T-psi-C: user friendly database of tRNA sequences and structures

Sajek, Marcin; Woźniak, Tomasz; Sprinzl, Mathias; Jaruzelska, Jadwiga; Barciszewski, Jan

doi:10.1093/nar/gkz922

Cited by 19 publications

(32 citation statements)

References 25 publications

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“…The presence and numbers of isoforms were extracted from the GtRNA database (http://gtrnadb.ucsc.edu/GtRNAdb2/ genomes/bacteria/Baci_subt_subtilis_168/) [26]. The RNA sequence data were extracted from Modomics (http://modomics.genesilico.pl/sequences/list/?type_field=tRNA&subtype=all&species=4& display=Display&nomenclature=abbrev) [27] from tRNAdb (http://trnadb.bioinf.uni-leipzig.de/) [28] and TpsiC databases (http://tpsic.igcz.poznan.pl/info/start/) [29]. The information on all genes involved in tRNA modification in E. coli and B. subtilis (Tables S1 and S2) were gathered from the literature and further checked using Subtiwiki [24], Uniprot Id mapping tools [30], and BlastP [31] searches at NCBI [32], as well as Pathosystems Resource Integration Center (PATRIC) feature group tools [33].…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

et al. 2020

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Extensive knowledge of both the nature and position of tRNA modifications in all cellular tRNAs has been limited to two bacteria, Escherichia coli and Mycoplasma capricolum. Bacillus subtilis sp subtilis strain 168 is the model Gram-positive bacteria and the list of the genes involved in tRNA modifications in this organism is far from complete. Mass spectrometry analysis of bulk tRNA extracted from B. subtilis, combined with next generation sequencing technologies and comparative genomic analyses, led to the identification of 41 tRNA modification genes with associated confidence scores. Many differences were found in this model Gram-positive bacteria when compared to E. coli. In general, B. subtilis tRNAs are less modified than those in E. coli, even if some modifications, such as m1A22 or ms2t6A, are only found in the model Gram-positive bacteria. Many examples of non-orthologous displacements and of variations in the most complex pathways are described. Paralog issues make uncertain direct annotation transfer from E. coli to B. subtilis based on homology only without further experimental validation. This difficulty was shown with the identification of the B. subtilis enzyme that introduces ψ at positions 31/32 of the tRNAs. This work presents the most up to date list of tRNA modification genes in B. subtilis, identifies the gaps in knowledge, and lays the foundation for further work to decipher the physiological role of tRNA modifications in this important model organism and other bacteria.

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Section: Bioinformatic Analysesmentioning

confidence: 99%

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

et al. 2020

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“…The tRNAdb provides a compendium of tRNA sequences, along with annotated modification sites from over 500 species across archaea, bacteria, eukarya, and viruses [121]. Most recently, Sajek and co-workers presented the T-psi-C resource [187], an up-to-date database of tRNA sequences from many species (including few viral molecules) enriched with 2D and 3D structure information, other than annotation of modified bases. The RNA modification Database (RNAMDB) provides a comprehensive collection of RNA modifications from archaea, bacteria, and eukaria that can be navigated by original nucleoside or RNA source [140].…”

Section: Epitranscriptomics Web Resourcesmentioning

confidence: 99%

A Census and Categorization Method of Epitranscriptomic Marks

Mathlin

Pera

Colombo

2020

IJMS

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In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.

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“…T-psi-C is a database for tRNA sequences and structures [ 35 ]. Information about circular RNA (circRNA) disease associations can be obtained from Circ2Traits [ 36 ] and circRNA disease [ 37 ] databases.…”

Section: Databases For Rna Variationsmentioning

confidence: 99%

Systematics for types and effects of RNA variations

Vihinen

2020

RNA Biology

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Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.

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T-psi-C: user friendly database of tRNA sequences and structures

Cited by 19 publications

References 25 publications

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

A Census and Categorization Method of Epitranscriptomic Marks

Systematics for types and effects of RNA variations

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