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D'Atri V, Imiołek M, Quinn C, Finny A, Lauber M, Fekete S, Guillarme D. Size exclusion chromatography of biopharmaceutical products: From current practices for proteins to emerging trends for viral vectors, nucleic acids and lipid nanoparticles. J Chromatogr A 2024; 1722:464862. [PMID: 38581978 DOI: 10.1016/j.chroma.2024.464862] [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: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The 21st century has been particularly productive for the biopharmaceutical industry, with the introduction of several classes of innovative therapeutics, such as monoclonal antibodies and related compounds, gene therapy products, and RNA-based modalities. All these new molecules are susceptible to aggregation and fragmentation, which necessitates a size variant analysis for their comprehensive characterization. Size exclusion chromatography (SEC) is one of the reference techniques that can be applied. The analytical techniques for mAbs are now well established and some of them are now emerging for the newer modalities. In this context, the objective of this review article is: i) to provide a short historical background on SEC, ii) to suggest some clear guidelines on the selection of packing material and mobile phase for successful method development in modern SEC; and iii) to highlight recent advances in SEC, such as the use of narrow-bore and micro-bore columns, ultra-wide pore columns, and low-adsorption column hardware. Some important innovations, such as recycling SEC, the coupling of SEC with mass spectrometry, and the use of alternative detectors such as charge detection mass spectrometry and mass photometry are also described. In addition, this review discusses the use of SEC in multidimensional setups and shows some of the most recent advances at the preparative scale. In the third part of the article, the possibility of SEC for the characterization of new modalities is also reviewed. The final objective of this review is to provide a clear summary of opportunities and limitations of SEC for the analysis of different biopharmaceutical products.
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Affiliation(s)
- Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland
| | | | | | - Abraham Finny
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | - Matthew Lauber
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | | | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland.
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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
ConspectusIn 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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Yared MJ, Yoluç Y, Catala M, Tisné C, Kaiser S, Barraud P. Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. Nucleic Acids Res 2023; 51:10653-10667. [PMID: 37650648 PMCID: PMC10602860 DOI: 10.1093/nar/gkad722] [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: 12/19/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
As essential components of the protein synthesis machinery, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of numerous posttranscriptional modifications. Defects in these tRNA maturation steps may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. We previously identified m1A58 as a late modification introduced after modifications Ψ55 and T54 in yeast elongator tRNAPhe. However, previous reports suggested that m1A58 is introduced early during the tRNA modification process, in particular on primary transcripts of initiator tRNAiMet, which prevents its degradation by RNA decay pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m1A58 incorporation, we examined its introduction into yeast elongator and initiator tRNAs. We used specifically modified tRNAs to report on the molecular aspects controlling the Ψ55 → T54 → m1A58 modification circuit in elongator tRNAs. We also show that m1A58 is efficiently introduced on unmodified tRNAiMet, and does not depend on prior modifications. Finally, we show that m1A58 has major effects on the structural properties of initiator tRNAiMet, so that the tRNA elbow structure is only properly assembled when this modification is present. This observation provides a structural explanation for the degradation of hypomodified tRNAiMet lacking m1A58 by the nuclear surveillance and RTD pathways.
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Affiliation(s)
- Marcel-Joseph Yared
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Marjorie Catala
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Carine Tisné
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| | - Pierre Barraud
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
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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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5
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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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Hagelskamp F, Kellner S. Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry. Methods Enzymol 2021; 658:111-135. [PMID: 34517944 DOI: 10.1016/bs.mie.2021.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA modifications gain growing attention as a new frontier in the life sciences but with the rise of RNA vaccines also in biomedical drug development. Impeccable characterization of RNA modifications within their sequence context remains an analytical challenge. Oligonucleotide mass spectrometry (ON-MS), an approach similar to bottom-up proteome analysis, is capable of defining a short 5-15 nucleotide sequence context of an RNA modification while delivering information on the chemical character of the modified nucleotide. Commonly, ON-MS requires the use of ion pairing reagents for ON separation which is not compatible with most other MS-based applications and only few laboratories run dedicated MS instruments for the task. Here, we present an ON-MS technique which is independent of ion pairing reagents and can be used on any available mass spectrometer without risking its sensitivity for other analytes. In this chapter, we describe the experiments necessary for ON-MS method development, ON-MS application to native and synthetic RNAs and finally a guideline for data analysis.
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Affiliation(s)
- Felix Hagelskamp
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany
| | - Stefanie Kellner
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany.
