ABSTRACT

Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding ‘intergenic regions’ (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.

摘要

比较序列分析方法对于从细菌基因组 DNA 序列数据集中发现新型结构化非编码 RNA (ncRNA) 非常有效。以前，我们开发了一个计算管道，以更全面地识别来自单个细菌基因组的结构化 ncRNA 代表。该搜索过程利用了这样一个事实，即作为结构化 RNA 转录模板的基因组区域往往存在于比基因组其余部分富含 G 和 C 核苷酸的平均非编码“基因间区域”（IGR）更长的时间。在本研究中，我们应用这种计算管道来识别来自 26 种不同细菌物种的结构化 ncRNA 候选者。发现了许多新的结构化 ncRNA 基序，包括几个候选核糖开关，一种其配体已被鉴定，另一种尚未经过实验验证。我们的研究结果支持最近的预测，即数百种新型核糖开关类和其他 ncRNA 在基因组已完全测序的有限数量的细菌物种中仍未被发现。