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

By Liron Argaman, Ruth Hershberg, Jörg Vogel, Gill Bejerano, E. H. Wagner, Hanah Margalit, S. Altuvia. Current Biology, 2001

802 citations recorded by the source corpus.

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.

Subfields: Astronomy and Astrophysics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/51156e1bb349fbe41cac0ee811fad7c7383f1202

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Citations in the corpus

The microRNAs of Caenorhabditis elegans. (2003, methodology): “Recent advances have been made in the computational identification of ncRNA genes through comparative genomics, and complex algorithms have been developed to identify ncRNAs in general (Argaman et al. 2001; Rivas et al. 2001; Wassarman et al. 2001), as well as specific ncRNA families such as tRNAs a”
σE Regulates and Is Regulated by a Small RNA in Escherichia coli (2007, background): “A number of genome-wide searches performed by various groups using computational and biochemical methods have uncovered close to 100 small RNAs (sRNAs) in Escherichia coli (6, 8, 27, 47, 57, 62).”
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti (2010, methodology): “These were probably generated by the activity of a single promoter with a diffuse transcription start site, as was previously described for the SraL sRNA [52].”
The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior (2008, background): “(2), with the following modifications.”
Hfq and its constellation of RNA (2011, background): “However, some undergo endonucleolytic processing to accumulate as a shorter 3′ for”
Computational analysis of bacterial RNA-Seq data (2013, methodology): “A 50 RACE was performed as described previously (22).”
Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles (2010, background): “coli, Salmonella, Yersinia pestis, and Klebsiella pneumoniae (3), suggesting a common mechanism for upregulating vesiculation.”
The small RNA regulators of Escherichia coli: roles and mechanisms*. (2004, background): “Two other groups (5, 19) used computational methods to predict a promoter and a terminator within a given intergenic region with an orientation and spacing consistent with a sRNA (orphan promoters, terminators); Argaman et al.”
Non–coding RNA genes and the modern RNA world (2001, background): “; and general ncRNA gene-finding exercises using computational comparative genomics in Escherichia coli”
Global Mapping of Small RNA-Target Interactions in Bacteria (2016, background): “While the sRNAs detected in the ﬁrst genome-wide surveys were predominantly independent transcripts encoded in intergenic regions (Argaman et al., 2001; Rivas et al., 2001; Wassar-man et al., 2001), recent studies revealed expression of candidate sRNAs originating from various genomic regions,…”
Identification of novel small RNAs using comparative genomics and microarrays. (2001, methodology): “), and others have found additional sRNAs using variations of the approaches used here (Argaman et al. 2001).”