Nucleic Acids Research Advance Access published online on January 26, 2007
Nucleic Acids Research, doi:10.1093/nar/gkl1096
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Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets
1Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France; INSERM, U604, Paris, F-75015 France; INRA, USC2020, Paris, F-75015 France, 2CNRS URA 2171, Institut Pasteur, UP Génétique in silico, Paris, F-75015 France and 3UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Srasbourg, F-67084 France
*To whom correspondence should be addressed. Tel: (33) 145688841; Fax: (33) 145688706; E-mail: pcossart{at}pasteur.fr
Received July 25, 2006. Revised November 15, 2006. Accepted December 1, 2006.
To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA–mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs.
Authors contributed equally
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