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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; 19:e202400115. [PMID: 38630955 DOI: 10.1002/cmdc.202400115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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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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3
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Janssen KA, Xie Y, Kramer MC, Gregory BD, Garcia BA. Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:885-893. [PMID: 35357823 PMCID: PMC9425428 DOI: 10.1021/jasms.2c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
RNA is dynamically modified in cells by a plethora of chemical moieties to modulate molecular functions and processes. Over 140 modifications have been identified across species and RNA types, with the highest density and diversity of modifications found in tRNA (tRNA). The methods used to identify and quantify these modifications have developed over recent years and continue to advance, primarily in the fields of next-generation sequencing (NGS) and mass spectrometry (MS). Most current NGS methods are limited to antibody-recognized or chemically derivatized modifications and have limitations in identifying multiple modifications simultaneously. Mass spectrometry can overcome both of these issues, accurately identifying a large number of modifications in a single run. Here, we present advances in MS data acquisition for the purpose of RNA modification identification and quantitation. Using this approach, we identified multiple tRNA wobble position modifications in Arabidopsis thaliana that are upregulated in salt-stressed growth conditions and may stabilize translation of salt stress induced proteins. This work presents improvements in methods for studying RNA modifications and introduces a possible regulatory role of wobble position modifications in A. thaliana translation.
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Affiliation(s)
- Kevin A. Janssen
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Corresponding Author: Correspondence to: Benjamin A. Garcia;
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4
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Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M, Helm M. Die stark wachsende chemische Vielfalt der RNA-Modifikationen enthält eine Thioacetalstruktur. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christina Dal Magro
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Patrick Keller
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Annika Kotter
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Stephan Werner
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
| | - Victor Duarte
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG, CNRS; 17 rue des martyrs 38000 Grenoble Frankreich
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, FR3209 Bioingénierie Moléculaire Cellulaire et Thérapeutique, CNRS; Lorraine University; 54505 Vandoeuvre-les-Nancy Frankreich
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine; Universität zu Köln; Kerpener Straße 62 50937 Cologne Deutschland
| | - Anja Freiwald
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Deutschland
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine; Universität zu Köln; Kerpener Straße 62 50937 Cologne Deutschland
| | - Christoph Dieterich
- Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK); Universitätsklinikum Heidelberg; Im Neuenheimer Feld 669 69120 Heidelberg Deutschland
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) UMR7365 CNRS-UL; BioPôle de l'Université de Lorraine Campus Biologie-Santé; 9 avenue de la Forêt de Haye, CS 50184 54505 Vandoeuvre-les-Nancy Frankreich
| | - Falk Butter
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Deutschland
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG, CNRS; 17 rue des martyrs 38000 Grenoble Frankreich
| | - Mark Helm
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Deutschland
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5
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Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M, Helm M. A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure. Angew Chem Int Ed Engl 2018; 57:7893-7897. [DOI: 10.1002/anie.201713188] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Christina Dal Magro
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Patrick Keller
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Stephan Werner
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
| | - Victor Duarte
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG; CNRS; 17 rue des martyrs 38000 Grenoble France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, FR3209 Bioingénierie Moléculaire Cellulaire et Thérapeutique, CNRS; Lorraine University; 54505 Vandoeuvre-les-Nancy France
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine; University of Cologne; Kerpener Strasse 62 50937 Cologne Germany
| | - Anja Freiwald
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine; University of Cologne; Kerpener Strasse 62 50937 Cologne Germany
| | - Christoph Dieterich
- German Center for Cardiovascular Research (DZHK); University Hospital Heidelberg; Im Neuenheimer Feld 669 69120 Heidelberg Germany
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) UMR7365 CNRS-UL; BioPôle de l'Université de Lorraine Campus Biologie-Santé; 9 avenue de la Forêt de Haye, CS 50184 54505 Vandoeuvre-les-Nancy France
| | - Falk Butter
- Institute of Molecular Biology (IMB); Ackermannweg 4 55128 Mainz Germany
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CEA/BIG; CNRS; 17 rue des martyrs 38000 Grenoble France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University Mainz; Staudingerweg 5 55128 Mainz Germany
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6
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Matuszewski M, Wojciechowski J, Miyauchi K, Gdaniec Z, Wolf WM, Suzuki T, Sochacka E. A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs. Nucleic Acids Res 2017; 45:2137-2149. [PMID: 27913732 PMCID: PMC5389693 DOI: 10.1093/nar/gkw1189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/25/2016] [Indexed: 02/06/2023] Open
Abstract
N6-Threonylcarbamoyladenosine (t6A) and its derivatives are universally conserved modified nucleosides found at position 37, 3΄ adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t6A is further modified to the cyclic t6A (ct6A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNALys. Previous work indicated that the chemical structure of ct6A is a cyclic active ester with an oxazolone ring. In this study, we solved the crystal structure of chemically synthesized ct6A nucleoside. Unexpectedly, we found that the ct6A adopted a hydantoin isoform rather than an oxazolone isoform, and further showed that the hydantoin isoform of ct6A was actually present in Escherichia coli tRNAs. In addition, we observed that hydantoin ct6A is susceptible to epimerization under mild alkaline conditions, warning us to avoid conventional deacylation of tRNAs. A hallmark structural feature of this isoform is the twisted arrangement of the hydantoin and adenine rings. Functional roles of ct6A37 in tRNAs should be reconsidered.
