathogenicity under the conditions tested.
Collapse
Affiliation(s)
- Jonathan M Palmer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Seul Lee
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Taylor R T Dagenais
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - David R Andes
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Disease, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
46
|
Soukup A, Keller NP. Western Analysis of Histone Modifications ( Aspergillus nidulans). Bio Protoc 2013; 3:e424. [PMID: 27275003 DOI: 10.21769/bioprotoc.424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Western blotting allows for the specific detection of proteins and/or modifications of proteins by an antibody of interest. This protocol utilizes a crude nuclei extraction protocol for Aspergillus nidulans to enrich for histones and other nuclear proteins prior to gel electrophoresis. Post translational modifications of histones may then be easily detected. After electrophoresis, the selected antibodies are used to detect and quantify levels of the modifications of interest.
Collapse
Affiliation(s)
- Alexandra Soukup
- Department of Genetics, University of Wisconsin - Madison, Madison, USA
| | - Nancy P Keller
- Department of Bacteriology and Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, USA
| |
Collapse
|
47
|
Soukup AA, Chiang YM, Bok JW, Reyes-Dominguez Y, Oakley BR, Wang CCC, Strauss J, Keller NP. Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol Microbiol 2012; 86:314-30. [PMID: 22882998 PMCID: PMC3514908 DOI: 10.1111/j.1365-2958.2012.08195.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Regulation of secondary metabolite (SM) gene clusters in Aspergillus nidulans has been shown to occur through cluster-specific transcription factors or through global regulators of chromatin structure such as histone methyltransferases, histone deacetylases, or the putative methyltransferase LaeA. A multicopy suppressor screen for genes capable of returning SM production to the SM deficient ΔlaeA mutant resulted in identification of the essential histone acetyltransferase EsaA, able to complement an esa1 deletion in Saccharomyces cereviseae. Here we report that EsaA plays a novel role in SM cluster activation through histone 4 lysine 12 (H4K12) acetylation in four examined SM gene clusters (sterigmatocystin, penicillin, terrequinone and orsellinic acid), in contrast to no increase in H4K12 acetylation of the housekeeping tubA promoter. This augmented SM cluster acetylation requires LaeA for full effect and correlates with both increased transcript levels and metabolite production relative to wild type. H4K12 levels may thus represent a unique indicator of relative production potential, notably of SMs.
Collapse
Affiliation(s)
- Alexandra A. Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan, ROC 71710,Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Jin Woo Bok
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yazmid Reyes-Dominguez
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, USA 66045
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033,Department of Chemistry, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Nancy P. Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Corresponding author: 3476 Microbial Sciences, 1550 Linden Drive, Madison, WI, USA 53706 Phone: (608) 262-9795 Fax: (608)262-8418
| |
Collapse
|
48
|
Lim FY, Sanchez JF, Wang CC, Keller NP. Toward awakening cryptic secondary metabolite gene clusters in filamentous fungi. Methods Enzymol 2012; 517:303-24. [PMID: 23084945 PMCID: PMC3703436 DOI: 10.1016/b978-0-12-404634-4.00015-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mining for novel natural compounds is of eminent importance owing to the continuous need for new pharmaceuticals. Filamentous fungi are historically known to harbor the genetic capacity for an arsenal of natural compounds, both beneficial and detrimental to humans. The majority of these metabolites are still cryptic or silent under standard laboratory culture conditions. Mining for these cryptic natural products can be an excellent source for identifying new compound classes. Capitalizing on the current knowledge on how secondary metabolite gene clusters are regulated has allowed the research community to unlock many hidden fungal treasures, as described in this chapter.
