Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics

The Serratia marcescens is a Gram-negative bacterium from the Enterobacteriaceae family. Recently, S. marcescens have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of S. marcescens was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from Salmonella typhi, Escherichia coli, and Yersinia pestis against S. marcescens was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from S. typhi showed expression in S. marcescens during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from S. marcescens, which can be useful for diagnostics and therapeutic applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01160-y.