Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner E G, Margalit H, Altuvia S
Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel.
Curr Biol. 2001 Jun 26;11(12):941-50. doi: 10.1016/s0960-9822(01)00270-6.
Small, untranslated RNA molecules were identified initially in bacteria, but examples can be found in all kingdoms of life. These RNAs carry out diverse functions, and many of them are regulators of gene expression. Genes encoding small, untranslated RNAs are difficult to detect experimentally or to predict by traditional sequence analysis approaches. Thus, in spite of the rising recognition that such RNAs may play key roles in bacterial physiology, many of the small RNAs known to date were discovered fortuitously.
To search the Escherichia coli genome sequence for genes encoding small RNAs, we developed a computational strategy employing transcription signals and genomic features of the known small RNA-encoding genes. The search, for which we used rather restrictive criteria, has led to the prediction of 24 putative sRNA-encoding genes, of which 23 were tested experimentally. Here we report on the discovery of 14 genes encoding novel small RNAs in E. coli and their expression patterns under a variety of physiological conditions. Most of the newly discovered RNAs are abundant. Interestingly, the expression level of a significant number of these RNAs increases upon entry into stationary phase.
Based on our results, we conclude that small RNAs are much more widespread than previously imagined and that these versatile molecules may play important roles in the fine-tuning of cell responses to changing environments.
小的非翻译RNA分子最初是在细菌中发现的，但在所有生物界中都能找到其例子。这些RNA执行多种功能，其中许多是基因表达的调节因子。编码小的非翻译RNA的基因很难通过实验检测到，也很难用传统的序列分析方法预测。因此，尽管越来越多的人认识到这类RNA可能在细菌生理学中起关键作用，但迄今为止已知的许多小RNA都是偶然发现的。
为了在大肠杆菌基因组序列中搜索编码小RNA的基因，我们开发了一种利用已知小RNA编码基因的转录信号和基因组特征的计算策略。我们使用了相当严格的标准进行搜索，结果预测出了24个假定的sRNA编码基因，其中23个进行了实验测试。在此，我们报告在大肠杆菌中发现了14个编码新型小RNA的基因及其在各种生理条件下的表达模式。大多数新发现的RNA含量丰富。有趣的是，这些RNA中有相当一部分在进入稳定期后表达水平会增加。
基于我们的结果，我们得出结论，小RNA比以前想象的要广泛得多，并且这些多功能分子可能在细胞对不断变化的环境的微调反应中发挥重要作用。
