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Nai YS, Huang YC, Yen MR, Chen PY. Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns. Front Microbiol 2021; 11:616922. [PMID: 33552027 PMCID: PMC7862722 DOI: 10.3389/fmicb.2020.616922] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
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Affiliation(s)
- Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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The perennial ryegrass endophyte Neotyphodium lolii genetically transformed with the green fluorescent protein gene (gfp) and visualization in the host plant. ACTA ACUST UNITED AC 2001. [DOI: 10.1017/s0953756201004075] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Liu G, Casqueiro J, Bañuelos O, Cardoza RE, Gutiérrez S, Martín JF. Targeted inactivation of the mecB gene, encoding cystathionine-gamma-lyase, shows that the reverse transsulfuration pathway is required for high-level cephalosporin biosynthesis in Acremonium chrysogenum C10 but not for methionine induction of the cephalosporin genes. J Bacteriol 2001; 183:1765-72. [PMID: 11160109 PMCID: PMC95063 DOI: 10.1128/jb.183.5.1765-1772.2001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeted gene disruption efficiency in Acremonium chrysogenum was increased 10-fold by applying the double-marker enrichment technique to this filamentous fungus. Disruption of the mecB gene by the double-marker technique was achieved in 5% of the transformants screened. Mutants T6 and T24, obtained by gene replacement, showed an inactive mecB gene by Southern blot analysis and no cystathionine-gamma-lyase activity. These mutants exhibited lower cephalosporin production than that of the control strain, A. chrysogenum C10, in MDFA medium supplemented with methionine. However, there was no difference in cephalosporin production between parental strain A. chrysogenum C10 and the mutants T6 and T24 in Shen's defined fermentation medium (MDFA) without methionine. These results indicate that the supply of cysteine through the transsulfuration pathway is required for high-level cephalosporin biosynthesis but not for low-level production of this antibiotic in methionine-unsupplemented medium. Therefore, cysteine for cephalosporin biosynthesis in A. chrysogenum derives from the autotrophic (SH(2)) and the reverse transsulfuration pathways. Levels of methionine induction of the cephalosporin biosynthesis gene pcbC were identical in the parental strain and the mecB mutants, indicating that the induction effect is not mediated by cystathionine-gamma-lyase.
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Affiliation(s)
- G Liu
- Area of Microbiology, Faculty of Biology, University of León, 24071 León, Spain
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Pignède G, Wang HJ, Fudalej F, Seman M, Gaillardin C, Nicaud JM. Autocloning and amplification of LIP2 in Yarrowia lipolytica. Appl Environ Microbiol 2000; 66:3283-9. [PMID: 10919782 PMCID: PMC92146 DOI: 10.1128/aem.66.8.3283-3289.2000] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We synthesized a Yarrowia lipolytica strain overproducing lipase for industrial applications by using long terminal repeat (zeta) of the Y. lipolytica retrotransposon Ylt1 and an allele of URA3 with a promoter deletion to construct JMP3. JMP3 is a derivative of plasmid pHSS6 carrying a NotI-NotI cassette which contains a defective URA3 allele, a polylinker sequence, and the zeta region for targeting to multiple sites in the genome of the recipient. We inserted the LIP2 gene (encoding extracellular lipase) under the control of the strong POX2 promoter into JMP3 to generate JMP6. The pHSS6 region was removed by NotI digestion prior to transformation. Two Y. lipolytica strains transformed with the JMP6 LIP2 cassette had a mean of 10 integrated copies devoid of the Escherichia coli region, corresponding to an autocloning event. The copy number in the transformants was stable even after 120 generations in nonselective and lipase-inducing conditions. The resulting strains could produce 0.5 g of active lipase per liter in the supernatant, 40 times more than the single-copy strain with the LIP2 promoter. This work provides a new expression system in Y. lipolytica that results in strains devoid of bacterial DNA and in strains producing a high level of lipase for industrial uses, waste treatment, and pancreatic insufficiency therapy.