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7
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Heiss M, Hagelskamp F, Marchand V, Motorin Y, Kellner S. Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo. Nat Commun 2021; 12:389. [PMID: 33452242 PMCID: PMC7810713 DOI: 10.1038/s41467-020-20576-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of the temporal processing of RNA transcripts. Here, we present nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. We design pulse chase experiments and study the temporal placement of modified nucleosides in tRNAPhe and 18S rRNA. In existing RNAs, we observe a time-dependent constant loss of modified nucleosides which is masked by post-transcriptional methylation mechanisms and thus undetectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing ones. Overall, we present a fast and reliable stable isotope labeling strategy which allows in-depth study of RNA modification dynamics in human cell culture.
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Affiliation(s)
- Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Felix Hagelskamp
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, CNRS, Inserm, UMS2008/US40 IBSLor and UMR7365 IMoPA, F-54000, Nancy, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str, 9, 60438, Frankfurt, Germany.
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8
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Heiss M, Borland K, Yoluç Y, Kellner S. Quantification of Modified Nucleosides in the Context of NAIL-MS. Methods Mol Biol 2021; 2298:279-306. [PMID: 34085252 DOI: 10.1007/978-1-0716-1374-0_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent progress in epitranscriptome research shows an interplay of enzymes modifying RNAs and enzymes dedicated for RNA modification removal. One of the main techniques to study RNA modifications is liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) as it allows sensitive detection of modified nucleosides. Although RNA modifications have been found to be highly dynamic, state-of-the-art LC-MS/MS analysis only gives a static view on modifications and does not allow the investigation of temporal modification placement. Here, we present the principles of nucleic acid isotope labeling coupled with mass spectrometry, termed NAIL-MS, which overcomes these limitations by stable isotope labeling in human cell culture and gives detailed instructions on how to label cells and process samples in order to get reliable results. For absolute quantification in the context of NAIL-MS, we explain the production of internal standards in detail. Furthermore, we outline the requirements for stable isotope labeling in cell culture and all subsequent steps to receive nucleoside mixtures of native RNA for NAIL-MS analysis. In the final section of this chapter, we describe the distinctive features of NAIL-MS data analysis with a special focus toward absolute quantification of modified nucleosides.
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Affiliation(s)
- Matthias Heiss
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany.
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Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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Quiles-Jiménez A, Gregersen I, Mittelstedt Leal de Sousa M, Abbas A, Kong XY, Alseth I, Holm S, Dahl TB, Skagen K, Skjelland M, Aukrust P, Bjørås M, Halvorsen B. N6-methyladenosine in RNA of atherosclerotic plaques: An epitranscriptomic signature of human carotid atherosclerosis. Biochem Biophys Res Commun 2020; 533:631-637. [PMID: 33004177 DOI: 10.1016/j.bbrc.2020.09.057] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND More than 170 post-transcriptional RNA modifications regulate the localization, processing and function of cellular RNAs, and aberrant RNA modifications have been linked to a range of human diseases. The RNA modification landscape in atherosclerosis, the main underlying cause of cardiovascular diseases, is still largely unknown. METHODS We used mass spectrometry to analyse a selection of RNA-modifying enzymes and the N6-methyladenosine (m6A) in carotid atherosclerotic lesion samples representing early and advanced stages of atherosclerosis as compared to non-atherosclerotic arteries from healthy controls. FINDINGS (i) the detection of different levels of several enzymes involved in methylations occurring in rRNA and mRNA; (ii) these findings included changes in the levels of methyltransferases ('writers'), binding proteins ('readers') and demethylases ('erasers') during atherosclerosis as compared to non-atherosclerotic control arteries, with generally the most prominent differences in samples from early atherosclerotic lesions; and (iii) these changes were accompanied by a marked downregulation of m6A in rRNA, the most abundant and well-studied modification in mRNA with a wide range of effects on cell biology. INTERPRETATION We show for the first time that RNA-modifying enzymes and the well-studied RNA modification m6A are differentially regulated in atherosclerotic lesions, which potentially could help creating new prognostic and treatment strategies.
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Affiliation(s)
- Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway; Faculty of Medicine, University of Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway; Faculty of Medicine, University of Oslo, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway; PROMEC Core Facility for Proteomics and Metabolomics, NTNU and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Azhar Abbas
- Department of Neurology, Østfold Hospital Trust Kalnes, Grålum, Norway
| | - Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway
| | - Tuva B Dahl
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway
| | - Karolina Skagen
- Department of Neurology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Mona Skjelland
- Department of Neurology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway; PROMEC Core Facility for Proteomics and Metabolomics, NTNU and the Central Norway Regional Health Authority, Trondheim, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Norway; Faculty of Medicine, University of Oslo, Norway.
