Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

Liron Argaman, Ruth Hershberg, Jörg Vogel, Gill Bejerano, E. Gerhart H. Wagner, Hanah Margalit, Shoshy Altuvia*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

646 Scopus citations


Background: 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. Results: 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. Conclusions: 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.

Original languageAmerican English
Pages (from-to)941-950
Number of pages10
JournalCurrent Biology
Issue number12
StatePublished - 26 Jun 2001

Bibliographical note

Funding Information:
The authors gratefully acknowledge the excellent technical assistance by Monica Tamasi and Anna Barladian. We also thank Julio Collado-Vides for providing the electronic list of terminators. This work was supported by the Human Frontier Science Program (G.W., H.M., and S.A.), the Swedish National Science Research Council (G.W.), the Israeli Ministry of Science (H.M., G.B.), Yeshaya Horowitz fellowship for distinction (L.A.), and THE ISRAEL SCIENCE FOUNDATION founded by The Academy of Sciences and Humanities – Centers of Excellence Program (S.A.).


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