1
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Goyon A, Scott B, Yehl P, Zhang K. Online Nucleotide Mapping of mRNAs. Anal Chem 2024; 96:8674-8681. [PMID: 38712815 DOI: 10.1021/acs.analchem.4c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Messenger RNA (mRNA) can be sequenced via indirect approaches such as Sanger sequencing and next generation sequencing (NGS), or direct approaches like bottom-up mass spectrometry (MS). Direct sequencing allows the confirmation of RNA modifications. However, the conventional bottom-up MS approach involves time-consuming in-solution digestions that require a large amount of sample, and can lead to the RNase contamination of the LC-MS system and column. Here, we describe a platform that enables online nucleotide mapping of mRNAs via the use of immobilized RNase cartridges and 2D-LC-MS instrumentation. The online approach was compared to conventional offline digestion protocols adapted from two published studies. For this purpose, five model mRNAs of varying lengths (996-4521 nucleotides) and chemistries (unmodified uridine vs 5-methoxyuridine (5moU)) were analyzed. The profiles and sequence coverages obtained after RNase T1 digestion were discussed. The online nucleotide mapping achieved comparable or slightly greater sequence coverage for the 5 mRNAs (5.8-51.5%) in comparison to offline approaches (3.7-50.4%). The sequence coverage was increased to 65.6-85.6 and 69.7-85.0% when accounting for the presence of nonunique digestion products generated by the RNase T1 and A, respectively. The online nucleotide mapping significantly reduced the digestion time (from 15 to <5 min), increased the signal intensity by more than 10-fold in comparison to offline approaches.
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Affiliation(s)
- Alexandre Goyon
- Synthetic Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Brandon Scott
- Synthetic Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Yehl
- Synthetic Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Synthetic Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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2
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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3
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Finkler M, Brandt J, Boutfol T, Grimm F, Hartz P, Ott A. Protocol to identify amino acids bound to tRNA by aminoacylation using mass spectrometry. STAR Protoc 2023; 4:102504. [PMID: 37585296 PMCID: PMC10436234 DOI: 10.1016/j.xpro.2023.102504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/12/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
tRNA-bound amino acids often need to be identified, for instance, in cases where different amino acids compete for binding to the same tRNA. Here, we present a mass-spectrometry-based protocol to determine the amino acids bound to tRNA by aminoacylation. We detail how to perform the aminoacylation reaction, the preparation of the aminoacyl-tRNA for measurement, and the mass spectrometric analysis. We use arginine acylation as an example; however, this protocol can be applied to any other amino acid.
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Affiliation(s)
- Marc Finkler
- Universität des Saarlandes, Biologische Experimentalphysik, Zentrum f. Biophysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123 Saarbrücken, Germany.
| | - Joshua Brandt
- Universität des Saarlandes, Biologische Experimentalphysik, Zentrum f. Biophysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123 Saarbrücken, Germany.
| | - Timothée Boutfol
- Universität des Saarlandes, Biologische Experimentalphysik, Zentrum f. Biophysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123 Saarbrücken, Germany
| | - Florent Grimm
- Universität des Saarlandes, Biologische Experimentalphysik, Zentrum f. Biophysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123 Saarbrücken, Germany
| | - Philip Hartz
- Universität des Saarlandes, Institut für Biochemie, Naturwissenschaftlich-Technische Fakultät, B2 2, Campus, 66123 Saarbrücken, Germany
| | - Albrecht Ott
- Universität des Saarlandes, Biologische Experimentalphysik, Zentrum f. Biophysik, Naturwissenschaftlich-Technische Fakultät, B2 1, Campus, 66123 Saarbrücken, Germany.
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4
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Macias LA, Garcia SP, Back KM, Wu Y, Johnson GH, Kathiresan S, Bellinger AM, Rohde E, Freitas MA, Madsen JA. Spacer Fidelity Assessments of Guide RNA by Top-Down Mass Spectrometry. ACS CENTRAL SCIENCE 2023; 9:1437-1452. [PMID: 37521788 PMCID: PMC10375574 DOI: 10.1021/acscentsci.3c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Indexed: 08/01/2023]
Abstract
The advancement of CRISPR-based gene editing tools into biotherapeutics offers the potential for cures to genetic disorders and for new treatment paradigms for even common diseases. Arguably, the most important component of a CRISPR-based medicine is the guide RNA, which is generally large (>100-mer) synthetic RNA composed of a "tracr" and "spacer" region, the latter of which dictates the on-target editing site as well as potential undesired off-target edits. Aiming to advance contemporary capabilities for gRNA characterization to ensure the spacer region is of high fidelity, top-down mass spectrometry was herein implemented to provide direct and quantitative assessments of highly modified gRNA. In addition to sequencing the spacer region and pinpointing modifications, top-down mass spectra were utilized to quantify single-base spacer substitution impurities down to <1% and to decipher highly dissimilar spacers. To accomplish these results in an automated fashion, we devised custom software capable of sequencing and quantifying impurities in gRNA spacers. Notably, we developed automated tools that enabled the quantification of single-base substitutions, including advanced isotopic pattern matching for C > U and U > C substitutions, and created a de novo sequencing strategy to facilitate the identification and quantification of gRNA impurities with highly dissimilar spacer regions.
