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Small is big in Arabidopsis mitochondrial ribosome

Nature Plants volume 5, pages 106–117 (2019)Cite this article

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Abstract

Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.

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Fig. 1: Strategy for the identification of Arabidopsis mitochondrial ribosome protein composition.
Fig. 2: rPPR1 immuno-precipitates the Arabidopsis mitochondrial ribosome.
Fig. 3: Macroscopic phenotyping of rPPR mutants.
Fig. 4: Arabidopsis rPPR1-deficient plants have lower ribosome density along mitochondrial mRNAs.
Fig. 5: Arabidopsis mitoribosome cryo-EM map compared to animal mitoribosome and Arabidopsis cytoribosome.
Fig. 6: Architecture of Arabidopsis mitoribosome fitted with E. coli and yeast mitochondria ribosomes.

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Data availability

Mass spectrometric data were deposited with the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD010324. Ribo-Seq sequencing data were deposited in the NCBI Gene Expression Omnibus under accession number GSE119655. Cryo-EM data were deposited in EMDataBank under accession number EMDB-4408 for Arabidopsis mitoribosome SSU, and EMDB-4409 for Arabidopsis mitoribosome LSU.

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Acknowledgements

This work was supported by Centre National de la Recherche Scientifique, the University of Strasbourg, by Agence Nationale de la Recherche (ANR) grants (MITRA, no. ANR-16-CE11-0024-02) and (CytoRP, no. ANR-16-CE21-0001-01) to P.G., Y.H. and H.M., and by the LabEx consortium MitoCross within the framework of the French National Program Investissement d’Avenir (no. ANR-11-LABX-0057_MITOCROSS) and LabEx Saclay Plant Sciences-SPS (no. ANR-10-LABX-0040-SPS). Mass spectrometry instruments were funded by the University of Strasbourg, IdEx Equipement mi-lourd 2015 and the LabEx consortium NetRNA within the framework of the French National Program Investissement d’Avenir (no. ANR-10-LABEX-0036_NETRNA). Y.H. was supported by the LabEx consortium NetRNA.

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Authors and Affiliations

  1. Institut de biologie de moléculaire des plantes UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France

    Florent Waltz, Mathilde Arrivé & Philippe Giegé

  2. Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France

    Tan-Trung Nguyen, Martine Quadrado & Hakim Mireau

  3. Institut Européen de Chimie et Biologie U1212 Inserm, Université de Bordeaux, Pessac, France

    Anthony Bochler & Yaser Hashem

  4. Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France

    Johana Chicher, Philippe Hammann & Lauriane Kuhn

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Contributions

P.G., F.W., H.M. and Y.H. designed and coordinated the experiments. F.W., T.T.N., M.A., A.B., J.C., M.Q., P.H. and L.K. performed the experiments and analysed the results. P.G., F.W., H.M., T.T.N. and Y.H. wrote the manuscript.

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Correspondence to Hakim Mireau, Yaser Hashem or Philippe Giegé.

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Waltz, F., Nguyen, TT., Arrivé, M. et al. Small is big in Arabidopsis mitochondrial ribosome. Nature Plants 5, 106–117 (2019). https://doi.org/10.1038/s41477-018-0339-y

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