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Schäck MA, Jablonski KP, Gräf S, Klassen R, Schaffrath R, Kellner S, Hammann C. Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. Nucleic Acids Res 2020; 48:7899-7913. [PMID: 32609816 PMCID: PMC7430636 DOI: 10.1093/nar/gkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
In the Elongator-dependent modification pathway, chemical modifications are introduced at the wobble uridines at position 34 in transfer RNAs (tRNAs), which serve to optimize codon translation rates. Here, we show that this three-step modification pathway exists in Dictyostelium discoideum, model of the evolutionary superfamily Amoebozoa. Not only are previously established modifications observable by mass spectrometry in strains with the most conserved genes of each step deleted, but also additional modifications are detected, indicating a certain plasticity of the pathway in the amoeba. Unlike described for yeast, D. discoideum allows for an unconditional deletion of the single tQCUG gene, as long as the Elongator-dependent modification pathway is intact. In gene deletion strains of the modification pathway, protein amounts are significantly reduced as shown by flow cytometry and Western blotting, using strains expressing different glutamine leader constructs fused to GFP. Most dramatic are these effects, when the tQCUG gene is deleted, or Elp3, the catalytic component of the Elongator complex is missing. In addition, Elp3 is the most strongly conserved protein of the modification pathway, as our phylogenetic analysis reveals. The implications of this observation are discussed with respect to the evolutionary age of the components acting in the Elongator-dependent modification pathway.
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Affiliation(s)
- Manfred A Schäck
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Kim Philipp Jablonski
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Stefanie Kellner
- Department of Chemistry and Pharmacy, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
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12
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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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13
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The rRNA m 6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 2020; 34:715-729. [PMID: 32217665 PMCID: PMC7197354 DOI: 10.1101/gad.333369.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
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14
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Erber L, Hoffmann A, Fallmann J, Betat H, Stadler PF, Mörl M. LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. RNA Biol 2020; 17:23-32. [PMID: 31486704 PMCID: PMC6948972 DOI: 10.1080/15476286.2019.1664250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 02/07/2023] Open
Abstract
Transfer RNAs belong to the most abundant type of ribonucleic acid in the cell, and detailed investigations revealed correlations between alterations in the tRNA pool composition and certain diseases like breast cancer. However, currently available methods do not sample the entire tRNA pool or lack specificity for tRNAs. A specific disadvantage of such methods is that only full-length tRNAs are analysed, while tRNA fragments or incomplete cDNAs due to RT stops at modified nucleosides are lost. Another drawback in certain approaches is that the tRNA fraction has to be isolated and separated from high molecular weight RNA, resulting in considerable labour costs and loss of material. Based on a hairpin-shaped adapter oligonucleotide selective for tRNA transcripts, we developed a highly specific protocol for efficient and comprehensive high-throughput analysis of tRNAs that combines the benefits of existing methods and eliminates their disadvantages. Due to a 3'-TGG overhang, the adapter is specifically ligated to the tRNA 3'-CCA end. Reverse transcription prior to the ligation of a second adapter allows to include prematurely terminated cDNA products, increasing the number of tRNA reads. This strategy renders this approach a powerful and universal tool to analyse the tRNA pool of cells and organisms under different conditions in health and disease.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Anne Hoffmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Facultad de Ciencias, Universidad Nacional de Colombia, Sede Botoga, Colombia
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Department of Theoretical Chemistry of the University of Vienna, Vienna, Austria
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
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15
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Abstract
Although the biological importance of post-transcriptional RNA modifications in gene expression is widely appreciated, methods to directly detect their introduction during RNA biosynthesis are rare and do not easily provide information on the temporal nature of events. Here, we introduce the application of NMR spectroscopy to observe the maturation of tRNAs in cell extracts. By following the maturation of yeast tRNAPhe with time-resolved NMR measurements, we show that modifications are introduced in a defined sequential order, and that the chronology is controlled by cross-talk between modification events. In particular, we show that a strong hierarchy controls the introduction of the T54, Ψ55 and m1A58 modifications in the T-arm, and we demonstrate that the modification circuits identified in yeast extract with NMR also impact the tRNA modification process in living cells. The NMR-based methodology presented here could be adapted to investigate different aspects of tRNA maturation and RNA modifications in general. Transfer RNA (tRNA) is regulated by RNA modifications. Here the authors employ time-resolved NMR to monitor modifications of yeast tRNAPhe in cellular extracts, revealing a sequential order and cross-talk between modifications.