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Affiliation(s)
- Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Jakub Wojciechowski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech M Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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7
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Kang BI, Miyauchi K, Matuszewski M, D'Almeida GS, Rubio M, Alfonzo JD, Inoue K, Sakaguchi Y, Suzuki T, Sochacka E, Suzuki T. Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs. Nucleic Acids Res 2017; 45:2124-2136. [PMID: 27913733 PMCID: PMC5389704 DOI: 10.1093/nar/gkw1120] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/09/2016] [Indexed: 02/01/2023] Open
Abstract
Transfer RNA modifications play pivotal roles in protein synthesis. N6-threonylcarbamoyladenosine (t6A) and its derivatives are modifications found at position 37, 3΄-adjacent to the anticodon, in tRNAs responsible for ANN codons. These modifications are universally conserved in all domains of life. t6A and its derivatives have pleiotropic functions in protein synthesis including aminoacylation, decoding and translocation. We previously discovered a cyclic form of t6A (ct6A) as a chemically labile derivative of t6A in tRNAs from bacteria, fungi, plants and protists. Here, we report 2-methylthio cyclic t6A (ms2ct6A), a novel derivative of ct6A found in tRNAs from Bacillus subtilis, plants and Trypanosoma brucei. In B. subtilis and T. brucei, ms2ct6A disappeared and remained to be ms2t6A and ct6A by depletion of tcdA and mtaB homologs, respectively, demonstrating that TcdA and MtaB are responsible for biogenesis of ms2ct6A.
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Affiliation(s)
- Byeong-il Kang
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Michal Matuszewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Lodz 90-924, Poland
| | - Gabriel Silveira D'Almeida
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mary Anne T. Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Juan D. Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kazuki Inoue
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Lodz 90-924, Poland
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
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8
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Abstract
A common feature of ribonucleic acids (RNAs) is that they can undergo a variety of chemical modifications. As nearly all of these chemical modifications result in an increase in the mass of the canonical nucleoside, mass spectrometry has long been a powerful approach for identifying and characterizing modified RNAs. Over the past several years, significant advances have been made in method development and software for interpreting tandem mass spectra resulting in approaches that can yield qualitative and quantitative information on RNA modifications, often at the level of sequence specificity. We discuss these advances along with instrumentation developments that have increased our ability to extract such information from relatively complex biological samples. With the increasing interest in how these modifications impact the epitranscriptome, mass spectrometry will continue to play an important role in bioanalytical investigations revolving around RNA.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172. and University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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10
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A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol 2012; 9:105-11. [PMID: 23242255 DOI: 10.1038/nchembio.1137] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/01/2012] [Indexed: 11/09/2022]
Abstract
N(6)-threonylcarbamoyladenosine (t(6)A) is a universally conserved, essential modified nucleoside found in transfer RNAs (tRNAs) responsible for ANN codons in all three domains of life. t(6)A has a crucial role in maintaining decoding accuracy during protein synthesis. The presence of t(6)A in cellular tRNAs has been well documented for more than four decades. However, under conditions optimized for nucleoside preparation, we detected little t(6)A in tRNAs from Escherichia coli. Instead, we identified a new modified base named 'cyclic t(6)A' (ct(6)A), which is a cyclized active ester with an oxazolone ring. An E1-like enzyme, CsdL (renamed as TcdA), which catalyzes ATP-dependent dehydration of t(6)A to form ct(6)A, was also identified. Two yeast homologs of tcdA, YHR003C (TCD1) and YKL027W (TCD2), were required for ct(6)A formation and respiratory cell growth. ct(6)A was involved in promoting decoding efficiency. Structural modeling suggests that ct(6)A recognizes the first adenine base of ANN codon at the ribosomal A site.
