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Herbert C, Valesyan S, Kist J, Limbach PA. Analysis of RNA and Its Modifications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:47-68. [PMID: 38594935 DOI: 10.1146/annurev-anchem-061622-125954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Ribonucleic acids (RNAs) are key biomolecules responsible for the transmission of genetic information, the synthesis of proteins, and modulation of many biochemical processes. They are also often the key components of viruses. Synthetic RNAs or oligoribonucleotides are becoming more widely used as therapeutics. In many cases, RNAs will be chemically modified, either naturally via enzymatic systems within a cell or intentionally during their synthesis. Analytical methods to detect, sequence, identify, and quantify RNA and its modifications have demands that far exceed requirements found in the DNA realm. Two complementary platforms have demonstrated their value and utility for the characterization of RNA and its modifications: mass spectrometry and next-generation sequencing. This review highlights recent advances in both platforms, examines their relative strengths and weaknesses, and explores some alternative approaches that lie at the horizon.
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Affiliation(s)
- Cassandra Herbert
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Jennifer Kist
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
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2
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Baek A, Rayhan A, Lee GE, Golconda S, Yu H, Kim S, Limbach PA, Addepalli B, Kim S. Mapping m 6A Sites on HIV-1 RNA Using Oligonucleotide LC-MS/MS. Methods Protoc 2024; 7:7. [PMID: 38251200 PMCID: PMC10801558 DOI: 10.3390/mps7010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC-MS/MS). LC-MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m6A) modifications. In our initial trial, we used target-specific DNA probes only and encountered insufficient RNA fragmentation due to inefficient S1 digestion near the target site. Recognizing that inefficient S1 digestion by HIV-1 RNA is likely due to the formation of secondary structures in proximity to the target site, we designed multiple DNA probes annealing to various sites of HIV-1 RNA to better control the structures of RNA substrates for S1 digestion. The use of these non-target DNA probes significantly improved the isolation of more homogeneous target RNA fragments of approximately 50 bases in length. Oligonucleotide LC-MS/MS analysis of these isolated target RNA fragments successfully separated and detected both m6A-methylated and non-methylated oligomers at the two m6A-predicted sites. The principle of this new target enrichment strategy holds promise and should be broadly applicable to the analysis of any lengthy RNA that was previously deemed infeasible for investigation using oligonucleotide LC-MS/MS.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Ga-Eun Lee
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Sarah Golconda
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah Yu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Sanggu Kim
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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3
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Jones JD, Simcox KM, Kennedy RT, Koutmou KS. Direct sequencing of total Saccharomyces cerevisiae tRNAs by LC-MS/MS. RNA (NEW YORK, N.Y.) 2023; 29:1201-1214. [PMID: 37169396 PMCID: PMC10351886 DOI: 10.1261/rna.079656.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/23/2023] [Indexed: 05/13/2023]
Abstract
Among RNAs, transfer RNAs (tRNAs) contain the widest variety of abundant posttranscriptional chemical modifications. These modifications are crucial for tRNAs to participate in protein synthesis, promoting proper tRNA structure and aminoacylation, facilitating anticodon:codon recognition, and ensuring the reading frame maintenance of the ribosome. While tRNA modifications were long thought to be stoichiometric, it is becoming increasingly apparent that these modifications can change dynamically in response to the cellular environment. The ability to broadly characterize the fluctuating tRNA modification landscape will be essential for establishing the molecular level contributions of individual sites of tRNA modification. The locations of modifications within individual tRNA sequences can be mapped using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). In this approach, a single tRNA species is purified, treated with ribonucleases, and the resulting single-stranded RNA products are subject to LC-MS/MS analysis. The application of LC-MS/MS to study tRNAs is limited by the necessity of analyzing one tRNA at a time, because the digestion of total tRNA mixtures by commercially available ribonucleases produces many short digestion products unable to be uniquely mapped back to a single site within a tRNA. We overcame these limitations by taking advantage of the highly structured nature of tRNAs to prevent the full digestion by single-stranded RNA-specific ribonucleases. Folding total tRNA prior to digestion allowed us to sequence Saccharomyces cerevisiae tRNAs with up to 97% sequence coverage for individual tRNA species by LC-MS/MS. This method presents a robust avenue for directly detecting the distribution of modifications in total tRNAs.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kaley M Simcox