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16
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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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17
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Oligonucleotide analysis by hydrophilic interaction liquid chromatography-mass spectrometry in the absence of ion-pair reagents. J Chromatogr A 2019; 1595:39-48. [PMID: 30772056 DOI: 10.1016/j.chroma.2019.02.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/02/2019] [Accepted: 02/06/2019] [Indexed: 01/09/2023]
Abstract
Improving our understanding of nucleic acids, both in biological and synthetic applications, remains a bustling area of research for both academic and industrial laboratories. As nucleic acids research evolves, so must the analytical techniques used to characterize nucleic acids. One powerful analytical technique has been coupled liquid chromatography - tandem mass spectrometry (LC-MS/MS). To date, the most successful chromatographic mode has been ion-pairing reversed-phase liquid chromatography. Hydrophilic interaction liquid chromatography (HILIC), in the absence of ion-pair reagents, has been investigated here as an alternative chromatographic approach to the analysis of oligonucleotides. By combining a mobile phase system using commonly employed in liquid chromatography-mass spectrometry (LC-MS) - i.e., water, acetonitrile, and ammonium acetate - and a new, commercially available diol-based HILIC column, high chromatographic and mass spectrometric performance for a wide range of oligonucleotides is demonstrated. Particular applications of HILIC-MS for the analysis of deoxynucleic acid (DNA) oligomers, modified and unmodified oligoribonucleotides, and phosphorothioate DNA oligonucleotides are presented. Based on the LC-MS performance, this HILIC-based approach provides an attractive, sensitive and robust alternative to prior ion-pairing dependent methods with potential utility for both qualitative and quantitative analyses of oligonucleotides without compromising chromatographic or mass spectrometric performance.
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18
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Borland K, Diesend J, Ito-Kureha T, Heissmeyer V, Hammann C, Buck AH, Michalakis S, Kellner S. Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes (Basel) 2019; 10:E26. [PMID: 30621251 PMCID: PMC6356711 DOI: 10.3390/genes10010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 12/04/2022] Open
Abstract
Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.
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Affiliation(s)
- Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Jan Diesend
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Taku Ito-Kureha
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Marchioninistr. 25, 81377 Munich, Germany.
| | - Christian Hammann
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Amy H Buck
- Institute of Immunology & Infection and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CiPSM at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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19
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Reichle VF, Weber V, Kellner S. NAIL-MS in E. coli Determines the Source and Fate of Methylation in tRNA. Chembiochem 2018; 19:2575-2583. [PMID: 30328661 PMCID: PMC6582434 DOI: 10.1002/cbic.201800525] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Indexed: 12/11/2022]
Abstract
In all domains of life, the nucleobases of tRNA can be methylated. These methylations are introduced either by enzymes or by the reaction of methylating agents with the nucleophilic centers of the nucleobases. Herein, we present a systematic approach to identify the methylation sites within RNA in vitro and in vivo. For discrimination between enzymatic tRNA methylation and tRNA methylation damage in bacteria, we used nucleic acid isotope labeling coupled mass spectrometry (NAIL‐MS). With NAIL‐MS, we clearly observed the formation of 7‐methylguanosine, 3‐methyluridine, and 6‐methyladenosine during exposure of bacteria to the alkylating agent methyl methanesulfonate (MMS) in vivo. These damage products were not reported to form in tRNA in vivo, as they were masked by the enzymatically formed modified nucleosides in previous studies. In addition, we found formation of the known damage products 1‐methyladenosine and 3‐methylcytidine in vivo. With a dynamic NAIL‐MS setup, we observed tRNA repair by demethylation of these two RNA modifications in vivo. Furthermore, we saw the potential repair of 6‐methyladenosine but not 7‐methylguanosine in bacterial tRNA.
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Affiliation(s)
- Valentin F Reichle
- Department of Chemistry, LMU Munich, Faculty of Chemistry and Pharmacy, Butenandtstrasse 5, 81377, Munich, Germany
| | - Verena Weber
- Department of Chemistry, LMU Munich, Faculty of Chemistry and Pharmacy, Butenandtstrasse 5, 81377, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, LMU Munich, Faculty of Chemistry and Pharmacy, Butenandtstrasse 5, 81377, Munich, Germany
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20
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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21
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Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR. tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. Mol Syst Biol 2018; 14:e8009. [PMID: 30287681 PMCID: PMC6171970 DOI: 10.15252/msb.20178009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/24/2022] Open
Abstract
Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.
