1
|
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.
Collapse
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
| |
Collapse
|
2
|
Albee SR, Mueller GM, Kropp BR. Polymorphisms in the large intergenic spacer of the nuclear ribosomal repeat identify Laccaria proxima strains. Mycologia 2018. [DOI: 10.1080/00275514.1996.12026738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Steven R. Albee
- Biology Department, Utah State University, Logan, Utah 84322-5305
| | - Gregory M. Mueller
- Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605-2496
| | - Bradley R. Kropp
- Biology Department, Utah State University, Logan, Utah 84322-5305
| |
Collapse
|
3
|
Utomo C, Werner S, Niepold F, Deising HB. Identification of Ganoderma, the causal agent of basal stem rot disease in oil palm using a molecular method. Mycopathologia 2005; 159:159-70. [PMID: 15750749 DOI: 10.1007/s11046-004-4439-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
From comparison of the alignments of the internally transcribed spacers (ITS) of ribosomal DNA from Ganoderma associated with oil palm basal stem rot (BSR) and other Ganoderma species, two specific primer pairs were selected to provide a specific DNA amplification of pathogenic Ganoderma in oil palm. Each primer pair produced a single PCR product of about 450 bp (for primer pair IT1-IT2) and 334 bp (for primer pair IT1-IT3) when oil palm Ganoderma DNA was used. No PCR amplification product was observed when other Ganoderma species DNA was used in PCR amplification with these primer pairs. Three specific restriction enzyme sites were identified in the ITS and intergenic spacer (IGS1) regions. The restriction enzymes MluI, SacI and HinfI were used to digest the ITS-PCR product and restriction enzymes TfiI, ScaI and HincII were used to digest the IGS1-PCR product. Of the three restriction enzymes used in each rDNA region, MluI specifically digested the ITS regions, and TfiI specifically digested the IGS1 region of oil palm Ganoderma. Analysis of the published ITS nucleotide sequences of 31 Ganoderma species showed that the MluI restriction site was not present in other Ganoderma species. The use of both specific primers and restriction enzyme analysis can be applied as a standard protocol to identify pathogenic Ganoderma in oil palm. In this study, the use of specific primers and PCR-RFLP analyses of the rDNA gave consistent results for the characterisation of pathogenic Ganoderma, and indicated that Ganoderma strains associated with BSR disease in oil palms belong to a single species.
Collapse
Affiliation(s)
- C Utomo
- Indonesian Oil Palm Research Institute (IOPRI), Jl. Brigjen Katamso No. 51, Medan 20158, North Sumatra, Indonesia.
| | | | | | | |
Collapse
|
4
|
Baird RE, Gitaitis RD, Carling DE, Baird SM, Alt PJ, Mullinix BG. Determination of Whole-Cell Fatty Acid Profiles for the Characterization and Differentiation of Isolates of Rhizoctonia solani AG-4 And AG-7. PLANT DISEASE 2000; 84:785-788. [PMID: 30832109 DOI: 10.1094/pdis.2000.84.7.785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fatty acid methyl esters (FAMEs) of isolates of Rhizoctonia solani AG-4 and AG-7 were characterized by gas chromatography and analyzed with Microbial Identification System software. Palmitic, stearic, and oleic acids were common in all isolates from both anastomosis groups (AGs) and accounted for 95% of the C14 to C18 fatty acids present. Oleic acid, most common in both R. solani AG-4 and AG-7 isolates, accounted for the greatest percentages of total FAMEs. The presence, quantities, or absence of individual fatty acids could not be used for distinguishing AG-4 and AG-7 isolates. Anteisopentadecanoic and 9-heptadecanoic acids, however, were specific to all three AG-7 isolates from Japan but absent in other AG-7 isolates and all AG-4 isolates. Pentadecanoic acid occurred in only two of the R. solani AG-4 isolates, but was not found in any of the AG-7 isolates. The AG-4 isolates could be distinguished from AG-7 isolates when quantities of FAMEs and key FAME ratios were analyzed with cluster analysis and principle components were plotted. Isolates of AG-7 from Arkansas, Indiana, and Georgia appeared to be more closely related to each other than to AG-7 isolates from Japan and Mexico. These differences in FAMEs were sufficiently distinct that isolate geographical variability could be determined. A dendrogram analysis cluster constructed from the FAMEs data showed results similar to that of the principal component analysis. Euclidean distances of total AG-4 isolates were distinct from total AG-7 isolates. The Arkansas and Indiana AG-7 isolates had a similar Euclidean distance to each another but the percentages were different for the AG-7 isolates from Japan and Mexico. In conclusion, variability of the FAMEs identified in this study would not be suitable as the main diagnostic tool for distinguishing individual isolates of R. solaniAG-4 from AG-7.
