Abstract
To understand the steps involved in the evolution of translation, we used Tetrahymena thermophila, a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.
Highlights
Mitoribosomes are composed of a catalytic rRNA core, encoded in the mitochondrial genome, and an outer shell of mitoribosomal proteins
Most of the newly identified proteins are associated with the small subunit and distributed across the head and the two regions that we named as the back protuberance and the body extension
We found the third protein encoded in the previously unknown Ymf64, which mainly corresponds to the functional C-terminal domain (CTD) of uS3 and forms a part of the N-terminal stabilizing domain (NTD) (Figure 3)
Summary
Mitoribosomes are composed of a catalytic rRNA core, encoded in the mitochondrial genome, and an outer shell of mitoribosomal proteins. Previous structural studies have reported atomic models of mitoribosomes from eukaryotic supergroups such as Holozoa, Holomycota (Brown et al, 2014; Amunts et al, 2014; Greber et al, 2014; Amunts et al, 2015; Greber et al, 2015; Desai et al, 2017), and Discoba (Ramrath et al, 2018), previously Excavata (Adl et al, 2019) These mitoribosomes translate only a few mRNAs, of which all but one code for hydrophobic membrane subunits of the oxygenic phosphorylation complexes. To generate data to understand the evolution and function of mitochondrial translation, new evidence representing a larger variation of species is needed (Lukeset al., 2018)
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