Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation
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.
Reviewing Editor
- Cynthia Wolberger, Johns Hopkins University School of Medicine, United States
Publication history
- Received: May 25, 2020
- Accepted: June 8, 2020
- Accepted Manuscript published: June 18, 2020 (version 1)
- Version of Record published: June 30, 2020 (version 2)
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
-
- 1,887
- Page views
-
- 307
- Downloads
-
- 23
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
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)
Further reading
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
Aurora B, together with IN-box, the C-terminal part of INCENP, forms an enzymatic complex that ensures faithful cell division. The [Aurora B/IN-box] complex is activated by autophosphorylation in the Aurora B activation loop and in IN-box, but it is not clear how these phosphorylations activate the enzyme. We used a combination of experimental and computational studies to investigate the effects of phosphorylation on the molecular dynamics and structure of [Aurora B/IN-box]. In addition, we generated partially phosphorylated intermediates to analyze the contribution of each phosphorylation independently. We found that the dynamics of Aurora and IN-box are interconnected, and IN-box plays both positive and negative regulatory roles depending on the phosphorylation status of the enzyme complex. Phosphorylation in the activation loop of Aurora B occurs intramolecularly and prepares the enzyme complex for activation, but two phosphorylated sites are synergistically responsible for full enzyme activity.
-
- Neuroscience
- Structural Biology and Molecular Biophysics
The cation-permeable TRPV2 channel is important for cardiac and immune cell function. Cannabidiol (CBD), a non-psychoactive cannabinoid of clinical relevance, is one of the few molecules known to activate TRPV2. Using the patch-clamp technique, we discover that CBD can sensitize current responses of the rat TRPV2 channel to the synthetic agonist 2-aminoethoxydiphenyl borate (2-APB) by over two orders of magnitude, without sensitizing channels to activation by moderate (40°C) heat. Using cryo-EM, we uncover a new small-molecule binding site in the pore domain of rTRPV2 in addition to a nearby CBD site that had already been reported. The TRPV1 and TRPV3 channels are also activated by 2-APB and CBD and share multiple conserved features with TRPV2, but we find that strong sensitization by CBD is only observed in TRPV3, while sensitization for TRPV1 is much weaker. Mutations at non-conserved positions between rTRPV2 and rTRPV1 in either the pore domain or the CBD sites failed to confer strong sensitization by CBD in mutant rTRPV1 channels. Together, our results indicate that CBD-dependent sensitization of rTRPV2 channels engages multiple channel regions, and that the difference in sensitization strength between rTRPV2 and rTRPV1 channels does not originate from amino acid sequence differences at the CBD binding site or the pore domain. The remarkably robust effect of CBD on TRPV2 and TRPV3 channels offers a promising new tool to both understand and overcome one of the major roadblocks in the study of these channels – their resilience to activation.