Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

Abstract

TET/JBP dioxygenases oxidize methylpyrimidines in nucleic acids and are implicated in generation of epigenetic marks and potential intermediates for DNA demethylation. We show that TET/JBP genes are lineage-specifically expanded in all major clades of basidiomycete fungi, with the majority of copies predicted to encode catalytically active proteins. This pattern differs starkly from the situation in most other organisms that possess just a single or a few copies of the TET/JBP family. In most basidiomycetes, TET/JBP genes are frequently linked to a unique class of transposons, KDZ (Kyakuja, Dileera, and Zisupton) and appear to have dispersed across chromosomes along with them. Several of these elements typically encode additional proteins, including a divergent version of the HMG domain. Analysis of their transposases shows that they contain a previously uncharacterized version of the RNase H fold with multiple distinctive Zn-chelating motifs and a unique insert, which are predicted to play roles in structural stabilization and target sequence recognition, respectively. We reconstruct the complex evolutionary history of TET/JBPs and associated transposons as involving multiple rounds of expansion with concomitant lineage sorting and loss, along with several capture events of TET/JBP genes by different transposon clades. On a few occasions, these TET/JBP genes were also laterally transferred to certain Ascomycota, Glomeromycota, Viridiplantae, and Amoebozoa. One such is an inactive version, calnexin-independence factor 1 (Cif1), from Schizosaccharomyces pombe, which has been implicated in inducing an epigenetically transmitted prion state. We argue that this unique transposon-TET/JBP association is likely to play important roles in speciation during evolution and epigenetic regulation.

Keywords: DNA modification; fungal evolution; genomic association; methylcytosine.

Fig. 1.

Phylogenetic tree shows lineage-specific expansions of TET/JBP proteins in different fungi. Branches and names are colored differentially based on their lineages. Clades entirely composed of monospecific representatives are collapsed into triangles and labeled with the species abbreviation and number of sequences in the clade. Nodes supported by bootstrap values >85% are marked with black circles. Each colored dot shown at the edge of the collapsed clades indicates a single association between a TET/JBP protein and a transposase, where Kyakuja (K) is shown in red, Dileera (D) in blue, Zisupton (Z) in green, and Plavaka (P) in purple. Genomic structures of representative examples of these associations are shown around the tree and are labeled with the species abbreviation, Genbank index number (gi) of the TET/JBP gene, and the type of associated transposase (i.e., K, D, Z, or P) in the association. Genes are shown as arrows pointing from the 5′ end to the 3′ end, with the name and domain architecture within. A fully expanded tree with individual branch labels is provided in SI Appendix, Fig. S1. Species abbreviations are provided in SI Appendix, Table S1.

Fig. 2.

(A) Multiple sequence alignment of KDZ transposases. Proteins are labeled with their species abbreviations and GenBank index numbers. Species abbreviations are provided in SI Appendix, Table S1. Conserved Zn-binding residues and catalytic residues of transposases are indicated. The coloring is based on 85% consensus using the following scheme: polar residues (CDEHKNQRST) shaded light blue, hydrophobic (ACFILMVWY) residues shaded yellow, and small (ACDGNPSTV) residues shaded gray. Catalytic residues are colored dark blue. Conserved cysteine and histidine residues predicted to be involved in coordinating a Zn ion are colored green and red, respectively. (B) Domain architectures of representative KDZ and Plavaka transposases. In each domain, the conserved Zn-chelating residues, cysteine and histidine, are shown as vertical green and red lines.

Fig. 3.

Evolutionary associations of fungal TET/JBP and KDZ transposases. On the top are shown the topological alignments of the phylogenetic trees of TET/JBP and KDZ transposases with the TET/JBP tree colored in blue and transposase tree in red and branches showing topological mismatch in green. TET/JBP and KDZ transposase genes predicted to be derived from the same mobile element are assigned the same number shown next to the leaf label (a complete description of the leaves is provided in SI Appendix, Fig. S18). The red bar in the bottom graph is the actual recovered nodal distance positioned with respect to the normally distributed nodal distances of 1000 randomly generated trees from the same set of terminal leaves and is labeled on top using the number of SDs from the mean distance of the random trees.