Characterisation of an evolutionarily conserved RNaseH-like domain in a domesticated transposase-derived protein

Abstract

The RNase-H fold is an ancient protein fold found in diverse nucleases that is characterised by a conserved structural core (five β strands and ⍺ helices), canonical DDE/D catalytic residues and catalytic mechanism. This study focuses on the evolutionary conservation of the RNaseH-like domain in the transposase-derived THAP9 family among different taxonomic groups. Phylogenetic analysis demonstrates that the structural framework required for catalysis has been maintained over the course of evolution, while other peripheral regions have undergone lineage-specific diversification. This is exemplified by a Lys residue, which is conserved across mammals, can be structurally superposed on a catalytic Asp residue found in active transposases, but is not important for DNA integration. Further, the importance of conserved motifs (YREK and YKEFR motifs) near the THAP9 catalytic residues are confirmed biochemically by performing site directed mutagenesis followed by functional assays which demonstrate that substitution mutants have decreased ability to integrate DNA. Overall, these results emphasize that DNA integration activity is controlled by interactions with several structural elements rather than by individual catalytic residues.