1
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Bessler L, Sirleaf J, Kampf CJ, Frankowska K, Leszczyńska G, Opatz T, Helm M. Esterification of Cyclic N 6-Threonylcarbamoyladenosine During RNA Sample Preparation. ChemMedChem 2024:e202400115. [PMID: 38630955 DOI: 10.1002/cmdc.202400115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
The continuous deciphering of crucial biological roles of RNA modifications and their involvement in various pathological conditions, together with their key roles in the use of RNA-based therapeutics, has reignited interest in studying the occurrence and identity of non-canonical ribonucleoside structures during the past years. Discovery and structural elucidation of new modified structures is usually achieved by combination of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) at the nucleoside level and stable isotope labeling experiments. This approach, however, has its pitfalls as demonstrated in the course of the present study: we structurally elucidated a new nucleoside structure that showed significant similarities to the family of (c)t6A modifications and was initially considered a genuine modification, but subsequently turned out to be an in vitro formed glycerol ester of t6A. This artifact is generated from ct6A during RNA hydrolysis upon addition of enzymes stored in glycerol containing buffers in a mildly alkaline milieu, and was moreover shown to undergo an intramolecular transesterification reaction. Our results demand for extra caution, not only in the discovery of new RNA modifications, but also with regard to the quantification of known modified structures, in particular chemically labile modifications, such as ct6A, that might suffer from exposure to putatively harmless reagents during the diverse steps of sample preparation.
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Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Jason Sirleaf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Katarzyna Frankowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Łódź, Poland
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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2
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Bessler L, Groß J, Kampf CJ, Opatz T, Helm M. Reversible oxidative dimerization of 4-thiouridines in tRNA isolates. RSC Chem Biol 2024; 5:216-224. [PMID: 38456039 PMCID: PMC10915967 DOI: 10.1039/d3cb00221g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
The occurrence of non-canonical nucleoside structures in RNA of biological or synthetic origin has encountered several recent boosts in attention, namely in the context of RNA modifications, and with an eye to RNA vaccines. New nucleoside structures introduce added functionality and function into biopolymers that are otherwise rather homogenous in their chemical structure. Here, we report the discovery of a presumed RNA modification that was identified by combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) with stable isotope labelling as a dimer of the known RNA modification 4-thiouridine (s4U). The disulfide-linked structure, which had previously been synthetically introduced into RNA, was here formed spontaneously in isolates of E. coli tRNA. Judicious application of stable isotope labelling suggested that this presumed new RNA modification was rather generated ex vivo by oxidation with ambient oxygen. These findings do not only underscore the need for caution in the discovery of new RNA modifications with respect to artifacts, but also raise awareness of an RNA vulnerability, especially to oxidative damage, during its transport or storage.
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Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz Duesbergweg 10-14 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
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3
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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4
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Ammann G, Berg M, Dalwigk JF, Kaiser SM. Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry. Acc Chem Res 2023; 56:3121-3131. [PMID: 37944919 PMCID: PMC10666278 DOI: 10.1021/acs.accounts.3c00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
In recent years, there has been a high interest in researching RNA modifications, as they are involved in many cellular processes and in human diseases. A substantial set of enzymes within the cell, called RNA writers, place RNA modifications selectively and site-specifically. Another set of enzymes, called readers, recognize these modifications which guide the fate of the modified RNA. Although RNA is a transient molecule and RNA modification could be removed by RNA degradation, a subclass of enzymes, called RNA erasers, remove RNA modifications selectively and site-specifically to alter the characteristics of the RNA. The detection of RNA modifications can be done by various methods including second and next generation sequencing but also mass spectrometry. An approach capable of both qualitative and quantitative RNA modification analysis is liquid chromatography coupled to mass spectrometry of enzymatic hydrolysates of RNA into nucleosides. However, for successful detection and quantification, various factors must be considered to avoid biased identification and inaccurate quantification. In this Account, we identify three classes of errors that may distort the analysis. These classes comprise (I) errors related to chemical instabilities, (II) errors revolving around enzymatic hydrolysis to nucleosides, and (III) errors arising from issues with chromatographic separation and/or subsequent mass spectrometric analysis.A prominent example for class 1 is Dimroth rearrangement of m1A to m6A, but class 1 also comprises hydrolytic reactions and reactions with buffer components. Here, we also present the conversion of m3C to m3U under mild alkaline conditions and propose a practical solution to overcome these instabilities. Class 2 errors-such as contaminations in hydrolysis reagents or nuclease specificities-have led to erroneous discoveries of nucleosides in the past and possess the potential for misquantification of nucleosides. Impurities in the samples may also lead to class 3 errors: For instance, issues with chromatographic separation may arise from residual organic solvents, and salt adducts may hamper mass spectrometric quantification. This Account aims to highlight various errors connected to mass spectrometry analysis of nucleosides and presents solutions for how to overcome or circumnavigate those issues. Therefore, the authors anticipate that many scientists, but especially those who plan on doing nucleoside mass spectrometry, will benefit from the collection of data presented in this Account as a raised awareness, toward the variety of potential pitfalls, may further enhance the quality of data.
