RRM1 variants cause a mitochondrial DNA maintenance disorder via impaired de novo nucleotide synthesis

Jonathan Shintaku, Wolfgang M. Pernice, Wafaa Eyaid, B. G.C. Jeevan, Zuben P. Brown, Marti Juanola-Falgarona, Javier Torres-Torronteras, Ewen W. Sommerville, Debby M.E.I. Hellebrekers, Emma L. Blakely, Alan Donaldson, Ingrid van de Laar, Cheng Shiun Leu, Ramon Marti, Joachim Frank, Kurenai Tanji, David A. Koolen, Richard J. Rodenburg, Patrick F. Chinnery, H. J.M. SmeetsGráinne S. Gorman, Penelope E. Bonnen, Robert W. Taylor, Michio Hirano*

*Corresponding author for this work

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Abstract

Mitochondrial DNA (mtDNA) depletion/deletions syndromes (MDDS) encompass a clinically and etiologically heterogenous group of mitochondrial disorders caused by impaired mtDNA maintenance. Among the most frequent causes of MDDS are defects in nucleoside/nucleotide metabolism, which is critical for synthesis and homeostasis of the deoxynucleoside triphosphate (dNTP) substrates of mtDNA replication. A central enzyme for generating dNTPs is ribonucleotide reductase, a critical mediator of de novo nucleotide synthesis composed of catalytic RRM1 subunits in complex with RRM2 or p53R2. Here, we report 5 probands from 4 families who presented with ptosis and ophthalmoplegia as well as other clinical manifestations and multiple mtDNA deletions in muscle. We identified 3 RRM1 loss-of-function variants, including a dominant catalytic site variant (NP_001024.1: p.N427K) and 2 homozygous recessive variants at p.R381, which has evolutionarily conserved interactions with the specificity site. Atomistic molecular dynamics simulations indicate mechanisms by which RRM1 variants affect protein structure. Cultured primary skin fibroblasts of probands manifested mtDNA depletion under cycling conditions, indicating impaired de novo nucleotide synthesis. Fibroblasts also exhibited aberrant nucleoside diphosphate and dNTP pools and mtDNA ribonucleotide incorporation. Our data reveal that primary RRM1 deficiency and, by extension, impaired de novo nucleotide synthesis are causes of MDDS.

Original languageEnglish
Article numbere145660
JournalJournal of Clinical Investigation
Volume132
Issue number13
DOIs
Publication statusPublished - 1 Jul 2022

Bibliographical note

Funding Information:
This work was supported by Department of Defense Focused Program Award W81XWH2010807 (to MH), NIH research grant P01 HD32062 (to MH), and NIH grant 35 GM139453 (to JF). MH is supported by the Arturo Estopinan TK2 Research Fund, Nicholas Nunno Foundation, JDM Fund for Mitochondrial Research, Shuman Mitochondrial Disease Fund, the Marriott Mitochondrial Disease Clinic Research Fund from the J. Willard and Alice S. Marriott Foundation, and NIH grant U54 NS078059. Work in Newcastle upon Tyne was supported by the Wellcome Centre for Mitochondrial Research (203105/Z/16/Z), Medical Research Council International Centre for Genomic Medicine in Neuromuscular Disease (MR/S005021/1), UK NIHR Biomedical Research Centre in Age and Age Related Diseases award to the Newcastle upon Tyne Hospitals NHS Foundation, the Lily Foundation, and the UK National Health Service Highly Specialised Service for Rare Mitochondrial Disorders. RWT receives financial support from the Pathological Society. EWS was funded by a Medical Research Council PhD studentship. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant ACI-1548562. JBGC is supported by grant BIO210070 from XSEDE. The authors thank the patients and their families for collaborating in this study and Saba Tadesse for technical support of mitochondrial respiratory chain enzyme activities. We also thank the Genome Technology Center at the Radboud University Medical Center and BGI Copenhagen for WES technical support.

Publisher Copyright:
Copyright: © 2022, Shintaku et al. This is an open access article published under the terms of the Creative Commons Attribution 4.0 International License.

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