Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion

Abstract

Mitochondrial DNA (mtDNA) depletion syndrome (MDS; MIM 251880) is a prevalent cause of oxidative phosphorylation disorders characterized by a reduction in mtDNA copy number. The hitherto recognized disease mechanisms alter either mtDNA replication (POLG (ref. 1)) or the salvage pathway of mitochondrial deoxyribonucleosides 5′-triphosphates (dNTPs) for mtDNA synthesis (DGUOK (ref. 2), TK2 (ref. 3) and SUCLA2 (ref. 4)). A last gene, MPV17 (ref. 5), has no known function. Yet the majority of cases remain unexplained. Studying seven cases of profound mtDNA depletion (1–2% residual mtDNA in muscle) in four unrelated families, we have found nonsense, missense and splice-site mutations and in-frame deletions of the RRM2B gene, encoding the cytosolic p53-inducible ribonucleotide reductase small subunit. Accordingly, severe mtDNA depletion was found in various tissues of the Rrm2b−/− mouse. The mtDNA depletion triggered by p53R2 alterations in both human and mouse implies that p53R2 has a crucial role in dNTP supply for mtDNA synthesis.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Pedigrees.
Figure 2: Real-time PCR quantification of the mtDNA content relative to that of MLH1 or Pde6b nuclear genes used as references for human or mouse respectively.
Figure 3: Computational modeling based on the crystal structure of the E. coli R1 and human R2 showing the putative R1-p53R2 interface of interaction.
Figure 4: Protein blot analysis.

Accession codes

Accessions

GenBank/EMBL/DDBJ

Protein Data Bank

References

  1. Ferrari, G. et al. Infantile hepatocerebral syndromes associated with mutations in the mitochondrial DNA polymerase-γA. Brain 128, 723–731 (2005).

    Article  Google Scholar 

  2. Mandel, H. et al. The deoxyguanosine kinase gene is mutated in individuals with depleted hepatocerebral mitochondrial DNA. Nat. Genet. 29, 337–341 (2001).

    Article  CAS  Google Scholar 

  3. Saada, A. et al. Mutant mitochondrial thymidine kinase in mitochondrial DNA depletion myopathy. Nat. Genet. 29, 342–344 (2001).

    Article  CAS  Google Scholar 

  4. Elpeleg, O. et al. Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion. Am. J. Hum. Genet. 76, 1081–1086 (2005).

    Article  CAS  Google Scholar 

  5. Spinazzola, A. et al. MPV17 encodes an inner mitochondrial membrane protein and is mutated in infantile hepatic mitochondrial DNA depletion. Nat. Genet. 38, 570–575 (2006).

    Article  CAS  Google Scholar 

  6. Nordlund, P. & Reichard, P. Ribonucleotide reductases. Annu. Rev. Biochem. 75, 681–706 (2006).

    Article  CAS  Google Scholar 

  7. Tanaka, H. et al. A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage. Nature 404, 42–49 (2000).

    Article  CAS  Google Scholar 

  8. Kimura, T. et al. Impaired function of p53R2 in Rrm2b-null mice causes severe renal failure through attenuation of dNTP pools. Nat. Genet. 34, 440–445 (2003).

    Article  CAS  Google Scholar 

  9. Comeau, S.R., Gatchell, D.W., Vajda, S. & Camacho, C.J. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 32, W96–W99 (2004).

    Article  CAS  Google Scholar 

  10. Comeau, S.R., Gatchell, D.W., Vajda, S. & Camacho, C.J. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20, 45–50 (2004).

    Article  CAS  Google Scholar 

  11. Eklund, H., Uhlin, U., Farnegardh, M., Logan, D.T. & Nordlund, P. Structure and function of the radical enzyme ribonucleotide reductase. Prog. Biophys. Mol. Biol. 77, 177–268 (2001).

    Article  CAS  Google Scholar 

  12. Lycksell, P.O., Ingemarson, R., Davis, R., Graslund, A. & Thelander, L. 1H NMR studies of mouse ribonucleotide reductase: the R2 protein carboxyl-terminal tail, essential for subunit interaction, is highly flexible but becomes rigid in the presence of protein R1. Biochemistry 33, 2838–2842 (1994).

    Article  CAS  Google Scholar 

  13. Kolberg, M., Strand, K.R., Graff, P. & Andersson, K.K. Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699, 1–34 (2004).