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Affiliation(s)
- Gregor Ammann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Maximilian Berg
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Felix Dalwigk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie M. Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
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5
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Wang C, Ulryck N, Herzel L, Pythoud N, Kleiber N, Guérineau V, Jactel V, Moritz C, Bohnsack M, Carapito C, Touboul D, Bohnsack K, Graille M. N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing. Nucleic Acids Res 2023; 51:7496-7519. [PMID: 37283053 PMCID: PMC10415138 DOI: 10.1093/nar/gkad487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last 'orphan' modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Lydia Herzel
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Nicole Kleiber
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, École polytechnique, ENSTA, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Chloé Moritz
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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6
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Huang G, Zhang F, Xie D, Ma Y, Wang P, Cao G, Chen L, Lin S, Zhao Z, Cai Z. High-throughput profiling of RNA modifications by ultra-performance liquid chromatography coupled to complementary mass spectrometry: Methods, quality control, and applications. Talanta 2023; 263:124697. [PMID: 37262985 DOI: 10.1016/j.talanta.2023.124697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides, were successfully monitored within a 16-min single run of UPLC-MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans (C. elegans) were developed using the coexisting C. elegans and Escherichia coli (E. coli) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans, E. coli, and Arabidopsis thaliana (A. thaliana). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
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Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Feng Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Pengxi Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Leijian Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Siyi Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China.
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7
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Libiad M, Douki T, Fontecave M, Atta M. Identification of 2-Methylthio-methylenethio-N 6 -(cis-4-hydroxyisopentenyl)adenosine (msms 2 io 6 A 37 ) as a Novel Modification at Adenosine 37 of tRNAs from Salmonella typhimurium. Chembiochem 2023; 24:e202300019. [PMID: 36640047 DOI: 10.1002/cbic.202300019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Post-transcriptional modifications of tRNA nucleotide are important determinants in folding, structure and function. We have successfully identified and characterized a new modified base named 2-methylthio-methylenethio-N6 -(cis-4-hydroxyisopentenyl)adenosine, which is present at position 37 in some tRNAs. We also showed that this new modified adenosine is derived from the known 2-methylthio-methylenethio-N6 -(isopentenyl)adenosine nucleoside by a catalytic cycle of the tRNA-diiron monooxygenase, MiaE, present in Salmonella typhimurium.
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Affiliation(s)
- Marouane Libiad
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11, place Marcellin-Berthelot, Paris, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000, Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11, place Marcellin-Berthelot, Paris, France
| | - Mohamed Atta
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, LCBM, UMR 5249, 38000, Grenoble, France.,Laboratoire de Chimie des Processus Biologiques, UMR 8229, Collège de France/CNRS/Sorbonne Université, 11, place Marcellin-Berthelot, Paris, France
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8
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Fang Z, Lu Z, Han S, Zhou Y, Yang W, Zhang X, Zhou X. The Transcriptome-Wide Mapping of 2-Methylthio- N6-isopentenyladenosine at Single-Base Resolution. J Am Chem Soc 2023; 145:5467-5473. [PMID: 36820840 DOI: 10.1021/jacs.2c13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hundreds of modified bases have been identified and enzymatically modified to transfer RNAs (tRNAs) to regulate RNA function in various organisms. 2-Methylthio-N6-isopentenyladenosine (ms2i6A), a hypermodified base found at tRNA position 37, exists in both prokaryotes and eukaryotes. ms2i6A is traditionally identified by separating and digesting each tRNA from total RNA using RNA mass spectrometry. A transcriptome-wide and single-base resolution method that enables absolute mapping of ms2i6A along with analysis of its distribution in different RNAs is lacking. Here, through chemoselective methylthio group bioconjugation, we introduce a new approach (redox activated chemical tagging sequencing, ReACT-seq) to detect ms2i6A transcriptome-wide at single-base resolution. Using the chemoselectivity between the methylthio group and oxaziridine group, ms2i6A is bio-orthogonally tagged with an azide group without interference of canonical nucleotides, advancing enrichment of methylthio group modified RNAs prior to sequencing. ReACT-seq was demonstrated on nine known tRNAs and proved to be highly accurate, and the reverse transcription stop (RT-stop) character enables ReACT-seq detection at single-base resolution. In addition, ReACT-seq identified that the modification of ms2i6A is conservative and may not exist in other RNAs.
