SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder
Valentina Del Dotto, … , Tommaso Pippucci, Valerio Carelli
Valentina Del Dotto, … , Tommaso Pippucci, Valerio Carelli
Published January 2, 2020; First published September 24, 2019
Citation Information: J Clin Invest. 2020;130(1):108-125. https://doi.org/10.1172/JCI128514.
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Research Article Genetics Ophthalmology

SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder

Abstract

Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase–negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.

Authors

Valentina Del Dotto, Farid Ullah, Ivano Di Meo, Pamela Magini, Mirjana Gusic, Alessandra Maresca, Leonardo Caporali, Flavia Palombo, Francesca Tagliavini, Evan Harris Baugh, Bertil Macao, Zsolt Szilagyi, Camille Peron, Margaret A. Gustafson, Kamal Khan, Chiara La Morgia, Piero Barboni, Michele Carbonelli, Maria Lucia Valentino, Rocco Liguori, Vandana Shashi, Jennifer Sullivan, Shashi Nagaraj, Mays El-Dairi, Alessandro Iannaccone, Ioana Cutcutache, Enrico Bertini, Rosalba Carrozzo, Francesco Emma, Francesca Diomedi-Camassei, Claudia Zanna, Martin Armstrong, Matthew Page, Nicholas Stong, Sylvia Boesch, Robert Kopajtich, Saskia Wortmann, Wolfgang Sperl, Erica E. Davis, William C. Copeland, Marco Seri, Maria Falkenberg, Holger Prokisch, Nicholas Katsanis, Valeria Tiranti, Tommaso Pippucci, Valerio Carelli

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Figure 4

Distribution of SSBP1 mutations and protein in silico model.

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Distribution of SSBP1 mutations and protein in silico model. (A) Lollipo...
(A) Lollipop (61) diagram of ultrarare population and patients’ variants along the protein: variants with ≤ 2 gnomAD alleles are represented by gray sticks with red circles on top, while patients’ variants sticks and circles are uniformly colored. The green box represents the SSB domain. (B) MTR diagram for SSBP1 and location of patients’ variants: MTR viewer, version 0.3 (62), was used with window size 31 on ENST00000481508 transcript. MTR is plotted against SSBP1 sequence, and locations of variants are represented with dots using the same color code as in A. Dotted lines represent neutrality (blue) or different percentiles — black (median), green (25th), yellow (5th) — of most missense depleted gene regions. (C) Structural model of the SSBP1 homotetramer (from PDB code 3ULL) with aligned ssDNA (from structural alignment to 3ULP): the 3 positions carrying the most deleterious predictions are highlighted on WT homotetramer with same color code as in A and B. Upper inset: Gly40 occurs close to the approximate ssDNA binding site, not directly contacting DNA, but forming a highly constrained loop coordinating DNA-contacting residues Arg38 and Lys104. Middle inset: Arg107 occurs on the outer surface of the homotetramer at both homodimeric and homotetrameric interfaces. It is spatially close to Glu27 (5.3°A away) and likely forms a stabilizing salt -bridge across the dimer interface. Lower inset: Glu111 occurs directly in the tetrameric interface and potentially forms a stabilizing salt bridge with His34, although the available model does not clearly indicate the monomer this interaction occurs with (both His34 residues on opposing dimers are spatially close to Glu111, 7.7°A and 8.7°A, respectively).