A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina.

Pierre Grognet,Frédérique Bidard,Jinane Aït-Benkhali,Robert Debuchy,Florian Carlier,Véronique Berteaux-Lecellier,Fabienne Malagnac,Hélène Timpano,Eugene Gladyshev

doi:10.1371/journal.pgen.1008086

Abstract

DNA methyltransferases are ubiquitous enzymes conserved in bacteria, plants and opisthokonta. These enzymes, which methylate cytosines, are involved in numerous biological processes, notably development. In mammals and higher plants, methylation patterns established and maintained by the cytosine DNA methyltransferases (DMTs) are essential to zygotic development. In fungi, some members of an extensively conserved fungal-specific DNA methyltransferase class are both mediators of the Repeat Induced Point mutation (RIP) genome defense system and key players of sexual reproduction. Yet, no DNA methyltransferase activity of these purified RID (RIP deficient) proteins could be detected in vitro. These observations led us to explore how RID-like DNA methyltransferase encoding genes would play a role during sexual development of fungi showing very little genomic DNA methylation, if any. To do so, we used the model ascomycete fungus Podospora anserina. We identified the PaRid gene, encoding a RID-like DNA methyltransferase and constructed knocked-out ΔPaRid defective mutants. Crosses involving P. anserina ΔPaRid mutants are sterile. Our results show that, although gametes are readily formed and fertilization occurs in a ΔPaRid background, sexual development is blocked just before the individualization of the dikaryotic cells leading to meiocytes. Complementation of ΔPaRid mutants with ectopic alleles of PaRid, including GFP-tagged, point-mutated and chimeric alleles, demonstrated that the catalytic motif of the putative PaRid methyltransferase is essential to ensure proper sexual development and that the expression of PaRid is spatially and temporally restricted. A transcriptomic analysis performed on mutant crosses revealed an overlap of the PaRid-controlled genetic network with the well-known mating-types gene developmental pathway common to an important group of fungi, the Pezizomycotina.

Highlights

A covalently modified DNA base, the 5-methylcytosine (5-meC) is common in genomes of organisms as diverse as bacteria, fungi, plants and animals
We report on a gene of the model fungus Podospora anserina, encoding a protein called perithecia obtained from wild-type crosses (PaRid) that share several features with known DNA methyltransferases
By establishing the transcriptional profile of PaRid mutant strain, we identified a set of PaRid target genes

Summary

Introduction

A covalently modified DNA base, the 5-methylcytosine (5-meC) is common in genomes of organisms as diverse as bacteria, fungi, plants and animals. Patterns of cytosine methylation are established and maintained through subsequent DNA replication cycles by the cytosine DNA methyltransferases (DMTs), a class of enzymes conserved from bacteria to mammals. Genes encoding putative DMTs can be found in genome of species having very few, if any, 5-meC (e.g., Dictyostelium discoideum [17], Drosophila melanogaster [18] and Aspergillus nidulans [19]). These DMT-like proteins might be endowed with a still undetermined function. Most of the ascomycetous yeasts, including the model organism Saccharomyces cerevisiae and the human pathogen Candida albicans, lack genes encoding putative DMT-like enzymes. The presence of 5-mC in the ascomycetous yeast genomes remains controversial [20,21]

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