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Affiliation(s)
- Luis A. Macias
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Sara P. Garcia
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Kayla M. Back
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Yue Wu
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - G. Hall Johnson
- MassMatrix,
Inc., 600 Teteridge Road, Columbus, Ohio 43214, United States
| | - Sekar Kathiresan
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Andrew M. Bellinger
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Ellen Rohde
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
| | - Michael A. Freitas
- MassMatrix,
Inc., 600 Teteridge Road, Columbus, Ohio 43214, United States
- The
Ohio State University, 281 West Lane Avenue, Columbus, Ohio 43210, United States
| | - James A. Madsen
- Verve
Therapeutics, 201 Brookline Avenue, Suite 601, Boston, Massachusetts 02215, United States
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5
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Chin S, Goyon A, Zhang K, Kurita KL. Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion. Anal Bioanal Chem 2023; 415:2809-2818. [PMID: 37093234 DOI: 10.1007/s00216-023-04693-9] [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: 02/14/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Accurate sequencing of single guide RNAs (sgRNAs) for CRISPR/Cas9 genome editing is critical for patient safety, as the sgRNA guides the Cas9 nuclease to target site-specific cleavages in DNA. An approach to fully sequence sgRNA using protective DNA primers followed by ribonuclease (RNase) T1 digestion was developed to facilitate the analysis of these larger molecules by hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC-HRMS). Without RNase digestion, top-down mass spectrometry alone struggles to properly fragment precursor ions in large RNA oligonucleotides to provide confidence in sequence coverage. With RNase T1 digestion of these larger oligonucleotides, however, bottom-up analysis cannot confirm full sequence coverage due to the presence of short, redundant digestion products. By combining primer protection with RNase T1 digestion, digestion products are large enough to prevent redundancy and small enough to provide base resolution by tandem mass spectrometry to allow for full sgRNA sequence coverage. An investigation into the general requirements for adequate primer protection of specific regions of the RNA was conducted, followed by the development of a generic protection and digestion strategy that may be applied to different sgRNA sequences. This middle-out technique has the potential to expedite accurate sequence confirmation of chemically modified sgRNA oligonucleotides.
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Affiliation(s)
- Steven Chin
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Alexandre Goyon
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kelly Zhang
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kenji L Kurita
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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6
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Analysis of RNA Sequences and Modifications Using NASE. Methods Mol Biol 2023; 2624:225-239. [PMID: 36723819 DOI: 10.1007/978-1-0716-2962-8_15] [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: 02/02/2023]
Abstract
Mass spectrometry is an ideal method for the discovery and characterization of modified RNAs. Unlike other traditional sequencing methods, mass spectrometry can identify and localize multiple types of modifications in tandem. One of the traditional hurdles to using this powerful technique has been a paucity of software to interpret the complicated data produced by these experiments. Here I describe how to use the NucleicAcidSearchEngine (NASE), a component of OpenMS as well as best practices for acquiring RNA data, and potential pitfalls in the analysis process.
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7
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Brégeon D, Pecqueur L, Toubdji S, Sudol C, Lombard M, Fontecave M, de Crécy-Lagard V, Motorin Y, Helm M, Hamdane D. Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification. ACS Chem Biol 2022; 17:1638-1657. [PMID: 35737906 DOI: 10.1021/acschembio.2c00307] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.
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Affiliation(s)
- Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Sabrine Toubdji
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Claudia Sudol
- IBPS, Biology of Aging and Adaptation, Sorbonne Université, Paris 75252, France
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- Genetics Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy F-54000, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy F-54000, France
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris, Cedex 05, France
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8
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Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Genes (Basel) 2022; 13:genes13061008. [PMID: 35741770 PMCID: PMC9222981 DOI: 10.3390/genes13061008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 12/10/2022] Open
Abstract
The reversible and substoichiometric modification of RNA has recently emerged as an additional layer of translational regulation in normal biological function and disease. Modifications are often enzymatically deposited in and removed from short (~5 nt) consensus motif sequences to carefully control the translational output of the cell. Although characterization of modification occupancy at consensus motifs can be accomplished using RNA sequencing methods, these approaches are generally time-consuming and do not directly detect post-transcriptional modifications. Here, we present a nuclease protection assay coupled with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to rapidly characterize modifications in consensus motifs, such as GGACU, which frequently harbor N6-methyladenosine (m6A). While conventional nuclease protection methods rely on long (~30 nt) oligonucleotide probes that preclude the global assessment of consensus motif modification stoichiometry, we investigated a series of ion-tagged oligonucleotide (ITO) probes and found that a benzylimidazolium-functionalized ITO (ABzIM-ITO) conferred significantly improved nuclease resistance for GGACU targets. After optimizing the conditions of the nuclease protection assay, we applied the ITO and MALDI-MS-based method for determining the stoichiometry of GG(m6A)CU and GGACU in RNA mixtures. Overall, the ITO-based nuclease protection and MALDI-MS method constitutes a rapid and promising approach for determining modification stoichiometries of consensus motifs.
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9
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Morreel K, t’Kindt R, Debyser G, Jonckheere S, Sandra P. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.jk3969w4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.
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10
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Vanhinsbergh CJ, Criscuolo A, Sutton JN, Murphy K, Williamson AJK, Cook K, Dickman MJ. Characterization and Sequence Mapping of Large RNA and mRNA Therapeutics Using Mass Spectrometry. Anal Chem 2022; 94:7339-7349. [PMID: 35549087 PMCID: PMC9134182 DOI: 10.1021/acs.analchem.2c00765] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Large RNA including
mRNA (mRNA) has emerged as an important new
class of therapeutics. Recently, this has been demonstrated by two
highly efficacious vaccines based on mRNA sequences encoding for a
modified version of the SARS-CoV-2 spike protein. There is currently
significant demand for the development of new and improved analytical
methods for the characterization of large RNA including mRNA therapeutics.
In this study, we have developed an automated, high-throughput workflow
for the rapid characterization and direct sequence mapping of large
RNA and mRNA therapeutics. Partial RNase digestions using RNase T1
immobilized on magnetic particles were performed in conjunction with
high-resolution liquid chromatography–mass spectrometry analysis.
Sequence mapping was performed using automated oligoribonucleotide
annotation and identifications based on MS/MS spectra. Using this
approach, a >80% sequence of coverage of a range of large RNAs
and
mRNA therapeutics including the SARS-CoV-2 spike protein was obtained
in a single analysis. The analytical workflow, including automated
sample preparation, can be completed within 90 min. The ability to
rapidly identify, characterize, and sequence map large mRNA therapeutics
with high sequence coverage provides important information for identity
testing, sequence validation, and impurity analysis.
