Upadhyay Roopam, Bawankar Praveen, Malhotra Deepti, Patankar Swati
School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
Mol Biochem Parasitol. 2005 Dec;144(2):149-58. doi: 10.1016/j.molbiopara.2005.08.012. Epub 2005 Sep 9.
Noncoding RNAs (ncRNAs) such as snRNAs, snoRNAs and microRNAs play important roles in transcription and translation control. These ncRNAs have yet to be discovered in the malarial parasite Plasmodium falciparum, an organism in which these basic biological processes are poorly understood. Inspired by a report by Klein et al., we initiated a bioinformatics screen to uncover several candidate ncRNAs from the parasite genome using two simple criteria: first, elevated GC content in the highly A-T rich intergenic regions of the P. falciparum genome and second, conservation of sequence homology between malaria parasite species. We show that all the annotated tRNAs can be successfully identified in our screen as well as several new candidates that show homology to snRNAs and snoRNAs, and ten candidate ncRNAs of unknown function. Three of the candidate snRNAs, a predicted selenocysteine tRNA and two candidates of unknown function are expressed in asexual stage parasites, further validating the screen. With these results, the biological processes underlying RNA-mediated regulation of transcription, translation and splicing can be studied in an important human pathogen.
诸如小核RNA（snRNAs）、核仁小RNA（snoRNAs）和微小RNA等非编码RNA（ncRNAs）在转录和翻译控制中发挥着重要作用。这些ncRNAs尚未在疟原虫恶性疟原虫中被发现，而在这种生物体中，这些基本的生物学过程还知之甚少。受克莱因等人的一篇报告启发，我们启动了一项生物信息学筛选，使用两个简单标准从该寄生虫基因组中发现了几个候选ncRNAs：第一，恶性疟原虫基因组中高度富含A-T的基因间区域中升高的GC含量；第二，疟原虫物种之间序列同源性的保守性。我们表明，在我们的筛选中可以成功鉴定出所有注释的转运RNA（tRNAs），以及几个与snRNAs和snoRNAs具有同源性的新候选物，还有十个功能未知的候选ncRNAs。三个候选snRNAs、一个预测的硒代半胱氨酸tRNA和两个功能未知的候选物在无性阶段寄生虫中表达，进一步验证了该筛选。有了这些结果，就可以在一种重要的人类病原体中研究RNA介导的转录、翻译和剪接调控的潜在生物学过程。
