The structure of the yeast mitochondrial ribosome

Abstract

Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 Å. The mitoribosomal small subunit has been built de novo and includes 15S rRNA and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeastspecific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded mRNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.Mitochondria are eukaryotic organelles that carry out aerobic respiration. Resulting from their likely ancestry as endosymbionts (1), mitochondria retain a vestigial genome of ~3-100 genes depending on the species. All mitochondrial DNA (mtDNA) encodes at least some of the essential transmembrane subunits of the oxidative phosphorylation complexes. To synthesize these proteins, mitochondria have dedicated ribosomes (mitoribosomes). Nearly all mitoribosomal proteins and all translational factors are encoded by nuclear DNA and imported from the cytoplasm, while mtDNA encodes the mitoribosomal RNA (rRNA) and mitochondria-specific transfer RNAs (mt-tRNAs).Mitochondrial translation displays considerable species-specific specialization, largely dictated by the translational requirements of the mitochondrial genome (2). This specialization manifests in the diverse compositions and structures of mitoribosomes, which are distinct from one another and from all known ribosomes despite sharing an ancestor with modern bacterial ribosomes (2, 3).Our current understanding of this diversity at the atomic level is limited to comparisons of the structure of the large subunit of the Saccharomyces cerevisiae mitoribosome (mt-LSU) (4) with the structures of the complete human (5) and porcine (6) mitoribosomes. These † To whom correspondence should be addressed: ramak@mrc-lmb.cam.ac.uk. * This manuscript has been accepted for publication in Science. This version has not undergone final editing. Please refer to the complete version of record at http://www.sciencemag.org/. The manuscript may not be reproduced or used in any manner that does not fall within the fair use provisions of the Copyright Act without the prior, written permission of AAAS. Europe PMC Funders Group Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts comparisons have revealed that the major evolutionary trajectory for mammalian mitoribosomes is the enlargement of the mitoribosomal proteome together with contraction of the mt-rRNA (2, 3, 7). In contrast, the yeast mitoribosome appears to be on an evolutionary path that has not experienced...

Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation

“…The equivalent mutations are at positions 71 and 72 of yeast and mouse MRPS12, such that the error‐prone mutant is K72I and the hyper‐accurate mutation is K71T. Recent structures of the mammalian and yeast mitoribosomes revealed that the loop containing these mutations forms a structurally conserved element of the decoding center in these ribosomes, as it does in bacteria, indicating that the mechanism of decoding is conserved (Fig A) (Amunts et al , ; Greber et al , ; Desai et al , ). To understand the effect of altering the fidelity of mitochondrial protein synthesis in yeast, we introduced both error‐prone ( ep , K72I) and hyper‐accurate ( ha , K71T) mutations into the Saccharomyces cerevisiae MRPS12 gene via homologous recombination (Fig EV1B).…”

Kinetics and Mechanism of Mammalian Mitochondrial Ribosome Assembly

“…(5) The tight organization of mitochondrial rRNA genes completely lacks intergenic spacer regions found in other rRNA gene regions, requiring precise incisions by RNases P and ELAC2 for rRNA maturation. (6) S. cerevisiae has followed a different evolutionary path to adopt unlinked rRNAs even larger than those found in E. coli , along with a distinct pattern of altered ribosomal proteins (Amunts et al, 2014; Desai et al, 2017). Thus, this organism is not a suitable model for studies of mammalian mitoribosome structure or function, although it bears its own intrinsic interest.…”

Structure determination of group II introns

“…For example, cryo-EM has been used to solve the atomic models of the ribosome [25, 26] and the spliceosome [4, 5, 27–31]. It is likely that the techniques regarding sample preparation and solubility screening described in this review could be applied to the structure determination of large RNAs using cryo-EM as well.…”