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Functions of polyamines in growth and development of Phycomyces blakesleeanus wild-type and mutant strains. Fungal Biol 2022; 126:429-437. [DOI: 10.1016/j.funbio.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/18/2022]
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2
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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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Couturier M, Lindås AC. The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. Front Microbiol 2018; 9:137. [PMID: 29472906 PMCID: PMC5809426 DOI: 10.3389/fmicb.2018.00137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is the most common epigenetic modification observed in the genomic DNA (gDNA) of prokaryotes and eukaryotes. Methylated nucleobases, N6-methyl-adenine (m6A), N4-methyl-cytosine (m4C), and 5-methyl-cytosine (m5C), detected on gDNA represent the discrimination mark between self and non-self DNA when they are part of restriction-modification systems in prokaryotes (Bacteria and Archaea). In addition, m5C in Eukaryotes and m6A in Bacteria play an important role in the regulation of key cellular processes. Although archaeal genomes present modified bases as in the two other domains of life, the significance of DNA methylations as regulatory mechanisms remains largely uncharacterized in Archaea. Here, we began by investigating the DNA methylome of Sulfolobus acidocaldarius. The strategy behind this initial study entailed the use of combined digestion assays, dot blots, and genome resequencing, which utilizes specific restriction enzymes, antibodies specifically raised against m6A and m5C and single-molecule real-time (SMRT) sequencing, respectively, to identify DNA methylations occurring in exponentially growing cells. The previously identified restriction-modification system, specific of S. acidocaldarius, was confirmed by digestion assay and SMRT sequencing while, the presence of m6A was revealed by dot blot and identified on the characteristic Dam motif by SMRT sequencing. No m5C was detected by dot blot under the conditions tested. Furthermore, by comparing the distribution of both detected methylations along the genome and, by analyzing DNA methylation profiles in synchronized cells, we investigated in which cellular pathways, in particular the cell cycle, this m6A methylation could be a key player. The analysis of sequencing data rejected a role for m6A methylation in another defense system and also raised new questions about a potential involvement of this modification in the regulation of other biological functions in S. acidocaldarius.
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Affiliation(s)
- Mohea Couturier
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Bartnicki-García S. José Ruiz-Herrera - biographical sketch. FEMS Yeast Res 2006; 6:949-56. [PMID: 17042745 DOI: 10.1111/j.1567-1364.2006.00104.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Salomón Bartnicki-García
- Division of Experimental and Applied Biology, Center for Scientific Investigation & Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico.
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Akiyama K, Thanonkeo P, Ogawa H, Ohguchi T, Takata R. Detection and cloning of the gene encoding a protein produced by nonpathogenic mutants of Fusarium oxysporum. J Biosci Bioeng 2000; 90:302-7. [PMID: 16232860 DOI: 10.1016/s1389-1723(00)80085-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2000] [Accepted: 06/15/2000] [Indexed: 11/24/2022]
Abstract
Treatment of Fusarium oxysporum with 5-azacytidine, a potent inhibitor of DNA methylation, induced nonpathogenic mutants. Analysis of the protein expression pattern by two-dimensional gel electrophoresis revealed a protein that is present in yeast-form cells of the mutants but absent in those of the wild-type strain. N-terminal amino acid analysis indicated that this protein is identical to a region of a polypeptide encoded by a cDNA clone, sti35, previously identified as a heat shock gene in F. oxysporum. A genomic clone for sti35 was isolated and sequence analysis revealed an intron and two heat shock elements upstream of sti35. The analysis also revealed the presence of a leader sequence composed of 27 amino acid residues, which shares a common amino acid composition with leader sequences of the proteins located in the mitochondrial matrix. Different expression patterns of sti35 in the mutants and wild-type strain were demonstrated.
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Affiliation(s)
- K Akiyama
- Center for Gene Research, Ehime University, Matsuyama 790-8566, Japan
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AKIYAMA KOUICHI, THANONKEO PORNTHAP, OGAWA HIRONOBU, OHGUCHI TOMIZO, TAKATA RENKICHI. Detection and Cloning of the Gene Encoding a Protein Produced by Nonpathogenic Mutants of Fusarium oxysporum. J Biosci Bioeng 2000. [DOI: 10.1263/jbb.90.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Ruiz-Herrera J, Ruiz-Medrano R, Domínguez A. Selective inhibition of cytosine-DNA methylases by polyamines. FEBS Lett 1995; 357:192-6. [PMID: 7805889 DOI: 10.1016/0014-5793(94)01360-d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have advanced the hypothesis that polyamines affect DNA methylation and thus promote the expression of developmentally controlled genes. We demonstrate that the activity of cytosine-DNA methyltransferases HpaII, HhaI, HaeIII and SssI is inhibited by physiological concentrations of polyamines. On the other hand, activity of the adenine-DNA methyltransferase EcoRI, and restriction enzymes HpaII, HhaI, HaeIII and EcoRI, is insensitive to polyamine concentrations up to 40 mM. Our results indicate that the effect of polyamines on cytosine-DNA methyltransferases is rather selective and suggest a possible mode of action in vivo.
