Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation

Abstract
Data availability
Article and author information
Metrics

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.

The following data sets were generated

1. Tobiasson V
2. Amunts A
(2020) monosome
EMDB, EMD-11032.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11032
1. Tobiasson V
2. Amunts A
(2020) LSU
EMDB, EMD-11033.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11033
1. Tobiasson V
2. Amunts A
(2020) SSU
EMDB, EMD-11034.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11034
1. Tobiasson V
2. Amunts A
(2020) CP
EMDB, EMD-11035.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11035
1. Tobiasson V
2. Amunts A
(2020) L7/L12 stalk
EMDB, EMD-11036.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11036
1. Tobiasson V
2. Amunts A
(2020) head
EMDB, EMD-11037.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11037
1. Tobiasson V
2. Amunts A
(2020) back protuberance
EMDB, EMD-11038.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11038
1. Tobiasson V
2. Amunts A
(2020) Model
Protein Data Bank, 6Z1P.

https://www.rcsb.org/structure/6Z1P

Article and author information

Author details

Victor Tobiasson

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden

Competing interests
The authors declare that no competing interests exist.
Alexey Amunts

Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden

For correspondence
amunts@scilifelab.se

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5302-1740

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

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.