Elucidating RNA-RNA interaction networks of Pseudomonas aeruginosa during interbacterial interactions with other bacterial species

Interbacterial interactions is a common phenomenon in many bacterial communities. Living in a community can lead to differences in the physiology of the bacteria in comparison to their growth in pure culture. Pseudomonas aeruginosa is a pathogen that cause acute and chronic infections in individuals with compromised immune systems. Commonly, P. aeruginosa found in relationship with other bacteria such as Staphylococcus aureus in chronic wounds. Understanding such interbacterial interactions can improve future treatment for infected patients. Short RNA molecules named small RNAs (sRNAs) are considered as post-transcriptional regulators which control bacterial adaptation to environmental changes. While sRNAs are important for the growth and survival of bacteria, little is known about the regulatory roles they play during interbacterial interactions. Here, we reveal the sRNA interaction network in P. aeruginosa during its interaction with other bacteria and decode the regulatory roles played by sRNAs throughout the course of these interactions. To achieve this, we used RNA-seq to uncover the bacterial transcriptome, and the RIL-seq (RNA Interaction by Ligation and sequencing) approach to identify the sRNA interaction network. Our analysis found that some sRNA-RNA pairs are unique to P. Aeruginosa that was exposed to S.aureus spent medium. Using translational reporter assays we tested the regulation of several sRNAs on their RIL-seq targets. Northern analysis demonstrated that the levels of P. Aeruginosa sRNAs change in co-culture with S.aureus, hinting on their importance for interbacterial interactions. Overall, our work starts to uncover the role sRNAs have in communication of bacteria with their surroundings.