Insights into the genotype-phenotype correlation and molecular function of SLC25A46

Abstract

Recessive SLC25A46 mutations cause a spectrum of neurodegenerative disorders with optic atrophy as a core feature. We report a patient with optic atrophy, peripheral neuropathy, ataxia, but not cerebellar atrophy, who is on the mildest end of the phenotypic spectrum. By studying seven different nontruncating mutations, we found that the stability of the SLC25A46 protein inversely correlates with the severity of the disease and the patient's variant does not markedly destabilize the protein. SLC25A46 belongs to the mitochondrial transporter family, but it is not known to have transport function. Apart from this possible function, SLC25A46 forms molecular complexes with proteins involved in mitochondrial dynamics and cristae remodeling. We demonstrate that the patient's mutation directly affects the SLC25A46 interaction with MIC60. Furthermore, we mapped all of the reported substitutions in the protein onto a 3D model and found that half of them fall outside of the signature carrier motifs associated with transport function. We thus suggest that there are two distinct molecular mechanisms in SLC25A46-associated pathogenesis, one that destabilizes the protein while the other alters the molecular interactions of the protein. These results have the potential to inform clinical prognosis of such patients and indicate a pathway to drug target development.

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease

“…We did Sanger-sequence cDNA made from mutant mRNA and we confirmed that it is the same as the genomic DNA sequence, eliminating the possibility of transcriptional alterations (S1 Fig). Additionally, although the quantitative real-time polymerase chain reaction (RT-PCR) did not show a notable decrease in either slc25a46 crispant or mutant transcript abundance (S2 Fig), it is likely that the truncated protein was quickly degraded due to its conformational instability, previously shown to adversely affect the protein in the targeted region [30,31,33,35,39,44].…”

“…We designed five non-overlapping single guide RNAs (sgRNA) targeting the beginning of the largest exon 8, which encodes a conserved mitochondrial substrate carrier domain (IPR018108, InterPro) [44,45] (Fig 1A). We also targeted this domain because most of the disease-causing mutations [30,31,44], and a frameshift in a mouse model, which developed ataxia, optic atrophy and peripheral neuropathy, reside in exon 8 [33]. Finally, by choosing exon 8, we minimized the chances of functional restoration of the protein by alternative mRNA processing [46].…”

Diseases Caused by Mutations in Mitochondrial Carrier Genes SLC25: A Review

“…Notably, mutations in other genes involved in the regulation of the mitochondrial shape cause similar clinical features as those found in SLC24A46 deficiency patients [174]. Furthermore, it has been suggested that (i) the pathogenic SLC25A46 mutations affect the stability of the protein and interfere with protein-protein interactions important in mitochondrial morphology dynamics, and (ii) the degree of the protein destabilization and interference effects determine the severity of the disease [181]. Five of the pathogenic point mutations are located in different matrix helices (Figure 2A,C, at positions 48, 52, 70, 157, and 165) and they could be involved in protein-protein interactions; the other four are all in the SMS of H5 (Figure 1).…”

Mitochondrial diseases: expanding the diagnosis in the era of genetic testing

“…Other patients present later in life with optic atrophy diffuse brain and cerebellar atrophy [272,273] .…”

“…Unlike other members of the solute carrier family, SLC25A46 localizes to the OMM and its precise function remains unknown [324] . SLC25A46 has been shown to interact with both OPA1 and MFN2 suggesting a direct role in fusion/fission dynamics, but also forms a complex with the cristae remodeling protein MIC60 [325] . Variants in SLC25A46 express range of disease, although all patients express optic atrophy and axonal neuropathy.…”