Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen

Abstract

DNA methylation is found throughout all domains of life, yet the extent and function of DNA methylation differ among eukaryotes. Strains of the plant pathogenic fungus Zymoseptoria tritici appeared to lack cytosine DNA methylation (5mC) because gene amplification followed by Repeat-Induced Point mutation (RIP) resulted in the inactivation of the dim2 DNA methyltransferase gene. 5mC is, however, present in closely related sister species. We demonstrate that inactivation of dim2 occurred recently as some Z. tritici isolates carry a functional dim2 gene. Moreover, we show that dim2 inactivation occurred by a different path than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains with or without functional dim2 alleles. Presence of functional dim2 correlates with high levels of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified low levels of 5mC in strains carrying non-functional dim2 alleles, suggesting that 5mC is maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration of a functional dim2 allele in strains with mutated dim2 restored normal 5mC levels, demonstrating de novo cytosine methylation activity of Dim2. To assess the importance of 5mC for genome evolution, we performed an evolution experiment, comparing genomes of strains with high levels of 5mC to genomes of strains lacking functional dim2. We found that presence of a functional dim2 allele alters nucleotide composition by promoting C to T transitions (C→T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation. Our results show that 5mC density at TEs is a polymorphic trait in Z. tritici populations that can impact genome evolution.

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

“…RIP mutations have been associated with meiosis, but alternative mechanisms during vegetative propagation could lead to RIP-like mutations ( Clutterbuck 2011 ). This has been recently observed in Z. tritici and N. crassa in which propagation through mitotic divisions generate RIP-like mutations ( Möller et al 2021 ; Wang et al 2020 ). Intriguingly, polymorphic TEs are depleted in RIP mutations.…”

Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

“…In N. crassa, the RIP process occurs during the sexual stage, and if it is also conserved in A. fumigatus, the result may suggest another mutually non-exclusive possibility that the two isolates have different levels of sexual activities. Alternatively, the C:G to T:A transitions may be due to a DNA methyltransferase-mediated mechanism that occurs during mitosis as found for the plant fungal pathogen Z. tritici [101]. Regardless of the mechanism, our result indicates differential TE inactivation activities between A. fumigatus clinical isolates.…”

Differential Regulation and Production of Secondary Metabolites among Isolates of the Fungal Wheat Pathogen Zymoseptoria tritici

“…Genome and transcriptome studies have demonstrated that infection of Z. tritici relies not on major virulence determinants but on a large repertoire of effector proteins that are produced to facilitate host invasion. Interspecific hybridization has occurred repeatedly in Z. tritici and has been demonstrated to be an important mechanism of gene exchange between species as well as a source of within-species variation ( 49 , 50 ). In addition to proteinaceous virulence determinants, fungal pathogens also produce secondary metabolites during host infection.…”