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Affiliation(s)
- Chee Sheng Ng
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ameya Sinha
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yaw Aniweh
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Qianhui Nah
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
| | - Indrakanti Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Microbiology and Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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22
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Xu L, Liu X, Sheng N, Oo KS, Liang J, Chionh YH, Xu J, Ye F, Gao YG, Dedon PC, Fu XY. Three distinct 3-methylcytidine (m 3C) methyltransferases modify tRNA and mRNA in mice and humans. J Biol Chem 2017; 292:14695-14703. [PMID: 28655767 DOI: 10.1074/jbc.m117.798298] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/23/2017] [Indexed: 01/05/2023] Open
Abstract
Chemical RNA modifications are central features of epitranscriptomics, highlighted by the discovery of modified ribonucleosides in mRNA and exemplified by the critical roles of RNA modifications in normal physiology and disease. Despite a resurgent interest in these modifications, the biochemistry of 3-methylcytidine (m3C) formation in mammalian RNAs is still poorly understood. However, the recent discovery of trm141 as the second gene responsible for m3C presence in RNA in fission yeast raises the possibility that multiple enzymes are involved in m3C formation in mammals as well. Here, we report the discovery and characterization of three distinct m3C-contributing enzymes in mice and humans. We found that methyltransferase-like (METTL) 2 and 6 contribute m3C in specific tRNAs and that METTL8 only contributes m3C to mRNA. MS analysis revealed that there is an ∼30-40% and ∼10-15% reduction, respectively, in METTL2 and -6 null-mutant cells, of m3C in total tRNA, and primer extension analysis located METTL2-modified m3C at position 32 of tRNAThr isoacceptors and tRNAArg(CCU) We also noted that METTL6 interacts with seryl-tRNA synthetase in an RNA-dependent manner, suggesting a role for METTL6 in modifying serine tRNA isoacceptors. METTL8, however, modified only mRNA, as determined by biochemical and genetic analyses in Mettl8 null-mutant mice and two human METTL8 mutant cell lines. Our findings provide the first evidence of the existence of m3C modification in mRNA, and the discovery of METTL8 as an mRNA m3C writer enzyme opens the door to future studies of other m3C epitranscriptomic reader and eraser functions.
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Affiliation(s)
- Luang Xu
- From the Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599 Singapore
| | - Xinyu Liu
- From the Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599 Singapore
| | - Na Sheng
- the Model Animal Research Center of Nanjing University, 12 Xuefu Road, 210032 Nanjing, China
| | - Kyaw Soe Oo
- From the Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599 Singapore
| | - Junxin Liang
- the Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117596 Singapore
| | - Yok Hian Chionh
- the Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
| | - Juan Xu
- the Model Animal Research Center of Nanjing University, 12 Xuefu Road, 210032 Nanjing, China
| | - Fuzhou Ye
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Yong-Gui Gao
- the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, and
| | - Peter C Dedon
- the Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore, .,the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Xin-Yuan Fu
- From the Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599 Singapore, .,the Model Animal Research Center of Nanjing University, 12 Xuefu Road, 210032 Nanjing, China.,the Department of Biochemistry, National University of Singapore, 8 Medical Drive, 117596 Singapore
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23
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Heiss M, Reichle VF, Kellner S. Observing the fate of tRNA and its modifications by nucleic acid isotope labeling mass spectrometry: NAIL-MS. RNA Biol 2017; 14:1260-1268. [PMID: 28488916 PMCID: PMC5699550 DOI: 10.1080/15476286.2017.1325063] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
RNA in yeast, especially rRNA and tRNA are heavily modified to fulfill their function in protein translation. Using biosynthetic stable isotope labeled internal standards we quantified 12 modified nucleosides in tRNA from S. cerevisiae over 24 hours. We observed different quantities of modified nucleosides in dependence of the growth phase. To elucidate the underlying mechanism of the observed tRNA modification profile adaptation, it is necessary to distinguish the pre-existing tRNA pool and its modifications from newly-synthesized tRNAs. By combination of 2 differentially isotope labeled media we developed NAIL-MS, nucleic acid isotope labeling coupled mass spectrometry. During the yeast growth cycle we observe dilution of pre-existing tRNAs by newly-synthesized tRNAs by the growing number of cells. tRNA was found to be highly stable with only little degradation over the observed period. The method was further used to quantify the levels of modified nucleosides in the original and new tRNA pools. By addition of deuterium-labeled methionine, we could observe the incorporation of new methyl marks on pre-existing tRNAs. For 2'-O-methylcytidine (Cm) we observed a global increase in log phase. We identified extensive 2'-OH-cytidine methylation of the pre-existing tRNAs and the new tRNAs which masks an actual decrease of pre-existing Cm. In contrast, global 5-methylcytidine (m5C) levels decreased during growth due to a drop in m5C quantities in the original tRNA pool. The NAIL-MS data suggests different mechanisms for tRNA modification adaptation depending on the individual modification observed. With this new tool it is possible to follow the fate of methylated RNAs during growth and potentially compare the impact of different stress conditions on the epitranscriptome.
