Identification of novel Hfq-binding sRNAs in Pseudomonas aeruginosa

Previously, we performed in vivo UV CLIP-seq to identify Hfq-binding RNAs in the Pseudomonas aeruginosa PAO1 transcriptome and found that sRNA SPA0079 and SPA0078 highly bound to Hfq in the early stationary phase and biofilm states, respectively. Both sRNAs were first identified in previously performed two size-selection RNA-seq studies in Pseudomonas aeruginosa (Ferrara, S. et al., PLoS One, 2012; Gomez-Lozano, M. et al., Environ. Microbiol., 2012). The purpose of this study is to characterize the trigger of each sRNA expression, the secondary structure, the posttranscriptional regulatory mechanism to the target mRNAs, and the effect of the P. aeruginosa phenotype.