A microeukaryotic PPR-DYW protein supports multisite C- and A-deamination RNA editing

RNA editing within mitochondria is crucial for numerous eukaryotes. In plants, the conversion of C to U during this process is carried out by dozens to hundreds of PPR-DYW proteins, each specializing in editing a specific site. Remarkably, in marine microeukaryotes known as diplonemids, despite the necessity for editing over 100 sites in their mitochondrial RNA, only one homolog of the PPR-DYW family is present. This study delves into one such unique deaminase, referred to as PPRD1, originating from Diplonema papillatum.

To better understand PPRD1, researchers employed native affinity pulldown, which unveiled approximately twenty partners that bind to the protein in a primarily sub-stoichiometric manner. Among these, a divergent PolX-like protein, termed DAPX1, was found to consistently and reciprocally co-purify with PPRD1 in nearly equal concentrations.

Through structural modeling, it was suggested that DAPX1 could potentially stabilize the deaminase's catalytic domain and broaden its interaction interface, thereby enhancing its function.

Further investigation revealed that the simultaneous absence of either PPRD1 or DAPX1 led to inhibited cell growth. Moreover, this absence resulted in a significant decrease in both C-to-U and A-to-I deamination across five mitochondrial RNA-editing clusters, each containing 110 sites. These findings collectively propose a model wherein PPRD1 and DAPX1 form the core of the Diplonema deamination-editing machinery.

It suggests that other sub-stoichiometric partners act as specificity factors, ensuring precise RNA editing with minimal instances of off-target effects.