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Affiliation(s)
- Zhentian Fang
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Yuanyuan Zhou
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Medicine, Wuhan 430071, People's Republic of China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Medicine, Wuhan 430071, People's Republic of China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
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9
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Bessler L, Vogt LM, Lander M, Dal Magro C, Keller P, Kühlborn J, Kampf CJ, Opatz T, Helm M. A New Bacterial Adenosine-Derived Nucleoside as an Example of RNA Modification Damage. Angew Chem Int Ed Engl 2023; 62:e202217128. [PMID: 36629490 DOI: 10.1002/anie.202217128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/12/2023]
Abstract
The fields of RNA modification and RNA damage both exhibit a plethora of non-canonical nucleoside structures. While RNA modifications have evolved to improve RNA function, the term RNA damage implies detrimental effects. Based on stable isotope labelling and mass spectrometry, we report the identification and characterisation of 2-methylthio-1,N6-ethenoadenosine (ms2 ϵA), which is related to 1,N6-ethenoadenine, a lesion resulting from exposure of nucleic acids to alkylating chemicals in vivo. In contrast, a sophisticated isoprene labelling scheme revealed that ms2 ϵA biogenesis involves cleavage of a prenyl moiety in the known transfer RNA (tRNA) modification 2-methylthio-N6-isopentenyladenosine (ms2 i6 A). The relative abundance of ms2 ϵA in tRNAs from translating ribosomes suggests reduced function in comparison to its parent RNA modification, establishing the nature of the new structure in a newly perceived overlap of the two previously separate fields, namely an RNA modification damage.
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Affiliation(s)
- Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christina Dal Magro
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Keller
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Jonas Kühlborn
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Christopher J Kampf
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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10
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Landscape of Post-Transcriptional tRNA Modifications in Streptomyces albidoflavus J1074 as Portrayed by Mass Spectrometry and Genomic Data Mining. J Bacteriol 2023; 205:e0029422. [PMID: 36468867 PMCID: PMC9879100 DOI: 10.1128/jb.00294-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Actinobacterial genus Streptomyces (streptomycetes) represents one of the largest cultivable group of bacteria famous for their ability to produce valuable specialized (secondary) metabolites. Regulation of secondary metabolic pathways inextricably couples the latter to essential cellular processes that determine levels of amino acids, carbohydrates, phosphate, etc. Post-transcriptional tRNA modifications remain one of the least studied aspects of streptomycete physiology, albeit a few of them were recently shown to impact antibiotic production. In this study, we describe the diversity of post-transcriptional tRNA modifications in model strain Streptomyces albus (albidoflavus) J1074 by combining mass spectrometry and genomic data. Our results show that J1074 can produce more chemically distinct tRNA modifications than previously thought. An in silico approach identified orthologs for enzymes governing most of the identified tRNA modifications. Yet, genetic control of certain modifications remained elusive, suggesting early divergence of tRNA modification pathways in Streptomyces from the better studied model bacteria, such as Escherichia coli and Bacillus subtilis. As a first point in case, our data point to the presence of a non-canonical MiaE enzyme performing hydroxylation of prenylated adenosines. A further finding concerns the methylthiotransferase MiaB, which requires previous modification of adenosines by MiaA to i6A for thiomethylation to ms2i6A. We show here that the J1074 ortholog, when overexpressed, yields ms2A in a ΔmiaA background. Our results set the working ground for and justify a more detailed studies of biological significance of tRNA modification pathways in streptomycetes. IMPORTANCE Post-transcriptional tRNA modifications (PTTMs) play an important role in maturation and functionality of tRNAs. Little is known about tRNA modifications in the antibiotic-producing actinobacterial genus Streptomyces, even though peculiar tRNA-based regulatory mechanisms operate in this taxon. We provide a first detailed description of the chemical diversity of PTTMs in the model species, S. albidoflavus J1074, and identify most plausible genes for these PTTMs. Some of the PTTMs are described for the first time for Streptomyces. Production of certain PTTMs in J1074 appears to depend on enzymes that show no sequence similarity to known PTTM enzymes from model species. Our findings are of relevance for interrogation of genetic basis of PTTMs in pathogenic actinobacteria, such as M. tuberculosis.
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11
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Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
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12
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Hertler J, Slama K, Schober B, Özrendeci Z, Marchand V, Motorin Y, Helm M. Synthesis of point-modified mRNA. Nucleic Acids Res 2022; 50:e115. [PMID: 36062567 PMCID: PMC9723659 DOI: 10.1093/nar/gkac719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/20/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic mRNA has recently moved into the focus of therapeutic and vaccination efforts. Incorporation of modified nucleotides during in vitro transcription can improve translation and attenuate immunogenicity, but is limited to triphosphate nucleotides which are accepted by RNA polymerases, and their incorporation is either random or complete. In contrast, site-specific modification, herein termed 'point modification' in analogy to point mutations, holds significant technical challenge. We developed fundamental techniques for isolation of long, translatable and internally point-modified mRNAs. Enabling concepts include three-way-one-pot splint ligations, and isolation of mRNA by real-time elution from agarose gels. The use of blue light permitted visualization of mRNA in pre-stained gels without the photochemical damage associated with the use of hard UV-radiation. This allowed visualization of the mRNA through its migration in the agarose gel, which in turn, was a prerequisite for its recovery by electroelution into precast troughs. Co-eluting agarose particles were quantified and found to not be detrimental to mRNA translation in vitro. Translation of EGFP-coding mRNA into functional protein was quantified by incorporation of 35S-labelled methionine and by in-gel EGFP fluorescence. This enabled the functional analysis of point modifications, specifically of ribose methylations in the middle of a 1371 nt long mRNA.