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Affiliation(s)
| | | | | | - Keeley Murphy
- ThermoFisher Scientific, San Jose, California 95134, United States
| | | | - Ken Cook
- ThermoFisher Scientific, Hemel Hempstead, Hertfordshire HP2 7GE, U.K
| | - Mark J Dickman
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield S1 3JD, U.K
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11
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Santos IC, Lanzillotti M, Shilov I, Basanta-Sanchez M, Roushan A, Lawler R, Tang W, Bern M, Brodbelt JS. Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:510-520. [PMID: 35157441 DOI: 10.1021/jasms.1c00340] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation. Activated electron photodetachment dissociation (a-EPD) has also been used as an alternative to capitalize on the dominant charge-reduction pathway prevalent in UVPD, facilitate dissociation, and produce high abundances of fragment ions. Here, we compare higher-energy collisional activation (HCD), UVPD using 193 and 213 nm photons, and a-EPD for the top-down sequencing of modified nucleic acids, including methylated, phosphorothioate, and locked nucleic acid-modified DNA. The presence of these modifications alters the fragmentation pathways observed upon UVPD and a-EPD, and extensive backbone cleavage is observed that results in the production of fragment ions that retain the modifications and allow them to be pinpointed. LNA and 2'-O-methoxy phosphorothioate modifications caused a significant suppression of fragmentation for UVPD but not for a-EPD, whereas phosphorothioate bonds did not cause any significant suppression for either method. The incorporation of 2'-O-methyl modifications suppressed fragmentation of the antisense strand of patisiran, which resulted in some gaps in sequence coverage. However, UVPD provided the highest sequence coverage when compared to a-EPD.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ignat Shilov
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Maria Basanta-Sanchez
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Abhishek Roushan
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Rose Lawler
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Wilfred Tang
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Marshall Bern
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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12
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Goyon A, Scott B, Kurita K, Maschinot C, Meyer K, Yehl P, Zhang K. On-line Sequencing of CRISPR Guide RNAs and Their Impurities via the Use of Immobilized Ribonuclease Cartridges Attached to a 2D/3D-LC-MS System. Anal Chem 2022; 94:1169-1177. [PMID: 34932902 DOI: 10.1021/acs.analchem.1c04350] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, for the first time, the automated digestion and sequencing of an RNA molecule via the use of immobilized RNase cartridges attached to a multidimensional liquid chromatography (LC)-mass spectrometry (MS) system are presented. We first developed an on-line digestion-HILIC two-dimensional (2D)-LC-MS method in order to sequence CRISPR guide RNAs for gene editing. Three RNases (T1, A, and U2) were immobilized on polyetheretherketone cartridges, and their performance was evaluated. Ultrafast digestions were performed within 2.3 min with the on-line approach versus 30 min via the conventional off-line approach. The higher sequence coverage was achieved by the RNase T1 (71%), which is the same as the off-line mode. A 20-fold reduction in the gRNA sample amount was achieved with the on-line digestion approach (6.5 μg) in comparison to that with the off-line approach (130 μg). In the second step, a three-dimensional (3D)-LC-MS method was developed for the sequencing of fractions collected on-line across the main peak and the partially separated tail by the reference ion-pairing RPLC method. Additional insights were gained in order to better understand the cause of the main peak tailing.
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Affiliation(s)
- Alexandre Goyon
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Brandon Scott
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenji Kurita
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Chad Maschinot
- Perfinity Biosciences, 1281 Win Hentschel Boulevard, West Lafayette, Indiana 47906, United States
| | - Kevin Meyer
- Perfinity Biosciences, 1281 Win Hentschel Boulevard, West Lafayette, Indiana 47906, United States
| | - Peter Yehl
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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13
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Goyon A, Scott B, Kurita K, Crittenden CM, Shaw D, Lin A, Yehl P, Zhang K. Full Sequencing of CRISPR/Cas9 Single Guide RNA (sgRNA) via Parallel Ribonuclease Digestions and Hydrophilic Interaction Liquid Chromatography-High-Resolution Mass Spectrometry Analysis. Anal Chem 2021; 93:14792-14801. [PMID: 34699173 DOI: 10.1021/acs.analchem.1c03533] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CRISPR/Cas9 is a powerful genome editing approach in which a Cas9 enzyme and a single guide RNA (sgRNA) form a ribonucleoprotein complex effectively targeting site-specific cleavages of DNA. Accurate sequencing of sgRNA is critical to patient safety and is the expectation by regulatory agencies. In this paper, we present the full sequencing of sgRNA via parallel ribonuclease (RNase) T1, A, and U2 digestions and the simultaneous separation and identification of the digestion products by hydrophilic interaction liquid chromatography (HILIC) coupled to high-resolution mass spectrometry (HRMS). When using RNase T1 digestion alone, a maximal sequence coverage of 81% was obtained excluding the nonunique fragments. Full sgRNA sequencing was achieved using unique fragments generated by RNase T1, A, and U2 parallel digestions. Thorough optimization of sgRNA digestions was performed by varying the nuclease-to-sgRNA ratio, buffer conditions, and reaction times. A biocompatible ethylene-bridged hybrid amide column was evaluated for the separation of RNase digestion products. To our knowledge, it is the first time that (i) RNA digests are separated and identified by HILIC-HRMS and (ii) chemically modified sgRNAs are directly sequenced via a bottom-up approach.
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Affiliation(s)
- Alexandre Goyon
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
| | - Brandon Scott
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenji Kurita
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M Crittenden
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
| | - David Shaw
- Cell Therapy Engineering and Development, 1 DNA Way, South San Francisco, California 94080, United States
| | - Andy Lin
- Technical Development Project and Portfolio Management Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Yehl
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, 1 DNA Way, South San Francisco, California 94080, United States
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14
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Ramos-Morales E, Bayam E, Del-Pozo-Rodríguez J, Salinas-Giegé T, Marek M, Tilly P, Wolff P, Troesch E, Ennifar E, Drouard L, Godin JD, Romier C. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic Acids Res 2021; 49:6529-6548. [PMID: 34057470 PMCID: PMC8216470 DOI: 10.1093/nar/gkab436] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/26/2023] Open
Abstract
Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determinants. We show that tRNA binding and deamination can vary depending on the cognate tRNA but absolutely rely on the eukaryote-specific ADAT3 N-terminal domain. This domain can rotate with respect to the ADAT catalytic domain to present and position the tRNA anticodon-stem-loop correctly in ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, which causes intellectual disability, does not affect tRNA binding despite the structural changes it induces but most likely hinders optimal presentation of the tRNA anticodon-stem-loop to ADAT2.