    Article  CAS  Google Scholar 

  14. Hakansson, P., Hofer, A. & Thelander, L. Regulation of mammalian ribonucleotide reduction and dNTP pools after DNA damage and in resting cells. J. Biol. Chem. 281, 7834–7841 (2006).

    Article  CAS  Google Scholar 

  15. Chabes, A.L., Pfleger, C.M., Kirschner, M.W. & Thelander, L. Mouse ribonucleotide reductase R2 protein: a new target for anaphase-promoting complex-Cdh1-mediated proteolysis. Proc. Natl. Acad. Sci. USA 100, 3925–3929 (2003).

    Article  CAS  Google Scholar 

  16. Zhou, B. et al. The human ribonucleotide reductase subunit hRRM2 complements p53R2 in response to UV-induced DNA repair in cells with mutant p53. Cancer Res. 63, 6583–6594 (2003).

    CAS  PubMed  Google Scholar 

  17. Matoba, S. et al. p53 regulates mitochondrial respiration. Science 312, 1650–1653 (2006).

    Article  CAS  Google Scholar 

  18. Liu, Z. & Butow, R.A. Mitochondrial retrograde signaling. Annu. Rev. Genet. 40, 159–185 (2006).

    Article  CAS  Google Scholar 

  19. Butow, R.A. & Avadhani, N.G. Mitochondrial signaling: the retrograde response. Mol. Cell 14, 1–15 (2004).

    Article  CAS  Google Scholar 

  20. Paquis-Flucklinger, V. et al. Early-onset fatal encephalomyopathy associated with severe mtDNA depletion. Eur. J. Pediatr. 154, 557–562 (1995).

    Article  CAS  Google Scholar 

  21. Abecasis, G.R., Cherny, S.S., Cookson, W.O. & Cardon, L.R. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30, 97–101 (2002).

    Article  CAS  Google Scholar 

  22. Rustin, P. et al. Biochemical and molecular investigations in respiratory chain deficiencies. Clin. Chim. Acta 228, 35–51 (1994).

    Article  CAS  Google Scholar 

  23. Sarzi, E. et al. Mitochondrial DNA depletion is a prevalent cause of multiple respiratory chain deficiency in childhood. J. Pediatr. (in the press).

  24. Schwede, T., Kopp, J., Guex, N. & Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381–3385 (2003).

    Article  CAS  Google Scholar 

  25. Hooft, R.W., Vriend, G., Sander, C. & Abola, E.E. Errors in protein structures. Nature 381, 272 (1996).

    Article  CAS  Google Scholar 

  26. Guex, N. & Peitsch, M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank T. Soussi for discussion and J. Bentata, B. Chabrol, C. Fallet-Bianco and J.M. Liet for referring the study subjects. This research was supported in part by the Association Française contre les Myopathies, Mitocircle European Union Project (contract number LSHB-CT-2004-005260), Eumitocombat within the European Union Sixth Framework Program for Research, Priority 1 'Life sciences, genomics and biotechnology for health' (contract number LSHM-CT-2004-503116) and the French Agence Nationale pour la Recherche.

Author information

Authors and Affiliations

Authors

Contributions

A.B. identified the p53R2 mutations and performed the protein blot and mtDNA quantification in mouse, L.M. performed protein blot analysis, V.S. performed the modeling of ribonucleotide reductase, J.-P.J. performed the linkage analysis using Merlin software, E.S. performed the mitochondrial DNA quantification, S.A. was in charge of cell culture, D.C. identified the respiratory chain enzyme activity, P.d.L. was responsible for clinical management of subjects 3, 4 and 7 and their diagnosis, V.P.-F. was responsible for clinical management of subject 7 and her diagnosis, H.A. and Y.N. produced the Rrm2b−/− mouse, A.M. was responsible for clinical management of subjects 1 and 2 and wrote the paper, and A.R. designed the project and wrote the paper.

Corresponding author

Correspondence to Agnès Rötig.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Sequence analysis of the RRM2B gene. (PDF 17 kb)

Supplementary Fig. 2

Sequence alignment of p53R2 and R2 proteins from human and nonhuman sources. (PDF 6 kb)

Supplementary Fig. 3

Protein blot analysis of Bax and Bcl2 in subject and control cells. (PDF 12 kb)

Supplementary Table 1

Oligonucleotide primers. (PDF 3 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bourdon, A., Minai, L., Serre, V. et al. Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion. Nat Genet 39, 776–780 (2007). https://doi.org/10.1038/ng2040

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng2040

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing