tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Abstract

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/.

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

“…This provided a general interest and a serious motivation for developing computational tools aiming at predicting the nature and the sites of modification in tRNA sequences from any organism. Some of these tools have been developed recently, the most comprehensive computational method for predicting posttranscriptional modifications in tRNAs being tRNAmodpred . The predictions performed by tRNAmodpred for organisms for which tRNA modification profiles are unknown but for which the complete sequence of the genome is available, are based on detection of homology to known tRNA modification enzymes conserved during evolution.…”

Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma

“…Spiroplasma holothuricola’ genome. A possible trmK gene responsible for A22 methylation was also identified, but likely was a false positive according to the phylogeny-based examination by the tRNAmodpred ( 24 ). However, we cannot exclude possible transport of tRNA modifying enzymes encoded by the sea cucumber host to the endoensymbiont.…”

“…The deduced proteins of all the CDSs were probed against the NCBI-nr database with BLASTp program with e-value cutoff of 1e–4 and seed size of 3. tRNA genes in the genome were searched using tRNAscan ( 23 ). The genes for potential tRNA posttranscriptional modifications and their targets were predicted with tRNAmodpred ( 24 ). Phylogeny-based filtration and NCBI SmartBLAST were performed to examine the output of tRNAmodpred.…”

Systematics for types and effects of RNA variations

“…Performance of methods for N 1 -methyladenosine (m 1 A) and m 6 A modifications have been benchmarked [152]. tRNAmodpred is an example of an RNA typespecific modification predictor [153].…”