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Affiliation(s)
- J Ruiz-Herrera
- Departmento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto., Mexico
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Feistner GJ. Metabolism of polyamines and basic amino acids in Erwinia amylovora: application of liquid chromatography/electrospray mass spectrometry to proferrioxamine precursor feeding and inhibition studies. BIOLOGICAL MASS SPECTROMETRY 1994; 23:793-803. [PMID: 7841214 DOI: 10.1002/bms.1200231212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Erwinia amylovora, the etiological agent of fire blight, produces a family of proferrioxamine siderophores, which may be essential for the pathogen to establish itself in its hosts. If so, then control of fire blight may perhaps be possible via interference with proferrioxamine biosynthesis. Proof of this hypothesis requires prior knowledge of the corresponding biosynthetic pathways in E. amylovora. As a first step towards understanding proferrioxamine biosynthesis, it was of interest to investigate the ability of the fire blight bacterium to utilize various potential biosynthetic pathways for diamines. Feeding of lysine, ornithine and diaminobutyric acid gave rise to highly elevated levels of cadaverine, putrescine and diaminopropane, respectively, indicating that the corresponding decarboxylase activities are all present in E. amylovora. The conclusion for lysine decarboxylase was confirmed with (15N2)lysine, which was converted to (15N2)cadaverine. Arginine did not increase putrescine levels substantially, but (13C6)arginine nevertheless gave rise to (13C4)putrescine while suppressing excretion of non-labeled putrescine. A serendipitous result of this study was the finding that the growth of E. amylovora can be inhibited with 5-hydroxylysine and 1,4-diamino-2-butanone. The mechanism of inhibition appears complex and is not yet understood. For 5-hydroxylysine, preliminary investigations point to a competitive inhibition of lysine decarboxylase. However, the growth inhibition cannot be reversed by providing cadaverine, the decarboxylation product of lysine.
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Affiliation(s)
- G J Feistner
- Beckman Research Institute of the City of Hope, Duarte, California 91010
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Elorza MV, Sentandreu R, Ruiz-Herrera J. Isolation and characterization of yeast monomorphic mutants of Candida albicans. J Bacteriol 1994; 176:2318-25. [PMID: 8157600 PMCID: PMC205355 DOI: 10.1128/jb.176.8.2318-2325.1994] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A method was devised for the isolation of yeast monomorphic (LEV) mutants of Candida albicans. By this procedure, about 20 stable yeast-like mutants were isolated after mutagenesis with ethyl methane sulfonate. The growth rate of the mutants in different carbon sources, both fermentable and not, was indistinguishable from that of the parental strain, but they were unable to grow as mycelial forms after application of any of the common effective inducers, i.e., heat shock, pH alterations, proline addition, or use of GlcNAc as the carbon source. Studies performed with one selected strain demonstrated that it had severe alterations in the chemical composition of the cell wall, mainly in the levels of chitin and glucans, and in specific mannoproteins, some of them recognizable by specific polyclonal and monoclonal antibodies. It is suggested that these structural alterations hinder the construction of a normal hyphal wall.
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Affiliation(s)
- M V Elorza
- Sección de Microbiología, Facultat de Farmacia, Universitat de Valencia, Spain
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Abstract
Mucorales constitute a group of fungi that, because of their growth characteristics, have been used extensively in the study of cell differentiation, cell morphogenesis, and stimuli perception. We have studied the role of polyamine metabolism in the development of different Mucorales, with emphasis on Mucor and Phycomyces species. It has been observed that previous to each differentiative step, the cellular levels of the most regulated enzyme of the pathway, ornithine decarboxylase (ODC), and polyamines suffer a noticeable increase. Addition of diaminobutanone (DAB), a competitive inhibitor of ODC, blocks all the corresponding differentiative phenomena. In its presence, germinating spores fail to produce germ tubes and keep growing isodiametrically; mycelia do not sporulate but continue their vegetative growth, and yeast cells are unable to engage in a dimorphic transition without alterations in their growth rate. This differential effect of the ODC inhibitor in growth and development is apparently due to the location of ODC in at least two different cell compartments, one of which is impermeable to the drug. Inhibition of development is counteracted by putrescine and more noticeably by 5-azacytidine (5AC), a strong inhibitor of DNA methylation. Methylation levels of DNA are high in spores, and they become reduced after germination. Demethylation is inhibited by hydroxyurea, which blocks DNA replication, and by DAB. The effect of the latter is reversed by 5AC. These results suggest a relationship between polyamines and DNA methylation. Analysis of metallothioneine gene (CUP) behavior and expression during spore germination has confirmed this hypothesis.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J Ruiz-Herrera
- Department of Genética y Biología Molecular, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Gto., México
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Affiliation(s)
- E U Selker
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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Effect of dibutyryl-cAMP on growth and morphology of germinatingMucor rouxii sporangiospores. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0147-5975(92)90015-j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cano-Canchola C, Sosa L, Fonzi W, Sypherd P, Ruiz-Herrera J. Developmental regulation of CUP gene expression through DNA methylation in Mucor spp. J Bacteriol 1992; 174:362-6. [PMID: 1729231 PMCID: PMC205725 DOI: 10.1128/jb.174.2.362-366.1992] [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: 12/28/2022] Open
Abstract
Inserts which carried the CUP gene from Saccharomyces cerevisiae or Mucor racemosus were used as hybridization probes to measure the methylation state and expression of the CUP gene from Mucor rouxii at different stages of growth. It was observed that the fungus contains a CUP multigene family. All the CUP genes were present in a hypermethylated DNA region in nongrowing and isodiametrically growing spores and were not transcribed at these stages. After germ tube emergence, CUP genes became demethylated and transcriptionally active. Development, demethylation, and transcription of CUP genes were blocked by the ornithine decarboxylase inhibitor 1,4-diaminobutanone. These results suggest that genes that are activated during development became demethylated in this fungus.
