Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex

Kinetoplastids are a clade of eukaryotic protozoans that include human parasitic pathogens like trypanosomes and Leishmania species. In these organisms, protein-coding genes are transcribed as polycistronic pre-mRNAs, which need to be processed by the coupled action of trans-splicing and polyadenylation to yield monogenic mature mRNAs. During trans-splicing, a universal RNA sequence, the spliced leader RNA (SL RNA) mini-exon, is added to the 5’-end of each mRNA. The 5’-end of this mini-exon carries a hypermethylated cap structure and is bound by a trypanosomatid-specific cap-binding complex (CBC). The function of three of the kinetoplastid CBC subunits is unknown, but an essential role in cap binding and trans-splicing has been suggested. Here, we report cryo-EM structures that reveal the molecular architecture of the Trypanosoma brucei CBC ( Tb CBC) complex. We find that Tb CBC interacts with two distinct features of the SL RNA. The Tb CBP20 subunit interacts with the m7G cap while Tb CBP66 recognizes double-stranded portions of the SL RNA. Our findings pave the way for future research on mRNA maturation in kinetoplastids. Moreover, the observed structural similarities and differences between Tb CBC and the mammalian cap-binding complex will be crucial for considering the potential of Tb CBC as a target for anti-trypanosomatid drug development. Highlights ### Competing Interest Statement The authors have declared no competing interest. The coordinates and cryo-EM maps were deposited in the PDB and EMDB database: Tb CBP20- Tb CBP110- Tb CBP30- Tb CBP66 tetramer cap0 PDB:9F3F and EMD-50173; Tb CBP20- Tb CBP110- Tb CBP30 trimer cap4 PDB:9F67 and EMD-50217.