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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4
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Jones JD, Grassmyer KT, Kennedy RT, Koutmou KS, Maloney TD. Nuclease P1 Digestion for Bottom-Up RNA Sequencing of Modified siRNA Therapeutics. Anal Chem 2023; 95:4404-4411. [PMID: 36812429 DOI: 10.1021/acs.analchem.2c04902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
siRNA therapeutics provide a selective and powerful approach to reduce the expression of disease-causing genes. For regulatory approval, these modalities require sequence confirmation which is typically achieved by intact tandem mass spectrometry sequencing. However, this process produces highly complex spectra which are difficult to interpret and typically results in less than full sequence coverage. We sought to develop a bottom-up siRNA sequencing platform to ease sequencing data analysis and provide full sequence coverage. Analogous to bottom-up proteomics, this process requires chemical or enzymatic digestion to reduce the oligonucleotide length down to analyzable lengths, but siRNAs commonly contain modifications that inhibit the degradation process. We tested six digestion schemes for their feasibility to digest the 2' modified siRNAs and identified that nuclease P1 provides an effective digestion workflow. Using a partial digestion, nuclease P1 provides high 5' and 3' end sequence coverage with multiple overlapping digestion products. Additionally, this enzyme provides high-quality and highly reproducible RNA sequencing no matter the RNA phosphorothioate content, 2'-fluorination status, sequence, or length. Overall, we developed a robust enzymatic digestion scheme for bottom-up siRNA sequencing using nuclease P1, which can be implemented into existing sequence confirmation workflows.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States.,Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Kathleen T Grassmyer
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States
| | - Todd D Maloney
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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Wolf EJ, Grünberg S, Dai N, Chen TH, Roy B, Yigit E, Corrêa I. Human RNase 4 improves mRNA sequence characterization by LC–MS/MS. Nucleic Acids Res 2022; 50:e106. [PMID: 35871301 PMCID: PMC9561288 DOI: 10.1093/nar/gkac632] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography–mass spectrometry (LC–MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a larger population of uniquely mappable cleavage products. We deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine–two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5′ cap incorporation into in vitro transcribed mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC–MS/MS.
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Affiliation(s)
- Eric J Wolf
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | | | - Nan Dai
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Tien-Hao Chen
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Bijoyita Roy
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Erbay Yigit
- New England Biolabs, Inc, 43/44 Dunham Ridge, Beverly, MA 01915, USA
| | - Ivan R Corrêa
- To whom correspondence should be addressed. Tel: +1 978 380 7504;
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Thakur P, Atway J, Limbach PA, Addepalli B. RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site. Int J Mol Sci 2022; 23:7021. [PMID: 35806025 PMCID: PMC9266746 DOI: 10.3390/ijms23137021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/05/2023] Open
Abstract
Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5-1% cleavage levels for a given dinucleotide sequence combination. While RNase MC1 efficiently cleaved the [A/U/C]pU dinucleotide bond, no cleavage was observed for the GpU bond. Similarly, cusativin efficiently cleaved Cp[U/A/G] dinucleotide combinations along with UpA and [A/U]pU, suggesting a broader specificity of dinucleotide preferences. The molecular interactions between the substrate and active site as determined by the dinucleotide docking studies of protein models offered additional evidence and support for the observed substrate specificity. Targeted alteration of the key amino acid residues in the nucleotide-binding site confirms the utility of this in silico approach for the identification of key interactions. Taken together, the use of bioanalytical and computational approaches, involving LC-MS and ligand docking of tertiary structural models, can form a powerful combination to help explain the RNA cleavage behavior of RNases.
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Affiliation(s)
| | | | | | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (P.T.); (J.A.); (P.A.L.)
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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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Huang G, Ding Q, Xie D, Cai Z, Zhao Z. Technical challenges in defining RNA modifications. Semin Cell Dev Biol 2021; 127:155-165. [PMID: 34838434 DOI: 10.1016/j.semcdb.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.
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Affiliation(s)
- Gefei Huang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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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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Grünberg S, Wolf EJ, Jin J, Ganatra MB, Becker K, Ruse C, Taron CH, Corrêa IR, Yigit E. Enhanced expression and purification of nucleotide-specific ribonucleases MC1 and Cusativin. Protein Expr Purif 2021; 190:105987. [PMID: 34637916 DOI: 10.1016/j.pep.2021.105987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Combinations of ribonucleases (RNases) are commonly used to digest RNA into oligoribonucleotide fragments prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The distribution of the RNase target sequences or nucleobase sites within an RNA molecule is critical for achieving a high mapping coverage. Cusativin and MC1 are nucleotide-specific endoribonucleases encoded in the cucumber and bitter melon genomes, respectively. Their high specificity for cytidine (Cusativin) and uridine (MC1) make them ideal molecular biology tools for RNA modification mapping. However, heterogenous recombinant expression of either enzyme has been challenging because of their high toxicity to expression hosts and the requirement of posttranslational modifications. Here, we present two highly efficient and time-saving protocols that overcome these hurdles and enhance the expression and purification of these RNases. We first purified MC1 and Cusativin from bacteria by expressing and shuttling both enzymes to the periplasm as MBP-fusion proteins in T7 Express lysY/IqE. coli strain at low temperature. The RNases were enriched using amylose affinity chromatography, followed by a subsequent purification via a C-terminal 6xHIS tag. This fast, two-step purification allows for the purification of highly active recombinant RNases significantly surpassing yields reported in previous studies. In addition, we expressed and purified a Cusativin-CBD fusion enzyme in P. pastoris using chitin magnetic beads. Both Cusativin variants exhibited a similar sequence preference, suggesting that neither posttranslational modifications nor the epitope-tags have a substantial effect on the sequence specificity of the enzyme.
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Affiliation(s)
| | - Eric J Wolf
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Jingming Jin
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Mehul B Ganatra
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Kelly Becker
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Cristian Ruse
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | | | - Ivan R Corrêa
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Erbay Yigit
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA.
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11
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Thakur P, Abernathy S, Limbach PA, Addepalli B. Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis. Methods Enzymol 2021; 658:1-24. [PMID: 34517943 PMCID: PMC9680040 DOI: 10.1016/bs.mie.2021.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge of the structural information is essential for understanding the functional details of modified RNA. Cellular non-coding RNA such as rRNA, tRNA and even viral RNAs contain a number of post-transcriptional modifications with varied degree of diversity and density. In this chapter, we discuss the use of a combination of biochemical and analytical tools such as ribonucleases and liquid chromatography coupled with mass spectrometry approaches for characterization of modified RNA. We present the protocols and alternate strategies for obtaining confident modified sequence information to facilitate the understanding of function.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States.
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12
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Hagelskamp F, Kellner S. Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry. Methods Enzymol 2021; 658:111-135. [PMID: 34517944 DOI: 10.1016/bs.mie.2021.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA modifications gain growing attention as a new frontier in the life sciences but with the rise of RNA vaccines also in biomedical drug development. Impeccable characterization of RNA modifications within their sequence context remains an analytical challenge. Oligonucleotide mass spectrometry (ON-MS), an approach similar to bottom-up proteome analysis, is capable of defining a short 5-15 nucleotide sequence context of an RNA modification while delivering information on the chemical character of the modified nucleotide. Commonly, ON-MS requires the use of ion pairing reagents for ON separation which is not compatible with most other MS-based applications and only few laboratories run dedicated MS instruments for the task. Here, we present an ON-MS technique which is independent of ion pairing reagents and can be used on any available mass spectrometer without risking its sensitivity for other analytes. In this chapter, we describe the experiments necessary for ON-MS method development, ON-MS application to native and synthetic RNAs and finally a guideline for data analysis.
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Affiliation(s)
- Felix Hagelskamp
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany
| | - Stefanie Kellner
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany.
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13
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Qin Y, Zhong Q, Zhang Y, Lin X, Fu P, Lin H. Micro-flow hydrophilic interaction liquid chromatography coupled with triple quadrupole mass spectrometry detects modified nucleosides in the transfer RNA pool of cyanobacteria. J Sep Sci 2021; 44:3208-3218. [PMID: 34212504 DOI: 10.1002/jssc.202100417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
Post-transcriptional modification of nucleosides is observed in almost all elements of RNA. Modified nucleosides finely tune the structure of RNA molecules and affect vital functions, such as the modified wobble position 34 of transfer RNAs expanding the reading preference of anticodons to codons. Recent investigations have revealed that the modification species and their frequencies in an RNA element are not stable but vary with specific cellular factors including metabolites and particular proteins (writers, readers, and erasers). To understand the link between dynamic RNA modifications and biological processes, sensitive and reliable methods for determining modified nucleosides are required. In this study, micro-flow (8 μL/min) hydrophilic interaction liquid chromatography was coupled with triple quadrupole mass spectrometry for the simultaneous determination of adenosine, uridine, cytidine, guanosine, and 20 modified nucleosides. The method was calibrated using 0.1-1000 nM standards (∼0.03-300 ng/mL) and successfully applied to the determination of transfer RNA modifications in the model cyanobacterium Synechococcus elongatus PCC 7942. A protocol for the isolation of a clean transfer RNA pool was optimized, requiring only 25 ng for the identification and quantification of transfer RNA modifications. This micro-flow liquid chromatography-tandem mass spectrometry method constitutes the first step toward monitoring dynamic ribonucleoside modifications in a limited RNA sample.
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Affiliation(s)
- Yichao Qin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China.,College of Tropical Crops, Hainan University, Haikou, P. R. China
| | - Qisheng Zhong
- Shimadzu Corporation, Guangzhou branch, Guangzhou, P. R. China
| | - Ying Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China.,College of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Xiuying Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China.,College of Food Science and Engineering, Hainan University, Haikou, P. R. China
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, P. R. China
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14
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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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15
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Pan Y, Yan TM, Wang JR, Jiang ZH. The nature of the modification at position 37 of tRNAPhe correlates with acquired taxol resistance. Nucleic Acids Res 2021; 49:38-52. [PMID: 33290562 PMCID: PMC7797046 DOI: 10.1093/nar/gkaa1164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 11/12/2022] Open
Abstract
Acquired drug resistance is a major obstacle in cancer therapy. Recent studies revealed that reprogramming of tRNA modifications modulates cancer survival in response to chemotherapy. However, dynamic changes in tRNA modification were not elucidated. In this study, comparative analysis of the human cancer cell lines and their taxol resistant strains based on tRNA mapping was performed by using UHPLC-MS/MS. It was observed for the first time in all three cell lines that 4-demethylwyosine (imG-14) substitutes for hydroxywybutosine (OHyW) due to tRNA-wybutosine synthesizing enzyme-2 (TYW2) downregulation and becomes the predominant modification at the 37th position of tRNAphe in the taxol-resistant strains. Further analysis indicated that the increase in imG-14 levels is caused by downregulation of TYW2. The time courses of the increase in imG-14 and downregulation of TYW2 are consistent with each other as well as consistent with the time course of the development of taxol-resistance. Knockdown of TYW2 in HeLa cells caused both an accumulation of imG-14 and reduction in taxol potency. Taken together, low expression of TYW2 enzyme promotes the cancer survival and resistance to taxol therapy, implying a novel mechanism for taxol resistance. Reduction of imG-14 deposition offers an underlying rationale to overcome taxol resistance in cancer chemotherapy.
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MESH Headings
- A549 Cells
- Base Sequence
- Cell Line, Tumor
- Chromatography, High Pressure Liquid
- Down-Regulation
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Female
- Gene Expression Regulation, Enzymologic
- Gene Knockdown Techniques
- Guanosine/analogs & derivatives
- Guanosine/chemistry
- Guanosine/metabolism
- HeLa Cells
- Humans
- Molecular Structure
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Nucleic Acid Conformation
- Ovarian Neoplasms/pathology
- Paclitaxel/pharmacology
- RNA Processing, Post-Transcriptional/genetics
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/physiology
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/physiology
- Tandem Mass Spectrometry
- Tumor Stem Cell Assay
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Affiliation(s)
- Yu Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jing-Rong Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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16
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Thakur P, Atway J, Limbach PA, Addepalli B. Identification of the amino acids associated with the novel ribonuclease activity of cusativin via protein engineering and LC‐MS. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.02404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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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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18
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Antoine L, Wolff P, Westhof E, Romby P, Marzi S. Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS. Biochimie 2019; 164:60-69. [PMID: 31295507 DOI: 10.1016/j.biochi.2019.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Abstract
RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base-pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.
