Letter | Published:

Mitochondrial translation requires folate-dependent tRNA methylation

Nature volume 554, pages 128132 (01 February 2018) | Download Citation

Abstract

Folates enable the activation and transfer of one-carbon units for the biosynthesis of purines, thymidine and methionine1,2,3. Antifolates are important immunosuppressive4 and anticancer agents5. In proliferating lymphocytes6 and human cancers7,8, mitochondrial folate enzymes are particularly strongly upregulated. This in part reflects the need for mitochondria to generate one-carbon units and export them to the cytosol for anabolic metabolism2,9. The full range of uses of folate-bound one-carbon units in the mitochondrial compartment itself, however, has not been thoroughly explored. Here we show that loss of the catalytic activity of the mitochondrial folate enzyme serine hydroxymethyltransferase 2 (SHMT2), but not of other folate enzymes, leads to defective oxidative phosphorylation in human cells due to impaired mitochondrial translation. We find that SHMT2, presumably by generating mitochondrial 5,10-methylenetetrahydrofolate, provides methyl donors to produce the taurinomethyluridine base at the wobble position of select mitochondrial tRNAs. Mitochondrial ribosome profiling in SHMT2-knockout human cells reveals that the lack of this modified base causes defective translation, with preferential mitochondrial ribosome stalling at certain lysine (AAG) and leucine (UUG) codons. This results in the impaired expression of respiratory chain enzymes. Stalling at these specific codons also occurs in certain inborn errors of mitochondrial metabolism. Disruption of whole-cell folate metabolism, by either folate deficiency or antifolate treatment, also impairs the respiratory chain. In summary, mammalian mitochondria use folate-bound one-carbon units to methylate tRNA, and this modification is required for mitochondrial translation and thus oxidative phosphorylation.

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Acknowledgements

We thank T. Pan, W. Lu, L. Chen, L. Parsons, W. Wang and T. Srikumar, and all members of the Rabinowitz laboratory. This work was supported by funding to J.D.R. from the US National Institutes of Health (NIH) (R01CA163591 and DP1DK113643) and StandUp to Cancer (SU2C-AACR-DT-20-16). G.S.D. was supported by a postdoctoral fellowship (PF-15-190-01- TBE) from the American Cancer Society. J.A.M. was supported by the science fund of the Paracelsus Medical University Salzburg (E-12/15/076-MAY). Z.G. was supported by the NIH (DP1AI124669).

Author information

Affiliations

  1. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA

    • Raphael J. Morscher
    • , Gregory S. Ducker
    •  & Joshua D. Rabinowitz
  2. Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA

    • Raphael J. Morscher
    • , Gregory S. Ducker
    •  & Joshua D. Rabinowitz
  3. Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA

    • Sophia Hsin-Jung Li
    •  & Zemer Gitai
  4. Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg 5020, Austria

    • Johannes A. Mayer
    •  & Wolfgang Sperl

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Contributions

R.J.M., G.S.D. and J.D.R. conceived the project and designed the experiments. R.J.M. and J.D.R. wrote the manuscript. R.J.M., G.S.D. and S.H.L performed biochemical experiments. Z.G. and W.S. were involved in study design and data interpretation. W.S. and J.A.M. contributed primary patient cell lines. All authors reviewed and edited the manuscript before submission.

Competing interests

J.D.R. is a founder of Raze Therapeutics, which aims to target 1C metabolism for cancer therapy.

Corresponding author

Correspondence to Joshua D. Rabinowitz.

Reviewer Information Nature thanks D. Appling, V. Gohil and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature25460

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