Minimum inhibitory concentration (MIC) determination The MICs of STI571 nmr all relevant strains in RDM to tigecycline, (gift from Wyeth Pharmaceuticals, US), tetracycline (Sigma-Aldrich, UK), ciprofloxacin and ampicillin (Sigma-Aldrich, UK) were determined and interpreted according to the BSAC protocols [51]. In order to check whether concentrations at half the MIC would induce stress

response rather than kill the cells in liquid medium, half of the MIC of the antibiotic was added to liquid culture at OD600 = 0.6 (sterilised water was added to the control). After growth for an hour or overnight, an aliquot of the culture was taken and spread on plates, to determine colony forming unit per ml (cfu/ml). Additionally growth curves were also generated based on the OD600 readings. The stress GSI-IX nmr response was confirmed by comparison of the antibiotic challenged cells to the control on both the growth curves

and the cfu/ml. RNA extraction Cells were grown to OD600 = 0.6 prior to the addition of the antibiotic. After 1 hour of exposure, cells were harvested by centrifugation. The cell pellet was then resuspended in TRIzol reagent (Invitrogen) and the total RNA was extracted according to Santhakumar et al.[52]. The resulting pellet was washed and resuspended in an appropriate amount of DEPC (Sigma, UK) treated water. cDNA library construction The cDNA library was constructed (according to the manufacturer’s instruction) using the Exact START Small RNA Cloning kit from Epicentre (Cambio,

UK). Briefly, total RNA was digested with DNase I to remove any contaminating DNA, and small RNAs were enriched with Epicentre enrichment solution by precipitating RNA molecules selleckchem longer than 200 nts. The enriched RNAs were treated with phosphatase (Cambio, UK) to convert 5’ triphosphate group of RNA molecules to 5’ monophosphate, and a poly-A tail was added to the 3’ end (according to the manufacturer’s instruction). The 5’ cAMP end of RNA was ligated with Acceptor Oligo that carries a NotI restriction site. Reverse transcription was performed to yield first cDNA strand, using a primer with poly-T at its 3’ end to cover the poly-A tail of RNA samples, and an AscI restriction site. After RNase digestion, the sample was subject to a PCR with Small RNA PCR Primer 1 and 2. The product was digested by NotI and AscI (New England Biolabs) and was subsequently cloned into the cloning-ready pCDC1-K vector (Cambio, UK). Since the 5’ ligation adaptor differs from the 3’ ligation adaptor, the cloning of these putative small RNA molecules is directional. All oligonucleotides used in this study are listed in Table 3.