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Affiliation(s)
- Laura Antoine
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade, CNRS, FR1589, F-67000, Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France.
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19
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Jiang T, Yu N, Kim J, Murgo JR, Kissai M, Ravichandran K, Miracco EJ, Presnyak V, Hua S. Oligonucleotide Sequence Mapping of Large Therapeutic mRNAs via Parallel Ribonuclease Digestions and LC-MS/MS. Anal Chem 2019; 91:8500-8506. [PMID: 31129964 DOI: 10.1021/acs.analchem.9b01664] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of mRNA sequences is a critical aspect of mRNA drug development and regulatory filing. Herein, we developed a novel bottom-up oligonucleotide sequence mapping workflow combining multiple endonucleases that cleave mRNA at different frequencies. RNase T1, colicin E5, and mazF were applied in parallel to provide complementary sequence coverage for large mRNAs. Combined use of multiple endonucleases resulted in significantly improved sequence coverage: greater than 70% sequence coverage was achieved on mRNAs near 3000 nucleotides long. Oligonucleotide mapping simulations with large human RNA databases demonstrate that the proposed workflow can positively identify a single correct sequence from hundreds of similarly sized sequences. In addition, the workflow is sensitive and specific enough to detect minor sequence impurities such as single nucleotide polymorphisms (SNPs) with a sensitivity of less than 1%. LC-MS/MS-based oligonucleotide sequence mapping can serve as an orthogonal sequence characterization method to techniques such as Sanger sequencing or next-generation sequencing (NGS), providing high-throughput sequence identification and sensitive impurity detection.
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Affiliation(s)
- Tao Jiang
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Ningxi Yu
- Department of Chemistry , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| | - Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy , University of Georgia , Athens , Georgia 30602 , United States
| | - John-Ross Murgo
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Mildred Kissai
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Kanchana Ravichandran
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Edward J Miracco
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Vladimir Presnyak
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
| | - Serenus Hua
- Moderna Inc. , 500 Technology Square , Cambridge , Massachusetts 02139 , United States
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20
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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: 33] [Impact Index Per Article: 6.6] [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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21
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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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22
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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23
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Lobue PA, Yu N, Jora M, Abernathy S, Limbach PA. Improved application of RNAModMapper - An RNA modification mapping software tool - For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. Methods 2018; 156:128-138. [PMID: 30366097 DOI: 10.1016/j.ymeth.2018.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/02/2018] [Accepted: 10/21/2018] [Indexed: 12/21/2022] Open
Abstract
Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven for over two decades to be a powerful ally in the elucidation of RNA modification identity and location, but the technique has not proceeded without its own unique technical challenges. The throughput of LC-MS/MS modification mapping experiments continues to be impeded by tedious and time-consuming spectral interpretation, particularly during for the analysis of complex RNA samples. RNAModMapper was recently developed as a tool to improve the interpretation and annotation of LC-MS/MS data sets from samples containing post-transcriptionally modified RNAs. Here, we delve deeper into the methodology and practice of RNAModMapper to provide greater insight into its utility, and remaining hurdles, in current RNA modification mapping experiments.
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Affiliation(s)
- Peter A Lobue
- 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
| | - Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Scott Abernathy
- 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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24
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Thakur P, Limbach PLA, Addepalli B. Improved RNA‐modification mapping through employment of novel ribonucleases and LC‐MS. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.532.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Priti Thakur
- Department of ChemistryUniversity of CincinnatiCincinnatiOH
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25
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Filippova JA, Semenov DV, Juravlev ES, Komissarov AB, Richter VA, Stepanov GA. Modern Approaches for Identification of Modified Nucleotides in RNA. BIOCHEMISTRY (MOSCOW) 2018; 82:1217-1233. [PMID: 29223150 DOI: 10.1134/s0006297917110013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
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Affiliation(s)
- J A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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26
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Yu N, Lobue PA, Cao X, Limbach PA. RNAModMapper: RNA Modification Mapping Software for Analysis of Liquid Chromatography Tandem Mass Spectrometry Data. Anal Chem 2017; 89:10744-10752. [PMID: 28942636 DOI: 10.1021/acs.analchem.7b01780] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven to be a powerful analytical tool for the characterization of modified ribonucleic acids (RNAs). The typical approach for analyzing modified nucleosides within RNA sequences by mass spectrometry involves ribonuclease digestion followed by LC-MS/MS analysis and data interpretation. Here we describe a new software tool, RNAModMapper (RAMM), to assist in the interpretation of LC-MS/MS data. RAMM is a stand-alone package that requires user-submitted DNA or RNA sequences to create a local database against which collision-induced dissociation (CID) data of modified oligonucleotides can be compared. RAMM can interpret MS/MS data containing modified nucleosides in two modes: fixed and variable. In addition, RAMM can also utilize interpreted MS/MS data for RNA modification mapping back against the input sequence(s). The applicability of RAMM was first tested using total tRNA isolated from Escherichia coli. It was then applied to map modifications found in 16S and 23S rRNA from Streptomyces griseus.
