Heterologous Inferential Analysis (HIA) as a Method to Understand the Role of Mitochondrial rRNA Mutations in Pathogenesis
Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis or HIA that can be used to make predictions on the disruptive potential of a large subset of mt-rRNA variants. First, due to the high evolutionary conservation of the rRNA fold, comparison of phylogenetically derived secondary structures of the human mt-rRNAs and those from model organisms allows the location of structurally equivalent residues. Second, visualization of the heterologous equivalent residue in high-resolution structures of the ribosome allows a preliminary structural characterization of the residue and its neighboring region. Third, an exhaustive search for biochemical and genetic information on the residue and its surrounding region is performed to understand their degree of involvement in ribosomal function. Additional rounds of visualization in biochemically relevant high-resolution structures will lead to the structural and functional characterization of the residue’s role in ribosomal function and to an assessment of the disruptive potential of mutations at this position. Notably, in the case of certain mitochondrial variants for which sufficient information regarding their genetic and pathological manifestation is available; HIA data alone can be used to predict their pathogenicity. In other cases, HIA will serve to prioritize variants for additional investigation. In the context of a scoring system specifically designed for these variants, HIA could lead to a powerful diagnostic tool.
Key wordsMitochondrial rRNA mtDNA Mitoribosome Mitochondrial deafness mtDNA mutation
Note added in proof
Recent advances in cryo-electron microscopy have allowed the groups led by R.K. Agrawal, N. Ban, and V. Ramakrishnan to achieve medium-resolution and near-atomic-resolution structures of mammalian mitoribosomal particles. Such advances now permit the placement of sites of mutation directly on mitoribosomal structures, thus dramatically improving the predictive power of the methods described here.
- 4.Mutai H, Kouike H, Teruya E, Takahashi-Kodomari I, Kakishima H, Taiji H, Usami S, Okuyama T, Matsunaga T (2011) Systematic analysis of mitochondrial genes associated with hearing loss in the Japanese population: DHPLC reveals a new candidate mutation. BMC Med Genet 12:135PubMedCentralPubMedCrossRefGoogle Scholar
- 9.Subhankar B, Dhananjaya S (2003) MITOMAP mtDNA sequence data: unpublished variant 20041220003Google Scholar
- 11.Smith PM, Elson JL, Greaves LC, Wortmann SB, Rodenburg RJ, Lightowlers RN, Chrzanowska-Lightowlers ZM, Taylor RW, Vila-Sanjurjo A (2014) The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential. Hum Mol Genet 23:949–956PubMedCentralPubMedCrossRefGoogle Scholar
- 13.Sayers E (2010) E-utilities quick start. In: Entrez programming utilities help [Internet]. National Center for Biotechnology Information (US), Bethesda (MD)Google Scholar
- 17.Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM et al (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:2PubMedCentralPubMedCrossRefGoogle Scholar
- 22.Jeffrey G (1997) An introduction to hydrogen bonding. Oxford University Press, OxfordGoogle Scholar