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Wang C, Feng J, Chen Y, Li D, Liu L, Wu Y, Zhang S, Du S, Zhang Y. Revealing mitogenome-wide DNA methylation and RNA editing of three Ascomycotina fungi using SMRT sequencing. Mitochondrion 2020; 51:88-96. [PMID: 31923469 DOI: 10.1016/j.mito.2020.01.003] [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: 06/12/2018] [Revised: 12/25/2019] [Accepted: 01/03/2020] [Indexed: 10/25/2022]
Abstract
Beauveria bassiana, Cordyceps militaris and Ophiocordyceps sinensis (Ascomycotina) are traditional Chinese medicines. Here, mitogenomes of these three Ascomycotina fungi were sequenced and de-novo assembled using single-molecule real-time sequencing. The results showed that their complete mitogenomes were 31,258, 31,854 and 157,584 bp, respectively, with sequencing depth approximately 278,760×, 326,283× and 69,385×. Types of repeat sequences were mainly (AA)n, (AAT)n, (TA)n and (TATT)n. DNA methylation motifs were revealed in DNA modifications of these three fungi. We discovered new models of RNA editing through analysis of transcriptomes from B. bassiana and C. militaris. These data lay a solid foundation for further genetic and biological studies about these three fungi, especially for elucidating the mitogenome evolution and exploring the regulatory mechanism of adapting environment.
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Affiliation(s)
- Chaoxia Wang
- Management Center of Tianjin Modern Agricultural Science and Technology Innovation Base, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China; Tianjin Lakeside Powergene Science Development Co. Ltd, Tianjin 300309, China.
| | - Jianhua Feng
- Tianjin Lakeside Powergene Science Development Co. Ltd, Tianjin 300309, China
| | - Yujiao Chen
- Tuke (Tianjing) Pharmaceutical Technology Co. Ltd, Tianjin 300457, China
| | - Dongmei Li
- Tianjin Lakeside Powergene Science Development Co. Ltd, Tianjin 300309, China
| | - Li Liu
- Tuke (Tianjing) Pharmaceutical Technology Co. Ltd, Tianjin 300457, China
| | - Yuqian Wu
- Gui'an Precision Medicine Academy Co. Ltd, GuiZhou 550029, China
| | - Shujun Zhang
- Research Center of Human Genome, Tianjin University, Tianjin 300309, China
| | - Simiao Du
- Zheng Yuan Tang (Tianjin) Biotechnology Co. Ltd, Tianjin 300457, China
| | - Yaozhou Zhang
- Research Center of Human Genome, Tianjin University, Tianjin 300309, China; Tianjin International Joint Academy of Biomedical, Tianjin 300457, China.
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2
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Li W, Wang Y, Zhu J, Wang Z, Tang G, Huang B. Differential DNA methylation may contribute to temporal and spatial regulation of gene expression and the development of mycelia and conidia in entomopathogenic fungus Metarhizium robertsii. Fungal Biol 2017; 121:293-303. [DOI: 10.1016/j.funbio.2017.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/17/2016] [Accepted: 01/17/2017] [Indexed: 12/17/2022]
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3
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Wang YL, Wang ZX, Liu C, Wang SB, Huang B. Genome-wide analysis of DNA methylation in the sexual stage of the insect pathogenic fungus Cordyceps militaris. Fungal Biol 2015; 119:1246-1254. [PMID: 26615747 DOI: 10.1016/j.funbio.2015.08.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 11/19/2022]
Abstract
DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes. However, its function in the sexual development of fungi remains unclear. Cordyceps militaris, readily performs sexual reproduction and thus provides a remarkably rich model for understanding epigenetic processes in sexual development. Here, we surveyed the methylome of C. militaris at single-base resolution to assess DNA methylation patterns during sexual development using genomic bisulfite sequencing (BS-Seq). The results showed that approximately 0.4 % of cytosines are methylated, similar to the DNA methylation level (0.39 %) during asexual development. Importantly, we found that DNA methylation in the fungi undergoes global reprogramming during fungal development. Moreover, RNA-Seq analysis indicated that the differentially methylated regions (DMRs) have no correlation with the genes that have roles during fungal sexual development in C. militaris. These results provide a comprehensive characterization of DNA methylation in the sexual development of C. militaris, which will contribute to future investigations of epigenetics in fungi.