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Affiliation(s)
- Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati , P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Peter A Lobue
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati , P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati , P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati , P.O. Box 210172, Cincinnati, Ohio 45221-0172, United States
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Novel ribonuclease activity of cusativin from Cucumis sativus for mapping nucleoside modifications in RNA. Anal Bioanal Chem 2017; 409:5645-5654. [PMID: 28730304 DOI: 10.1007/s00216-017-0500-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/14/2017] [Accepted: 06/27/2017] [Indexed: 01/05/2023]
Abstract
A recombinant ribonuclease, cusativin, was characterized for its cytidine-specific cleavage ability of RNA to map chemical modifications. Following purification of native cusativin protein as described before (Rojo et al. Planta 194:328, 17), partial amino acid sequencing was carried out to identify the corresponding protein coding gene in cucumber genome. Cloning and heterologous expression of the identified gene in Escherichia coli resulted in successful production of active protein as a C-terminal His-tag fusion protein. The ribonuclease activity and cleavage specificity of the fusion protein were confirmed with a variety of tRNA isoacceptors and total tRNA. Characterization of cusativin digestion products by ion-pairing reverse-phase liquid chromatography coupled with mass spectrometry (IP-RP-LC-MS) analysis revealed cleavage of CpA, CpG, and CpU phosphodiester bonds at the 3'-terminus of cytidine under optimal digestion conditions. Ribose methylation or acetylation of cytosine inhibited RNA cleavage. The CpC phosphodiester bond was also resistant to cusativin-mediated RNA cleavage; a feature to our knowledge has not been reported for other nucleobase-specific ribonucleases. Here, we demonstrate the analytical utility of such a novel feature for obtaining high-sequence coverage and accurate mapping of modified residues in substrate RNAs. Graphical abstract Cytidine-specific novel ribonuclease activity of cusativin.
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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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Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry. Biomolecules 2017; 7:biom7010021. [PMID: 28241457 PMCID: PMC5372733 DOI: 10.3390/biom7010021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/15/2017] [Indexed: 01/07/2023] Open
Abstract
Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments. With biological discoveries relating to ribonucleic acid happening more frequently, mass spectrometry has been invaluable in helping to understand what is happening at the molecular level. Here we present a brief overview of the methods that have been developed and refined for the analysis of modified tRNAs by liquid chromatography tandem mass spectrometry.
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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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Ross R, Cao X, Yu N, Limbach PA. Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. Methods 2016; 107:73-8. [PMID: 27033178 DOI: 10.1016/j.ymeth.2016.03.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry is a powerful analytical tool for identifying and characterizing structural modifications to the four canonical bases in RNA, information that is lost when using techniques such as PCR for RNA analysis. Here we described an updated method for sequence mapping of modified nucleosides in transfer RNA. This modification mapping approach utilizes knowledge of the modified nucleosides present in the sample along with the genome-derived tRNA sequence to readily locate modifications site-specifically in the tRNA sequence. The experimental approach involves isolation of the tRNA of interest followed by separate enzymatic digestion to nucleosides and oligonucleotides. Both samples are analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) and the data sets are then combined to yield the modification profile of the tRNA. Data analysis is facilitated by the use of unmodified sequence exclusion lists and new developments in software that can automate MS/MS spectral annotation. The method is illustrated using tRNA-Asn isolated from Thermus thermophilus.
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Affiliation(s)
- Robert Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States.
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