In silico model of mtDNA mutations effect on secondary structure of mitochondrial rRNA and tRNA in Leber's hereditary optical neuropathy.

Rovcanin, Branislav; Jancic, Jasna; Samardzic, Janko; Rovcanin, Marija; Nikolic, Blazo; Ivancevic, Nikola; Novakovic, Ivana; Kostic, Vladimir

The Leber's hereditary optical neuropathy (LHON) is a rare disease caused by mitochondrial DNA (mtDNA) mutations. Beside primary mutations, the effect of secondary mtDNA mutations in still unclear. We examined the effect of secondary mtDNA mutations on secondary structure of different mitochondrial RNAs. Whole mitochondrial genome sequence of LHON patients has been obtained from in six non related pedigrees by Sanger sequencing method. The effect of mutations located in mitochondrial RNA genes was examined by creating in silico models of RNA secondary structure, accompanied by sequence conservation analysis. All three primary LHON mutations (m.3460G > A, m.11778G > A and m.14,484 T > C) were revealed in study families. Four mutations in MT-RNR1 gene (m.750 A > G, m.956delC, m.1438 A > G and m.1555 A > G) were identified and only a m.1555 A > G causes significant changes of secondary structure of mitochondrial 12 S ribosomal RNA (rRNA). Five mutations (m.1811A > G, m.2706 A > G, m.2831G > A, m.3010G > A and m.3197 T > C) were discovered in MT-RNR2 gene and all of them induced substantial alterations of mitochondrial 16 S rRNA secondary structure. A single insertion variant (m.15986insG) has been found in the MT-TP gene which encodes mitochondrial transfer RNA for Proline (tRNA Pro). This mutation does not cause substantial changes of tRNA Pro secondary structure. Most of the mutation loci exhibited high level of sequence conservation. Presence of multiple mutations in a single family can either be of no influence on secondary RNA structure, or it can be a correctable factor for some deleterious effects of individual mutations. The effect of discovered mutations on in silico modeled RNA structure is in a significant correlation with the present knowledge about the potential of these mutation to participate in the pathophysiology of LHON and other human diseases. The presence of certain multiple mitochondrial RNA mutations could be a possible explanation of LHON clinical presentation in some families. All revealed mutations have been evaluated for the first time in terms of in silico structural modeling. The application of bioinformatics tools such as secondary RNA structure prediction can have a great advantage in better understanding of the molecular standpoint of the LHON pathophysiology and clinical phenotype.