In silico 'fishing' using known small regulatory RNA (sRNA) candidates as the decoy from Escherichia coli, Salmonella typhi and Salmonella typhimurium manifested 14 novel sRNA candidates in the orthologous region of Proteus mirabilis

Proteus mirabilis, a gram-negative bacterium of the family Enterobacteriaceae, is a leading cause of urinary tract infection (UTI) with rapid development of multi-drug resistance. Identification of small regulatory RNAs (sRNAs), which belongs to a class of RNAs that do not translate into a protein, could permit the comprehension of the regulatory roles this molecules play in mediating pathogenesis and multi-drug resistance of the organism. In this study, comparative sRNA analysis across three different members of Enterobacteriaceae (Escherichia coli, Salmonella typhi and Salmonella typhimurium) was carried out to identify the sRNA homologs in P. mirabilis. A total of 232 sRNA genes that were reported in E. coli, S. typhi and S. typhimurium were subjected to comparative analysis against P. mirabilis HI4320 genome. We report the detection of 14 sRNA candidates, conserved in the orthologous regions of P. mirabilis, that are not included in Rfam database. Northern-blot analysis was carried out for selected three sRNA candidates from the current investigation and three known sRNA from Rfam of P. mirabilis. The expression pattern of the six sRNA candidates shows that they are growth stage-dependant. To the best of our knowledge, this is the first report on the identification of sRNA candidates in P. mirabilis.