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      Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology

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          Abstract

          Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA would also stabilize its pathogenic variants is unknown. Here we show that the N 1-methylation of guanosine at position 9 (m 1G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has a destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated, as removal of the m 1G9 methylation, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving the structure and activity of the variant. These results have therapeutic implications, suggesting that the N 1-methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.

          Abstract

          Here the authors show that the m 1G9 post-transcriptional methylation differentially regulates the stability of the native and the MELAS variants of human mt-Leu(UAA) tRNA, contributing to mitochondrial pathology.

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          Most cited references80

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          Sequence and organization of the human mitochondrial genome.

          The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
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            Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.

            Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) interrogates local backbone flexibility in RNA at single-nucleotide resolution under diverse solution environments. Flexible RNA nucleotides preferentially sample local conformations that enhance the nucleophilic reactivity of 2'-hydroxyl groups toward electrophiles, such as N-methylisatoic anhydride (NMIA). Modified sites are detected as stops in an optimized primer extension reaction, followed by electrophoretic fragment separation. SHAPE chemistry scores local nucleotide flexibility at all four ribonucleotides in a single experiment and discriminates between base-paired versus unconstrained or flexible residues with a dynamic range of 20-fold or greater. Quantitative SHAPE reactivity information can be used to establish the secondary structure of an RNA, to improve the accuracy of structure prediction algorithms, to monitor structural differences between related RNAs or a single RNA in different states, and to detect ligand binding sites. SHAPE chemistry rarely needs significant optimization and requires two days to complete for an RNA of 100-200 nucleotides.
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              Universal rules and idiosyncratic features in tRNA identity.

              Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities.
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                Author and article information

                Contributors
                ya-ming.hou@jefferson.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                18 October 2024
                18 October 2024
                2024
                : 15
                : 9008
                Affiliations
                [1 ]Department of Biochemistry and Molecular Biology, Thomas Jefferson University, ( https://ror.org/00ysqcn41) Philadelphia, PA USA
                [2 ]Department of Physics, Northeastern University, ( https://ror.org/04t5xt781) Boston, MA USA
                [3 ]Department of Chemistry, University of Chicago, ( https://ror.org/024mw5h28) Chicago, IL USA
                [4 ]Faculty of Medicine, University of the Ryukyus, ( https://ror.org/02z1n9q24) Okinawa, Japan
                [5 ]Department of Chemistry and Biotechnology, University of Tokyo, ( https://ror.org/057zh3y96) Tokyo, Japan
                [6 ]Department of Pathology, Thomas Jefferson University, ( https://ror.org/00ysqcn41) Philadelphia, PA USA
                [7 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, , University of Pennsylvania, ; Philadelphia, PA USA
                Author information
                http://orcid.org/0000-0002-7099-1802
                http://orcid.org/0000-0001-9007-8546
                http://orcid.org/0000-0003-2457-7296
                http://orcid.org/0000-0002-9731-1731
                http://orcid.org/0000-0002-0541-6270
                http://orcid.org/0000-0002-9837-0004
                http://orcid.org/0000-0001-6546-2597
                Article
                53318
                10.1038/s41467-024-53318-x
                11489592
                39424798
                437cacc8-2cb4-4430-971e-2ee58f1fbffc
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

                History
                : 16 January 2024
                : 8 October 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000009, Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.);
                Award ID: R35 GM134931
                Award Recipient :
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                © Springer Nature Limited 2024

                Uncategorized
                rna,neurological disorders
                Uncategorized
                rna, neurological disorders

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