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Affiliation(s)
| | | | - Benedikt Schober
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Zeynep Özrendeci
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Virginie Marchand
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Yuri Motorin
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mark Helm
- To whom correspondence should be addressed. Tel: +49 6131 392 5731; Fax: +49 6131 392 0373;
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13
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Espadas G, Morales-Sanfrutos J, Medina R, Lucas MC, Novoa EM, Sabidó E. High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry. J Chromatogr A 2022; 1665:462803. [PMID: 35042139 DOI: 10.1016/j.chroma.2022.462803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 01/10/2023]
Abstract
Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.
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Affiliation(s)
- Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Julia Morales-Sanfrutos
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Rebeca Medina
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Morghan C Lucas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eva Maria Novoa
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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14
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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15
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Biosynthesis and Degradation of Sulfur Modifications in tRNAs. Int J Mol Sci 2021; 22:ijms222111937. [PMID: 34769366 PMCID: PMC8584467 DOI: 10.3390/ijms222111937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Various sulfur-containing biomolecules include iron–sulfur clusters that act as cofactors for enzymes, sulfur-containing vitamins such as thiamin, and sulfur-modified nucleosides in RNA, in addition to methionine and cysteine in proteins. Sulfur-containing nucleosides are post-transcriptionally introduced into tRNA molecules, where they ensure precise codon recognition or stabilization of tRNA structure, thereby maintaining cellular proteome integrity. Modulating sulfur modification controls the translation efficiency of specific groups of genes, allowing organisms to adapt to specific environments. The biosynthesis of tRNA sulfur nucleosides involves elaborate ‘sulfur trafficking systems’ within cellular sulfur metabolism and ‘modification enzymes’ that incorporate sulfur atoms into tRNA. This review provides an up-to-date overview of advances in our knowledge of the mechanisms involved. It covers the functions, biosynthesis, and biodegradation of sulfur-containing nucleosides as well as the reaction mechanisms of biosynthetic enzymes catalyzed by the iron–sulfur clusters, and identification of enzymes involved in the de-modification of sulfur atoms of RNA. The mechanistic similarity of these opposite reactions is discussed. Mutations in genes related to these pathways can cause human diseases (e.g., cancer, diabetes, and mitochondrial diseases), emphasizing the importance of these pathways.
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16
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Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategien zur Vermeidung von Artefakten in der massenspektrometrischen Epitranskriptomanalytik. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Tim Gehrke
- Ella Biotech GmbH 82152 München Deutschland
| | - Felix Hagelskamp
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
| | - Lili Liu
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Qinghua Zhang
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group Singapore-Massachusetts Institute of Technology Alliance for Research and Technology 138602 Singapore Singapur
| | - Bo Cao
- College of Life Sciences Qufu Normal University Qufu Shandong 273165 China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität München Butenandtstr. 5–13 81137 München Deutschland
- Institut für Pharmazeutische Chemie Goethe-Universität Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Deutschland
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17
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Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S. Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses. Angew Chem Int Ed Engl 2021; 60:23885-23893. [PMID: 34339593 PMCID: PMC8597057 DOI: 10.1002/anie.202106215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Indexed: 11/05/2022]
Abstract
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2'-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.
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Affiliation(s)
- Steffen Kaiser
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Shane R. Byrne
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Gregor Ammann
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Paria Asadi Atoi
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Kayla Borland
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | | | - Michael S. DeMott
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
| | | | - Felix Hagelskamp
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Matthias Heiss
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Yasemin Yoluç
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
| | - Lili Liu
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Qinghua Zhang
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMA02139USA
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore-Massachusetts Institute of Technology Alliance for Research and Technology138602SingaporeSingapore
| | - Bo Cao
- College of Life SciencesQufu Normal UniversityQufuShandong273165China
| | - Stefanie Kellner
- Ludwig-Maximilians Universität MünchenButenandtstr. 5–1381137MünchenDeutschland
- Institute of Pharmaceutical ChemistryGoethe-University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
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18
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Helm M, Schmidt-Dengler MC, Weber M, Motorin Y. General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents. Adv Biol (Weinh) 2021; 5:e2100866. [PMID: 34535986 DOI: 10.1002/adbi.202100866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Indexed: 12/16/2022]
Abstract
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Martina C Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, F-54000, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, F-54000, France
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19
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Clark K, Lee C, Gillette R, Sweedler JV. Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization. ACS CENTRAL SCIENCE 2021; 7:1183-1190. [PMID: 34345669 PMCID: PMC8323240 DOI: 10.1021/acscentsci.1c00351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 05/12/2023]
Abstract
Subtle changes in the landscape of post-transcriptional modifications have emerged as putative regulators of central nervous system plasticity and activity-induced protein synthesis. However, simultaneous characterization of multiple RNA modifications and their covariation during learning and memory paradigms has been impeded by the complexity of animal models and lack of untargeted approaches for identifying pathway-relevant RNA modifications in small-volume samples. Here, we used mass spectrometry to profile spatiotemporal changes in dozens of neuronal RNA modifications in Aplysia californica during behavioral sensitization of a simple defensive reflex. Unique RNA modification patterns were observed in the major ganglia of trained and naı̇ve animals, with two tRNA modifications, namely, 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 1-methyladenosine (m1A), at significantly higher levels in trained subjects. We report that tRNAs, and their modifications, correlate with increased polyglutamine synthesis and excitability in neurons, characterizing the first link between noncoding RNA modifications and non-associative learning.
