Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns

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.

Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts

“…The virulence of plant pathogens have been reported to be partially controlled by epigenetic mechanisms, such as DNA methylation and histone modifications, because these modifications change protein structure and function; therefore, the fungal development and pathogenicity also could be regulated for fungal survival during infection. PTMs modulate not only protein production and activity but also the host response ( Dubey and Jeon, 2017 ; Kong et al, 2018 ; Nai et al, 2020 ; Retanal et al, 2021 ). Khib has recently been reported in F. oxysporum , B. cinerea , and U. virens .…”

Global analysis of cytosine and adenine DNA modifications across the tree of life

“…A notable exception was that we detected hardly any of these DNA modifications in the unicellular fungi studied ( Supplementary file 1 ). Hence it is not merely 5mdC ( Capuano et al, 2014 ; Binz et al, 2018 ; Nai et al, 2020 ), but also its oxidized form 5hmdC along with N6mdA that are very low if not absent in typical yeast species. It is interesting in this context that the insects Trichoplusia ni, Spodoptera frugiperda , and D. melanogaster ( Supplementary file 1 ) all had DNA modifications, but also at much lower levels compared to both, higher organisms but also bacteria.…”

The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses

“…Protein complexes involved in writing, reading, and erasing these modifications have been reported in few model fungal species to date (16,22), but the evolution and conservation of these complexes in diverse fungal species have not been largely systematically explored. Besides some research on DNA methyltransferases (21,23) and SET domain-containing proteins (17) that have been performed throughout the fungal kingdom, we still lack the evolutionary overview of other chromatin modifiers and in depth analyses for important fungal groups. To start uncovering the occurrence and evolutionary histories of chromatin modifiers involved in these major modifications in the fungal genus Aspergillus, we first focused on six conserved catalytic domains reported to be involved in histone modifications: DNA methyltransferase domain for DNMTs, SET domain for histone methyltransferases (HMTs), acetyltransferase domain and MOZ/SAS FAMILY domain for histone acetyltransferases (HATs), histone deacetylase domain for histone deacetylases (HDACs), and JmjC domain for histone demethylases (HDMTs).…”

“…In addition to ancient chromatin modifiers, also lineage-specific innovations such as duplications and losses were found in fungi. For example, Dim-2 and RID (Repeat-Induced Point Mutation (RIP)-Defective) are considered to be fungal-specific DNMTs, while DNMT3 that is typically found in animals and plants seems to be absent in fungi (21)(22)(23). However, S. cerevisiae is not representative of the complete fungal kingdom, and detailed studies on PTMs are needed for other, less studied fungal species.…”