Identification and Characterization of Non-Protein Coding RNA Homologs in Citrobacter rodentium by Comparative Genomics

Abstract

This experiment was conducted to identify homologous non-protein coding RNAs (npcRNA) in Citrobacter rodentium as an alternate for solving health issues caused by this bacteria. Abuse of antimicrobial leads to the emergence of antimicrobial resistance pathogen. Aim of this research is to screen homologous npcRNAs from known bacteria in C. rodentium, to study the expression of homologous npcRNAs in C. rodentium and to predict the regulatory roles of identified homologous npcRNA in C. rodentium. Firstly, screening for presence of homologous npcRNA in Citrobacter rodentium was conducted by collecting known npcRNAs from S. typhi, E. coli and Y. pestis falling under the same genus of Enterobacteriaceae. Secondly, screening the homolog npcRNA identified from previous step (BLASTn) through Rfam (RNA family) to identify unannotated homologs. Then, target mRNA prediction for homologous npcRNA was done using TargetRNA2 webtool to find the compliment mRNA binding of the homologous sequence and the regulatory activities of this transcript. The npcRNA homologs which predicted to regulate virulence target mRNA were assessed for its expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using Image J tool. The known npcRNA Styr-296 from S. typhi showed expression in C. rodentium during three growth stages (lag, log and stationary). The expression was observed to be high during lag phase followed by no expression during log and stationary phase. This Styr-296 homolog was predicted to regulate mRNA translating modulator drug activity B which is associated with the bacterial virulence. Hence, this is a preliminary study promising for further elucidation of more virulence associated npcRNAs that are yet to be discovered from C. rodentium developing strategy to unveil alternate therapeutic options for diseases caused by this bacterium.