Collapse
Affiliation(s)
- R E Baird
- Entomology and Plant Pathology Department, Mississippi State University, Mississippi State 39762
| | - R D Gitaitis
- Plant Pathology Department, University of Georgia, CPES, Tifton 31793
| | - D E Carling
- Agricultural and Forestry Experiment Station, University of Alaska-Fairbanks, Palmer 99645
| | - S M Baird
- Entomology and Plant Pathology Department, Mississippi State University
| | - P J Alt
- Plant Pathology Department, Mississippi State University
| | - B G Mullinix
- Experimental Statistics Unit, University of Georgia, CPES
| |
Collapse
|
5
|
Use of RFLP and SSCP analysis to differentiate the pine rusts Cronartium flaccidum and Peridermium pini. ACTA ACUST UNITED AC 1998. [DOI: 10.1017/s0953756297005467] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
6
|
Variation in the ITS and IGS regions of ribosomal DNA among the biological species of European Armillaria. ACTA ACUST UNITED AC 1998. [DOI: 10.1017/s0953756297005315] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
7
|
Kwon-Chung KJ, Chang YC, Penoyer L. Species of the genus Filobasidielladiffer in the organization of their 5S rRNA genes. Mycologia 1997. [DOI: 10.1080/00275514.1997.12026777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- K. J. Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Yun C. Chang
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - L. Penoyer
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| |
Collapse
|
8
|
Jeng R, Hintz WE, Bowden CG, Horgen PA, Hubbes M. A comparison of the nucleotide sequence of the cerato-ulmin gene and the rDNA ITS between aggressive and non-aggressive isolates of Ophiostoma ulmi sensu lato, the causal agent of Dutch elm disease. Curr Genet 1996; 29:168-73. [PMID: 8821664 DOI: 10.1007/bf02221581] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Little genetic information exists comparing aggressive and non-aggressive isolates of the causal agent of Dutch elm disease, Ophiostoma ulmi. Two genetic elements were compared between the subgroups. The ceratoulmin cu gene product has been associated with disease symptoms. Nucleotide-sequence analysis of cu and the internal transcribed spacer (ITS) region of the rDNA were made from three aggressive and three non-aggressive isolates of the pathogen. Our results suggested uniformity within, and unique differences between, subgroups. Differences were detected for cu in the promoter, coding, and transcription termination regions. Sequence data for the ITS clearly distinguish the subgroups.