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Affiliation(s)
- G Pignède
- Laboratoire Mayoly-Spindler, Service Recherche, Chatou Cedex, France
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Inoue S, Turgeon BG, Yoder OC, Aist JR. Role of fungal dynein in hyphal growth, microtubule organization, spindle pole body motility and nuclear migration. J Cell Sci 1998; 111 ( Pt 11):1555-66. [PMID: 9580563 DOI: 10.1242/jcs.111.11.1555] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytoplasmic dynein is a microtubule-associated motor protein with several putative subcellular functions. Sequencing of the gene (DHC1) for cytoplasmic dynein heavy chain of the filamentous ascomycete, Nectria haematococca, revealed a 4,349-codon open reading frame (interrupted by two introns) with four highly conserved P-loop motifs, typical of cytoplasmic dynein heavy chains. The predicted amino acid sequence is 78.0% identical to the cytoplasmic dynein heavy chain of Neurospora crassa, 70.2% identical to that of Aspergillus nidulans and 24.8% identical to that of Saccharomyces cerevisiae. The genomic copy of DHC1 in N. haematococca wild-type strain T213 was disrupted by inserting a selectable marker into the central motor domain. Mutants grew at 33% of the wild-type rate, forming dense compact colonies composed of spiral and highly branched hyphae. Major cytological phenotypes included (1) absence of aster-like arrays of cytoplasmic microtubules focused at the spindle pole bodies of post-mitotic and interphase nuclei, (2) limited post-mitotic nuclear migration, (3) lack of spindle pole body motility at interphase, (4) failure of spindle pole bodies to anchor interphase nuclei, (5) nonuniform distribution of interphase nuclei and (6) small or ephemeral Spitzenkorper at the apices of hyphal tip cells. Microtubule distribution in the apical region of tip cells of the mutant was essentially normal. The nonuniform distribution of nuclei in hyphae resulted primarily from a lack of both post-mitotic nuclear migration and anchoring of interphase nuclei by the spindle pole bodies. The results support the hypothesis that DHC1 is required for the motility and functions of spindle pole bodies, normal secretory vesicle transport to the hyphal apex and normal hyphal tip cell morphogenesis.
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Affiliation(s)
- S Inoue
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853, USA
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MIGHELI Q, FRIARD O, TEDESCO DDEL, MUSSO MR, GULLINO ML. Stability of transformed antagonistic Fusarium oxysporum strains in vitro and in soil microcosms. Mol Ecol 1996. [DOI: 10.1111/j.1365-294x.1996.tb00359.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Judelson HS, Whittaker SL. Inactivation of transgenes in Phytophthora infestans is not associated with their deletion, methylation, or mutation. Curr Genet 1995; 28:571-9. [PMID: 8593689 DOI: 10.1007/bf00518171] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The mitotic and meiotic stabilities of transgenes were evaluated in the oomycete, Phytophthora infestans. Genes encoding beta-glucuronidase (GUS), neomycin phosphotransferase (NPT) and hygromycin phosphotransferase (HPT), fused to one of six promoters from P. infestans or other oomycetes, were usually stably expressed during continued asexual culture and transmitted to progeny. However, the activity of these genes became undetectable in many strains during asexual or sexual propagation. Over 33 months of growth, transgene expression stopped each month in 1-3% of the transformants. Silencing of the genes was not associated with their deletion, mutation, or hypermethylation. The conformation of the integrated sequences was similar in strains destined to continue or terminate expression of the transgenes. Expression of the genes was not associated with a loss of fitness during growth in vitro and in planta, which might otherwise have selected for silencing events.
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Affiliation(s)
- H S Judelson
- Department of Plant Pathology, University of California, Riverside 92521, USA
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Pilgeram AL, Goins T, Henson JM. The fate of integrated DNA inGaeumannomyces graministransformants. FEMS Microbiol Lett 1993. [DOI: 10.1111/j.1574-6968.1993.tb06532.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Walz M, Kück U. Targeted integration into the Acremonium chrysogenum genome: disruption of the pcbC gene. Curr Genet 1993; 24:421-7. [PMID: 8299158 DOI: 10.1007/bf00351851] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cephalosporin C-producing fungus Acremonium chrysogenum was transformed to hygromycin B resistance using different vector constructs. These constructs contain sequences of the pcbC gene from A. chrysogenum, encoding isopenicillin N synthetase. Detailed analysis of transformants, including pulsed-field gel electrophoresis (PFGE), suggests that integration of multiple vector copies takes place predominantly via non-homologous integration. By increasing the length of vector-DNA homologous to genomic DNA, integration occurs more frequently into chromosome VI, carrying the endogenous pcbC gene copy. In gene disruption experiments, the length of vector homology required to obtain cephalosporin C-minus transformants was investigated. Inactivation of the pcbC gene was observed only when homologous fragments of more than 3.0 kb were used on both sites of the resistance cassette. Southern analysis indicated homologous, as well as heterologous, integration of recombinant DNA. The integration of multiple vector copies leads to the appearance of truncated pcbC transcripts.
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Affiliation(s)
- M Walz
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität Bochum, Germany
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Judelson HS, Dudler R, Pieterse CM, Unkles SE, Michelmore RW. Expression and antisense inhibition of transgenes in Phytophthora infestans is modulated by choice of promoter and position effects. Gene 1993; 133:63-9. [PMID: 8224895 DOI: 10.1016/0378-1119(93)90225-r] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Procedures were identified for manipulating the expression of genes in the oomycete fungus, Phytophthora infestans. The activities of five putative promoter sequences, derived from the 5' regions of oomycete genes, were measured in transient assays performed in protoplasts and in stable transformants. The sequences tested were from the ham34 and hsp70 genes of Bremia lactucae, the actin-encoding genes of P. infestans and P. megasperma, and a polyubiquitin-encoding gene of P. infestans. Experiments using the GUS reporter gene (encoding beta-glucuronidase) demonstrated that each 5' fragment had promoter activity, but that their activities varied over a greater than tenfold range. Major variation was revealed in the level of transgene expression in individual transformants containing the same promoter::GUS or promoter::lacZ fusion. The level of expression was not simply related to the number of genes present, suggesting that position effects were also influencing expression. Fusions between the ham34 promoter, and full-length and partial GUS genes in the antisense orientation blocked the expression of GUS in protoplasts and in stable transformants.