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Affiliation(s)
- Matthias Heiss
- a Department of Chemistry , Ludwig-Maximilians-Universität München , Munich , Germany
| | - Valentin F Reichle
- a Department of Chemistry , Ludwig-Maximilians-Universität München , Munich , Germany
| | - Stefanie Kellner
- a Department of Chemistry , Ludwig-Maximilians-Universität München , Munich , Germany
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24
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Wang J, Dong H, Chionh YH, McBee ME, Sirirungruang S, Cunningham RP, Shi PY, Dedon PC. The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. Nucleic Acids Res 2016; 44:8962-8975. [PMID: 27365049 PMCID: PMC5062971 DOI: 10.1093/nar/gkw572] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/16/2022] Open
Abstract
The misincorporation of 2′-deoxyribonucleotides (dNs) into RNA has important implications for the function of non-coding RNAs, the translational fidelity of coding RNAs and the mutagenic evolution of viral RNA genomes. However, quantitative appreciation for the degree to which dN misincorporation occurs is limited by the lack of analytical tools. Here, we report a method to hydrolyze RNA to release 2′-deoxyribonucleotide-ribonucleotide pairs (dNrN) that are then quantified by chromatography-coupled mass spectrometry (LC-MS). Using this platform, we found misincorporated dNs occurring at 1 per 103 to 105 ribonucleotide (nt) in mRNA, rRNAs and tRNA in human cells, Escherichia coli, Saccharomyces cerevisiae and, most abundantly, in the RNA genome of dengue virus. The frequency of dNs varied widely among organisms and sequence contexts, and partly reflected the in vitro discrimination efficiencies of different RNA polymerases against 2′-deoxyribonucleoside 5′-triphosphates (dNTPs). Further, we demonstrate a strong link between dN frequencies in RNA and the balance of dNTPs and ribonucleoside 5′-triphosphates (rNTPs) in the cellular pool, with significant stress-induced variation of dN incorporation. Potential implications of dNs in RNA are discussed, including the possibilities of dN incorporation in RNA as a contributing factor in viral evolution and human disease, and as a host immune defense mechanism against viral infections.
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Affiliation(s)
- Jin Wang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Yok Hian Chionh
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Microbiology & Immunology Programme, Center for Life Sciences, National University of Singapore, Singapore 117545
| | - Megan E McBee
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Sasilada Sirirungruang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, Albany, NY 12222, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Phamarcology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Peter C Dedon
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Biological Engineering & Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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25
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Köse K, Uzun L. PolyGuanine methacrylate cryogels for ribonucleic acid purification. J Sep Sci 2016; 39:1998-2005. [PMID: 27004613 DOI: 10.1002/jssc.201600199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 11/10/2022]
Abstract
The isolation and purification of ribonucleic acid have attracted attention recently for the understanding of the functions in detail because of the necessity for the treatment of genetic diseases. In this study, guanine-incorporated polymeric cryogels were developed to obtain highly purified ribonucleic acid. The satisfactory purification performance was achieved with the guanine-incorporated poly (2-hydroxyethyl methacrylate-guanine methacrylate) cryogels. The most crucial advantages to use guanine as a functional monomer are to obtain a real natural interaction between guanine on the polymeric material and cytosine on the ribonucleic acid. Moreover, using cryogel with a highly porous structure and high swelling ratio provide advantages of getting more water within the structure to get more analyte to interact. The characterization of cryogels has proved the success of the synthesis and the perfect natural interaction to be taken place between the ligand (guanine methacrylate) and the cytosine in the ribonucleic acid molecules. Although the pores within the structure of cryogels are small, they provide efficient and fast adsorption. The chromatographic separation performance was investigated for different conditions (pH, temperature etc.). The desorption ratio and reusability were also analyzed at the end of the five adsorption-desorption cycles with no significant changes.
