YBEY as a ribosome biogenesis factor

<p>The ultraconserved RNA-binding protein YbeY has been associated with ribosomal RNA processing in numerous bacteria. However, mechanistic understanding of its function is still lacking, in particular in the light of the generally poor conservation of rRNA processing pathways across the bacterial kingdom. By leveraging the fact that YbeY homologues are wide-spread not only in bacteria but also in most eukaryotes harbouring bacteria-derived organelles, we addressed the functional significance of this protein in the highly divergent genetic system of human mitochondria.</p> <p>Mammalian mitochondrial rRNAs are known to be fully processed by dedicated RNase P and RNase Z enzymes, making additional ribonucleases superfluous. Indeed, <em>YBEY</em> knockout mitochondria were found to process all their ribosomal RNAs normally. Nevertheless, in the absence of YBEY, the mitochondrial small subunit (SSU) rRNA showed significant destabilisation, associated with a late SSU assembly defect. Component analysis identified a significant depletion of the mitoribosomal protein uS11m and several other, structurally dependent SSU constituents forming the platform and the head of the subunit. Our biochemical and genetic data suggest that this assembly defect renders the mitochondrial SSU initiation-incompetent, leading to a nearly complete translational shutdown in the mitochondrial compartment. Consequently, <em>YBEY</em> KO cells completely lose the ability to carry out oxidative phosphorylation.</p> <p>Coimmunoprecipitation and FLIM-FRET <em>in situ</em> interactomics, further supported by analyses in a heterologous system, identified direct and tight interactions between YBEY, uS11m and p32, a deeply conserved RNA-binding protein involved in mitoribosome assembly in a variety of eukaryotes. The three proteins form together stable and stoichiometric complexes. We propose that YBEY, together with p32, helps to efficiently deliver and/or correctly position uS11m on the nascent mitochondrial SSU&nbsp;in order to complete the assembly of the platform. Based on existing data, this YBEY function appears to be broadly conserved.</p>