Small Non-Coding sRNA53 Modulates the Quorum Sensing System to Enhance Drug Resistance in Escherichia coli Exposed to Heavy Ion and X-ray Irradiation

Abstract

Small non-coding RNAs (sRNAs, also called sncRNAs) known as gene expression regulatory factors are capable of modulating mRNA functions through complementary base pairing. A number of studies has shown that when exposed to radiation, the expression of drug resistance genes increases in some cells. Here, in Escherichia coli subjected to ¹²C⁶⁺ heavy ion beams or X-ray exposure, five sRNAs (sRNA120, sRNA127, sRNA109, sRNA72, sRNA53) with elevated expression were identified by deep sequencing and sRNAscanner prediction. To investigate whether they have a potential role in drug resistance, we engineered strains overexpressing these sRNAs, and assessed their survival rate under sub-lethal antibiotic concentrations. It was noteworthy that under Gentamicin, Norfloxacin, Chloramphenicol and Cfotaxime, the survival rate of ::sRNA53 strain was 1.0667, 1.0251, 1.3797 and 3.9327 times higher, respectively, than for the control and strains overexpressing other sncRNAs. TargetRNA2 software identified lsrA as a likely target gene regulated by sRNA53 based on binding free energy calculations. We analyzed the interaction sites between sRNA53 and lsrA and measured the expression of these molecules in various mutants using RT-qPCR. We also investigated the regulation of Luxs/AI-2 system by the lsr operon and the biofilm formation of mutants. In the ::sRNA53 strain, the log₂FC for sRNA53 and lsrA concurrently escalated by 1.8533 and 1.7367-fold. Additionally, the biofilm formation ability of ::sRNA53, ::lsrA, and ::sRNA53::lsrA (co-expression) strains was increased 5.4542, 3.946, and 7.1758-fold, respectively, compared to wild-type MG1655. Based on these data, we can conclude that sRNA53 plays a critical role in the development of antibiotic resistance in E. coli. Apparently, the action of sRNA53 targets the lsrA gene, which, by modulating the Luxs/AI-2 system, affects the ability to biofilm formation and drug resistance of the bacterium. The study shows that a new sRNA, named sRNA53, is involved in the formation of tolerance to sub-lethal doses of various antibiotics.