Collapse
Affiliation(s)
- R Jeng
- Faculty of Forestry, University of Toronto, Ontario, Canada
| | | | | | | | | |
Collapse
|
9
|
Béatrice L, Georgios Z. Molecular systematics of the genus Pleurotus: analysis of restriction polymorphisms in ribosomal DNA. Microbiology (Reading) 1995; 141:1479-1490. [DOI: 10.1099/13500872-141-6-1479] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Part of the nuclear ribosomal DNA unit of Pleurotus cornucopiae, including most of the intergenic sequences, was used as a probe to hybridize with DNA from eleven Pleurotus taxa (29 isolates), digested with nine restriction endonucleases. For all digests, a high level of rDNA heterogeneity between and within species was detected, which is in agreement with the phenetic variability already reported in previous studies on Pleurotus taxa. Numerical analysis of the results, performed by use of two different tree-making methods, clearly distinguished among well-defined species, i.e. P. dryinus, P. eryngii and P. flabellatus, which presented large phenetic distances with the rest of the taxa tested. P. abalonus, despite morphological similarity and interfertility with P. cystidiosus, appears to be a discrete taxon. Although they showed relative affinity, P. cornucopiae, P. columbinus and P. ostreatus presented large distances among their representative isolates, supporting the idea that they correspond to distinct taxa. All strains of P. pulmonarius, P. sajor-caju and P. sapidus having small phenetic distances were closely positioned on dendrograms; in relation to results from recent interfertility and isozyme studies, these results support the common genetic background of P. pulmonarius and P. sajor-caju; the position of P. sapidus remains controversial. Furthermore, the rDNA analysis identified ten fragments suitable for species identification: eight allowed the characterization of five taxa (P. cornucopiae. P. ostreatus, P. sajor-caju, P. abalonus and P. columbinus) and two distinguished among clusters including related taxa. By a combination of just two restriction enzymes, the rDNA probe used seems to be the appropriate tool for both varietal characterization and protection of commercially valuable strains.
Collapse
Affiliation(s)
| | - Zervakis Georgios
- Laboratoire de Génétique Moléculaire et d'Amélioration des Champignons Cultivés, Université de Bordeaux II -INRA, CRA de Bordeaux, BP 81, 33883 Villenave d'Ornon Cedex, France
| |
Collapse
|
10
|
Iraçabal B, Labarère J. Restriction site and length polymorphism of the rDNA unit in the cultivated basidiomycetePleurotus cornucopiae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 88:824-830. [PMID: 24186184 DOI: 10.1007/bf01253992] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/1993] [Accepted: 12/21/1993] [Indexed: 06/02/2023]
Abstract
In the ribosomal DNA unit ofPleurotus cornucopiae, the rDNA coding regions are in the order 5', 5S-18S-5.8S-25S, 3', with the 5' location of the 5S gene differing from its 3' location found in other basidiomycetes. The most discriminating probe used to study the rDNA polymorphism consisted of a fragment that included the 5S, 18S and part of the 5.8S and 25S genes flanking three intergenic sequences. A high degree of rDNA polymorphism was observed in the sevenP. cornucopiae dikaryons studied. For the first time within a basidiomycete species, the restrictions maps distinguished two types of rDNA units (I and II). In each rDNA type, length variations in the external intergenic sequence IGS 1 located between the 25S and 5S genes allowed characterization of two different rDNA units in type I and four rDNA units in type II. This suggested that theP. cornucopiae rDNA units were derived from two kinds of ancestors (type I and II) by insertion or deletion events (100-700 bp) in the IGS 1. In four dikaryotic strains, two rDNA units of the same type (I or II) differing only by the IGS 1 length, were found in a similar number of copies, and presented a meiotic segregation in homokaryotic progeny. In one progeny, some homokaryotic strains possessed two different rDNA units: one with a high copy number and another with a lower one, showing that two different rDNA units could coexist in a single nucleus.
Collapse
Affiliation(s)
- B Iraçabal
- Laboratoire de Génétique Moléculaire et Amélioration des Champignons Cultivés, Université de Bordeaux II-INRA, CRA. de Bordeaux, B.P. 81, 33883, Villenave d'Ornon Cedex, France
| | | |
Collapse
|
11
|
Yao C, Frederiksen RA, Magill CW. Length heterogeneity in ITS 2 and the methylation status of CCGG and GCGC sites in the rRNA genes of the genus Peronosclerospora. Curr Genet 1992; 22:415-20. [PMID: 1423729 DOI: 10.1007/bf00352443] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The polymerase chain reaction (PCR) was used with primers complementary to conserved flanking sequences to amplify the internal transcribed spacer 2 (ITS 2) of the rDNA repeat units of five Peronoscleropora isolates, one each of P. sorghi, P. maydis, P. sacchari and two of P. zeae. In contrast to the situation found in most-fungi that have been examined, length heterogeneity was evident in each sample. The rDNA composition of the amplified bands was confirmed by Southern hybridizations using an ITS 2 amplified from P. sorghi and cloned rDNA from Neurospora crassa as probes. Length heterogeneity was also detected in genomic DNA digests using the same probes. In addition to one dominant fragment for each isolate, there were several less frequent fragments of different sizes, and the isolate(s) for each species had a unique banding pattern for ITS 2. The absence of 5-methylcytosine residues in CCGG and GCGC sequences in the ribosomal genes of these four Peronosclerospora species was demonstrated by the production of identical banding patterns with ribosomal DNA probes following digestion of genomic DNA with MspI and HpaII, and by complete digestion with CfoI.
