TY - JOUR A1 - Bencurova, Elena A1 - Akash, Aman A1 - Dobson, Renwick C.J. A1 - Dandekar, Thomas T1 - DNA storage-from natural biology to synthetic biology JF - Computational and Structural Biotechnology Journal N2 - Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades). KW - DNA KW - RNA KW - data storage KW - natural processing KW - synthetic biology Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-349971 SN - 2001-0370 VL - 21 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 - TY - JOUR A1 - Ye, Liqing A1 - Ambi, Uddhav B. A1 - Olguin-Nava, Marco A1 - Gribling-Burrer, Anne-Sophie A1 - Ahmad, Shazeb A1 - Bohn, Patrick A1 - Weber, Melanie M. A1 - Smyth, Redmond P. T1 - RNA structures and their role in selective genome packaging JF - Viruses N2 - To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution. KW - RNA virus KW - RNA KW - RNA structure KW - genome packaging KW - viral assembly KW - evolution Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-246101 SN - 1999-4915 VL - 13 IS - 9 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 - Bakari-Soale, Majeed A1 - Ikenga, Nonso Josephat A1 - Scheibe, Marion A1 - Butter, Falk A1 - Jones, Nicola G. A1 - Kramer, Susanne A1 - Engstler, Markus T1 - The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei JF - Scientific Reports N2 - The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process. KW - infection KW - parasite evolution KW - parasite genetics KW - RNA Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-263872 VL - 11 IS - 1 ER - TY - JOUR A1 - Ji, Changhe A1 - Bader, Jakob A1 - Ramanathan, Pradhipa A1 - Hennlein, Luisa A1 - Meissner, Felix A1 - Jablonka, Sibylle A1 - Mann, Matthias A1 - Fischer, Utz A1 - Sendtner, Michael A1 - Briese, Michael T1 - Interaction of 7SK with the Smn complex modulates snRNP production JF - Nature Communications N2 - Gene expression requires tight coordination of the molecular machineries that mediate transcription and splicing. While the interplay between transcription kinetics and spliceosome fidelity has been investigated before, less is known about mechanisms regulating the assembly of the spliceosomal machinery in response to transcription changes. Here, we report an association of the Smn complex, which mediates spliceosomal snRNP biogenesis, with the 7SK complex involved in transcriptional regulation. We found that Smn interacts with the 7SK core components Larp7 and Mepce and specifically associates with 7SK subcomplexes containing hnRNP R. The association between Smn and 7SK complexes is enhanced upon transcriptional inhibition leading to reduced production of snRNPs. Taken together, our findings reveal a functional association of Smn and 7SK complexes that is governed by global changes in transcription. Thus, in addition to its canonical nuclear role in transcriptional regulation, 7SK has cytosolic functions in fine-tuning spliceosome production according to transcriptional demand. KW - Molecular neuroscience KW - RNA KW - RNA splicing KW - Transcription Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-259125 VL - 12 IS - 1 ER - 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 - 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 - Van Haute, Lindsey A1 - Dietmann, Sabine A1 - Kremer, Laura A1 - Hussain, Shobbir A1 - Pearce, Sarah F. A1 - Powell, Christopher A. A1 - Rorbach, Joanna A1 - Lantaff, Rebecca A1 - Blanco, Sandra A1 - Sauer, Sascha A1 - Kotzaeridou, Urania A1 - Hoffmann, Georg F. A1 - Memari, Yasin A1 - Kolb-Kokocinski, Anja A1 - Durbin, Richard A1 - Mayr, Johannes A. A1 - Frye, Michaela A1 - Prokisch, Holger A1 - Minczuk, Michal T1 - Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3 JF - Nature Communications N2 - Epitranscriptome modifications are required for structure and function of RNA and defects in these pathways have been associated with human disease. Here we identify the RNA target for the previously uncharacterized 5-methylcytosine (m5C) methyltransferase NSun3 and link m5C RNA modifications with energy metabolism. Using whole-exome sequencing, we identified loss-of-function mutations in NSUN3 in a patient presenting with combined mitochondrial respiratory chain complex deficiency. Patient-derived fibroblasts exhibit severe defects in mitochondrial translation that can be rescued by exogenous expression of NSun3. We show that NSun3 is required for deposition of m5C at the anticodon loop in the mitochondrially encoded transfer RNA methionine (mt-tRNAMet). Further, we demonstrate that m5C deficiency in mt-tRNAMet results in the lack of 5-formylcytosine (f5C) at the same tRNA position. Our findings demonstrate that NSUN3 is necessary for efficient mitochondrial translation and reveal that f5C in human mitochondrial RNA is generated by oxidative processing of m5C. KW - Methylation KW - RNA KW - Transferases Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-165998 VL - 7 ER - TY - JOUR A1 - Binas, Oliver A1 - Bessi, Irene A1 - Schwalbe, Harald T1 - Structure Validation of G‐Rich RNAs in Noncoding Regions of the Human Genome JF - ChemBioChem N2 - We present the rapid biophysical characterization of six previously reported putative G‐quadruplex‐forming RNAs from the 5′‐untranslated region (5′‐UTR) of silvestrol‐sensitive transcripts for investigation of their secondary structures. By NMR and CD spectroscopic analysis, we found that only a single sequence—[AGG]\(_{2}\)[CGG]\(_{2}\)C—folds into a single well‐defined G‐quadruplex structure. Sequences with longer poly‐G strands form unspecific aggregates, whereas CGG‐repeat‐containing sequences exhibit a temperature‐dependent equilibrium between a hairpin and a G‐quadruplex structure. The applied experimental strategy is fast and provides robust readout for G‐quadruplex‐forming capacities of RNA oligomers. KW - biophysical investigation KW - circular dichroism KW - G-quadruplexes KW - NMR spectroscopy KW - RNA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-214892 VL - 21 IS - 11 SP - 1656 EP - 1663 ER -