GSE134960
YBEY is an essential biogenesis factor for mitochondrial ribosomes
Ribosome biogenesis relies on a number of specific factors. Some of them are remarkably conserved, suggesting that they play essential roles even in distant evolutionary contexts. This is namely the case for the UPF0054 protein YBEY found in all bacteria, but also in many Eukarya. Proposed to act as an endoribonuclease processing the 3' end of 16S rRNA, YBEY is critically required for translation in model bacteria and plant chloroplasts. However, ribosomal RNA processing pathways are poorly conserved between distant phyla, suggesting that YBEY may have another important function in ribosome biogenesis. We studied the human YBEY homologue and found that it localises in mitochondria. The human mitochondrial rRNAs are flanked by tRNA genes and thereby processed by mitochondrial RNase P and RNase Z, making other ribonucleases superfluous. Yet, CRISPR-mediated knockout of the YBEY gene resulted in a decrease of the mitochondrial small ribosomal subunits (SSU), abolished translation in the organelles and, as a result, led to the inability of the knockout cells to respire. Mapping the ends of the mitochondrial rRNAs revealed no processing defects. Similarly, although human YBEY did show robust RNase activity in vitro and in vivo, mutations in key catalytic residues did not abolish its ability to complement the knockout phenotypes. The analysis of the mitoribosomes identified a distinct set of SSU proteins, mostly located in the head and the platform, to be significantly depleted in the absence of YBEY, including uS11m, required for translation initiation. Importantly, uS11m was the only SSU protein found to directly interact with YBEY in vitro, in vivo and in situ, and forming a stable stoichiometric complex with YBEY. The sum of our data supports the model where YBEY functions primarily as an essential ribosome biogenesis factor by recruiting uS11m in order to complete the assembly of translationally active SSUs. Overall design: RNA was isolated from mitochondria of three independent YBEY+ and three independent YBEY KO cell lines and analysed by standard RNA-seq.