@article{KleiberLemusDiazStilleretal.2022,
  author    = {Kleiber, Nicole and Lemus-Diaz, Nicolas and Stiller, Carina and Heinrichs, Marleen and Mong-Quyen Mai, Mandy and Hackert, Philipp and Richter-Dennerlein, Ricarda and H{\"o}bartner, Claudia and Bohnsack, Katherine E. and Bohnsack, Markus T.},
  title     = {The RNA methyltransferase METTL8 installs m\(^3\)C\(_{32}\) in mitochondrial tRNAs\(^{Thr/Ser(UCN)}\) to optimise tRNA structure and mitochondrial translation},
  series = {Nature Communication},
  volume    = {13},
  journal   = {Nature Communication},
  doi       = {10.1038/s41467-021-27905-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-254592},
  year      = {2022},
  abstract  = {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.},
  language  = {en}
}
@unpublished{ScheitlMieczkowskiSchindelinetal.2022,
  author    = {Scheitl, Carolin P. M. and Mieczkowski, Mateusz and Schindelin, Hermann and H{\"o}bartner, Claudia},
  title     = {Structure and mechanism of the methyltransferase ribozyme MTR1},
  series = {Nature Chemical Biology},
  journal   = {Nature Chemical Biology},
  edition   = {submitted version},
  doi       = {10.1038/s41589-022-00976-x},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-272170},
  year      = {2022},
  abstract  = {RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m\(^1\)A) in RNA, using O\(^6\)-methylguanine (m\(^6\)G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 {\AA}, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.},
  language  = {en}
}
@article{KokicHillenTegunovetal.2021,
  author    = {Kokic, Goran and Hillen, Hauke S. and Tegunov, Dimitry and Dienermann, Christian and Seitz, Florian and Schmitzova, Jana and Farnung, Lucas and Siewert, Aaron and H{\"o}bartner, Claudia and Cramer, Patrick},
  title     = {Mechanism of SARS-CoV-2 polymerase stalling by remdesivir},
  series = {Nature Communications},
  volume    = {12},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-020-20542-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-220979},
  year      = {2021},
  abstract  = {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.},
  language  = {en}
}
@incollection{LiaqatSednevHoebartner2022,
  author    = {Liaqat, Anam and Sednev, Maksim V. and H{\"o}bartner, Claudia},
  title     = {In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications},
  series = {Ribosome Biogenesis: Methods and Protocols},
  booktitle = {Ribosome Biogenesis: Methods and Protocols},
  publisher = {Humana Press},
  isbn      = {978-1-0716-2501-9},
  doi       = {10.1007/978-1-0716-2501-9_10},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-279208},
  publisher      = {Universit{\"a}t W{\"u}rzburg},
  pages     = {167-179},
  year      = {2022},
  abstract  = {Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.},
  language  = {en}
}
@article{MieczkowskiSteinmetzgerBessietal.2021,
  author    = {Mieczkowski, Mateusz and Steinmetzger, Christian and Bessi, Irene and Lenz, Ann-Kathrin and Schmiedel, Alexander and Holzapfel, Marco and Lambert, Christoph and Pena, Vladimir and H{\"o}bartner, Claudia},
  title     = {Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine},
  series = {Nature Communications},
  volume    = {12},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-021-23932-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-254527},
  pages     = {3549},
  year      = {2021},
  abstract  = {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.},
  language  = {en}
}
@article{MieczkowskiSteinmetzgerBessietal.2021,
  author    = {Mieczkowski, Mateusz and Steinmetzger, Christian and Bessi, Irene and Lenz, Ann-Kathrin and Schmiedel, Alexander and Holzapfel, Marco and Lambert, Christoph and Pena, Vladimir and H{\"o}bartner, Claudia},
  title     = {Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine},
  series = {Nature Communications},
  volume    = {12},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-021-23932-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-270274},
  year      = {2021},
  abstract  = {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.},
  language  = {en}
}
@article{OkudaLenzSeitzetal.2023,
  author    = {Okuda, Takumi and Lenz, Ann-Kathrin and Seitz, Florian and Vogel, J{\"o}rg and H{\"o}bartner, Claudia},
  title     = {A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells},
  series = {Nature Chemistry},
  journal   = {Nature Chemistry},
  doi       = {10.1038/s41557-023-01320-z},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328762},
  year      = {2023},
  abstract  = {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.},
  language  = {en}
}