Combating an intrinsic antibiotic resistance mechanism by interfering with small RNA regulation of an outer membrane porin

The discovery of novel antibiotics has not kept pace with the growing threat of bacterial resistance. Bacteria have remarkable genetic plasticity that allows them to respond to a wide array of environmental threats, including the presence of antibiotic molecules that may jeopardize their existence. Compared to Gram-positive species, Gram-negative bacteria are intrinsically resistant to many antibiotics due to the presence of an outer membrane. Permeability through the outer membrane is the first step involved in the resistance of bacteria to an antibiotic. Among several outer membrane porins, outer membrane porin F (OmpF), is one of the largest porin proteins that enable the entry of several antibiotics. Therefore, the loss of OmpF highlights a devastating effect on the success rate of the current antimicrobial agents. The MicF sRNA is a small, antisense RNA found in Escherichia coli and related bacteria that shows extensive sequence complementarity with the 5' end of ompF mRNA and negatively regulates expression of OmpF, by hybridizing to ompF at its ribosome-binding domain and start codon. In this case, peptides engineered to bind to MicF specifically would interfere with its capacity to bind to ompF. ARMs are an excellent candidate for the design and selection of the peptides since they are known to bind RNA effectively and specifically, as well as having cell penetrating abilities. By using the arginine-rich RNA-binding motifs (ARMs) as a framework, a random mutation peptide library was developed to produce peptides that have enhanced binding affinity for the MicF sRNA. Bacterial fluorescent colony selection was established as a rapid screening method to identify specific peptides available from a library containing thousands of peptide molecules using a fluorescent reporter. Two peptides with a high binding affinity for MicF were successfully discovered and the altered areas of these peptides were thoroughly investigated. Furthermore, the efficiency of these peptides in countering the effects of MicF mediated antibiotic resistance was demonstrated by minimum inhibitory concentration analysis. The E. coli MG1655 bacteria appear to be 30 percent more susceptible to antibiotics tested on average when the developed peptides were present inside the cell. In conclusion, this study focuses on the design and screening of the peptide molecules capable of binding to sRNA targets and aims to pave the way for future discussions about how targeting sRNAs could aid in the fight against drug-resistant infections.