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Affiliation(s)
- Elizabeth Ramos-Morales
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Efil Bayam
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Jordi Del-Pozo-Rodríguez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Martin Marek
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Peggy Tilly
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Edouard Troesch
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Juliette D Godin
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Christophe Romier
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
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15
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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16
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Yan TM, Pan Y, Yu ML, Hu K, Cao KY, Jiang ZH. Full-Range Profiling of tRNA Modifications Using LC-MS/MS at Single-Base Resolution through a Site-Specific Cleavage Strategy. Anal Chem 2021; 93:1423-1432. [PMID: 33382261 DOI: 10.1021/acs.analchem.0c03307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transfer RNAs (tRNAs) are the most heavily modified RNA species. Liquid chromatography coupled with mass spectrometry (LC-MS/MS) is a powerful tool for characterizing tRNA modifications, which involves pretreating tRNAs with base-specific ribonucleases to produce smaller oligonucleotides amenable to MS. However, the quality and quantity of products from base-specific digestions are severely impacted by the base composition of tRNAs. This often leads to a loss of sequence information. Here, we report a method for the full-range profiling of tRNA modifications at single-base resolution by combining site-specific RNase H digestion with the LC-MS/MS and RNA-seq techniques. The key steps were designed to generate high-quality products of optimal lengths and ionization properties. A linear correlation between collision energies and the m/z of oligonucleotides significantly improved the information content of collision-induced dissociation (CID) spectra. False positives were eliminated by up to 95% using novel inclusion criteria for collecting a census of modifications. This method is illustrated by the mapping of mouse mitochondrial tRNAHis(GUG) and tRNAVal(UAC), which were hitherto not investigated. The identities and locations of the five species of modifications on these tRNAs were fully characterized. This approach is universally applicable to any tRNA species and provides an experimentally realizable pathway to the de novo sequencing of post-transcriptionally modified tRNAs with high sequence coverage.
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Affiliation(s)
- Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yu Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Meng-Lan Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Kua Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Kai-Yue Cao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
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17
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Sun C, Limbach PA, Addepalli B. Characterization of UVA-Induced Alterations to Transfer RNA Sequences. Biomolecules 2020; 10:E1527. [PMID: 33171700 PMCID: PMC7695249 DOI: 10.3390/biom10111527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its modified version, suggesting an auxiliary role for nucleoside modifications. The type of oxidation product formed in the anticodon stem-loop region varied with the modification type, status, and whether the tRNA was inside or outside the cell during exposure. Oligonucleotide-based characterization of tRNA following UVA exposure also revealed the presence of novel photoproducts and stable intermediates not observed by nucleoside analysis alone. This approach provides sequence-specific information revealing potential hotspots for UVA-induced damage in tRNAs.
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Affiliation(s)
| | | | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA; (C.S.); (P.A.L.)
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18
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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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19
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Herkt M, Foinquinos A, Batkai S, Thum T, Pich A. Pharmacokinetic Studies of Antisense Oligonucleotides Using MALDI-TOF Mass Spectrometry. Front Pharmacol 2020; 11:220. [PMID: 32269522 PMCID: PMC7109322 DOI: 10.3389/fphar.2020.00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/18/2020] [Indexed: 11/21/2022] Open
Abstract
Cardiac diseases are the most frequent causes of death in industrialized countries. Pathological remodeling of the heart muscle is caused by several etiologies such as prolonged hypertension or injuries that can lead to myocardial infarction and in serious cases also the death of the patient. The micro-RNA miR-132 has been identified as a master-switch in the development of cardiac hypertrophy and adverse remodeling. In this study, MALDI-TOF mass spectrometry (MS) was utilized to establish a robust and fast method to sensitively detect and accurately quantify anti-microRNA (antimiR) oligonucleotides in blood plasma. An antimiR oligonucleotide isolation protocol containing an ethanol precipitation step with glycogen as oligonucleotide carrier as well as a robust and reproducible MS-analysis procedure has been established. Proteinase K treatment was crucial for releasing antimiR oligonucleotides from plasma- as well as cellular proteins and reducing background derived from biological matrices. AntimiR oligonucleotide detection was achieved from samples of studies in different animal models such as mouse and pig where locked nucleic acids-(LNA)-modified antimiR oligonucleotides have been used to generate pharmacokinetic data.
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Affiliation(s)
- Markus Herkt
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Ariana Foinquinos
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Sandor Batkai
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Thomas Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies, Hanover, Germany
| | - Andreas Pich
- Hannover Medical School, Institute for Toxicology - Core Unit Proteomics, Hanover, Germany
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20
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Thakur P, Estevez M, Lobue PA, Limbach PA, Addepalli B. Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases. Analyst 2020; 145:816-827. [PMID: 31825413 PMCID: PMC7002195 DOI: 10.1039/c9an02111f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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21
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tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii. J Bacteriol 2019; 201:JB.00690-18. [PMID: 30745370 DOI: 10.1128/jb.00690-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies.IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.
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22
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Solivio B, Yu N, Addepalli B, Limbach PA. Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant. Anal Chim Acta 2018; 1036:73-79. [PMID: 30253839 PMCID: PMC6214470 DOI: 10.1016/j.aca.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 11/21/2022]
Abstract
We report the identification and use of a mutant of the purine selective ribonuclease RNase U2 that randomly cleaves RNA in a manner that is directly compatible with RNA modification mapping by mass spectrometry. A number of RNase U2 mutants were generated using site-saturation mutagenesis. The enzyme activity and specificity were tested using oligonucleotide substrates, which revealed an RNase U2 E49A mutant with limited specificity and a tendency to undercut RNA. Using this mutant, RNA digestion conditions were optimized to yield long, overlapping digestion products, which improve sequence coverage in RNA modification mapping experiments. The analytical utility of this mutant was demonstrated by liquid chromatography tandem mass spectrometry (LC-MS/MS) mapping of several modified RNAs where 100% sequence coverage could be obtained using only a single enzymatic digestion. This new mutant facilitates more accurate and efficient RNA modification mapping than traditional highly base-specific RNases that are currently used.
