Fig. 2

In silico analyses suggests RsmW involvement in RsmA regulation. a Secondary structure prediction of RsmW. Using Mfold and sequence based on 5’ RLM-RACE and RNA sequencing reveals that 3 out of 7 GGA motifs can be located on outer stem loops, patterns reminiscent of that of the small regulatory RNAs RsmX, RsmY and RsmZ, thus suggesting RsmW’s role in binding/sequestering the global regulator RsmA. Transcription of rsmY and rsmZ require GacA binding to upstream activating sequence (UAS; TGTAAG-N₆-CTTACA). There is a weakly conserved GacA binding motif approximately 830 bp upstream of rsmW. b Promoter analysis of rsmW. Virtual Footprint/PRODORIC predictions (Munch et al. [40]) suggests binding sites and regulation of rsmW by RhlR, Fur, and IHF (shown in boxes). A conserved σ⁷⁰ 35 site but not a -10 site appear upstream of rsmW within the PA4570 open reading frame (underlined). A -35 site 58 bp upstream of the 5’end of rsmW is predicted to overlap with a binding site for the heat shock sigma factor RpoH. Directly downstream of the -35 site is a putative IHF binding site, 46 bp upstream of the rsmW 5’end. The RLM-RACE predicted 5’end of RsmW is indicated with +1 and arrow. The first nucleotide of the start codons of the open reading frames are indicated with a downward arrow. Transcriptional terminator of ispB gene, upstream of PA4570, is indicated in bold. No transcriptional terminator can be predicted between PA4570 and rsmW