tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs
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DOI：
10.1016/j.ymeth.2016.03.013
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发表时间：
2016-09-01
期刊：
影响因子：
4.8
通讯作者：
Bujnicki, Janusz M.
中科院分区：
文献类型：
--
作者：
Machnicka, Magdalena A.;Dunin-Horkawicz, Stanislaw;Bujnicki, Janusz M.
TRNA分子含有许多化学变化的核苷，这些核苷是在复杂的tRNA成熟过程中对初级转录本进行酶修饰而形成的。一些修饰是通过单一反应引入的，而另一些则需要由几种不同的酶进行复杂的一系列反应。在不同的tRNA分子、生物和器官中，不同类型的修饰的位置和分布有很大的差异。我们开发了一种计算方法tRNAmodpred，用于预测tRNA序列中的修饰。简而言之，我们的方法以一个或多个未修改的tRNA序列和一组对应于细胞蛋白质组的蛋白质序列作为输入。随后，它鉴定了蛋白质组中已知tRNA修饰酶的同源物，预测了tRNA修饰活性，并将它们映射到MODOMICS数据库中已知的RNA修饰途径上。从而，确定了理论上可能的修饰路径，并提出了这些修饰反应的产物以供查询tRNA。这种方法可以预测新测序的基因组的修改模式，以及检查一个物种用来自另一个来源的酶处理的tRNA的试探性修改状态，例如预测在细菌中表达的真核tRNA的可能修改。TRNAmodpred可在http://genesilico.pl/trnamodprecli.上作为Web服务器免费获得(C)2016年提交人。由爱思唯尔公司出版。
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 a web server at http://genesilico.pl/trnamodprecli. (C) 2016 The Authors. Published by Elsevier Inc.