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Affiliation(s)
- Yu-Long Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Zhang-Xun Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China; School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Chun Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Si-Bao Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China.
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4
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Zhu F, Bryson PK, Schnabel G. Influence of storage approaches on instability of propiconazole resistance in Monilinia fructicola. PEST MANAGEMENT SCIENCE 2012; 68:1003-1009. [PMID: 22345072 DOI: 10.1002/ps.3255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 10/31/2011] [Accepted: 12/16/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND The long-term preservation of interesting phenotypes in plant pathogenic fungi allows for follow-up studies in the future. Twelve storage approaches were investigated to determine their effects on instability of propiconazole resistance for three demethylation inhibitor (DMI) fungicide-resistant and two DMI-sensitive isolates of Monilinia fructicola. They included mycelium in PDA slants under mineral oil, in PDA plugs under 10% glycerol, on dried filter paper and conidia on silica gel, each stored for 36 weeks at 4, - 20, and - 80 °C. RESULTS None of the storage approaches prevented the rapid decline of EC(50) values for propiconazole in the three resistant isolates, and no significant differences were found among storage approaches (P = 0.787) or between storage approaches and consecutive transfers (P = 0.053). Most of the decline in resistance occurred during the first 4 weeks of storage. The DMI resistance-associated genetic element Mona, located in the immediate upstream region of the MfCYP51 gene, was still present in the three resistant isolates after 36 weeks of storage and weekly transfers. Furthermore, the Mona element and a portion of the MfCYP51 gene, which encodes the target enzyme for DMIs, did not reveal signs of DNA methylation. Resistance to propiconazole was partially regained in resistant isolates after two growth cycles on fresh peach fruit. CONCLUSIONS Obtained data indicate that the decline of DMI resistance in M. fructicola cannot be prevented using commonly employed storage methods at various temperatures. The number of consecutive transfers and the storage duration prior to fungicide sensitivity tests in M. fructicola should be indicated in scientific papers.
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Affiliation(s)
- Fuxing Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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5
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Liu SY, Lin JQ, Wu HL, Wang CC, Huang SJ, Luo YF, Sun JH, Zhou JX, Yan SJ, He JG, Wang J, He ZM. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation. PLoS One 2012; 7:e30349. [PMID: 22276181 PMCID: PMC3262820 DOI: 10.1371/journal.pone.0030349] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/14/2011] [Indexed: 12/12/2022] Open
Abstract
Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.
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Affiliation(s)
- Si-Yang Liu
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Cheng-Cheng Wang
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Yan-Feng Luo
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Jian-Xiang Zhou
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Jian-Guo He
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (J-GH); (JW); (Z-MH)
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (J-GH); (JW); (Z-MH)
| | - Zhu-Mei He
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (J-GH); (JW); (Z-MH)
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Herrera CM, Pozo MI, Bazaga P. Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast. Mol Ecol 2011; 21:2602-16. [PMID: 22171717 DOI: 10.1111/j.1365-294x.2011.05402.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In addition to genetic differences between individuals as a result of nucleotide sequence variation, epigenetic changes that occur as a result of DNA methylation may also contribute to population niche width by enhancing phenotypic plasticity, although this intriguing possibility remains essentially untested. Using the nectar-living yeast Metschnikowia reukaufii as study subject, we examine the hypothesis that changes in genome-wide DNA methylation patterns underlie the ability of this fugitive species to exploit a broad resource range in its heterogeneous and patchy environment. Data on floral nectar characteristics and their use by M. reukaufii in the wild were combined with laboratory experiments and methylation-sensitive amplified polymorphism (MSAP) analyses designed to detect epigenetic responses of single genotypes to variations in sugar environment that mimicked those occurring naturally in nectar. M. reukaufii exploited a broad range of resources, occurring in nectar of 48% of species and 52% of families surveyed, and its host plants exhibited broad intra- and interspecific variation in sugar-related nectar features. Under experimental conditions, sugar composition, sugar concentration and their interaction significantly influenced the mean probability of MSAP markers experiencing a transition from unmethylated to methylated state. Alterations in methylation status were not random but predictably associated with certain markers. The methylation inhibitor 5-azacytidine (5-AzaC) had strong inhibitory effects on M. reukaufii proliferation in sugar-containing media, and a direct relationship existed across sugar × concentration experimental levels linking inhibitory effect of 5-AzaC and mean per-marker probability of genome-wide methylation. Environmentally induced DNA methylation polymorphisms allowed genotypes to grow successfully in extreme sugar environments, and the broad population niche width of M. reukaufii was largely made possible by epigenetic changes enabling genotype plasticity in resource use.