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Affiliation(s)
- Beulah Solivio
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States.
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23
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Nwokeoji AO, Earll ME, Kilby PM, Portwood DE, Dickman MJ. High resolution fingerprinting of single and double-stranded RNA using ion-pair reverse-phase chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1104:212-219. [PMID: 30530113 PMCID: PMC6329874 DOI: 10.1016/j.jchromb.2018.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
Abstract
The emergence of new sustainable approaches for insect management using RNA interference (RNAi) based insecticides has created the demand for high throughput analytical techniques to fully characterise and accurately quantify double stranded RNA (dsRNA) prior to downstream RNAi applications. In this study we have developed a method for the rapid characterisation of single stranded and double stranded RNA using high resolution RNase mapping in conjunction with ion-pair reverse-phase chromatography utilising a column with superficially porous particles. The high resolution oligoribonucleotide map provides an important 'fingerprint' for identity testing and bioprocess monitoring. Reproducible RNA mapping chromatograms were generated from replicate analyses. Moreover, this approach was used to provide a method to rapidly distinguish different RNA sequences of the same size, based on differences in the resulting chromatograms. Principal components analysis of the high resolution RNA mapping data enabled us to rapidly compare multiple HPLC chromatograms and distinguish two dsRNA sequences of different size which share 72% sequence homology. We used the high resolution RNase mapping method to rapidly fingerprint biomanufactured dsRNA across a number of different batches. The resulting chromatograms in conjunction with principal components analysis demonstrated high similarity in the dsRNA produced across the different batches highlighting the potential ability of this method to provide information for batch release in a high throughput manner.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK
| | - Mark E Earll
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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24
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Kung AW, Kilby PM, Portwood DE, Dickman MJ. Quantification of dsRNA using stable isotope labeling dilution liquid chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:590-596. [PMID: 29397006 DOI: 10.1002/rcm.8074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 06/07/2023]
Abstract
RATIONALE Recent developments in RNA interference (RNAi) have created a need for cost-effective and large-scale synthesis of double-stranded RNA (dsRNA), in conjunction with high-throughput analytical techniques to fully characterise and accurately quantify dsRNA prior to downstream RNAi applications. METHODS Stable isotope labeled dsRNA was synthesised both in vivo (15 N) and in vitro (13 C,15 N-guanosine-containing dsRNA) prior to purification and quantification. The stable isotope labeled dsRNA standards were subsequently spiked into total RNA extracted from E. coli engineered to express dsRNA. RNase mass mapping approaches were subsequently performed using liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS) for both the identification and absolute quantification of the dsRNA using the ratios of the light and heavy oligonucleotide pairs. RESULTS Absolute quantification was performed based on the resulting light and heavy oligoribonucleotides identified using MS. Using this approach we determined that 624.6 ng/μL and 466.5 ng/μL of dsRNA was present in 80 μL total RNA extracted from 108 E. coli cells expressing 765 bp and 401 bp dsRNAs, respectively. CONCLUSIONS Stable isotope labeling of dsRNA in conjunction with MS enabled the characterisation and quantification of dsRNA in complex total RNA mixtures.
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Affiliation(s)
- An-Wen Kung
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, Sheffield, S1 3JD, UK
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, Sheffield, S1 3JD, UK
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25
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Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017; 9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.
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Affiliation(s)
- Mónica Marín
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Tamara Fernández-Calero
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Ricardo Ehrlich
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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Borland K, Limbach PA. Applications and Advantages of Stable Isotope Phosphate Labeling of RNA in Mass Spectrometry. Top Curr Chem (Cham) 2017; 375:33. [DOI: 10.1007/s41061-017-0121-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/17/2017] [Indexed: 01/17/2023]
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Paulines MJ, Limbach PA. Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:551-561. [PMID: 28105550 DOI: 10.1007/s13361-017-1593-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Even with the advent of high throughput methods to detect modified ribonucleic acids (RNAs), mass spectrometry remains a reliable method to detect, characterize, and place post-transcriptional modifications within an RNA sequence. Here we have developed a stable isotope labeling comparative analysis of RNA digests (SIL-CARD) approach, which improves upon the original 18O/16O labeling CARD method. Like the original, SIL-CARD allows sequence or modification information from a previously uncharacterized in vivo RNA sample to be obtained by direct comparison with a reference RNA, the sequence of which is known. This reference is in vitro transcribed using a 13C/15N isotopically enriched nucleoside triphosphate (NTP). The two RNAs are digested with an endonuclease, the specificity of which matches the labeled NTP used for transcription. As proof of concept, several transfer RNAs (tRNAs) were characterized by SIL-CARD, where labeled guanosine triphosphate was used for the reference in vitro transcription. RNase T1 digestion products from the in vitro transcript will be 15 Da higher in mass than the same digestion products from the in vivo tRNA that are unmodified, leading to a doublet in the mass spectrum. Singlets, rather than doublets, arise if a sequence variation or a post-transcriptional modification is present that results in a relative mass shift different from 15 Da. Moreover, the use of the in vitro synthesized tRNA transcript allows for quantitative measurement of RNA abundance. Overall, SIL-CARD simplifies data analysis and enhances quantitative RNA modification mapping by mass spectrometry. Graphical Abstract ᅟ.
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Affiliation(s)
- Mellie June Paulines
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, USA.
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Abstract
We describe the comparative analysis of ribonucleic acid digests (CARD) approach for RNA modification analysis. This approach employs isotope labeling during RNase digestion, which allows the direct comparison of a tRNA of unknown modification status against a reference tRNA, whose sequence or modification status is known. The reference sample is labeled with 18O during RNase digestion while the candidate (unknown) sample is labeled with 16O. These RNase digestion products are combined and analyzed by mass spectrometry. Identical RNase digestion products will appear in the mass spectrum as characteristic doublets, separated by 2 Da due to the 16O/18O mass difference. Singlets arise in the mass spectrum when the sequence or modification status of a particular RNase digestion product from the reference is not matched in the candidate (unknown) sample. This CARD approach for RNA modification analysis simplifies the determination of differences between reference and candidate samples, providing a route for higher throughput screening of samples for modification profiles, including determination of tRNA methylation patterns.
