Projects / Programmes
Structural and dynamic characterisation of mitochondrial transfer RNAs (mt-tRNAs) and their fragments
| Code |
Science |
Field |
Subfield |
| 1.04.00 |
Natural sciences and mathematics |
Chemistry |
|
| Code |
Science |
Field |
| 1.04 |
Natural Sciences |
Chemical sciences |
mitochondria, tRNA, mt-tRNA, tRNA fragments, RNA structure, pathological mutation, modified nucleotides, pseudouridine, NMR spectroscopy, RDC, nanodiscs, PRORP1, tRNA maturation enzymes, maturation
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
35144 |
PhD Vojč Kocman |
Chemistry |
Head |
2021 - 2023 |
46 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0104 |
National Institute of Chemistry |
Ljubljana |
5051592000 |
21,023 |
Abstract
Mitochondrial diseases impact 1/5000 individuals and are caused by changes in the structure of protein or RNA molecules present in the mitochondria. These changes can be directly linked to pathological mutations in mitochondrial or nuclear DNA with over 50% of disease-causing mitochondrial DNA (mt-DNA) mutations found in mt-tRNA encoding genes. Interestingly, more than 250 pathogenic mt-tRNA mutations primarily lie outside of the anticodon or discriminator bases critical for codon recognition and aminoacylation which suggests that these mutations cause perturbations in local or global mt-tRNA structure and dynamics that negatively impact the interactions between mt-tRNA and maturation enzymes or the mitochondrial translation machinery. Scientists are still missing the high-resolution structures of mt-tRNA that would allow them to mechanistically explain a lot of mt-tRNA pathologies and help them in the rational design of novel therapeutics. Additionally, mt-tRNAs also engage in a still poorly understood biogenesis to produce mt-tRNA fragments which are highly regulated entities that are important for cell biology and participate in processes such as gene/oncogene silencing, RNA processing, protein translation and epigenetic regulation. Importantly, even though they play important biological roles they are still almost completely structurally uncharacterized. Based on my preliminary data on B. Subtilis tRNA Asp and the analysis of scarce NMR spectra found in the literature I observed that tRNA molecules have the potential to produce very favorable NMR spectral properties. Previous studies have suggested that the main limitation in structurally characterizing mt-tRNAs is the fact that mt-tRNAs are very dynamic and need to include a lot of modified nucleotides, that are added by maturation enzymes, to adopt stable structures. I believe I am in a unique position to tackle these challenges since I can do both in vitro T7 transcription and chemical synthesis on solid phase support which gives me site specific control in introducing modified and (13C, 15N and 2H) isotopically enriched residues into mt-tRNAs and have access to mt-tRNA maturation enzymes from my collaborator from the University of Michigan. In the case of mt-tRNA fragments I believe that based on their short RNA sequences they are ideal systems to be studied by NMR spectroscopy. Since the high-resolution structures of mt-tRNAs and mt-tRNA fragments are mostly missing, this work will significantly contribute to the RNA structural database. High-resolution structures of mt-tRNA fragments will start the discussion on the importance of the mt-tRNA structure for cell biology. With the help of mt-tRNA structures, it will be possible to answer what role does structure and dynamics play in the interactions between mt-tRNAs and maturation enzymes or the mitochondrial translation machinery. It will also be possible to understand how these interactions break down in case of pathological mutations.