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Affiliation(s)
- Kazım Köse
- Department of Chemistry, Hacettepe University, Ankara, Turkey.,Scientific Technical Research and Application Center, Hitit University, Çorum, Turkey
| | - Lokman Uzun
- Department of Chemistry, Hacettepe University, Ankara, Turkey
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26
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Nie W, Yan L, Lee YH, Guha C, Kurland IJ, Lu H. Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma. MASS SPECTROMETRY REVIEWS 2016; 35:331-349. [PMID: 24890331 DOI: 10.1002/mas.21439] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 04/17/2014] [Accepted: 04/17/2014] [Indexed: 06/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.
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Affiliation(s)
- Wenna Nie
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Leyu Yan
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Yie H Lee
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology, Singapore, 138602, Singapore
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center, New York, New York, 10461
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research and Training Center, Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Haitao Lu
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia
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Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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28
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Hia F, Chionh YH, Pang YLJ, DeMott MS, McBee ME, Dedon PC. Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides. Nucleic Acids Res 2014; 43:e32. [PMID: 25539917 PMCID: PMC4357692 DOI: 10.1093/nar/gku1317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.
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Affiliation(s)
- Fabian Hia
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Yok Hian Chionh
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Microbiology and Immunology Programme, National University of Singapore, 117456, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Megan E McBee
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Peter C Dedon
- Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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29
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Pang YLJ, Abo R, Levine SS, Dedon PC. Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res 2014; 42:e170. [PMID: 25348403 PMCID: PMC4267671 DOI: 10.1093/nar/gku945] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3′-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H2O2) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H2O2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
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Affiliation(s)
- Yan Ling Joy Pang
- Department of Biological Engineering and Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan Abo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stuart S Levine
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter C Dedon
- Department of Biological Engineering and Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Gu C, Begley TJ, Dedon PC. tRNA modifications regulate translation during cellular stress. FEBS Lett 2014; 588:4287-96. [PMID: 25304425 DOI: 10.1016/j.febslet.2014.09.038] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression in response to stress is an essential cellular protection mechanism. Recent advances in tRNA modification analysis and genome-based codon bias analytics have facilitated studies that lead to a novel model for translational control, with translation elongation dynamically regulated during stress responses. Stress-induced increases in specific anticodon wobble bases are required for the optimal translation of stress response transcripts that are significantly biased in the use of degenerate codons keyed to these modified tRNA bases. These findings led us to introduce the notion of tRNA modification tunable transcripts (MoTTs - transcripts whose translation is regulated by tRNA modifications), which are identifiable using genome-wide codon counting algorithms. In support of this general model of translational control of stress response, studies making use of detailed measures of translation, tRNA methyltransferase mutants, and computational and mass spectrometry approaches reveal that stress reprograms tRNA modifications to translationally regulate MoTTs linked to arginine and leucine codons, which helps cells survive insults by damaging agents. These studies highlight how tRNA methyltransferase activities and MoTTs are key components of the cellular stress response.
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Affiliation(s)
- Chen Gu
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas J Begley
- State University of New York - College of Nanoscale Science and Engineering, Albany, NY, United States; The RNA Institute at the University at Albany, Albany, NY, United States.
| | - Peter C Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
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31
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Martins R, Queiroz J, Sousa F. Ribonucleic acid purification. J Chromatogr A 2014; 1355:1-14. [DOI: 10.1016/j.chroma.2014.05.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 11/24/2022]
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32
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Chen P, Jeannotte R, Weimer BC. Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier. Trends Microbiol 2014; 22:292-300. [PMID: 24725482 DOI: 10.1016/j.tim.2014.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 02/08/2023]
Abstract
Epigenetics has an important role for the success of foodborne pathogen persistence in diverse host niches. Substantial challenges exist in determining DNA methylation to situation-specific phenotypic traits. DNA modification, mediated by restriction-modification systems, functions as an immune response against antagonistic external DNA, and bacteriophage-acquired methyltransferases (MTase) and orphan MTases - those lacking the cognate restriction endonuclease - facilitate evolution of new phenotypes via gene expression modulation via DNA and RNA modifications, including methylation and phosphorothioation. Recent establishment of large-scale genome sequencing projects will result in a significant increase in genome availability that will lead to new demands for data analysis including new predictive bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing technologies that detect modification coupled with mass spectrometry to discover new adducts is a powerful tactic to study bacterial epigenetics, which is poised to make novel and far-reaching discoveries that link biological significance and the bacterial epigenome.
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Affiliation(s)
- Poyin Chen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile
| | - Richard Jeannotte
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile; Facultad de Ciencias, Universidad de Tarapacá, Arica, Chile
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile.
