Bi-allelic Mutations in the Mitochondrial Ribosomal Protein MRPS2 Cause Sensorineural Hearing Loss, Hypoglycemia, and Multiple OXPHOS Complex Deficiencies

Abstract

Biogenesis of the mitochondrial oxidative phosphorylation system, which produces the bulk of ATP for almost all eukaryotic cells, depends on the translation of 13 mtDNA-encoded polypeptides by mitochondria-specific ribosomes in the mitochondrial matrix. These mitoribosomes are dual-origin ribonucleoprotein complexes, which contain mtDNA-encoded rRNAs and tRNAs and $80 nucleus-encoded proteins. An increasing number of gene mutations that impair mitoribosomal function and result in multiple OXPHOS deficiencies are being linked to human mitochondrial diseases. Using exome sequencing in two unrelated subjects presenting with sensorineural hearing impairment, mild developmental delay, hypoglycemia, and a combined OXPHOS deficiency, we identified mutations in the gene encoding the mitochondrial ribosomal protein S2, which has not previously been implicated in disease. Characterization of subjects' fibroblasts revealed a decrease in the steady-state amounts of mutant MRPS2, and this decrease was shown by complexome profiling to prevent the assembly of the small mitoribosomal subunit. In turn, mitochondrial translation was inhibited, resulting in a combined OXPHOS deficiency detectable in subjects' muscle and liver biopsies as well as in cultured skin fibroblasts. Reintroduction of wild-type MRPS2 restored mitochondrial translation and OXPHOS assembly. The combination of lactic acidemia, hypoglycemia, and sensorineural hearing loss, especially in the presence of a combined OXPHOS deficiency, should raise suspicion for a ribosomal-subunit-related mitochondrial defect, and clinical recognition could allow for a targeted diagnostic approach. The identification of MRPS2 as an additional gene related to mitochondrial disease further expands the genetic and phenotypic spectra of OXPHOS deficiencies caused by impaired mitochondrial translation. Mitochondria are essential organelles that harbor the oxidative phosphorylation system (OXPHOS), an ATP-producing system encompassing five multi-subunit enzymatic complexes whose biogenesis is strictly dependent on the coordinated expression of genes encoded by nuclear and mitochondrial DNA (mtDNA). mtDNA encodes 13 subunits that are essential structural components of OXPHOS complexes I, III, IV, and V, in addition to encoding two rRNAs (16S and 12S) and 22 tRNAs required for the translation of the subunits. 1 Mitochondrial translation is executed by a dedicated translation machinery that includes many regulatory factors and a mitochondrial-specific ribosome composed of two subunits: the 28S (mt-SSU) and 39S (mt-LSU) ribosomal subunits. These subunits are large ribonucleoprotein complexes containing around 80 nuclear-encoded structural mitoribosomal proteins (MRPs) and mt-DNA-encoded RNAs: 12S rRNA in the mt-SSU and 16S rRNA, in addition to either mt-tRNA Val or mt-tRNA Phe , in the mt-LSU subunit. 2-5 The threedimensional structures of the mammalian 3,6,7 and human 2 mitoribosomes have only been elucidated recently. Considering the many factors involved in this process, it is not surpri...

Structural basis of mitochondrial translation

“…Translation in mitochondria is carried out by specialized mitoribosomes that are structurally distinct with 2-fold reduced mt-rRNA and ~1 MDa increased protein mass. Specific autosomal recessive mutations associated with these extra proteins cause severe, infantile onset disease with growth retardation, neurological phenotypes and cardiac involvement, and are associated with Perrault syndrome ( De Silva et al, 2015 ; D'Souza and Minczuk, 2018 ; Boczonadi et al, 2018 ; Gardeitchik et al, 2018 ; Bugiardini et al, 2019 ). Analysis of individuals with variations in mitoribosomal proteins demonstrated that mutations result in Leigh syndrome ( Lake et al, 2017 ).…”

Inhibition of mitochondrial translation in fibroblasts from a patient expressing the KARS p.(Pro228Leu) variant and presenting with sensorineural deafness, developmental delay, and lactic acidosis

“…This analysis revealed significant assembly defects of all complexes whose biogenesis depends on the synthesis of the 13 mtDNA‐encoded subunits in mitochondria (Figure b and c). Moreover, we observed an accumulation of the F1 subcomplex of complex V indicative of a biogenesis defect of this OXPHOS complex (Gardeitchik et al., ; Metodiev et al., ).…”

Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus that are Necessary for Synapse Function

“…This dearth of information about mitochondrial protein synthesis and proteostasis in synapses is in stark contrast with the numerous human mutations affecting mitochondrial protein synthesis and degradation. These mutations associate with pathology ranging from epileptic encephalopathy to neurodevelopmental and psychiatric disorders, which are also frequent phenotypes in mutations affecting bona fide synaptic genes (Akbergenov et al, 2018;Gardeitchik et al, 2018;Lake et al, 2017;Lightowlers et al, 2015;Nimmo et al, 2019;Pei and Wallace, 2018;Shutt and Shadel, 2010;Wallace et al, 2010). Here we make a case for mitochondrial protein translation and proteostasis in synapse biology focusing on genes encoded in a neurodevelopmental risk mutation, the 22q11.2 microdeletion syndrome locus…”