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Affiliation(s)
- Kevin
D. Clark
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Colin Lee
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rhanor Gillette
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
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20
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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21
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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22
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Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
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23
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Kimura S. Distinct evolutionary pathways for the synthesis and function of tRNA modifications. Brief Funct Genomics 2021; 20:125-134. [PMID: 33454776 DOI: 10.1093/bfgp/elaa027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Transfer ribonucleicacids (RNAs) (tRNAs) are essential adaptor molecules for translation. The functions and stability of tRNAs are modulated by their post-transcriptional modifications (tRNA modifications). Each domain of life has a specific set of modifications that include ones shared in multiple domains and ones specific to a domain. In some cases, different tRNA modifications across domains have similar functions to each other. Recent studies uncovered that distinct enzymes synthesize the same modification in different organisms, suggesting that such modifications are acquired through independent evolution. In this short review, I outline the mechanisms by which various modifications contribute to tRNA function, including modulation of decoding and tRNA stability, using recent findings. I also focus on modifications that are synthesized by distinct biosynthetic pathways.
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Affiliation(s)
- Satoshi Kimura
- Dr Matthew Waldor's lab at the Brigham and Women's Hospital. He completed his PhD and early postdoc work in Dr Tsutomu Suzuki's lab at the University of Tokyo
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24
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Jora M, Borland K, Abernathy S, Zhao R, Kelley M, Kellner S, Addepalli B, Limbach PA. Chemical Amination/Imination of Carbonothiolated Nucleosides During RNA Hydrolysis. Angew Chem Int Ed Engl 2020; 60:3961-3966. [DOI: 10.1002/anie.202010793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/17/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Kayla Borland
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Ruoxia Zhao
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Melissa Kelley
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Stefanie Kellner
- Department of Chemistry Ludwig Maximilians University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry Department of Chemistry University of Cincinnati PO Box 210172 Cincinnati OH 45221-0172 USA
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25
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Kristen M, Plehn J, Marchand V, Friedland K, Motorin Y, Helm M, Werner S. Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides. Genes (Basel) 2020; 11:genes11080950. [PMID: 32824672 PMCID: PMC7466121 DOI: 10.3390/genes11080950] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022] Open
Abstract
Reverse transcription of RNA templates containing modified ribonucleosides transfers modification-related information as misincorporations, arrest or nucleotide skipping events to the newly synthesized cDNA strand. The frequency and proportion of these events, merged from all sequenced cDNAs, yield a so-called RT signature, characteristic for the respective RNA modification and reverse transcriptase (RT). While known for DNA polymerases in so-called error-prone PCR, testing of four different RTs by replacing Mg2+ with Mn2+ in reaction buffer revealed the immense influence of manganese chloride on derived RT signatures, with arrest rates on m1A positions dropping from 82% down to 24%. Additionally, we observed a vast increase in nucleotide skipping events, with single positions rising from 4% to 49%, thus implying an enhanced read-through capability as an effect of Mn2+ on the reverse transcriptase, by promoting nucleotide skipping over synthesis abortion. While modifications such as m1A, m22G, m1G and m3C showed a clear influence of manganese ions on their RT signature, this effect was individual to the polymerase used. In summary, the results imply a supporting effect of Mn2+ on reverse transcription, thus overcoming blockades in the Watson-Crick face of modified ribonucleosides and improving both read-through rate and signal intensity in RT signature analysis.
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Affiliation(s)
- Marco Kristen
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg, University Mainz, Staudingerweg 5, 55128 Mainz, Germany; (M.K.); (J.P.); (K.F.); (M.H.)
| | - Johanna Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg, University Mainz, Staudingerweg 5, 55128 Mainz, Germany; (M.K.); (J.P.); (K.F.); (M.H.)
