Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation
- Stockholm University, Sweden
Abstract
To reveal steps in the evolution of translation, we identified ciliates as a model with high coding capacity of the mitochondrial genome and characterized its mitoribosomes by cryo-EM. It revealed a 94-protein and 4-rRNA assembly with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure 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 intrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate 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.
Data availability
The electron density maps have been deposited into EMDB, with accession codes EMD-11032 (monosome), EMD-11033 (LSU), EMD-11034 (SSU), EMD-11035 (CP), EMD-11036 (L7/L12 stalk), EMD-11037 (head), EMD-11038 (back protuberance). The model has been deposited in the PDB, with accession code 6Z1P.
Article and author information
Author details
Funding
Ragnar Söderbergs stiftelse (M44/16)
- Alexey Amunts
Cancerfonden (2017/1041)
- Alexey Amunts
H2020 European Research Council (ERC-2018-StG- 805230)
- Alexey Amunts
Knut och Alice Wallenbergs Stiftelse (2018.0080)
- Alexey Amunts
European Molecular Biology Organization (EMBO Young Investigator Program)
- Alexey Amunts
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Tobiasson & Amunts
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,113
- views
-
- 332
- downloads
-
- 40
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation
eLife 9:e59264.
https://doi.org/10.7554/eLife.59264
Further reading
-
- Structural Biology and Molecular Biophysics
Ciliary rootlets are striated bundles of filaments that connect the base of cilia to internal cellular structures. Rootlets are critical for the sensory and motile functions of cilia. However, the mechanisms underlying these functions remain unknown, in part due to a lack of structural information of rootlet organization. In this study, we obtain 3D reconstructions of membrane-associated and purified rootlets from mouse retina using cryo-electron tomography. We show that flexible protrusions on the rootlet surface, which emanate from the cross-striations, connect to intracellular membranes. In purified rootlets, the striations were classified into amorphous (A)-bands, associated with accumulations on the rootlet surface, and discrete (D)-bands corresponding to punctate lines of density that run through the rootlet. These striations connect a flexible network of longitudinal filaments. Subtomogram averaging suggests the filaments consist of two intertwined coiled coils. The rootlet’s filamentous architecture, with frequent membrane-connecting cross-striations, lends itself well for anchoring large membranes in the cell.
-
- Structural Biology and Molecular Biophysics
Although the αC-β4 loop is a stable feature of all protein kinases, the importance of this motif as a conserved element of secondary structure, as well as its links to the hydrophobic architecture of the kinase core, has been underappreciated. We first review the motif and then describe how it is linked to the hydrophobic spine architecture of the kinase core, which we first discovered using a computational tool, local spatial Pattern (LSP) alignment. Based on NMR predictions that a mutation in this motif abolishes the synergistic high-affinity binding of ATP and a pseudo substrate inhibitor, we used LSP to interrogate the F100A mutant. This comparison highlights the importance of the αC-β4 loop and key residues at the interface between the N- and C-lobes. In addition, we delved more deeply into the structure of the apo C-subunit, which lacks ATP. While apo C-subunit showed no significant changes in backbone dynamics of the αC-β4 loop, we found significant differences in the side chain dynamics of K105. The LSP analysis suggests disruption of communication between the N- and C-lobes in the F100A mutant, which would be consistent with the structural changes predicted by the NMR spectroscopy.
