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T1TAdb: the database of type I toxin–antitoxin systems
RNA ( IF 4.5 ) Pub Date : 2021-12-01 , DOI: 10.1261/rna.078802.121
Nicolas J Tourasse 1 , Fabien Darfeuille 1
Affiliation  

Type I toxin–antitoxin (T1TA) systems constitute a large class of genetic modules with antisense RNA (asRNA)-mediated regulation of gene expression. They are widespread in bacteria and consist of an mRNA coding for a toxic protein and a noncoding asRNA that acts as an antitoxin preventing the synthesis of the toxin by directly base-pairing to its cognate mRNA. The co- and post-transcriptional regulation of T1TA systems is intimately linked to RNA sequence and structure, therefore it is essential to have an accurate annotation of the mRNA and asRNA molecules to understand this regulation. However, most T1TA systems have been identified by means of bioinformatic analyses solely based on the toxin protein sequences, and there is no central repository of information on their specific RNA features. Here we present the first database dedicated to type I TA systems, named T1TAdb. It is an open-access web database (https://d-lab.arna.cnrs.fr/t1tadb) with a collection of ∼1900 loci in ∼500 bacterial strains in which a toxin-coding sequence has been previously identified. RNA molecules were annotated with a bioinformatic procedure based on key determinants of the mRNA structure and the genetic organization of the T1TA loci. Besides RNA and protein secondary structure predictions, T1TAdb also identifies promoter, ribosome-binding, and mRNA-asRNA interaction sites. It also includes tools for comparative analysis, such as sequence similarity search and computation of structural multiple alignments, which are annotated with covariation information. To our knowledge, T1TAdb represents the largest collection of features, sequences, and structural annotations on this class of genetic modules.

中文翻译:

T1TAdb:I 型毒素-抗毒素系统数据库

I 型毒素-抗毒素 (T1TA) 系统构成了一大类具有反义 RNA (asRNA) 介导的基因表达调控的遗传模块。它们广泛存在于细菌中,由一个编码有毒蛋白质的 mRNA 和一个非编码 asRNA 组成,后者作为一种抗毒素,通过与其同源 mRNA 直接碱基配对来阻止毒素的合成。T1TA 系统的共转录和转录后调控与 RNA 序列和结构密切相关,因此必须对 mRNA 和 asRNA 分子进行准确注释以了解该调控。然而,大多数 T1TA 系统都是通过仅基于毒素蛋白质序列的生物信息学分析来识别的,并且没有关于其特定 RNA 特征的中央信息库。在这里,我们介绍了第一个专用于 I 型 TA 系统的数据库,名为 T1TAdb。它是一个开放式网络数据库 (https://d-lab.arna.cnrs.fr/t1tadb),收集了约 500 种细菌菌株中的约 1900 个基因座,之前已在其中鉴定了毒素编码序列。基于 mRNA 结构的关键决定因素和 T1TA 基因座的遗传组织,使用生物信息学程序对 RNA 分子进行注释。除了 RNA 和蛋白质二级结构预测外,T1TAdb 还识别启动子、核糖体结合和 mRNA-asRNA 相互作用位点。它还包括用于比较分析的工具,例如序列相似性搜索和结构多重比对的计算,这些工具用协变信息进行注释。据我们所知,T1TAdb 代表了最大的特征、序列、
更新日期:2021-11-16
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