RNAModMapper: RNA Modification Mapping Software for Analysis of Liquid Chromatography Tandem Mass Spectrometry Data

Yu, Ningxi; Lobue, Peter A.; Cao, Xiaoyu; Limbach, Patrick A.

doi:10.1021/acs.analchem.7b01780

Cited by 53 publications

(57 citation statements)

References 52 publications

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“…The complete list of genomic tRNA sequences used for modification mapping is in Table S3 in the supplemental material. LC-MS/MS data from RNA modification mapping experiments were analyzed using variable sequence position modification of RNAModMapper (91). All the .RAW data files were converted to .MGF files by MSConvert from ProteoWizard, and the mass tolerance of both precursor ion and fragment ion was set to 1 Da.…”

Section: Methodsmentioning

confidence: 99%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

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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 codondecoding 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 (cnm 5 s 2 U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNA Phe 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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Section: Methodsmentioning

confidence: 99%

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Jora

Solivio

et al. 2019

J Bacteriol

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“…Sequence informative product ions in LC-MS/MS data of each digestion product were analyzed by RNAModmapper (RAMM) in a variable mode. The mass tolerance was set to 0.8 Da, and p-scores of 55 and above were considered to be significant [14].…”

Section: Discussionmentioning

confidence: 99%

“…For a long time, great deal of research efforts have been put into discovering and characterizing the chemical modifications in tRNAs, which have been found to significantly impact structural and functional activities of these biomolecules [10,11]. The most efficient approach for discovering and characterizing tRNA modifications has been based on liquid chromatography tandem mass spectrometry (LC-MS/MS) [12][13][14]. To date, more than 100 modified nucleosides have been identified in 715 tRNAs of 77 different organisms, including mainly bacteria, archaea, animal tissues, and plant leaves [15].…”

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confidence: 99%

LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method

Yan

Ren

et al. 2020

Biomolecules

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Transfer RNAs (tRNAs) are the most heavily modified RNA species in life entities. Post-transcriptional modifications severely impact the structure and function of tRNAs. To date, hundreds of modifications have been identified in tRNAs, mainly from microorganisms and animals. However, tRNAs in plant roots or tubers that have been widely used for food and medical purpose for centuries are rarely studied because isolation of RNA from plants still remains a challenge. In this paper, a polysaccharase-aided RNA isolation (PARI) method for extraction of high-quality RNA from plants containing large quantities of polysaccharides is developed. This method presents a new strategy of “digesting” polysaccharides that is completely different from the conventional method of “dissolving” the contaminants. By using this method, RNA of high integrity and purity were successfully extracted from ginseng roots because polysaccharide contaminations were removed efficiently with α-amylase digestion. Ginseng tRNAs were first sequenced by NGS and a total of 41 iso acceptors were identified. ChloroplastictRNAGly(GCC) in ginseng root was purified and four modified nucleosides, including m7G, D, T, and Ψ, were identified by LC-MS/MS. The results also revealed that the m7G occurs at a novel position 18, which may be related to the deformation of D-loop. PARI is the first enzyme-assisted technique for RNA isolation from plants, which could fundamentally solve the problem of polysaccharide contaminations. By using the PARI method, more individual tRNAs could be isolated easily from polysaccharide-rich plant tissues, which would have a positive impact on the feasibility of research on structure and function of tRNA in plants.

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“…RNAModMapper (RAMM) is tool that enables in the interpretation of LC‐MS/MS data generated from DNA or RNA sequences by creating a local DB against which collision‐induced dissociation (CID) MS/MS data of modified oligonucleotides (and modified nucleosides) are compared .…”

Section: Miscellaneous Tools Of Interestmentioning

confidence: 99%

New tools and resources in metabolomics: 2016–2017

Misra¹

2018

Electrophoresis

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Rapid advances in mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based platforms for metabolomics have led to an upsurge of data every single year. Newer high-throughput platforms, hyphenated technologies, miniaturization, and tool kits in data acquisition efforts in metabolomics have led to additional challenges in metabolomics data pre-processing, analysis, interpretation, and integration. Thanks to the informatics, statistics, and computational community, new resources continue to develop for metabolomics researchers. The purpose of this review is to provide a summary of the metabolomics tools, software, and databases that were developed or improved during 2016-2017, thus, enabling readers, developers, and researchers access to a succinct but thorough list of resources for further improvisation, implementation, and application in due course of time.

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RNAModMapper: RNA Modification Mapping Software for Analysis of Liquid Chromatography Tandem Mass Spectrometry Data

Cited by 53 publications

References 52 publications

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method

New tools and resources in metabolomics: 2016–2017

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