Collapse
Affiliation(s)
- Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - James F. Sanchez
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California, USA
| | - Clay C.C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California, USA,Department of Chemistry, University of Southern California, College of Letters, Arts, and Sciences, Los Angeles, California, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA,Corresponding author:
| |
Collapse
|
49
|
Gacek A, Strauss J. The chromatin code of fungal secondary metabolite gene clusters. Appl Microbiol Biotechnol 2012; 95:1389-404. [PMID: 22814413 PMCID: PMC3427479 DOI: 10.1007/s00253-012-4208-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/24/2012] [Accepted: 05/24/2012] [Indexed: 01/07/2023]
Abstract
Secondary metabolite biosynthesis genes in fungi are usually physically linked and organized in large gene clusters. The physical linkage of genes involved in the same biosynthetic pathway minimizes the amount of regulatory steps necessary to regulate the biosynthetic machinery and thereby contributes to physiological economization. Regulation by chromatin accessibility is a proficient molecular mechanism to synchronize transcriptional activity of large genomic regions. Chromatin regulation largely depends on DNA and histone modifications and the histone code hypothesis proposes that a certain combination of modifications, such as acetylation, methylation or phosphorylation, is needed to perform a specific task. A number of reports from several laboratories recently demonstrated that fungal secondary metabolite (SM) biosynthesis clusters are controlled by chromatin-based mechanisms and histone acetyltransferases, deacetylases, methyltransferases, and proteins involved in heterochromatin formation were found to be involved. This led to the proposal that establishment of repressive chromatin domains over fungal SM clusters under primary metabolic conditions is a conserved mechanism that prevents SM production during the active growth phase. Consequently, transcriptional activation of SM clusters requires reprogramming of the chromatin landscape and replacement of repressive histone marks by activating marks. This review summarizes recent advances in our understanding of chromatin-based SM cluster regulation and highlights some of the open questions that remain to be answered before we can draw a more comprehensive picture.
Collapse
Affiliation(s)
- Agnieszka Gacek
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Science, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Science, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria ,Health and Environment Department, Austrian Institute of Technology, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria
| |
Collapse
|
50
|
Wilkinson JR, Kale SP, Bhatnagar D, Yu J, Ehrlich KC. Expression profiling of non-aflatoxigenic Aspergillus parasiticus mutants obtained by 5-azacytosine treatment or serial mycelial transfer. Toxins (Basel) 2011; 3:932-48. [PMID: 22069749 PMCID: PMC3202869 DOI: 10.3390/toxins3080932] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/19/2011] [Accepted: 07/26/2011] [Indexed: 11/17/2022] Open
Abstract
Aflatoxins are carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. Previous studies found that repeated serial mycelial transfer or treatment of A. parasiticus with 5-azacytidine produced colonies with a fluffy phenotype and inability to produce aflatoxins. To understand how these treatments affect expression of genes involved in aflatoxin production and development, we carried out expressed sequence tag (EST)-based microarray assays to identify genes in treated clones that are differentially expressed compared to the wild-type. Expression of 183 genes was significantly dysregulated. Of these, 38 had at least two-fold or lower expression compared to the untreated control and only two had two-fold or higher expression. The most frequent change was downregulation of genes predicted to encode membrane-bound proteins. Based on this result we hypothesize that the treatments cause changes in the structure of cellular and organelle membranes that prevent normal development and aflatoxin biosynthesis.
Collapse
Affiliation(s)
- Jeffrey R. Wilkinson
- Southern Regional Research Center, ARS/USDA, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA; (J.R.W.); (D.B.); (J.Y)
| | - Shubha P. Kale
- Department of Biology, 1 Drexel Dr., Box 85B, Xavier University of Louisiana, New Orleans, LA 70125, USA;
| | - Deepak Bhatnagar
- Southern Regional Research Center, ARS/USDA, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA; (J.R.W.); (D.B.); (J.Y)
| | - Jiujiang Yu
- Southern Regional Research Center, ARS/USDA, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA; (J.R.W.); (D.B.); (J.Y)
| | - Kenneth C. Ehrlich
- Southern Regional Research Center, ARS/USDA, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA; (J.R.W.); (D.B.); (J.Y)
| |
Collapse
|