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33
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Su D, Chan CTY, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC. Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat Protoc 2014; 9:828-41. [PMID: 24625781 DOI: 10.1038/nprot.2014.047] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Post-transcriptional modification of RNA is an important determinant of RNA quality control, translational efficiency, RNA-protein interactions and stress response. This is illustrated by the observation of toxicant-specific changes in the spectrum of tRNA modifications in a stress-response mechanism involving selective translation of codon-biased mRNA for crucial proteins. To facilitate systems-level studies of RNA modifications, we developed a liquid chromatography-mass spectrometry (LC-MS) technique for the quantitative analysis of modified ribonucleosides in tRNA. The protocol includes tRNA purification by HPLC, enzymatic hydrolysis, reversed-phase HPLC resolution of the ribonucleosides, and identification and quantification of individual ribonucleosides by LC-MS via dynamic multiple reaction monitoring (DMRM). In this approach, the relative proportions of modified ribonucleosides are quantified in several micrograms of tRNA in a 15-min LC-MS run. This protocol can be modified to analyze other types of RNA by modifying the steps for RNA purification as appropriate. By comparison, traditional methods for detecting modified ribonucleosides are labor- and time-intensive, they require larger RNA quantities, they are modification-specific or require radioactive labeling.
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Affiliation(s)
- Dan Su
- 1] Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. [2]
| | - Clement T Y Chan
- 1] Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. [2]
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- 1] Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. [2]
| | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore
| | - Brandon S Russell
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- 1] Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. [2] Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore. [3] Center for Environmental Health Science, MIT, Cambridge, Massachusetts, USA
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Dedon PC, Begley TJ. A system of RNA modifications and biased codon use controls cellular stress response at the level of translation. Chem Res Toxicol 2014; 27:330-7. [PMID: 24422464 PMCID: PMC3997223 DOI: 10.1021/tx400438d] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cells respond to environmental stressors and xenobiotic exposures using regulatory networks to control gene expression, and there is an emerging appreciation for the role of numerous postsynthetic chemical modifications of DNA, RNA, and proteins in controlling transcription and translation of the stress response. In this Perspective, we present a model for a new network that regulates the cellular response to xenobiotic exposures and other stresses in which stress-induced reprogramming of a system of dozens of post-transcriptional modifications on tRNA (tRNA) promotes selective translation of codon-biased mRNAs for critical response proteins. As a product of novel genomic and bioanalytical technologies, this model has strong parallels with the regulatory networks of DNA methylation in epigenetics and the variety of protein secondary modifications comprising signaling pathways and the histone code. When present at the tRNA wobble position, the modified ribonucleosides enhance the translation of mRNAs in which the cognate codons of the tRNAs are highly over-represented and that represent critical stress response proteins. A parallel system may also downregulate the translation of families of proteins. Notably, dysregulation of the tRNA methyltransferase enzymes in humans has also been implicated in cancer etiology, with demonstrated oncogenic and tumor-suppressive effects.
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Affiliation(s)
- Peter C Dedon
- Department of Biological Engineering, Center for Environmental Health Science, Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures. J Biotechnol 2014; 174:16-21. [PMID: 24480570 DOI: 10.1016/j.jbiotec.2014.01.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 11/21/2022]
Abstract
The mTOR pathway is a conserved master regulator of translational activity that influences the fate of industrially relevant CHO cell cultures, yet its molecular mechanisms remain unclear. Interestingly, rapamycin specific inhibition of the mTOR pathway in CHO cells was found to down-regulate the small nucleolar RNA U19 (snoRNA U19) by 2-fold via translatome profiling. snoRNA U19 guides the two most conserved pseudouridylation modifications on 28S ribosomal RNA (rRNA) that are important for the biogenesis and proper function of ribosomes. In order to further understand the role of snoRNA U19 as a potential player in the mTOR pathway, we measured 28S rRNA pseudouridylation upon rapamycin treatments and/or snoRNA U19 overexpression conditions, thereby characterizing the subsequent effects on ribosome efficiency and global translation by polysome profiling. We showed that 28S rRNA pseudouridylation was increased by rapamycin treatment and/or overexpression of snoRNA U19, but only the latter condition improved ribosome efficiency toward higher global translation, thus implying that the mTOR pathway induces pseudouridylation at different sites along the 28S rRNA possibly with either positive or negative effects on the cellular phenotype. This discovery of snoRNA U19 as a new downstream effector of the mTOR pathway suggests that cell engineering of snoRNAs can be used to regulate translation and improve cellular growth in CHO cell cultures in the future.
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