Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae
Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae
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DOI：
10.1261/rna.027359.111
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发表时间：
2012-03-01
期刊：
影响因子：
4.5
通讯作者：
Amblar, Monica
中科院分区：
文献类型：
--
作者：
Acebo, Paloma;Martin-Galiano, Antonio J.;Amblar, Monica
肺炎链球菌是社区获得性肺炎的主要病原体，也是儿童和老年人死亡和发病的主要原因。几种肺炎球菌菌株的基因组测序揭示了关于这种流行的人类病原体的潜在蛋白质和遗传多样性的有价值的信息。然而，很少有人知道它的转录调控和它的小调控非编码RNA。在这项研究中，我们进行了深度测序的S。pneumoniae TIGR 4菌株RNome鉴定在该病原体中表达的小调节RNA候选物。我们发现了1047个潜在的小RNA，包括基因内，5 '和/或3'-重叠RNA和88个小RNA编码的基因间区域。通过这种方法，我们回收了许多以前鉴定的基因间小RNA，并鉴定了68个新的候选者，其中大多数在其他S. pneumoniae菌株我们确认了17个基因间小RNA的独立表达，并使用生物信息学工具预测了其中6个的假定mRNA靶点。初步结果表明，这六个是一个关键的球员在监管能力的发展。这项研究是迄今为止报道的最大的S.肺炎，并提供了一个高度完整的看法，小RNA网络在这种病原体。
Streptococcus pneumoniae is the main etiological agent of community-acquired pneumonia and a major cause of mortality and morbidity among children and the elderly. Genome sequencing of several pneumococcal strains revealed valuable information about the potential proteins and genetic diversity of this prevalent human pathogen. However, little is known about its transcriptional regulation and its small regulatory noncoding RNAs. In this study, we performed deep sequencing of the S. pneumoniae TIGR4 strain RNome to identify small regulatory RNA candidates expressed in this pathogen. We discovered 1047 potential small RNAs including intragenic, 5'-and/or 3'-overlapping RNAs and 88 small RNAs encoded in intergenic regions. With this approach, we recovered many of the previously identified intergenic small RNAs and identified 68 novel candidates, most of which are conserved in both sequence and genomic context in other S. pneumoniae strains. We confirmed the independent expression of 17 intergenic small RNAs and predicted putative mRNA targets for six of them using bioinformatics tools. Preliminary results suggest that one of these six is a key player in the regulation of competence development. This study is the biggest catalog of small noncoding RNAs reported to date in S. pneumoniae and provides a highly complete view of the small RNA network in this pathogen.