A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA.

Unlike most eukaryotes, Trypanosoma brucei processes its cytosolic large subunit (LSU) RNA into six fragments. The factors responsible for these processing events were previously unknown. Here, we identify TbLrRP1 and TbLrRP2 as essential components of this trypanosome-specific LSU RNA processing pathway. Each contains a single transmembrane domain and localizes to the ER membrane and the nuclear envelope, forming a heterodimeric complex. Depletion of either protein disrupts LSU RNA processing, causing accumulation of unprocessed intermediates that are incorporated into translationally active cytosolic polysomes. This disruption impairs, but does not fully halt, growth of both procyclic and bloodstream form trypanosomes. The nuclease-related domain (NERD) of TbLrRP2 is essential for LSU RNA processing. Intriguingly, NERD-containing proteins were predicted to have DNase activity; however, our results suggest that the NERD of TbLrRP2 is a ribonuclease. In contrast, the DEDDh domain of TbLrRP1 is dispensable for LSU RNA processing, indicating it may have a scaffolding role. Both proteins require their transmembrane domains for full functionality. Our findings reveal a lineage-specific processing complex acting at a late stage of LSU RNA maturation, highlighting the unique adaptations of trypanosomal cytosolic ribosome biogenesis.Trypanosomes, unlike most other eukaryotes, cut their large ribosomal RNA (LSU rRNA) into six pieces, but how and why this happens was unclear. Our study identified two essential proteins, TbLrRP1 and TbLrRP2, that work together to process the LSU rRNA. TbLrRP1 shares similarities with exonucleases, while TbLrRP2 contains a NERD domain likely acquired from bacteria through horizontal gene transfer. The NERD acts as an RNase and is required for processing. Both proteins must be integrated into the endoplasmic reticulum membrane to fullfill their function. When either protein is depleted, trypanosome growth slows, but translation still occurs, showing that ribosomes can function with unprocessed rRNA. These findings reveal a flexible and unique ribosome biogenesis pathway in trypanosomes.