The CsrA/RsmA family of post-transcriptional regulators in bacteria is involved in regulating many cellular processes, including pathogenesis. Using a bioinformatics approach, we identified an RsmA binding motif, A(N)GGA, in the Shine–Dalgarno regions of 901 genes. Among these genes with the predicted RsmA binding motif, 358 were regulated by RsmA according to our previously published gene expression profiling analysis (WT negative mutant; Kõiv , 2013 ). A small subset of the predicted targets known to be important as virulence factors was selected for experimental validation. RNA footprint analyses demonstrated that RsmA binds specifically to the ANGGA motif in the 5′UTR sequences of , , , and . RsmA-dependent regulation of these five genes was examined using plasmid-borne translational and transcriptional fusions with a reporter gene. They were all affected negatively by RsmA. However, we demonstrated that whereas the overall effect of RsmA on and was determined on both the translational and transcriptional level, expression of pectinolytic enzyme genes ( and ) was affected mainly on the level of transcription in tested conditions. In summary, these data indicate that RsmA controls virulence by integration of its regulatory activities at various levels.


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