Detection, genomic context, predicted secondary structure, and target prediction of sRNAs isolated from the S. pneumoniae TIGR4 strain. (A) srn491 and (B) srn206. srn206 was detected with a probe labeled internally with biotin, whereas srn491 was hybridized to either forward or reverse biotinylated oligonucleotides, as indicated. The arrows indicate the size of the sRNA detected by Northern blotting, which agrees with the size predicted by sequencing. (C) RNA molecular weight marker. The shadowed rectangles show the coordinates in the genome and the flanking genes for each sRNA. The figure also shows candidate mRNA targets for srn491 and srn206 (P-values of 3.63 × 10−3 and 4.88 × 10−5, respectively) predicted by TargetRNA software. The secondary structures were predicted using RNAfold server (ΔG values of −29.8 and −26.9 kcal/mol for srn491 and srn206, respectively). The sRNA region predicted to associate with the target mRNA is highlighted in gray. The start codons and SD are in bold, underlined letters.
