Is the Fungus Magnaporthe Losing DNA Methylation?

Abstract

The long terminal repeat retrotransposon, Magnaporthe gypsy-like element (MAGGY), has been shown to be targeted for cytosine methylation in a subset of Magnaporthe oryzae field isolates. Analysis of the F 1 progeny from a genetic cross between methylation-proficient (Br48) and methylation-deficient (GFSI1-7-2) isolates revealed that methylation of the MAGGY element was governed by a single dominant gene. Positional cloning followed by gene disruption and complementation experiments revealed that the responsible gene was the DNA methyltransferase, MoDMT1, an ortholog of Neurospora crassa Dim-2. A survey of MAGGY methylation in 60 Magnaporthe field isolates revealed that 42 isolates from rice, common millet, wheat, finger millet, and buffelgrass were methylation proficient while 18 isolates from foxtail millet, green bristlegrass, Japanese panicgrass, torpedo grass, Guinea grass, and crabgrass were methylation deficient. Phenotypic analyses showed that MoDMT1 plays no major role in development and pathogenicity of the fungus. Quantitative polymerase chain reaction analysis showed that the average copy number of genomic MAGGY elements was not significantly different between methylation-deficient and -proficient field isolates even though the levels of MAGGY transcript were generally higher in the former group. MoDMT1 gene sequences in the methylation-deficient isolates suggested that at least three independent mutations were responsible for the loss of MoDMT1 function. Overall, our data suggest that MoDMT1 is not essential for the natural life cycle of the fungus and raise the possibility that the genus Magnaporthe may be losing the mechanism of DNA methylation on the evolutionary time scale.C YTOSINE methylation is a chemical modification of DNA and is at the heart of an epigenetic mechanism involved in the control of a variety of biological processes, such as embryogenesis, cell differentiation, X-chromosome inactivation, genomic imprinting, and gene silencing (Laird and Jaenisch 1996). Cytosine methylation occurs in all three domains of life, namely, Eubacteria, Archaebacteria, and Eukaryota, and is regarded as an ancestral mechanism that antedates the divergence of eukaryotes and prokaryotes (Tajima and Suetake 1998). Consistent with this, the catalytic enzymes of cytosine methylation, the cytosine DNA methyltransferases (DMTs), are conserved in eukaryotes and prokaryotes and contain nine well-conserved motifs arranged in the same order along their primary structure (Kumar et al. 1994;Jurkowski and Jeltsch 2011).Interestingly, however, the pattern and extent of genomic DNA methylation shows considerable diversity among eukaryotes (Yoder et al. 1997; Colot and Rossignol 1999;Rabinowicz et al. 1999). While cytosine DNA methylation is common in higher plants and vertebrates, it is virtually absent in certain lower organisms, such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Caenorhabditis elegans (Antequera et al. 1984;Proffitt et al. 1984;Hodgkin 1994). Consistent with this observation, ...

Epigenetic regulation of development and pathogenesis in fungal plant pathogens

“…Although the DNA methylation status of a long terminal repeat retrotransposon (LTR), Magnaporthe gypsy‐like element (MAGGY), differs among various Magnaporthe grisea subgroups (fungal isolates derived from rice, common millets, foxtail millet and torpedo grass) (Nakayashiki et al ., ), its inactivation could not be attributed to DNA methylation in M. grisea (Nakayashiki et al ., ). Analyses of the F1 progeny derived through the cross of methylation‐proficient (Br‐48) and methylation‐deficient (GFSI1‐7‐2) isolates revealed the role of MoDMT1 (DNMT), an orthologue of N. crassa Dim‐2 , in the methylation of MAGGY elements (Ikeda et al ., ). However, phenotypic analyses of the MoDMT1 mutant revealed no significant role of MoDMT1 in the regulation of the development and pathogenicity of M. oryzae (Ikeda et al ., ).…”

“…Analyses of the F1 progeny derived through the cross of methylation‐proficient (Br‐48) and methylation‐deficient (GFSI1‐7‐2) isolates revealed the role of MoDMT1 (DNMT), an orthologue of N. crassa Dim‐2 , in the methylation of MAGGY elements (Ikeda et al ., ). However, phenotypic analyses of the MoDMT1 mutant revealed no significant role of MoDMT1 in the regulation of the development and pathogenicity of M. oryzae (Ikeda et al ., ). Furthermore, a trend of a loss in DNA methylation was observed in 60 field isolates of M. oryzae .…”

“…The significance of DNA methylation in governing the pathogenicity of M. oryzae has not been proven to date (Ikeda et al ., ; Jeon et al ., ; Nakayashiki et al ., ). Although the DNA methylation status of a long terminal repeat retrotransposon (LTR), Magnaporthe gypsy‐like element (MAGGY), differs among various Magnaporthe grisea subgroups (fungal isolates derived from rice, common millets, foxtail millet and torpedo grass) (Nakayashiki et al ., ), its inactivation could not be attributed to DNA methylation in M. grisea (Nakayashiki et al ., ).…”

“…Interestingly, the decoupled frequencies of genotypic mutations and phenotypic variations (Jablonka and Raz, ; Pigliucci, ; Skinner, ) can be explained on the basis of epigenetics. Instances of the loss or retention of epigenetic modifications in subsequent generations can throw light onto the trend of epigenetic evolution of any organism and explain the phenotypic variability (Billmyre et al ., ; Bird, ; Hu et al ., ; Ikeda et al ., ; Iyer et al ., ; Nakayashiki et al ., ). In addition, the epigenetic processes influenced by environmental factors (Skinner, ) can affect the molecular basis of inheritance, indicating a plausible combinatorial effect of epigenetics and genetic variation in evolution.…”

Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology

“…Genomic evidence indicates that RIP occurs or at least has occurred in the life history of most fungi including several Aspergilli (e.g., Aspergillus nidulans, Aspergillus niger, Aspergillus fumigatus, and Aspergillus oryzae (Clutterbuck et al 2008)) and other biotechnologically relevant taxa such as Trichoderma and Penicillium (Kubicek et al 2011;Braumann et al 2008). In Magnaporthe oryzae and Magnaporthe grisea, Ikeda et al (2013) detected mutations in DNA methyltransferases (see below) in a high portion of wild-type isolates and concluded that DNA methylation is on the way to be lost from this fungus. It is possible that this is also the case with other fungi, which would explain the partially conflicting results.…”