TY - JOUR A1 - Kleiber, Nicole A1 - Lemus-Diaz, Nicolas A1 - Stiller, Carina A1 - Heinrichs, Marleen A1 - Mong-Quyen Mai, Mandy A1 - Hackert, Philipp A1 - Richter-Dennerlein, Ricarda A1 - Höbartner, Claudia A1 - Bohnsack, Katherine E. A1 - Bohnsack, Markus T. T1 - The RNA methyltransferase METTL8 installs m\(^3\)C\(_{32}\) in mitochondrial tRNAs\(^{Thr/Ser(UCN)}\) to optimise tRNA structure and mitochondrial translation JF - Nature Communication N2 - Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m\(^3\)C\(_{32}\) in the human mitochondrial (mt-)tRNA\(^{Thr}\) and mt-tRNA\(^{Ser(UCN)}\). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mttRNA recognition elements revealed U\(_{34}\)G\(_{35}\) and t\(^6\)A\(_{37}\)/(ms\(^2\))i\(^6\)A\(_{37}\), present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C\(_{32}\). Several lines of evidence demonstrate the influence of U\(_{34}\), G\(_{35}\), and the m\(^3\)C\(_{32}\) and t\(^6\)A\(_{37}\)/(ms\(^2\))i\(^6\)A\(_{37}\) modifications in mt-tRNA\(^{Thr/Ser(UCN)}\) on the structure of these mt-tRNAs. Although mt-tRNA\(^{Thr/Ser(UCN)}\) lacking METTL8-mediated m\(^3\)C\(_{32}\) are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m\(^3\)C\(_{32}\) within mt-tRNAs. KW - Modified Nucleotides in tRNAs KW - METTL8 KW - Mitochondrial Matrix Protein KW - RNA Methyltransferase KW - RNA KW - Enzymes KW - Organelles Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-254592 VL - 13 ER - TY - JOUR A1 - Kokic, Goran A1 - Hillen, Hauke S. A1 - Tegunov, Dimitry A1 - Dienermann, Christian A1 - Seitz, Florian A1 - Schmitzova, Jana A1 - Farnung, Lucas A1 - Siewert, Aaron A1 - Höbartner, Claudia A1 - Cramer, Patrick T1 - Mechanism of SARS-CoV-2 polymerase stalling by remdesivir JF - Nature Communications N2 - Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryoelectron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3ʹ-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3ʹ-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3ʹ-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication. KW - SARS-CoV-2 polymerase KW - Remdesivir KW - RNA-dependent RNA polymerase KW - Molecular mechanism KW - Biochemistry KW - Cryoelectron microscopy KW - RNA Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-220979 VL - 12 ER - TY - JOUR A1 - Mieczkowski, Mateusz A1 - Steinmetzger, Christian A1 - Bessi, Irene A1 - Lenz, Ann-Kathrin A1 - Schmiedel, Alexander A1 - Holzapfel, Marco A1 - Lambert, Christoph A1 - Pena, Vladimir A1 - Höbartner, Claudia T1 - Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine JF - Nature Communications N2 - Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer. KW - Fluorogenic RNA Aptamers KW - Synthetic Functional RNAs KW - Chili RNA Aptamer KW - Co-Crystal Structures of Chili RNA KW - RNA KW - Optical Spectroscopy KW - Structural Biology KW - X-ray Crystallography Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-254527 VL - 12 ER - TY - JOUR A1 - Mieczkowski, Mateusz A1 - Steinmetzger, Christian A1 - Bessi, Irene A1 - Lenz, Ann-Kathrin A1 - Schmiedel, Alexander A1 - Holzapfel, Marco A1 - Lambert, Christoph A1 - Pena, Vladimir A1 - Höbartner, Claudia T1 - Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine JF - Nature Communications N2 - Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer. KW - RNA KW - optical spectroscopy KW - structural biology KW - X-ray crystallography Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-270274 VL - 12 ER - TY - JOUR A1 - Okuda, Takumi A1 - Lenz, Ann-Kathrin A1 - Seitz, Florian A1 - Vogel, Jörg A1 - Höbartner, Claudia T1 - A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells JF - Nature Chemistry N2 - Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes. KW - Alkyltransferase Ribozyme SAMURI KW - Site-specific RNA labelling KW - bioorthogonal SAM analogue ProSeDMA KW - Chemical modification KW - RNA Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-328762 ER -