Systematic identification of <scp>tRNAome</scp> and its dynamics in <scp><i>L</i></scp><i>actococcus lactis</i>

Puri, Pranav; Wetzel, Collin; Saffert, Paul; Gaston, Kirk W.; Russell, Susan P.; Varela, Juan Antonio Cordero; Vlies, Pieter van der; Zhang, Gong; Limbach, Patrick A.; Ignatova, Zoya; Poolman, Bert

doi:10.1111/mmi.12710

Cited by 56 publications

(58 citation statements)

References 45 publications

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“…21 ) and Lactococcus lactis (published during the preparation of this manuscript). 22 Also, the complete landscape of mammalian mitochondrial tRNAs has been recently updated and the consequence of their defects on mitochondrial dysfunctions ultimately causing pathological changes were discussed. 23 To date nearly 600 tRNA sequences have been investigated with respect to the presence of modified nucleosides.…”

Section: Introductionmentioning

confidence: 99%

Distribution and frequencies of post-transcriptional modifications in tRNAs

Olchowik²,

et al. 2014

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Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.

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Section: Introductionmentioning

confidence: 99%

Distribution and frequencies of post-transcriptional modifications in tRNAs

Olchowik²,

et al. 2014

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“…However, optimal RNA modification mapping requires generating sufficient overlapping digestion products from multiple RNases to reduce redundancies in digestion product sequences and modification placement . Alternative strategies for generating overlapping digestion products include partial ribonuclease digestion, the use of nonspecific nucleases and alkaline hydrolysis (Wurst et al 1978;Novikova et al 2013;Puri et al 2014). While such strategies can be effective, the RNA modification mapping approach would be enhanced by identifying new RNases with complementary nucleoside specificity.…”

Section: Introductionmentioning

confidence: 99%

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

Addepalli

Lesner

Limbach

2015

RNA

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A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA Tyr I . Analysis of MC1 digestion products by ion-pairing reverse phase liquidchromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5 ′ -termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.

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“…tRNA sequences from E. coli , M. capricolum, H. volcanii, B. subtilis and S. cerevisiae were obtained from the MODOMICS database (version from September 2015). tRNA sequences from L. lactis were obtained from [20]. For each species except L. lactis tRNAmodpred was started either with the complete library of HMMs (referred to as “sanity-check”) or with a library in which HMMs derived from species for which the prediction was being done were excluded (referred to as “cross validation”).…”

Section: Methodsmentioning

confidence: 99%

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Machnicka

Dunin-Horkawicz

Crécy‐Lagard

et al. 2016

Methods

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tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as web server at http://genesilico.pl/trnamodpred/.

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Systematic identification of tRNAome and its dynamics in Lactococcus lactis

Cited by 56 publications

References 45 publications

Distribution and frequencies of post-transcriptional modifications in tRNAs

Distribution and frequencies of post-transcriptional modifications in tRNAs

Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 fromMomordica charantia

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

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