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor CNRS, Université de Lorraine-INSERM, Biopôle, 9 Avenue de la Forêt de Haye, 54505 Vandœuvre-lès-Nancy, France; (V.M.); (Y.M.)
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg, University Mainz, Staudingerweg 5, 55128 Mainz, Germany; (M.K.); (J.P.); (K.F.); (M.H.)
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor CNRS, Université de Lorraine-INSERM, Biopôle, 9 Avenue de la Forêt de Haye, 54505 Vandœuvre-lès-Nancy, France; (V.M.); (Y.M.)
- IMoPA, UMR7365 CNRS, Université de Lorraine, Biopôle, 9 Avenue de la Forêt de Haye, 54505 Vandœuvre-lès-Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg, University Mainz, Staudingerweg 5, 55128 Mainz, Germany; (M.K.); (J.P.); (K.F.); (M.H.)
| | - Stephan Werner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg, University Mainz, Staudingerweg 5, 55128 Mainz, Germany; (M.K.); (J.P.); (K.F.); (M.H.)
- Correspondence: ; Tel.: +49-6131-392-5738
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26
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Bartosik K, Debiec K, Czarnecka A, Sochacka E, Leszczynska G. Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach. Molecules 2020; 25:E3344. [PMID: 32717917 PMCID: PMC7436257 DOI: 10.3390/molecules25153344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
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Affiliation(s)
| | | | | | | | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.B.); (K.D.); (A.C.); (E.S.)
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27
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Genetic analysis of Streptomyces albus J1074 mia mutants suggests complex relationships between post-transcriptional tRNA XXA modifications and physiological traits. Folia Microbiol (Praha) 2020; 65:1009-1015. [PMID: 32676973 DOI: 10.1007/s12223-020-00811-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Proteins MiaA and MiaB catalyze sequential isopentenylation and methylthiolation, respectively, of adenosine residue in 37th position of tRNAXXA. The mia mutations were recently shown by us to affect secondary metabolism and morphology of Streptomyces. However, it remained unknown as to whether both or one of the aforementioned modifications is critical for colony development and antibiotic production. Here, we addressed this issue through analysis of Streptomyces albus J1074 strains carrying double miaAmiaB knockout or extra copy of miaB gene. The double mutant differed from wild-type and miaA-minus strains in severity of morphological defects, growth dynamics, and secondary metabolism. Introduction of extra copy of miaB gene into miaA mutant restored aerial mycelium formation to the latter on certain solid media. Hence, miaB gene might be involved in tRNA thiomethylation in the absence of miaA; either MiaA- or MiaB-mediated modification appears to be enough to support normal metabolic and morphological processes in Streptomyces.
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28
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Kimura S, Srisuknimit V, Waldor MK. Probing the diversity and regulation of tRNA modifications. Curr Opin Microbiol 2020; 57:41-48. [PMID: 32663792 DOI: 10.1016/j.mib.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/28/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
Transfer RNAs (tRNAs) are non-coding RNAs essential for protein synthesis. tRNAs are heavily decorated with a variety of post-transcriptional modifications (tRNA modifications). Recent methodological advances provide new tools for rapid profiling of tRNA modifications and have led to discoveries of novel modifications and their regulation. Here, we provide an overview of the techniques for investigating tRNA modifications and of the expanding knowledge of their chemistry and regulation.
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Affiliation(s)
- Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States.
| | - Veerasak Srisuknimit
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, United States; Department of Microbiology, Harvard Medical School, United States; Howard Hughes Medical Institute, United States.
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29
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Hagelskamp F, Borland K, Ramos J, Hendrick AG, Fu D, Kellner S. Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Res 2020; 48:e41. [PMID: 32083657 PMCID: PMC7144906 DOI: 10.1093/nar/gkaa091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/23/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA.
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Affiliation(s)
- Felix Hagelskamp
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alan G Hendrick
- STORM Therapeutics, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT UK
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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30
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Begik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. Genome Biol 2020; 21:97. [PMID: 32375858 PMCID: PMC7204298 DOI: 10.1186/s13059-020-02009-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type. RESULTS Here, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers. CONCLUSIONS Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.