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30
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Abstract
tRNAs are fundamental components of translation and emerging evidence places them more centrally in various other cellular processes. However, rather than being uniformly conserved, tRNA abundance is instead highly variable and adaptable. The amount of tRNA genes greatly differs among species. Moreover, even within the same genome, tRNA abundance shapes the proteome in a tissue- and cell-specific manner and is dynamically regulated in response to stress. Here, we review approaches for identification and quantification of tRNAs and their functional integrity. We discuss the resolution of each method and highlight new approaches with cell-wide resolution based on deep-sequencing technologies.
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Addepalli B, Limbach PA. Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF. J Biol Chem 2016; 291:22327-22337. [PMID: 27551044 DOI: 10.1074/jbc.m116.747865] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Indexed: 02/02/2023] Open
Abstract
Pseudouridine is found in almost all cellular ribonucleic acids (RNAs). Of the multiple characteristics attributed to pseudouridine, making messenger RNAs (mRNAs) highly translatable and non-immunogenic is one such feature that directly implicates this modification in protein synthesis. We report the existence of pseudouridine in the anticodon of Escherichia coli tyrosine transfer RNAs (tRNAs) at position 35. Pseudouridine was verified by multiple detection methods, which include pseudouridine-specific chemical derivatization and gas phase dissociation of RNA during liquid chromatography tandem mass spectrometry (LC-MS/MS). Analysis of total tRNA isolated from E. coli pseudouridine synthase knock-out mutants identified RluF as the enzyme responsible for this modification. Furthermore, the absence of this modification compromises the translational ability of a luciferase reporter gene coding sequence when it is preceded by multiple tyrosine codons. This effect has implications for the translation of mRNAs that are rich in tyrosine codons in bacterial expression systems.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Patrick A Limbach
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
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32
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Gaston KW, Limbach PA. The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. RNA Biol 2015; 11:1568-85. [PMID: 25616408 PMCID: PMC4615682 DOI: 10.4161/15476286.2014.992280] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.
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Affiliation(s)
- Kirk W Gaston
- a Rieveschl Laboratories for Mass Spectrometry; Department of Chemistry ; University of Cincinnati ; Cincinnati , OH USA
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33
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Cao X, Limbach PA. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem 2015; 87:8433-40. [PMID: 26176336 PMCID: PMC4542202 DOI: 10.1021/acs.analchem.5b01826] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
There
has been a renewed appreciation for the dynamic nature of
ribonucleic acid (RNA) modifications and for the impact of modified
RNAs on organism health resulting in an increased emphasis on developing
analytical methods capable of detecting modifications within specific
RNA sequence contexts. Here we demonstrate that a DNA-based exclusion
list enhances data dependent liquid chromatography tandem mass spectrometry
(LC-MS/MS) detection of post-transcriptionally modified nucleosides
within specific RNA sequences. This approach is possible because all
post-transcriptional modifications of RNA, except pseudouridine, result
in a mass increase in the canonical nucleoside undergoing chemical
modification. Thus, DNA-based sequences reflect the state of the RNA
prior to or in the absence of modification. The utility of this exclusion
list strategy is demonstrated through the RNA modification mapping
of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently
enhance the number of detected modified ribonuclease (RNase) digestion
products by ∼20%. All modified RNase digestion products that
were detected during standard data dependent acquisition (DDA) LC-MS/MS
were also detected when the DNA-based exclusion list was used. Consequently,
the increase in detected modified RNase digestion products is attributed
to new experimental information only obtained when using the exclusion
list. This exclusion list strategy should be broadly applicable to
any class of RNA and improves the utility of mass spectrometry approaches
for discovery-based analyses of RNA modifications, such as are required
for studies of the epitranscriptome.
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Affiliation(s)
- Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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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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Houser WM, Butterer A, Addepalli B, Limbach PA. Combining recombinant ribonuclease U2 and protein phosphatase for RNA modification mapping by liquid chromatography–mass spectrometry. Anal Biochem 2015; 478:52-8. [DOI: 10.1016/j.ab.2015.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/21/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
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36
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Li MM, Addepalli B, Tu MJ, Chen QX, Wang WP, Limbach PA, LaSalle JM, Zeng S, Huang M, Yu AM. Chimeric MicroRNA-1291 Biosynthesized Efficiently in Escherichia coli Is Effective to Reduce Target Gene Expression in Human Carcinoma Cells and Improve Chemosensitivity. Drug Metab Dispos 2015; 43:1129-36. [PMID: 25934574 DOI: 10.1124/dmd.115.064493] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/29/2015] [Indexed: 01/19/2023] Open
Abstract
In contrast to the growing interests in studying noncoding RNAs (ncRNAs) such as microRNA (miRNA or miR) pharmacoepigenetics, there is a lack of efficient means to cost effectively produce large quantities of natural miRNA agents. Our recent efforts led to a successful production of chimeric pre-miR-27b in bacteria using a transfer RNA (tRNA)-based recombinant RNA technology, but at very low expression levels. Herein, we present a high-yield expression of chimeric pre-miR-1291 in common Escherichia coli strains using the same tRNA scaffold. The tRNA fusion pre-miR-1291 (tRNA/mir-1291) was then purified to high homogeneity using affinity chromatography, whose primary sequence and post-transcriptional modifications were directly characterized by mass spectrometric analyses. Chimeric tRNA/mir-1291 was readily processed to mature miR-1291 in human carcinoma MCF-7 and PANC-1 cells. Consequently, recombinant tRNA/mir-1291 reduced the protein levels of miR-1291 target genes, including ABCC1, FOXA2, and MeCP2, as compared with cells transfected with the same doses of control methionyl-tRNA scaffold with a sephadex aptamer (tRNA/MSA). In addition, tRNA-carried pre-miR-1291 suppressed the growth of MCF-7 and PANC-1 cells in a dose-dependent manner, and significantly enhanced the sensitivity of ABCC1-overexpressing PANC-1 cells to doxorubicin. These results indicate that recombinant miR-1291 agent is effective in the modulation of target gene expression and chemosensitivity, which may provide insights into high-yield bioengineering of new ncRNA agents for pharmacoepigenetics research.