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Affiliation(s)
- C Cano-Canchola
- Instituto de Investigación en Biología Experimental, Facultad de Química, Universidad de Guanajuato, Mexico
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Abstract
Mucor dimorphism has interested microbiologists since the time of Pasteur. When deprived of oxygen, these fungi grow as spherical, multipolar budding yeasts. In the presence of oxygen, they propagate as branching coenocytic hyphae. The ease with which these morphologies can be manipulated in the laboratory, the diverse array of morphopoietic agents available, and the alternative developmental fates that can be elicited from a single cell type (the sporangiospore) make Mucor spp. a highly propitious system in which to study eukaryotic cellular morphogenesis. The composition and organization of the cell wall differ greatly in Mucor yeasts and hyphae. The deposition of new wall polymers is isodiametric in yeasts and apically polarized in hyphae. Current research has focused on the identity and control of enzymes participating in wall synthesis. An understanding of how the chitosome interacts with appropriate effectors, specific enzymes, and the plasma membrane to assemble chitin-chitosan microfibrils and to deposit them at the proper sites on the cell exterior will be critical to elucidating dimorphism. Several biochemical and physiological parameters have been reported to fluctuate in a manner that correlates with Mucor morphogenesis. The literature describing these has been reviewed critically with the intent of distinguishing between causal and casual connections. The advancement of molecular genetics has afforded powerful new tools that researchers have begun to exploit in the study of Mucor dimorphism. Several genes, some encoding products known to correlate with development in Mucor spp. or other fungi, have been cloned, sequenced, and examined for transcriptional activity during morphogenesis. Most have appeared in multiple copies displaying independent transcriptional control. Selective translation of stored mRNA molecules occurs during sporangiospore germination. Many other correlates of Mucor morphogenesis, presently described but not yet explained, should prove amenable to analysis by the emerging molecular technology.
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Affiliation(s)
- M Orlowski
- Department of Microbiology, Louisiana State University, Baton Rouge 70803
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Calvo-Mendez C, Ruiz-Herrerax J. Regulation of S-adenosylmethionine decarboxylase during the germination of sporangiospores of Mucor rouxii. Microbiology (Reading) 1991. [DOI: 10.1099/00221287-137-2-307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Summary
General properties of S-adenosylmethionine decarboxylase (SAMDC) from Mucor rouxii were studied. Dormant spores of the fungus did not contain detectable levels of the enzyme, but it started to be synthesized at early stages of spore germination. Kinetics of synthesis changed before emergence of the germ tube, with a corresponding increase in a second SAMDC activity which, in contrast to the one originally synthesized, was not activated by putrescine. Development of the second enzyme activity required de novo protein synthesis. Neither enzymic activity was stimulated by Mg2+. Addition of the SAMDC inhibitor methylglyoxal bis-(guanylhydrazone) (MGBG) stopped fungal development in growth phase Ia: cells became spherical and showed ultrastructural alterations. Although MGBG inhibited polyamine formation, it barely inhibited protein and RNA biosynthesis during the first hour of incubation. However, at later periods, biosynthesis of both macromolecules was strongly decreased. When MGBG was added to growth media 3 h after inoculation of spores, it did not affect spore germination and outgrowth. A hypothesis for two different roles of spermidine and putrescine in spore germination is discussed.
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Affiliation(s)
- Carlos Calvo-Mendez
- Departamento de Genética y Biología Molecular, Centro de Investigatión y Estudios Avanzados, IPN, and Instituto de Investigatión en Biología Experimental, Universidad de Guanajuato, Apartado Postal 187, Guanajuato, Gto. 36000, Mexico
| | - Jose Ruiz-Herrerax
- Departamento de Genética y Biología Molecular, Centro de Investigatión y Estudios Avanzados, IPN, and Instituto de Investigatión en Biología Experimental, Universidad de Guanajuato, Apartado Postal 187, Guanajuato, Gto. 36000, Mexico
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Rodri´guez C, Lo´pez MC, Domi´nguez A. Macromolecular synthesis during the yeast-mycelium transition in Yarrowia lipolytica. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0147-5975(90)90054-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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