A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome
A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome
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DOI：
10.1016/s0303-2647(02)00013-8
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发表时间：
2002-03-01
期刊：
影响因子：
1.6
通讯作者：
Blyn, LB
中科院分区：
文献类型：
--
作者：
Chen, S;Lesnik, EA;Blyn, LB
近年来，细菌基因组序列的爆炸式增长已经开始需要提高以快速、高效和准确的方式注释重要序列和结构元素的能力。特别是小的非编码rna （sRNAs）一直难以预测。sRNAs在细胞中起着重要的结构、催化和调控作用。虽然最近有一些研究小组发表了细菌基因组中sRNAs注释的预测方法，但在这一领域还有很多工作要做。为了开发一种有效的方法来预测大肠杆菌基因组中未知的sRNA基因，我们采用了生物信息学方法，在rho非依赖性终止子的短距离内寻找含有sigma70启动子的DNA区域。在最初鉴定的227个候选sRNA基因中，32个是先前描述的sRNA、孤儿tRNA、部分tRNA和rRNA操作子。51个mrna基因在可接受的核糖体结合位点后编码带注释的极小开放阅读框（orf）。144个是潜在的新的不可翻译的sRNA基因。利用从四种不同条件下生长的大肠杆菌MG1655细胞中分离的总RNA，通过Northern杂交验证了部分基因的转录本。在这里，我们总结了我们的数据，并讨论了使用这种方法在细菌基因组上注释sRNA基因的规则和优点/缺点。(C) 2002爱思唯尔科学爱尔兰有限公司版权所有。
The recent explosion in available bacterial genome sequences has initiated the need to improve an ability to annotate important sequence and structural elements in a fast, efficient and accurate manner. In particular, small non-coding RNAs (sRNAs) have been difficult to predict. The sRNAs play an important number of structural, catalytic and regulatory roles in the cell. Although a few groups have recently published prediction methods for annotating sRNAs in bacterial genome, much remains to be done in this field. Toward the goal of developing an efficient method for predicting unknown sRNA genes in the completed Escherichia coli genome, we adopted a bioinformatics approach to search for DNA regions that contain a sigma70 promoter within a short distance of a rho-independent terminator. Among a total of 227 candidate sRNA genes initially identified, 32 were previously described sRNAs, orphan tRNAs, and partial tRNA and rRNA operons. Fifty-one are mRNAs genes encoding annotated extremely small open reading frames (ORFs) following an acceptable ribosome binding site. One hundred forty-four are potentially novel non-translatable sRNA genes. Using total RNA isolated from E. coli MG1655 cells grown under four different conditions, we verified transcripts of some of the genes by Northern hybridization. Here we summarize our data and discuss the rules and advantages/disadvantages of using this approach in annotating sRNA genes on bacterial genomes. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.