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Open Access Research article

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

Vincent M Ulvé1, Emeric W Sevin1, Angélique Chéron1 and Frédérique Barloy-Hubler12*

Author Affiliations

1 CNRS UMR6061 Génétique et Développement, Groupe Modèles Génétiques, Université de Rennes 1, IFR140 GFAS, Faculté de médecine, 2 avenue du Professeur Léon Bernard, CS 34317, 35043 Rennes Cedex, France

2 CNRS UMR6026 Interactions Cellulaires et Moléculaires, Groupe DUALS, Université de Rennes 1, IFR140 GFAS, Campus de Beaulieu, avenue du Général Leclerc, 35042 Rennes, France

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BMC Genomics 2007, 8:467  doi:10.1186/1471-2164-8-467

Published: 19 December 2007

Abstract

Background

Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years.

Results

We used a combination of in silico comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between Sinorhizobium meliloti and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization.

Conclusion

Small non coding RNA (sra) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium.