VARS2andTARS2Mutations in Patients with Mitochondrial Encephalomyopathies

Diodato, Daria; Melchionda, Laura; Haack, Tobias B.; Dallabona, Cristina; Baruffini, Enrico; Donnini, Claudia; Granata, Tiziana; Ragona, Francesca; Balestri, Paolo; Margollicci, Maria; Lamantea, Eleonora; Nasca, Alessia; Powell, Christopher A.; Minczuk, Michal; Strom, Tim M.; Meitinger, Thomas; Prokisch, Holger; Lamperti, Costanza; Zeviani, Massimo; Ghezzi, Daniele

doi:10.1002/humu.22590

Cited by 88 publications

(114 citation statements)

References 26 publications

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“…Loss of function mutations selected in yeast ThrRS and transplanted in human cytoplasmic ThrRS induce very similar defects, indicating that the yeast strain can be used to gain insights into the pathological mechanisms induced by human ThrRS mutations in the future, although no mutations have currently been linked pathologically with the human cytoplasmic ThrRS gene. Recently, a spontaneous mutation of human mitochondrial ThrRS P282L was reported to cause mitochondrial encephalopathies (54). The ThrRS knock-out system designed to test cellular function might also be helpful to examine the effects of this P282L mutation and establish an in vivo functional diagnosis.…”

Section: A Genetic Screen To Identify Functional Elements In Thrrs-mentioning

confidence: 99%

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog

Ruan

Fang

et al. 2015

Journal of Biological Chemistry

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Background: Eukaryotic ThrRSs exhibit four structural domains similar to bacterial ThrRSs and evolve a eukaryote-specific N-terminal extension domain. Results: Essential roles of 12 crucial residues in aminoacylation and editing reactions were revealed. Conclusion:The identified critical residues affected activities of ThrRS in various manners. Significance: We elucidated the synthetic and editing functions of selected residues and confirmed the functional consistency between yeast and human ThrRSs.

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Section: A Genetic Screen To Identify Functional Elements In Thrrs-mentioning

confidence: 99%

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog

Ruan

Fang

et al. 2015

Journal of Biological Chemistry

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“…TIMM9 was found to be up regulated in colorectal cancer case 145 . Consistent with these, our pipeline indicated the down regulation of TIMM9 by ETC-1922159 51 , with an assignment of low rank of 124. TARS2 has been found to be implicated in epilipsey 159 . Its role in colorectal cancer is not much known and after ETC-1922159 treatment TARS2 was found to be down regulated.…”

Section: Dicationmentioning

confidence: 99%

Revealing ETC-1922159 Affected Unknown 3rd order WNT10B-X-X Combinations, in Silico

Sinha¹

2017

Preprint

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WNT10B belongs to the family of WNT proteins that are implicated in a range of phenomena that are affected by the Wnt signaling pathway. Recent studies have shown that WNT10B plays a role in colorectal cancer. WNTs have been found to directly affect the stemness of the tumor cells via regulation of ASCL2. Switching off the ASCL2 literally blocks the stemness process of the tumor cells and vice versa. Furthermore, recent findings suggest BVES to be highly suppressed in malignancies and in vitro deletions of BVES show higher Wnt signaling activity to induce stemness. WNT10B was found to be highly expressed in such cases. Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. For example, WNT10B-ASCL2 is one such 2 nd order combination whose relation needs to be tested under the influence of recently developed porcupine-WNT inhibitor ETC-1922159. The inhibitor is known to suppress PORCN (porcupine) and thus inhibit a range of oncogenes known to be directly or indirectly affected by the Wnts. In a recent unpublished work in bioRxiv, Sinha 1 , we had the opportunity to rank these unknown biological hypotheses for down regulated genes at 2 nd order level after the drug was administered. The in silico observations showed that the combination of WNT10B-ASCL2 was assigned a relatively lower rank, thus validating the pipeline's efficacy with the confirmed wet lab experiment that indicate that both WNT10B and ASCL2 were down regulated after treatment in cancer cells. Here, we take one step further by in silico analysis of the 3 rd order combinations of WNT10B-X-X (X can be known or unknown factor), from a range of 100 randomly picked down regulated genes after ETC-1922159 treatment. The pipeline uses the density based HSIC (Hilbert Schmidt Information Criterion) sensitivity index with an rbf (radial basis function) kernel, which is known to be highly effective in sensitivity analysis. Various unknown/unexplored/untested 3 rd order biological hypotheses emerge some of which are confirmed in wet lab, while others need to be tested. The potential of such ranking is indispensable in the current era of search in a vast combinatorial forest. KEYWORDS -WNT pathway; porcupine inhibitor ETC-1922159; sensitivity analysis; colorectal cancer; unknown biological hypotheses; combinatorial search space; support vector ranking Conference, from 6-11 August 2017, held Significance WNT10B belongs to the family of WNT proteins that are implicated in a range of phenomena that are affected by the Wnt signaling pathway. Recent studies have shown that WNT10B plays a role in colorectal cancer. Often, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be involved in the pathway. The current work reveals at in silico level, the 3rd order WNT10B associated combinations that might be affected by the admin...