Collapse
Affiliation(s)
- C Yao
- Department of Plant Pathology and Microbiology, Texas A and M University, College Station 77843
| | | | | |
Collapse
|
12
|
Russo P, Juuti JT, Raudaskoski M. Cloning, sequence and expression of a beta-tubulin-encoding gene in the homobasidiomycete Schizophyllum commune. Gene X 1992; 119:175-82. [PMID: 1398097 DOI: 10.1016/0378-1119(92)90269-u] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The beta-tubulin (beta Tub)-encoding gene (tub-2) of Schizophyllum commune is the first tubulin gene isolated, cloned and sequenced from higher filamentous fungi (homobasidiomycetes). The S. commune tub-2 gene is organized into nine exons and eight introns. The introns vary from 48 to 107 nt in length, and are distributed throughout the gene. The tub-2 exons code for a protein of 445 amino acids (aa), which shows great homology with beta Tubs of filamentous ascomycetes, plants, and animals, but less homology with yeasts. The codon usage of tub-2 from S. commune is biased, as it is in most beta Tub-encoding genes of filamentous fungi. The S. commune beta Tub shows a conserved aa sequence in the C-terminal domain, which is suggested to interact with microtubule-associated proteins in animals. In contrast, the S. commune beta Tub deviates from most known beta Tubs by having a Cys165 residue, which might be significant for the insensitivity of S. commune haploid strains to the antimicrotubule drug, benomyl. In tub-2 of different haploid strains, sequence polymorphisms occur in the 5' and 3' flanking regions. The expression of tub-2 is high in young mycelium, which has a high number of extending apical cells, but decreases with the aging of the mycelium. No significant difference in the hybridization signal intensity for the tub-2 transcripts was recorded either during intercellular nuclear migration at early mating, or in mycelia with a mutation in the B mating-type gene.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- P Russo
- Department of Botany, University of Helsinki, Finland
| | | | | |
Collapse
|
13
|
|
14
|
Chen W, Hoy JW, Schneider RW. Species-specific polymorphisms in transcribed ribosomal DNA of fivePythium species. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0147-5975(92)90038-s] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
15
|
Ullrich RC, Specht CA, Stankis MM, Yang H, Giasson L, Novotny CP. Molecular biology of mating-type determination in Schizophyllum commune. GENETIC ENGINEERING 1991; 13:279-306. [PMID: 1367417 DOI: 10.1007/978-1-4615-3760-1_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- R C Ullrich
- Department of Botany, University of Vermont, Burlington 05405
| | | | | | | | | | | |
Collapse
|
16
|
Vilgalys D, Gonzalez D. Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola. Curr Genet 1990; 18:277-80. [PMID: 2249259 DOI: 10.1007/bf00318394] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
17
|
Duchesne LC, Anderson JB. Location and direction of transcription of the 5S rRNA gene in Armillaria. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0953-7562(09)80626-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
18
|
Affiliation(s)
- J M Magill
- Department of Biochemistry, Texas A&M University, College Station 77843
| | | |
Collapse
|
19
|
Developmental regulation of the methylation of the ribosomal DNA in the basidiomycete fungusSchizophyllum commune. Curr Genet 1988. [DOI: 10.1007/bf00569333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|