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EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation

Nature Cell Biology volume 20, pages 162–174 (2018)Cite this article

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Abstract

Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3′–5′ domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.

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Fig. 1: EXD2 is a mitochondrial protein.
Fig. 2: EXD2 is required for metabolic homeostasis.
Fig. 3: Characterization of EXD2-deficient cells.
Fig. 4: EXD2 interacts with complex I and the mitoribosome.
Fig. 5: EXD2 prevents aberrant mRNA association with the mitoribosome and facilitates translation.
Fig. 6: EXD2 preferentially targets ssRNA.
Fig. 7: Metabolic and developmental defects in dExd2-deficient flies.
Fig. 8: Germline stem cell attrition and increased lifespan in dEXD2-deficient flies.

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Acknowledgements

We are grateful to A. Zorzano, A. Vaquero, E. Hidalgo, W. M. Keyes, M. Milan, J. Casanova, M. Solà, V. Mootha, J. Guinovart and the Stracker Lab for input and discussions, N. Gallisa for help generating BioID constructs, J. J. P. Perry and J.A. Tainer for the WRN-EXO expression construct, A. Bratic and N.G. Larsson for sharing advice and protocols, and the Advanced Digital Microscopy and Biostatistics/Bioinformatics IRB core facilities. We thank the following bodies for funding: Ministerio de Economía y Competitividad (MINECO) (T.H.S.: BFU2012-39521, BFU2015-68354, Ayudas para incentivar la incorporación estable de doctores (IED) 2015; L.R.d.P.: BIO2015-64572; T.H.S. and L.R.d.P: institutional funding through the Centres of Excellence Severo Ochoa award and from the CERCA Programme of the Catalan Government; and O.Y.: SAF2011-30578 and BFU2014-57466); the Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), an initiative of Instituto de Investigacion Carlos III (ISCIII) to O.Y.; and the Biotechnology and Biological Sciences Research Council (BBSRC: BB/H019723/1 and BB/M008800/1) to A.J.D. and L.B. S.A. was supported by a Finnish Cultural Society Fellowship, J.S. by a fellowship from Fundação para a Ciência e a Tecnologia (SFRH/BD/87025/2012), P.A.K. by an Advanced Postdoc Mobility fellowship from the Swiss National Science Foundation (SNF), I.G.-C. by an Asociación Española Contra el Cáncer (AECC) fellowship, A.A.-F. by a Severo Ochoa FPI fellowship (MINECO; SVP2014068398), and A.A.J. by an EMBO long-term fellowship (ALTF 554-2015).

Author information

Author notes

  1. Joana Silva

    Present address: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

  2. Suvi Aivio

    Present address: Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA

  3. Philip A. Knobel

    Present address: Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland

  4. Pablo Pérez-Ferreros

    Present address: EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia

Authors and Affiliations

  1. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Suvi Aivio, Philip A. Knobel, Andreu Casali, Isabel Garcia-Cao, Pablo Pérez-Ferreros, Albert Antolin-Fontes, Lluís Ribas de Pouplana & Travis H. Stracker

  2. Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK

    Laura J. Bailey & Aidan J. Doherty

  3. Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain

    Maria Vinaixa, Sara Samino-Gené & Oscar Yanes

  4. Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain

    Maria Vinaixa, Sara Samino-Gené & Oscar Yanes

  5. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada

    Étienne Coyaud & Brian Raught

  6. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

    Étienne Coyaud & Brian Raught

  7. Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA

    Alexis A. Jourdain

  8. Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    Alexis A. Jourdain

  9. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Alexis A. Jourdain

  10. Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain

    Ana M. Rojas

  11. Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain

    Acaimo González-Reyes

  12. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

    Lluís Ribas de Pouplana

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Contributions

J.S. and S.A. performed the majority of experiments characterizing cell lines and effects of EXD2 deficiency. J.S. performed sucrose gradient fractionations, and L.J.B. and A.J.D. purified and characterized bacterial EXD2 and WRN, performed mtDNA replication assays and analysed data. J.S., S.A., A.C. and A.G.-R. characterized Drosophila. P.A.K. and P.P.-F. performed BioID assays, and M.V., S.S.-G. and O.Y. carried out metabolomics and mass spectrometry, analysed data and prepared figures. E.C. and B.R. purified biotinylated peptides, performed mass spectrometry and analysed data. A.A.J. performed the MitoString assay, and I.G.-C., J.S., S.A. and T.H.S. performed survival assays and analysed DNA damage responses. T.H.S. and J.S. performed mitochondrial translation assays, and P.A.K. and A.A.F. performed immunofluorescence analysis in Drosophila S2 cells. A.M.R. performed computational and evolutionary analysis, and L.R.d.P. provided critical technical expertise and advice. T.H.S. analysed data, prepared figures, supervised experiments and wrote the manuscript with editorial contributions from all authors.

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Correspondence to Travis H. Stracker.

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Silva, J., Aivio, S., Knobel, P.A. et al. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 20, 162–174 (2018). https://doi.org/10.1038/s41556-017-0016-9

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