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“…Mutation Causing Human Mitochondrial Encephalomyopathies Affects Protein Structure/Stability and Enzymatic Activities of ThrRS-Recently, a mutation of Pro to Leu at position 282 of hmtThrRS was identified in a patient presenting mitochondrial disorders (26). Despite decreased levels of protein and charged tRNA Thr , the molecular consequence of the mutation could not be understood (26).…”

Section: Human Mitochondrial Thrrs Misactivates Ser and Mainly Uses Tmentioning

confidence: 99%

“…Both hmtThrRS protein and aminoacylated tRNA Thr levels are decreased in the patients' cells. The g.4255AϾG mutation has no influence in mRNA splicing (26); therefore, it was proposed that the c.845CϾT mutation is responsible for patient phenotypes. However, how the mutation affects protein structure, stability, and catalytic activities remains largely unknown.…”

mentioning

confidence: 99%

“…According to the increasing number of mutations in aaRS genes causing mitochondrial dysfunctions, including hmtThrRS (26), there is an interest in analyzing the functional properties of these molecules and developing new tools to examine their in vivo properties. Recently, two mutations (c.845CϾT, encoding hmtThrRS-P282L and a nucleotide change in position ϩ3 of intron 6 (g.4255AϾG; c.695 ϩ 3AϾG)) were identified in TARS2 in two siblings presenting axial hypotonia and severe psychomotor delay associated with multiple mitochondrial respiratory chain defects (26). Both hmtThrRS protein and aminoacylated tRNA Thr levels are decreased in the patients' cells.…”

mentioning

confidence: 99%

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A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects

Wang

Zhou

Ruan

et al. 2016

Journal of Biological Chemistry

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Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a noncanonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs.Aminoacyl-tRNA synthetases (aaRSs) 4 supply the ribosome with aminoacyl-tRNA substrates for protein synthesis (1, 2). This process starts with amino acid activation by condensation with ATP to form the aminoacyl adenylate aa-AMP and pyrophosphate. The activated amino acid then reacts with the 3Ј-end of the cognate tRNA to yield the aminoacyl-tRNA (aatRNA), which is transferred by EF-Tu to the protein biosynthesis machinery as a building block. Highly accurate protein synthesis is indispensable for cell growth. To maintain fidelity during protein synthesis, aaRS needs to select the correct amino acid and tRNA substrates from a large number of structurally similar molecules in the cells. The specificity of aaRS is greatly challenged by the presence of the 20 amino acids in which the physicochemical properties are sometimes very similar and by non-proteogenous amino acids and diverse metabolites produced by cell metabolism. aaRSs that do not show an overall selectivity above 1 in 3000 are predicted to require proofreading (editing) activity to maintain sufficient accuracy during aa-tRNA synthesis (3). In fact, editing activity has evolved in half of the currently identified aaRS to remove aberrantly produced aa-AMP (pretransfer editing) and/or aa-tRNA (posttransfer editing) (4). tRNA mischarging may be toxic and deleterious for cells. Even a slight decrease in aminoacylation accuracy could cause an intracellular accumulation of misfolded proteins and up-regulation of cytoplasmic protein chaperones in neurons, leading to severe...

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VARS2andTARS2Mutations in Patients with Mitochondrial Encephalomyopathies

Cited by 88 publications

References 26 publications

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog

Revealing ETC-1922159 Affected Unknown 3<em><sup>rd</sup></em> order WNT10B-X-X Combinations, in Silico

A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects

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