The complete structure of the 55 S mammalian mitochondrial ribosome

Abstract

Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.

Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome

“…2,3 In humans, 30 mitochondrial ribosomal small subunit proteins (MRPSs) assemble with the 12S mt-rRNA to form the small 28S subunit, while 50 mitochondrial ribosomal large subunit proteins (MRPLs) assemble with the 16S mt-rRNA and mt-tRNA Val to form the large 39S subunit. [4][5][6] Molecular defects that impair different components of the mitochondrial translation machinery can cause combined OXPHOS deficiency. 7 Specifically, 7 of the 80 genes encoding mitochondrial ribosomal proteins have had pathogenic mutations reported, including autosomal-recessive mutations in MRPS7 (MIM: 611974), 8 MRPS16 (MIM: 609204), 9 MRPS22 (MIM: 605810), 10 MRPS23 (MIM: 611985), 11 MRPL3 (MIM: 607118), 12 MRPL12 (MIM: 602375), 13 and MRPL44 (MIM: 611849).…”

“…MRPS34, which lies within the foot of the small 28S mitoribosome subunit, is one of 15 mammalian mitochondria-specific MRPSs not found in the ancestral bacterial ribosome. 5 We previously showed that mice with a homozygous Mrps34 missense mutation that caused reduced MRPS34 protein stability developed cardiac hypertrophy and pronounced liver dysfunction due to impaired mitoribosome assembly. 18 We now demonstrate that human MRPS34 mutations cause Leigh or Leigh-like syndrome by destabilizing the small mitoribosomal subunit and impairing mitochondrial protein translation.…”

Human mitochondrial ribosomes can switch their structural RNA composition

“…Of the 80 known mitoribosomal proteins, 36 are mitospecific and lack bacterial orthologs, and those with orthologs often carry mitospecific extensions (1). Further idiosyncrasies have been revealed by recent subnanometer-resolution cryo-EM structures, which simultaneously resolved a long-debated question concerning mitoribosomal rRNA content (1,2). Until recently, mammalian mitoribosomes were considered divergent by containing only one rRNA species per subunit, although the potential presence of the 5S species in the mitochondrial large subunit (mt-LSU) remained a contentious issue (3).…”

“…Recent data have shown that there is indeed a third RNA moiety present in mammalian mitoribosomes. It is not, however, a 5S species, but a tRNA encoded by the mitochondrial genome (mtDNA) (1,2,(4)(5)(6). Interestingly, which tRNA was selected differed between mammalian species, with mt-tRNA Val predominating in human mt-LSU, in contrast to mt-tRNA Phe being selected for incorporation into the porcine mt-LSU ( Fig.…”

Hybrid Mass Spectrometry: Towards Characterization of Protein Conformational States

“…Integrative structure determination using advanced modelling was introduced by the Sali group [8] and, since then, it has been used for modelling large macromolecular complexes, such as the proteasome [9], ribosomes [10], and others. A milestone in integrative modelling approaches was the merging of heterogeneous data from different MS-based methods [1] enabling atomic-level characterization of dynamic (sub)complexes and their transient associations with other biomolecules.…”