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Affiliation(s)
- H S Judelson
- Center for Engineering Plants for Resistance Against Pathogens, University of California, Davis 95616
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11
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Arnau J, Oliver RP. Inheritance and alteration of transforming DNA during an induced parasexual cycle in the imperfect fungus Cladosporium fulvum. Curr Genet 1993; 23:508-11. [PMID: 8319310 DOI: 10.1007/bf00312643] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Protoplasts of a pAN7-1-transformed isolate of Cladosporium fulvum race 4, harbouring a tandem duplication of the vector, and an untransformed race 5 isolate were fused, without selection for the presence of vector sequences. Fusion products were allowed to haploidize spontaneously. The inheritance of pAN7-1 sequences and the expression of the hph gene was studied in 85 progeny. A very high proportion (80%) of the progeny contained vector sequences and 70% of the progeny were resistant to hygromycin. Inactivation of the hph gene occurred in eight progeny. Rearrangement of vector sequences can account for the inactivation: there is no evidence for any RIP-like mechanism. A number of novel bands were observed.
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Affiliation(s)
- J Arnau
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Salch YP, Beremand MN. Gibberella pulicaris transformants: state of transforming DNA during asexual and sexual growth. Curr Genet 1993; 23:343-50. [PMID: 8467533 DOI: 10.1007/bf00310897] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A genetically fertile, trichothecene-producing plant pathogen, Gibberella pulicaris (Fusarium sambucinum), was transformed with three different vectors: cosHyg1, pUCH1, and pDH25. All three vectors carry hph (encoding hygromycin B phosphotransferase) as the selectable marker. Transformation frequency was 0.03 transformants per mumg of DNA for pDH25 and 0.5 for pUCH1 or cosHyg1. The vector DNA sequences integrated at different sites into the fungal genome. Transformants were classified into three types based upon distinctive integration patterns: type A contained a single, intact copy of the vector at one site per genome; type B contained multiple tandem copies or a combination of single and multiple tandem copies at one or more sites per genome; type C contained a partial vector copy at one site per genome. While the transformants with cosHyg1 and pUCH1 were type A or B, type C was unique to pDH25 transformants. Type A and C transformants were both meiotically and mitotically stable. However, type B multiple inserts were unstable in mitosis and meiosis since: (1) multiple tandem copies were deleted; (2) rearrangements occurred during premeiosis; and (3) inserts in one of the type B transformants became methylated during premeiosis. Differential expression of transforming sequences between spore germination and mycelial growth was also observed among type B transformants. The ability to transform G. pulicaris with the resulting varied features of integration patterns and the behavior of transforming DNA during mitosis and meiosis provides a means to isolate, manipulate, and study cloned genes in this mycotoxin-producing plant pathogen.
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Affiliation(s)
- Y P Salch
- USDA/ARS, National Center for Agricultural Utilization Research, St., Peoria, IL 61604
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13
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Affiliation(s)
- E U Selker
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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14
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Peng M, Singh NK, Lemke PA. Recovery of recombinant plasmids from Pleurotus ostreatus transformants. Curr Genet 1992; 22:53-9. [PMID: 1611668 DOI: 10.1007/bf00351742] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A transformation system employing selectable resistance to hygromycin B has been developed for the mushroom-forming fungus, Pleurotus ostreatus. Vector pAN7-1, a commonly used non-replicative vector for integrative transformation in fungi, yielded 5-46 resistant colonies per micrograms of DNA per 10(7) viable protoplasts. Southern blot analysis of certain transformants revealed unexpected replicative plasmids containing pAN7-1 sequences, but modified for size, methylation and restriction enzyme pattern when compared to the initial transforming vector. Two such replicative derivatives of pAN7-1 have been rescued from P. ostreatus by cloning into Escherichia coli. Rescued plasmids have been used to probe DNA from untransformed P. ostreatus in an effort to identify fungal sequences that recombined in vivo with pAN7-1 to form replicative plasmids. Such replicative sequences have been localized in high molecular weight (chromosomal) DNA of wild-type P. ostreatus. Transformation has been obtained for P. ostreatus using a rescued plasmid, thereby confirming the role of this recombinant plasmid as a shuttle vector.
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Affiliation(s)
- M Peng
- Department of Botany and Microbiology, Auburn University, AL 36849-5407
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Durand N, Reymond P, F�vre M. Transmission and modification of transformation markers during an induced parasexual cycle in Penicillium roqueforti. Curr Genet 1992. [DOI: 10.1007/bf00351698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Meiotic and mitotic stability of transforming DNA in the phytopathogenic fungus Magnaporthe grisea. Curr Genet 1992. [DOI: 10.1007/bf00318655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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