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11
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Krog JS, Español Y, Giessing AMB, Dziergowska A, Malkiewicz A, Ribas de Pouplana L, Kirpekar F. 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine is one of two novel post-transcriptional modifications in tRNALys(UUU) from Trypanosoma brucei. FEBS J 2011; 278:4782-96. [PMID: 22040320 DOI: 10.1111/j.1742-4658.2011.08379.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
tRNA is the most heavily modified of all RNA types, with typically 10-20% of the residues being post-transcriptionally altered. Unravelling the modification pattern of a tRNA is a challenging task; there are 92 currently known tRNA modifications, many of which are chemically similar. Furthermore, the tRNA has to be investigated with single-nucleotide resolution in order to ensure complete mapping of all modifications. In the present work, we characterized tRNA(Lys)(UUU) from Trypanosoma brucei, and provide a complete overview of its post-transcriptional modifications. The first step was MALDI-TOF MS of two independent digests of the tRNA, with RNase A and RNase T1, respectively. This revealed digestion products harbouring mass-changing modifications. Next, the modifications were mapped at the nucleotide level in the RNase products by tandem MS. Comparison with the sequence of the unmodified tRNA revealed the modified residues. The modifications were further characterized at the nucleoside level by chromatographic retention time and fragmentation pattern upon higher-order tandem MS. Phylogenetic comparison with modifications in tRNA(Lys) from other organisms was used through the entire analysis. We identified modifications on 12 nucleosides in tRNA(Lys)(UUU), where U47 exhibited a novel modification, 3-(3-amino-3-carboxypropyl)-5,6-dihydrouridine, based on identical chromatographic retention and MS fragmentation as the synthetic nucleoside. A37 was observed in two versions: a minor fraction with the previously described 2-methylthio-N(6)-threonylcarbamoyl-modification, and a major fraction with A37 being modified by a 294.0-Da moiety. The latter product is the largest adenosine modification reported so far, and we discuss its nature and origin.
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Affiliation(s)
- Jesper S Krog
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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12
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Commans S, Lazard M, Delort F, Blanquet S, Plateau P. tRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases. J Mol Biol 1998; 278:801-13. [PMID: 9614943 DOI: 10.1006/jmbi.1998.1711] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subclass IIb aminoacyl-tRNA synthetases (Asn-, Asp- and LysRS) recognize the anticodon triplet of their cognate tRNA (GUU, GUC and UUU, respectively) through an OB-folded N-terminal extension. In the present study, the specificity of constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli was analyzed by cross-mutagenesis of the tRNA(Lys) anticodon, on the one hand, and of the amino acid residues composing the anticodon binding site on the other. From this analysis, a tentative model is deduced for both the recognition of the cognate anticodon and the rejection of non-cognate anticodons. In this model, the enzyme offers a rigid scaffold of amino acid residues along the beta-strands of the OB-fold for tRNA binding. Phe85 and Gln96 play a critical role in this spatial organization. This scaffold can recognize directly U35 at the center of the anticodon. Specification of the correct enzyme:tRNA complex is further achieved through the accommodation of U34 and U36. The binding of these bases triggers the conformationnal change of a flexible seven-residue loop between strands 4 and 5 of the OB-fold (L45). Additional free energy of binding is recovered from the resulting network of cooperative interactions. Such a mechanism would not depend on the modifications of the anticodon loop of tRNA(Lys) (mnm5s2U34 and t6A37). In the model, exclusion by the synthetase of non-cognate anticodons can be accounted for by a hindrance to the positioning of the L45 loop. In addition, Glu135 would repulse a cytosine base at position 35. Sequence comparisons show that the composition and length of the L45 loop are markedly conserved in each of the families composing subclass IIb aminoacyl-tRNA synthetases. The possible role of the loop is discussed for each case, including that of archaebacterial aspartyl-tRNA synthetases.
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Affiliation(s)
- S Commans
- Laboratoire de Biochimie, URA 1970 du CNRS, Ecole Polytechnique, Palaiseau, France
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13
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14
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Pomerantz SC, McCloskey JA. Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol 1990; 193:796-824. [PMID: 1706064 DOI: 10.1016/0076-6879(90)93452-q] [Citation(s) in RCA: 179] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Adamiak RW, Górnicki P. Hypermodified nucleosides of tRNA: synthesis, chemistry, and structural features of biological interest. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1985; 32:27-74. [PMID: 3911278 DOI: 10.1016/s0079-6603(08)60345-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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Dirheimer G. Chemical nature, properties, location, and physiological and pathological variations of modified nucleosides in tRNAs. Recent Results Cancer Res 1983; 84:15-46. [PMID: 6342070 DOI: 10.1007/978-3-642-81947-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)30183-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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