A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Putative trans-acting sRNAs predicted for A. pleuropneumoniae. Expression was validated by Northern blotting under aerobic (1) and anaerobic (2) conditions. The predicted secondary structures show the formation of several hairpin regions, defined by the presence of palindromic sequences. Target prediction with TargetRNA2 reveals preferable binding sites (except for RNA polymerase-interacting 6S—Arrc10 sRNA), highlighted in gray. Genomic context is shown for the A. pleuropneumoniae reference strain L20.