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Affiliation(s)
- C M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092 Sevilla, Spain.
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7
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Binz T, D'Mello N, Horgen PA. A comparison of DNA methylation levels in selected isolates of higher fungi. Mycologia 1998. [DOI: 10.1080/00275514.1998.12026971] [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)
- Thomas Binz
- Biology Group, University of Toronto at Mississauga, Mississauga, Ontario, L5L 1C6 Canada
| | - Nisha D'Mello
- Biology Group, University of Toronto at Mississauga, Mississauga, Ontario, L5L 1C6 Canada
| | - Paul A. Horgen
- Biology Group, University of Toronto at Mississauga, Mississauga, Ontario, L5L 1C6 Canada
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8
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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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9
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Li A, Begin M, Kokurewicz K, Bowden C, Horgen PA. Inheritance of Strain Instability (Sectoring) in the Commercial Button Mushroom,
Agaricus bisporus. Appl Environ Microbiol 1994; 60:2384-8. [PMID: 16349322 PMCID: PMC201660 DOI: 10.1128/aem.60.7.2384-2388.1994] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The button mushroom,
Agaricus bisporus
, is a commercially important cultivated filamentous fungus. During the last decade, the button mushroom industry has depended mainly on two strains (or derivatives of these two strains). Using one of these highly successful strains (strain U1) we examined the phenomenon of strain instability, specifically, the production of irreversible sectors. Three “stromatal” and three “fluffy” sectors were compared with a healthy type U1 strain and with a wild-collected isolate. Compost colonization and fruit body morphology were examined. The main objective of this study, however, was to examine the meiotic stability of the sectored phenotype. Single basidiospores were isolated and subjected to a grain bioassay in which the ability to produce sectors was measured. Our results were as follows: (i) basidiospore cultures obtained from a wild-collected isolate showed no tendency to produce sectors; (ii) approximately 5% of the basidiospore cultures obtained from healthy type U1 strains produced irreversible sectors in the grain bioassay; (iii) the five primary sectors examined produced basidiospore cultures, half of which produced normal-looking growth in the grain bioassay and half of which produced some degree of sectoring; and (iv) the one sectored isolate that represented the F2 generation gave ratios similar to the 1:1 ratio observed for the F1 cultures.
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Affiliation(s)
- A Li
- Center for Plant Biotechnology, Department of Botany, Erindale Campus, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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10
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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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11
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Smith SS. Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 49:65-111. [PMID: 7863011 DOI: 10.1016/s0079-6603(08)60048-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- S S Smith
- Department of Cell and Tumor Biology, City of Hope National Medical Center, Duarte, California 91010
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12
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Wilke NW, Wach MP. Detection of Methylated Mushroom DNA by Restriction Enzyme Analysis. Mycologia 1993. [DOI: 10.1080/00275514.1993.12026312] [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)
- Norbert W. Wilke
- Monterey Laboratories, Monterey Mushrooms Inc., Watsonville, California 95077
| | - Mark P. Wach
- Monterey Laboratories, Monterey Mushrooms Inc., Watsonville, California 95077
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13
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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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14
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Fronk J, Tank GA, Langmore JP. DNA methylation pattern changes during development of a sea urchin. Biochem J 1992; 283 ( Pt 3):751-3. [PMID: 1590764 PMCID: PMC1130949 DOI: 10.1042/bj2830751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytosine methylation of developmentally regulated genes of the sea urchin Strongylocentrotus purpuratus was studied by using restriction-endonuclease digestion and Southern blotting. The single-copy bindin gene, the family of five cytoplasmic actin genes and the 400-fold-repeated set of five early histone genes were mostly unmethylated, but some sites exhibited partial methylation that varied throughout development. This shows that in echinoderms the methylation of DNA is not confined to the non-transcribed portion of the genome, as previously believed [Bird, Tagart & Smith (1979) Cell 17, 889-901], and may play a role in transcriptional regulation.
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Affiliation(s)
- J Fronk
- Biophysics Research Division, University of Michigan, Ann Arbor 48109
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15
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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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16
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Abstract
We find no evidence for the presence of 5-methylcytosine in the DNA of Dictyostelium discoideum. Methylation was absent from CCGG sites in repetitive DNA and in DNA from the actin multigene family. Nor was 5-methylcytosine detected in total DNA when base composition was determined by means of h.p.l.c.
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Affiliation(s)
- S S Smith
- Department of Cell and Tumor Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010
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17
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Rothnie HM, McCurrach KJ, Glover LA, Hardman N. Retrotransposon-like nature of Tp1 elements: implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum. Nucleic Acids Res 1991; 19:279-86. [PMID: 1707520 PMCID: PMC333591 DOI: 10.1093/nar/19.2.279] [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: 12/28/2022] Open
Abstract
The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in the hypermethylated (M+) fraction of the genome where they have been found exclusively in scrambled clusters of up to 50kb long. Scrambling is thought to have arisen by insertion of Tp1 into further copies of the same sequence. In the present study, sequence analysis of cloned Tp1 elements has revealed striking homologies of the predicted amino acid sequence to several highly conserved domains characteristic of retrotransposons. The relative order of the predicted coding regions indicates that Tp1 elements are more closely related to copia and Ty than to retroviruses. Self-integration and methylation of Tp1 elements may function to limit transposition frequency. Such mechanisms provide a possible explanation for the origin and organisation of M + DNA in the Physarum genome.
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Affiliation(s)
- H M Rothnie
- Department of Molecular and Cell Biology, University of Aberdeen, Marischal College, UK
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19
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Mooibroek H, Kuipers AG, Sietsma JH, Punt PJ, Wessels JG. Introduction of hygromycin B resistance into Schizophyllum commune: preferential methylation of donor DNA. MOLECULAR & GENERAL GENETICS : MGG 1990; 222:41-8. [PMID: 1700269 DOI: 10.1007/bf00283021] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cotransformation of a trp1 strain of Schizophyllum commune with the homologous TRP gene and the Escherichia coli HPT gene was used to study the feasibility of transformation of S. commune to hygromycin B resistance. Southern blot analysis showed that 75% of the TRP transformants contained multiple integrated copies of the HPT gene. However only 7% of the transformants were resistant to 25 micrograms/ml hygromycin B and direct selection for hygromycin B resistance was hampered by the high incidence of spontaneously arising resistant colonies. Rescue of the HPT gene was possible with E. coli JA221 (mcr-) but not with JM83, suggesting methylation of the integrated donor DNA. Isoschizomer analyses confirmed heavy methylation in the HPT gene and flanking vector sequences but not in the homologous donor TRP gene and its flanking vector sequences. Also cotransforming S. commune Sc4 gene and flanking vector sequences were not methylated. A fusion between the S. commune TRP1 and the E. coli HPT genes resulted in only slight or no methylation of both vector and HPT sequences and in a higher hygromycin B resistance level. This suggests that transformation with DNA exclusively containing foreign sequences results in integration into regions where methylation occurs, possibly entailing poor transcription. Methylation of the HPT gene was also indicated by the stimulation of growth by 5-azacytidine of transformants on hygromycin B containing medium.
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Affiliation(s)
- H Mooibroek
- Department of Plant Biology, University of Groningen, Haren, The Netherlands
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