sYJ20 was previously identified by Vogel et al. in E. coli as SroA [5], encoded by a sequence downstream of yabN (encoding SgrR, a transcriptional regulator in E. coli[33]) and upstream of tbpA (encoding the thiamine-binding check details periplasmic protein, homologous to thiB in E. coli) (Figures 2C (ii) and 5A). Figure 5 The chromosomal location of the sYJ20 (SroA) encoding region and its encoding sequence. sYJ20 is encoded upstream of the tbpA-yabK-yabJ operon, and the shared

TSS of sYJ20 and tbpA as determined by 5’ RACE analysis is represented by the dark-black arrow. The DNA sequence of sYJ20 (SroA) is shown in bold letters, which is also the region that was deleted in YJ104 and used for TargetRNA prediction (Table 1). The THI-box sequence is underlined. The start codon of tbpA is displayed at larger size as GTG, where the first G is considered +1 in the numbering system. sYJ5, sYJ20 (SroA) and sYJ118 are all highly conserved within the different members of Enterobacteriaceae, although the coding sequences of sYJ5, sYJ20 and sYJ118 are also found in other families of bacteria (such as sYJ5 and sYJ118 in Prevotella ruminicola,

sYJ20 in Marinobacter aquaeolei VT8), in plants (such as sYJ20 and sYJ118 in Zea mays cultivar line T63) and in animals (sYJ118 in Gryllus bimaculatus). In contrast, sYJ75 is only found in Salmonella, Enterobacter, Photorhabdus and Citrobacter. sYJ20 (SroA), sYJ5, sYJ75 and sYJ118 in other species and relevance to other drug classes We proceeded PF-562271 in vitro to determine whether the increased expression of these sRNAs would be Salmonella specific or drug-class specific. Hence, we assessed the levels of our sRNA candidates (sYJ5, sYJ20 and sYJ118) in other members of Enterobacteriaceae (Klebsiella pneumoniae and Escherichia coli) when challenged with sub-inhibitory Atorvastatin levels of tigecycline (sYJ75 was not included since it is

not encoded in the tested species). Additionally, in order to determine whether these sRNAs are upregulated solely as a result of tigecycline challenge or are generally upregulated as a result of sub-inhibitory antibiotic challenge, S. Typhimurium SL1344 was challenged with either half the MIC of ampicillin (1 μg/ml) or ciprofloxacin (0.0156 μg/ml). As shown in Figure 3B, none of the four tested sRNAs were upregulated in response to ciprofloxacin exposure, whilst three (sYJ5, sYJ75 and sYJ118) were found to be upregulated in the presence of ampicillin. Interestingly, E. coli did not upregulate the expression of the three candidate sRNAs (sYJ5, sYJ20 and sYJ118) in response to challenge at half the MIC of tigecycline. However, sYJ118 exhibited an elevated level of expression in K. pneumoniae in the presence of tigecycline (Figure 3B). Of note, although the sYJ20 (SroA) coding sequence is present in K. pneumoniae, two transcripts were detected after hybridisation.