Selection of biofilm-degradation aptamers against Pseudomonas aeruginosa and isolation, identification, and interaction analysis of their binding proteins

The Pseudomonas aeruginosa biofilm exhibits strong survivability and resistance against conventional antibacterial treatments. In this study, we identified two biofilm-degrading aptamers (T1 and T2) against P. aeruginosa biofilm using systematic evolution of ligands by exponential enrichment (SELEX) technology. The T1 and T2 aptamers exhibited significant degradation efficacy against the P. aeruginosa biofilm, with degradation rates of 69.21% and 70.50%, respectively. However, the two aptamers exhibited < 20% degradation rates for the biofilms of Vibrio anguillarum , Vibrio alginolyticus , Vibrio harveyi , Escherichia coli , Pseudomonas plecoglossicida, Edwardsiella tarda, and Aeromonas hydrophilia demonstrating high target specificity. Magnetic separation, SDS-PAGE, and mass spectrometry analyses identified three stable, hydrophilic, and acidic T2-binding proteins, namely catalase (55 kDa), elongation factor-Tu (EF-Tu, 43 kDa), and transaldolase (34 kDa), in the P. aeruginosa biofilm. Molecular docking revealed that T2 bound to catalase and EF-Tu via hydrogen bonds and electrostatic interactions, while it primarily bound to transaldolase via electrostatic interactions. This study provides the theoretical and technical foundation for the prevention and control of P. aeruginosa biofilm as well as the identification of biofilm-degrading aptamers. • Pseudomonas aeruginosa biofilm-degrading aptamers were identified using SELEX. • Aptamer T2 exhibited > 70% P. aeruginosa biofilm-degradation rates. • Catalase, EF-Tu, and transaldolase were identified as aptamer-binding proteins. • T2 and its binding proteins interacted via H-bonds and electrostatic interactions.