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Morán Torres JP, Lyu J, Chen X, Klaas AM, Vonk PJ, Lugones LG, de Cock H, Wösten HAB. Single and combinatorial gene inactivation in Aspergillus niger using selected as well as genome-wide gRNA library pools. Microbiol Res 2025; 298:128204. [PMID: 40359875 DOI: 10.1016/j.micres.2025.128204] [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: 03/17/2025] [Revised: 04/30/2025] [Accepted: 05/02/2025] [Indexed: 05/15/2025]
Abstract
Aspergillus niger is a saprotroph, a pathogen, an endophyte, a food spoiler and an important cell factory. Only a minor fraction of its genes has been experimentally characterized. We here set up a CRISPR/Cas9 mutagenesis screen for functional gene analysis using co-transformation of a pool of gene editing plasmids that are maintained under selection pressure and that each contain a gRNA. First, a pool of gRNA vectors was introduced in A. niger targeting five genes with easy selectable phenotypes. Transformants were obtained with all possible single, double, triple, quadruple and quintuple gene inactivation phenotypes. Their genotypes were confirmed using the gRNA sequences in the transforming vector as barcodes. Next, a gRNA library was introduced in A. niger targeting > 9600 genes. Gene nsdC was identified as a sporulation gene using co-transformation conditions that favored uptake of one or two gRNA construct(s) from the genome-wide vector pool. Together, CRISPR/Cas9 vectors with a (genome-wide) pool of gRNAs can be used for functional analysis of genes in A. niger with phenotypes that are the result of the inactivation of a single or multiple genes.
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Affiliation(s)
- Juan Pablo Morán Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Jun Lyu
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Antonia M Klaas
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Peter Jan Vonk
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Hans de Cock
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands.
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Liu Y, Wang Y, Bao D, Chen H, Gong M, Sun S, Zou G. Cross-Kingdom DNA Methylation Dynamics: Comparative Mechanisms of 5mC/6mA Regulation and Their Implications in Epigenetic Disorders. BIOLOGY 2025; 14:461. [PMID: 40427651 PMCID: PMC12108942 DOI: 10.3390/biology14050461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Revised: 04/17/2025] [Accepted: 04/22/2025] [Indexed: 05/29/2025]
Abstract
DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns-characterized by spatial-temporal dysregulation and stochastic molecular noise-serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation.
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Affiliation(s)
- Yu Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Ying Wang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Hongyu Chen
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Ming Gong
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Shujing Sun
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Gen Zou
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
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Chen X, Moran Torres JP, Tedjai SVK, Lugones LG, Wösten HAB. Functional analysis of FlbA-regulated transcription factor genes in Aspergillus niger using a multiplexed CRISPRoff system. Int J Biol Macromol 2024; 277:134326. [PMID: 39089555 DOI: 10.1016/j.ijbiomac.2024.134326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
FlbA of Aspergillus niger (indirectly) regulates 36 transcription factor (TF) genes. As a result, it promotes sporulation and represses vegetative growth, protein secretion and lysis. In this study, the functions of part of the FlbA-regulated TF genes were studied by using CRISPRoff. This system was recently introduced as an epigenetic tool for modulating gene expression in A. niger. A plasmid encompassing an optimized CRISPRoff system as well as a library of sgRNA genes that target the promoters of the 36 FlbA-regulated TF genes was introduced in A. niger. Out of 24 transformants that exhibited a sporulation phenotype, 12 and 18 strains also showed a biomass and secretion phenotype, respectively. The transforming sgRNAs, and thus the genes responsible for the phenotypes, were identified from five of the transformants. The results show that the genes dofA, dofB, dofC, dofD, and socA are involved in sporulation and extracellular enzyme activity, while dofA and socA also play roles in biomass formation. Overall, this study shows that the multiplexed CRISPRoff system can be effectively used for functional analysis of genes in a fungus.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - S Vyanjan K Tedjai
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
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Zhang Y, Yu W, Lu Y, Wu Y, Ouyang Z, Tu Y, He B. Epigenetic Regulation of Fungal Secondary Metabolism. J Fungi (Basel) 2024; 10:648. [PMID: 39330408 PMCID: PMC11433216 DOI: 10.3390/jof10090648] [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: 08/06/2024] [Revised: 09/01/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
Secondary metabolism is one of the important mechanisms by which fungi adapt to their living environment and promote survival and reproduction. Recent studies have shown that epigenetic regulation, such as DNA methylation, histone modifications, and non-coding RNAs, plays key roles in fungal secondary metabolism and affect fungal growth, survival, and pathogenicity. This review describes recent advances in the study of epigenetic regulation of fungal secondary metabolism. We discuss the way in which epigenetic markers respond to environmental changes and stimulate the production of biologically active compounds by fungi, and the feasibility of these new findings applied to develop new antifungal strategies and optimize secondary metabolism. In addition, we have deliberated on possible future directions of research in this field. A deeper understanding of epigenetic regulatory networks is a key focus for future research.
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Affiliation(s)
| | | | | | | | | | - Yayi Tu
- Jiangxi Key Laboratory of Natural Microbial Medicine Research, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China; (Y.Z.); (W.Y.); (Y.L.); (Y.W.); (Z.O.)
| | - Bin He
- Jiangxi Key Laboratory of Natural Microbial Medicine Research, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China; (Y.Z.); (W.Y.); (Y.L.); (Y.W.); (Z.O.)
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