Center for Endocrine Surgery, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
Clinic of Neurology and Psychiatry for Children and Youth, Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
Exp Eye Res. 2020 Dec;201:108277. doi: 10.1016/j.exer.2020.108277. Epub 2020 Sep 28.
The Leber's hereditary optic 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 and regional 3D structure, accompanied by sequence conservation analysis. All three primary LHON mutations (m.3460G>A, m.11778G>A and m.14484 T>C) were revealed in study families. Four mutations in MT-RNR1 gene (m.750A>G, m.956delC, m.1438A>G and m.1555A>G) were identified and only an m.1555A>G causes significant changes of secondary structure of mitochondrial 12S ribosomal RNA (rRNA), while it is the only mutation which does not alter its 3D structure. Five mutations (m.1811A>G, m.2706A>G, m.2831G>A, m.3010G>A and m.3197T>C) were discovered in MT-RNR2 gene and all of them induced substantial alterations of mitochondrial 16S rRNA secondary structure. Significant changes of mitochondrial 16S rRNA 3D structure are caused by m.1811A>G, m.2706A>G, m.3010G>A and m.3197T>C. 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 for Proline secondary structure, while the 3D geometry remains without major changes. Most of the mutation loci exhibited high level of sequence conservation. Presence of multiple mutations in a single family appears to cause more extensive changes in mitochondrial 12S and 16S rRNA, then their individual influence. The effect of discovered mutations on in silico modelled 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 modelling. The application of bioinformatics tools such as secondary and 3D RNA structure prediction can have a great advantage in better understanding of the molecular standpoint of the LHON pathophysiology and clinical phenotype.
Leber 遗传性视神经病变（LHON）是一种由线粒体 DNA（mtDNA）突变引起的罕见疾病。除了主要突变外，次要 mtDNA 突变的影响仍不清楚。我们研究了次要 mtDNA 突变对不同线粒体 RNA 二级结构的影响。通过桑格测序方法，从六个非相关家族中获得了 LHON 患者的整个线粒体基因组序列。通过创建 RNA 二级和区域 3D 结构的计算机模型，并结合序列保守性分析，研究了位于线粒体 RNA 基因中的突变的影响。在研究的家族中发现了三种主要的 LHON 突变（m.3460G>A、m.11778G>A 和 m.14484 T>C）。在 MT-RNR1 基因中发现了四个突变（m.750A>G、m.956delC、m.1438A>G 和 m.1555A>G），只有 m.1555A>G 导致线粒体 12S 核糖体 RNA（rRNA）的二级结构发生显著变化，而它是唯一不改变其 3D 结构的突变。在 MT-RNR2 基因中发现了五个突变（m.1811A>G、m.2706A>G、m.2831G>A、m.3010G>A 和 m.3197T>C），它们都导致线粒体 16S rRNA 二级结构发生了实质性的改变。m.1811A>G、m.2706A>G、m.3010G>A 和 m.3197T>C 导致线粒体 16S rRNA 3D 结构发生显著变化。MT-TP 基因（编码线粒体脯氨酸转移 RNA（tRNA Pro））中发现了一个单一的插入变体（m.15986insG）。该突变不会导致 tRNA Pro 二级结构发生实质性变化，而 3D 几何形状保持不变。大多数突变位点表现出高度的序列保守性。单个家族中存在多种突变似乎会导致线粒体 12S 和 16S rRNA 的变化比它们各自的影响更为广泛。发现的突变对计算机建模 RNA 结构的影响与这些突变参与 LHON 和其他人类疾病的病理生理学的潜在能力的现有知识显著相关。某些线粒体 RNA 突变的存在可能是某些家族中 LHON 临床表现的一个可能解释。所有揭示的突变都首次进行了计算机模拟结构评估。二级和 3D RNA 结构预测等生物信息学工具的应用在更好地理解 LHON 病理生理学和临床表型的分子观点方面具有巨大优势。