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Affiliation(s)
- Mei-Mei Li
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Balasubrahmanyam Addepalli
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Qiu-Xia Chen
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Wei-Peng Wang
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Patrick A Limbach
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Janine M LaSalle
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Su Zeng
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Min Huang
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
| | - Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, University of California-Davis School of Medicine, Sacramento, California (M.-M.L., M.-J.T., Q.-X.C., W.-P.W., A.-M.Y.); Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China (M.-M.L, M.H.); Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio (B.A., P.A.L.); Laboratory of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China (Q.-X.C., S.Z.); and Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, California (J.M.L.)
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, Cordero Varela JA, van der Vlies P, Zhang G, Limbach PA, Ignatova Z, Poolman B. Systematic identification of tRNAome and its dynamics in Lactococcus lactis. Mol Microbiol 2014; 93:944-56. [PMID: 25040919 DOI: 10.1111/mmi.12710] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2014] [Indexed: 01/29/2023]
Abstract
Transfer RNAs (tRNAs) through their abundance and modification pattern significantly influence protein translation. Here, we present a systematic analysis of the tRNAome of Lactococcus lactis. Using the next-generation sequencing approach, we identified 40 tRNAs which carry 16 different post-transcriptional modifications as revealed by mass spectrometry analysis. While small modifications are located in the tRNA body, hypermodified nucleotides are mainly present in the anticodon loop, which through wobbling expand the decoding potential of the tRNAs. Using tRNA-based microarrays, we also determined the dynamics in tRNA abundance upon changes in the growth rate and heterologous protein overexpression stress. With a fourfold increase in the growth rate, the relative abundance of tRNAs cognate to low abundance codons decrease, while the tRNAs cognate to major codons remain mostly unchanged. Significant changes in the tRNA abundances are observed upon protein overexpression stress, which does not correlate with the codon usage of the overexpressed gene but rather reflects the altered expression of housekeeping genes.
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Affiliation(s)
- Pranav Puri
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Wetzel C, Li S, Limbach PA. Metabolic de-isotoping for improved LC-MS characterization of modified RNAs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1114-1123. [PMID: 24760295 DOI: 10.1007/s13361-014-0889-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/15/2014] [Accepted: 03/17/2014] [Indexed: 06/03/2023]
Abstract
Mapping, sequencing, and quantifying individual noncoding ribonucleic acids (ncRNAs), including post-transcriptionally modified nucleosides, by mass spectrometry is a challenge that often requires rigorous sample preparation prior to analysis. Previously, we have described a simplified method for the comparative analysis of RNA digests (CARD) that is applicable to relatively complex mixtures of ncRNAs. In the CARD approach for transfer RNA (tRNA) analysis, two complete sets of digestion products from total tRNA are compared using the enzymatic incorporation of (16)O/(18)O isotopic labels. This approach allows one to rapidly screen total tRNAs from gene deletion mutants or comparatively sequence total tRNA from two related bacterial organisms. However, data analysis can be challenging because of convoluted mass spectra arising from the natural (13)C and (15) N isotopes present in the ribonuclease-digested tRNA samples. Here, we demonstrate that culturing in (12)C-enriched/(13)C-depleted media significantly reduces the isotope patterns that must be interpreted during the CARD experiment. Improvements in data quality yield a 35 % improvement in detection of tRNA digestion products that can be uniquely assigned to particular tRNAs. These mass spectral improvements lead to a significant reduction in data processing attributable to the ease of spectral identification of labeled digestion products and will enable improvements in the relative quantification of modified RNAs by the (16)O/(18)O differential labeling approach.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221-0172, USA
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Wetzel C, Limbach PA. The global identification of tRNA isoacceptors by targeted tandem mass spectrometry. Analyst 2013; 138:6063-72. [DOI: 10.1039/c3an01224g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Gao X, Sugrue RJ, Tan BH, Tang K. Screening of influenza mutations using base-specific cleavage and MALDI mass spectrometry. Clin Chim Acta 2012; 420:89-93. [PMID: 23078853 DOI: 10.1016/j.cca.2012.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/09/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND The hemagglutinin (HA) and neuraminidase (NA) genes encode surface glycoproteins of influenza virus. These two proteins are involved in pathogenicity and are the primary targets of the immune system. Mutations in the HA and NA genes can result in antigenic drift in an influenza viral strain. A comparative sequencing method using MALDI MS combined with base-specific cleavage has been applied for the surveillance of these viral mutations. This approach shows advantages in high throughput and efficiency than the traditional direct sequencing methods in targeted sequence analysis. METHODS Base-specific cleavage assay with RNAse A was combined with MALDI-MS for the analysis of the HA and NA genes of 2 influenza viral strains. The mass peak patterns from the spectra were compared with the in silico digest result of reference gene sequences from the database to achieve comparative sequencing and screening of novel mutations. RESULTS The HA and NA genes of two influenza lab strains were comparatively sequenced using the base-specific cleavage and MALDI-MS approach. Mutations could be exactly identified if more than one observation (mass peak changes) were detected in the spectrum. Mutations with only one observation could be located in a small area for further validation. CONCLUSIONS We showed a proof of a principle that base-specific combined with MALDI-MS comparative sequencing approach can be utilized for targeted sequence analysis and potentially rapid and cost effective screening of emerging viral mutations.
