YBEY is an essential biogenesis factor for mitochondrial ribosomes

Abstract

Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3'-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter recruits uS11m to the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation. INTRODUCTIONRibosome biogenesis is a highly complex process that starts co-transcriptionally and includes ribosomal RNA processing, modification, and binding of ribosomal proteins (1). Each of these steps relies on specific factors, some of which are remarkably conserved. One such factor is the UPF0054 family protein YbeY found in all classified bacteria (2). Based on studies in various bacteria, YbeY has been implicated in ribosome maturation and quality control, with a particularly important role in small subunit (SSU) biogenesis (3-8), and post-transcriptional gene expression regulation (9-14). The deletion of ybeY is often lethal or associated with severe alterations of cellular metabolism and growth, indicating its indispensability for a wide variety of bacterial-type ribosomes (4,6,7,(13)(14)(15)(16)(17).Mechanistically, YbeY has been described as a metal-dependent endoribonuclease (5,12), and in some bacteria, ybeY mutants accumulate 16S rRNA with an unprocessed 3' end (3,5,7,8). Therefore, YbeY was proposed to be the "missing" 3' endoribonuclease required for 16S rRNA maturation to obtain the correct anti-Shine-Dalgarno sequence, which is needed for translation initiation on most bacterial mRNAs. However, this 16S rRNA 3'-misprocessing phenotype could equally be caused by the loss of a ribosome biogenesis factor that is not per se involved in rRNA cleavage (18), and so the precise role of YbeY in ribosome biogenesis remains unclear.By carrying out an in-depth phylogenetic analysis, we found that YBEY is also conserved in many eukaryal lineages, including animals, plants, most stramenopiles and alveolates (Supplementary Figure 1). Indeed, YbeY of Arabidopsis thaliana was reported to be an essential ribosome biogenesis factor in chloroplasts, and its absence was associated with severe misprocessing of nearly all chloroplast rRNAs, resulting in deficiency of organellar translation, and hence, the absence of photosynthesis (16). Human YBEY, which shares 27% of identity with YbeY of...

Schizosaccharomyces pombe Ppr10 and Mpa1 together mediate mitochondrial translational initiation

“…For reasons that are not clear, mitochondrial polysomes cannot be separated from monosomes under the experimental conditions used here. Similar observations have been made in other species including S. cerevisiae (41,42) and humans (43)(44)(45).…”

Suborganellar Localization of Mitochondrial Proteins and Transcripts in Human Cells

“…We found that smRNA bDNA FISH can be adapted for the detection and quantification of mitochondrially encoded rRNAs, low-abundance noncoding RNAs, and even short transcripts like tRNAs. We applied this technology for imaging the MT-CYB mRNA, the mitochondrial 12S rRNA, the mitochondrial tRNA Val , and the mirror RNAs for MT-CYB and 12S rRNA (17,18). As expected, 12S rRNA and tRNA Val (which is not only a transfer RNA but also a structural component of the mitoribosome (19)), were very abundant and nearly filled the entire mitochondrion (Fig.…”

The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments

“…Recent studies suggest that MAM33-family proteins might be involved in mitoribosome biogenesis. Indeed, they are linked to the LSU biogenesis in yeast (Hillman and Henry, 2019), in Trypanosoma, the recent structure of the SSU "assemblosome" includes a heterotrimeric p22, directly highlighting its role in mitoribosome biogenesis (Saurer et al, 2019;Sprehe et al, 2010) and in humans, the protein YBEY forms a complex with p32 and is involved in the SSU biogenesis (Summer et al, 2020). We observed that p32 is an integral component of the Chlamydomonas mitoribosome.…”

“…S4A). This MAM33-family protein is seemingly conserved in all eukaryotes, and has been described to have several functions in mitochondria, some related to mitoribosome assembly (Hillman and Henry, 2019;Jiang et al, 1999;Summer et al, 2020;Yagi et al, 2012). However, this is the first time that mS105/p32 has been identified as a core component of a ribosome.…”