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Open Access Highly Accessed Research article

Identification of small RNAs in Francisella tularensis

Guillaume Postic12, Eric Frapy12, Marion Dupuis12, Iharilalao Dubail12, Jonathan Livny34, Alain Charbit12 and Karin L Meibom12*

Author Affiliations

1 INSERM U1002, Paris, France

2 Université Paris Descartes, Faculté de Médecine Necker-Enfants Malades, Paris, France

3 Broad Institute of MIT and Harvard, Cambridge, USA

4 Channing Laboratories, Brigham and Women's Hospital, Harvard Medical School, Boston, USA

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BMC Genomics 2010, 11:625  doi:10.1186/1471-2164-11-625

Published: 10 November 2010

Abstract

Background

Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far.

Results

We have used a combination of experimental assays and in silico prediction to identify sRNAs in F. tularensis strain LVS. Using a cDNA cloning and sequencing approach we have shown that F. tularensis expresses homologues of several sRNAs that are well-conserved among diverse bacteria. We have also discovered two abundant putative sRNAs that share no sequence similarity or conserved genomic context with any previously annotated regulatory transcripts. Deletion of either of these two loci led to significant changes in the expression of several mRNAs that likely include the cognate target(s) of these sRNAs. Deletion of these sRNAs did not, however, significantly alter F. tularensis growth under various stress conditions in vitro, its replication in murine cells, or its ability to induce disease in a mouse model of F. tularensis infection. We also conducted a genome-wide in silico search for intergenic loci that suggests F. tularensis encodes several other sRNAs in addition to the sRNAs found in our experimental screen.

Conclusion

Our findings suggest that F. tularensis encodes a significant number of non-coding regulatory RNAs, including members of well conserved families of structural and housekeeping RNAs and other poorly conserved transcripts that may have evolved more recently to help F. tularensis deal with the unique and diverse set of environments with which it must contend.