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Affiliation(s)
- Xiang Gao
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Abstract
A method of analysis is presented that utilizes matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to monitor the kinetics and products of RNA cleavage, by use of a program designed to mass-match observed MS peaks with predicted RNA cleavage products. The method is illustrated through application to the study of targeted oxidation of RNA stem loops from HIV-1 Rev Response Element mRNA (RRE RNA) and ribosomal 16S A-site RNA (16S RNA) by metallonucleases. Following incubation of each RNA with catalysts and/or redox co-reactants, reaction mixtures were desalted, and MALDI-TOF MS was used to monitor both time-resolved formation of cleavage products and disappearance of full-length RNA. For each RNA, a unique list was generated that contained the predicted masses of both the full-length, and all of the possible RNA cleavage fragments that resulted from the combination of all possible cleavage sites and each of the six expected overhangs formed at nascent termini adjacent to the cleavage sites. The overhangs corresponded to 2′,3′-cyclic phosphate, 3′-phosphate, 3′-phosphoglycolate, 5′- hydroxyl and 5′- phosphate, which corresponded to differing oxidative, hydrolytic, and/or 2′-OH-mediated-endonucleolytic modes of scission. Each mass spectrum was compared with a corresponding list of predicted masses, and peaks were rapidly assigned by use of a Perl script, with a mass-matching tolerance of 200 ppm. Both time-dependent cleavage mediated by metallonucleases and MALDI-TOF-induced fragmentation were observed, and these were distinguished by time-dependent experiments. The resulting data allowed a semi-quantitative assessment of the rate of formation of each overhang at each nucleotide position. Limitations included artifactual skewing of quantification by mass bias, a limited mass range for quantification, and a lack of detection of secondary cleavage products. Nevertheless, the method presented herein provides a rapid, accurate, highly-detailed and semi-quantitative analysis of RNA cleavage that should be widely applicable.
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Affiliation(s)
- Jeff C Joyner
- Department of Chemistry and Biochemistry, Evans Laboratory of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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Global identification of transfer RNAs by liquid chromatography–mass spectrometry (LC–MS). J Proteomics 2012; 75:3450-64. [DOI: 10.1016/j.jprot.2011.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 09/18/2011] [Accepted: 09/21/2011] [Indexed: 11/17/2022]
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Izumi Y, Takimura S, Yamaguchi S, Iida J, Bamba T, Fukusaki E. Application of electrospray ionization ion trap/time-of-flight mass spectrometry for chemically-synthesized small RNAs. J Biosci Bioeng 2012; 113:412-9. [DOI: 10.1016/j.jbiosc.2011.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/06/2011] [Accepted: 11/08/2011] [Indexed: 12/13/2022]
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Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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Nakayama H, Takahashi N, Isobe T. Informatics for mass spectrometry-based RNA analysis. MASS SPECTROMETRY REVIEWS 2011; 30:1000-1012. [PMID: 21328601 DOI: 10.1002/mas.20325] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 07/01/2010] [Accepted: 07/01/2010] [Indexed: 05/30/2023]
Abstract
Mass spectrometry (MS) allows the sensitive and direct characterization of biological macromolecules and therefore has the potential to complement the more conventional genetic and biochemical methods used for RNA characterization. Although MS has been used much less frequently for RNA research than it has been for protein research, recent technical improvements in both instrumentation and software make MS a powerful tool for RNA analysis because it can now be used to sequence, quantify, and chemically analyze RNAs. Mass spectrometry is particularly well suited for the characterization of RNAs associated with ribonucleoprotein complexes. This review focuses on the software and databases that can be used for MS-based RNA studies. Software for the processing of raw mass spectra, the identification and characterization of RNAs by mass mapping, de novo sequencing, and tandem MS-based database searching are available.
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Affiliation(s)
- Hiroshi Nakayama
- Biomolecular Characterization Team, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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McGinnis AC, Chen B, Bartlett MG. Chromatographic methods for the determination of therapeutic oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 883-884:76-94. [PMID: 21945211 DOI: 10.1016/j.jchromb.2011.09.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/31/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Both DNA and RNA are being explored for their therapeutic potential against a wide range of diseases. As these new drugs emerge, new demands arise for the analysis and quantitation of these biomolecules. Pharmacokinetic and pharmacodynamic analysis requirements for drug approval place enormous challenges on the methods for analyzing these therapeutics. This review will focus on bioanalytical methods for DNA antisense and aptamers as well as small-interfering RNA (siRNA) therapeutics. Chromatography methods employing ultraviolet (UV), fluorescence and mass spectrometric (MS) detection along with matrix-assisted laser desorption/ionization (MALDI) will be covered. Sample preparation from biological matrices will be reviewed as well as metabolite analysis and identification. All of these techniques are important contributions toward oligonucleotide therapeutic development. They will also be important in microRNA (miRNA) biomarker discovery and RNomics in general, as more non-coding RNAs are inevitably discovered.
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Affiliation(s)
- A Cary McGinnis
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
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Taucher M, Ganisl B, Breuker K. Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:91-97. [PMID: 21960742 PMCID: PMC3180913 DOI: 10.1016/j.ijms.2010.05.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The constitutional isomers uridine (U) and pseudouridine (Ψ) cannot be distinguished from each other by simple mass measurements of RNA or its fragments because the conversion of U into Ψ is a "mass-silent" post-transcriptional modification. Here we propose a new mass spectrometry based method for identification, localization, and relative quantitation of Ψ in RNA consisting of ∼20 nucleotides that does not require chemical labeling. Our approach takes advantage of the different fragmentation behavior of uridine (N-glycosidic bond) and pseudouridine (C-glycosidic bond) residues in RNA upon collisionally activated dissociation.
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Affiliation(s)
| | | | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Sharma VK, Vouros P, Glick J. Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 304:172-183. [PMID: 21765648 PMCID: PMC3134299 DOI: 10.1016/j.ijms.2010.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the past decade, cell free DNA, or circulating cell free DNA, or cell free circulating DNA, isolated from body fluids such as plasma/serum/urine has emerged as an important tool for clinical diagnostics. The molecular biology of circulating cell free DNA is poorly understood but there is currently an increased effort to understand the origin, mechanism of its circulation, and sensitive characterization for the development of diagnostic applications. There has been considerable progress towards these goals using real time polymerase chain reaction technique (rt-PCR). More recently, new attempts to incorporate mass spectrometric techniques to develop accurate and highly sensitive high-throughput clinical diagnostic tests have been reported. This review focuses on the methods to isolate circulating cell free DNA from body fluids, their quantitative analysis and mass spectrometry based characterization in evolving applications as prenatal and cancer diagnostic tools.
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Affiliation(s)
- Vaneet K Sharma
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, Massachusetts 02115
| | - Paul Vouros
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, Massachusetts 02115
| | - James Glick
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, Massachusetts 02115
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