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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 .

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