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Affiliation(s)
- Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Morghan C Lucas
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Huanle Liu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Jose Miguel Ramirez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- UNSW, Sydney, Sydney, NSW, 2052, Australia.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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31
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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32
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Meyer B, Immer C, Kaiser S, Sharma S, Yang J, Watzinger P, Weiß L, Kotter A, Helm M, Seitz HM, Kötter P, Kellner S, Entian KD, Wöhnert J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res 2020; 48:1435-1450. [PMID: 31863583 PMCID: PMC7026641 DOI: 10.1093/nar/gkz1191] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
tRNAs from all domains of life contain modified nucleotides. However, even for the experimentally most thoroughly characterized model organism Escherichia coli not all tRNA modification enzymes are known. In particular, no enzyme has been found yet for introducing the acp3U modification at position 47 in the variable loop of eight E. coli tRNAs. Here we identify the so far functionally uncharacterized YfiP protein as the SAM-dependent 3-amino-3-carboxypropyl transferase catalyzing this modification and thereby extend the list of known tRNA modification enzymes in E. coli. Similar to the Tsr3 enzymes that introduce acp modifications at U or m1Ψ nucleotides in rRNAs this protein contains a DTW domain suggesting that acp transfer reactions to RNA nucleotides are a general function of DTW domain containing proteins. The introduction of the acp3U-47 modification in E. coli tRNAs is promoted by the presence of the m7G-46 modification as well as by growth in rich medium. However, a deletion of the enzymes responsible for the modifications at position 46 and 47 in the variable loop of E. coli tRNAs did not lead to a clearly discernible phenotype suggesting that these two modifications play only a minor role in ensuring the proper function of tRNAs in E. coli.
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Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Steffen Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Sunny Sharma
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Peter Watzinger
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Lena Weiß
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Hans-Michael Seitz
- Institute for Geosciences, Research Unit Mineralogy, and Frankfurt Isotope and Element Research Center (FIERCE), Goethe-Universität Frankfurt, Altenhöferallee 1, 60438 Frankfurt/M., Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
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33
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Asadi-Atoi P, Barraud P, Tisne C, Kellner S. Benefits of stable isotope labeling in RNA analysis. Biol Chem 2020; 400:847-865. [PMID: 30893050 DOI: 10.1515/hsz-2018-0447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles.
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Affiliation(s)
- Paria Asadi-Atoi
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Pierre Barraud
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Carine Tisne
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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34
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Reichle VF, Petrov DP, Weber V, Jung K, Kellner S. NAIL-MS reveals the repair of 2-methylthiocytidine by AlkB in E. coli. Nat Commun 2019; 10:5600. [PMID: 31811240 PMCID: PMC6898146 DOI: 10.1038/s41467-019-13565-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 01/12/2023] Open
Abstract
RNAs contain post-transcriptional modifications, which fulfill a variety of functions in translation, secondary structure stabilization and cellular stress survival. Here, 2-methylthiocytidine (ms2C) is identified in tRNA of E. coli and P. aeruginosa using NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) in combination with genetic screening experiments. ms2C is only found in 2-thiocytidine (s2C) containing tRNAs, namely tRNAArgCCG, tRNAArgICG, tRNAArgUCU and tRNASerGCU at low abundances. ms2C is not formed by commonly known tRNA methyltransferases. Instead, we observe its formation in vitro and in vivo during exposure to methylating agents. More than half of the s2C containing tRNA can be methylated to carry ms2C. With a pulse-chase NAIL-MS experiment, the repair mechanism by AlkB dependent sulfur demethylation is demonstrated in vivo. Overall, we describe ms2C as a bacterial tRNA modification and damage product. Its repair by AlkB and other pathways is demonstrated in vivo by our powerful NAIL-MS approach. Bacterial tRNA is modified by thiolation of nucleosides. Here the authors identify 2-methylthiocytidine in bacterial tRNA using nucleic acid isotope labeling coupled mass spectrometry. Exposure to methylating agents converts 2-thiocytidine to 2-methylthiocytidine, which is repaired by demethylase AlkB in vivo.
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Affiliation(s)
- Valentin F Reichle
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Dimitar P Petrov
- Department of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Verena Weber
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Kirsten Jung
- Department of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
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Koshla O, Yushchuk O, Ostash I, Dacyuk Y, Myronovskyi M, Jäger G, Süssmuth RD, Luzhetskyy A, Byström A, Kirsebom LA, Ostash B. Gene miaA for post-transcriptional modification of tRNA XXA is important for morphological and metabolic differentiation in Streptomyces. Mol Microbiol 2019; 112:249-265. [PMID: 31017319 DOI: 10.1111/mmi.14266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2019] [Indexed: 12/14/2022]
Abstract
Members of actinobacterial genus Streptomyces possess a sophisticated life cycle and are the deepest source of bioactive secondary metabolites. Although morphogenesis and secondary metabolism are subject to transcriptional co-regulation, streptomycetes employ an additional mechanism to initiate the aforementioned processes. This mechanism is based on delayed translation of rare leucyl codon UUA by the only cognate tRNALeu UAA (encoded by bldA). The bldA-based genetic switch is an extensively documented example of translational regulation in Streptomyces. Yet, after five decades since the discovery of bldA, factors that shape its function and peculiar conditionality remained elusive. Here we address the hypothesis that post-transcriptional tRNA modifications play a role in tRNA-based mechanisms of translational control in Streptomyces. Particularly, we studied two Streptomyces albus J1074 genes, XNR_1074 (miaA) and XNR_1078 (miaB), encoding tRNA (adenosine(37)-N6)-dimethylallyltransferase and tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase respectively. These enzymes produce, in a sequential manner, a hypermodified ms2 i6 A37 residue in most of the A36-A37-containing tRNAs. We show that miaB and especially miaA null mutant of S. albus possess altered morphogenesis and secondary metabolism. We provide genetic evidence that miaA deficiency impacts translational level of gene expression, most likely through impaired decoding of codons UXX and UUA in particular.
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Affiliation(s)
- Oksana Koshla
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Yuriy Dacyuk
- Department of Physics of Earth, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
| | - Maksym Myronovskyi
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, Saarbrucken, 66123, Germany
| | - Gunilla Jäger
- Department of Molecular Biology, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90197, Sweden
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straβe des 17 Juni 124/TC2, Berlin, 10623, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Saarland Campus, Building C2.3, Saarbrucken, 66123, Germany
| | - Anders Byström
- Department of Molecular Biology, Umeå University, 6K och 6L, Sjukhusområdet, Umeå, 90197, Sweden
| | - Leif A Kirsebom
- Uppsala Biomedicinska Centrum BMC, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Lviv, 79005, Ukraine
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Xiong J, Yuan BF, Feng YQ. Mass Spectrometry for Investigating the Effects of Toxic Metals on Nucleic Acid Modifications. Chem Res Toxicol 2019; 32:808-819. [PMID: 30920205 DOI: 10.1021/acs.chemrestox.9b00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The extensive use of toxic metals in industry and agriculture leads to their wide distribution in the environment, which raises critical concerns over their toxic effects on human health. Many toxic metals are reported to be mildly mutagenic or non-mutagenic, indicating that genetic-based mechanisms may not be primarily responsible for toxic metal-induced carcinogenesis. Increasing evidence has demonstrated that exposure to toxic metals can alter epigenetic modifications, which may lead to the dysregulation of gene expression and disease susceptibility. It is now becoming clear that a full understanding of the effects of toxic metals on cellular toxicity and carcinogenesis will need to consider both genetic- and epigenetic-based mechanisms. Uncovering the effects of toxic metals on epigenetic modifications in nucleic acids relies on the detection and quantification of these modifications. Mass spectrometry (MS)-based methods for deciphering epigenetic modifications have substantially advanced over the past decade, and they are now becoming widely used and essential tools for evaluating the effects of toxic metals on nucleic acid modifications. This Review provides an overview of MS-based methods for analysis of nucleic acid modifications. In addition, we also review recent advances in understanding the effects of exposure to toxic metals on nucleic acid modifications.
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Affiliation(s)
- Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
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Reichle VF, Kaiser S, Heiss M, Hagelskamp F, Borland K, Kellner S. Surpassing limits of static RNA modification analysis with dynamic NAIL-MS. Methods 2019; 156:91-101. [DOI: 10.1016/j.ymeth.2018.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 01/27/2023] Open
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Shigi N. Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs. Front Microbiol 2018; 9:2679. [PMID: 30450093 PMCID: PMC6225789 DOI: 10.3389/fmicb.2018.02679] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Sulfur is an essential element in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, introduced post-transcriptionally, that function to ensure proper codon recognition or stabilization of tRNA structure, thereby enabling accurate and efficient translation. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems that are closely related to cellular sulfur metabolism, and “modification enzymes” that incorporate sulfur atoms into tRNA. Herein, recent biochemical and structural characterization of the biosynthesis of sulfur modifications in tRNA is reviewed, with special emphasis on the reaction mechanisms of modification enzymes. It was recently revealed that TtuA/Ncs6-type 2-thiouridylases from thermophilic bacteria/archaea/eukaryotes are oxygen-sensitive iron-sulfur proteins that utilize a quite different mechanism from other 2-thiouridylase subtypes lacking iron-sulfur clusters such as bacterial MnmA. The various reaction mechanisms of RNA sulfurtransferases are also discussed, including tRNA methylthiotransferase MiaB (a radical S-adenosylmethionine-type iron-sulfur enzyme) and other sulfurtransferases involved in both primary and secondary sulfur-containing metabolites.
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Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Slama K, Galliot A, Weichmann F, Hertler J, Feederle R, Meister G, Helm M. Determination of enrichment factors for modified RNA in MeRIP experiments. Methods 2018; 156:102-109. [PMID: 30394295 DOI: 10.1016/j.ymeth.2018.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing different pulldown and elution conditions, we measure enrichment factors of 4-5 using m6A-containing mRNAs against an unmodified control of identical sequence. Both types of mRNA carry 32P labels at different nucleotides, allowing their relative quantification in a mixture after digestion to nucleotides, separation by TLC and quantitative phosphorimaging of the labels.
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Affiliation(s)
- Kaouthar Slama
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Aurellia Galliot
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Franziska Weichmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Jasmin Hertler
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Regina Feederle
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Munich, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany.
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40
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Affiliation(s)
- Bei Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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