coli. KanR, SucS transformants were then transformed with the PCR SOEing product and selected for growth on sucrose. Transformants were then screened by PCR and sequenced to confirm the presence of the 5 bp insertion and the absence of additional mutations. The resultant strains, JWJ159 (2019cyaA+5 bp) and JWJ160 (2019cyaAnagB+5 bp) were used for subsequent analysis. RNA extraction and
transcriptional analysis RNA was extracted using the hot acid phenol method as described previously . DNA was removed selleck from extracted RNA by digestion with DNase I (New England Biolabs) and cleaned up with the RNeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) CHIR98014 purchase and the concentration was determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). For real time RT-PCR analysis, primer/probe sets were obtained using the Custom TaqMan Gene Expression Service (Applied Biosystems, Foster City, CA). Primer/probe sets were designed using the sequence of HI0145 and HI0146 from H. influenzae 2019. A primer/probe set for the 16S rRNA of H. influenzae was designed and used as a control. The TaqMan RNA-To-CT 1-Step Kit (Applied Biosystems) was used following the manufacturer’s protocol. Reactions were set up in triplicate using 20 ng of RNA. Reactions
were carried out using the StepOnePlus Real Time PCR System (Applied Biosystems) with StepOne analysis software. Osimertinib Results were calculated using the comparative CT method to determine the relative expression ratio between RNA samples. The primer and probe set for HI16S rRNA was used as the endogenous reference to normalize the results. Two independent sets of RNA Trichostatin A in vitro samples were used for each experiment and the mean fold change is reported. Data are expressed as mean +/- SD. Protein expression and purification SiaR was expressed and purified as described previously , with modified buffers to enhance stability of the purified
protein and an additional purification step. Cells were resuspended in the SiaR lysis and equilibration buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 0.1% CHAPS) prior to lysis by French press. After protein binding, the resin was washed with the SiaR wash buffer (10 mM Tris, pH 8.0, 1,150 mM NaCl, 10% glycerol, 0.1% CHAPS, 5 mM imidazole) and protein was eluted with the SiaR elution buffer (10 mM Tris, pH 8.0, 150 mM NaCl, 10% glycerol, 0.1% CHAPS, 500 mM imidazole). The purified protein was concentrated using an Amicon Ultra centrifugation filter (Millipore, Billerica, MA) with a 10 kDa molecular weight cutoff. The protein sample was then desalted into the SiaR storage buffer (10 mM Tris, pH 8.0, 150 mM NaCl, 10% glycerol, 0.1% CHAPS) using FPLC through a 10 ml (2-5 ml) HiTrap Desalting Column (GE Healthcare, Piscataway, NJ). Protein concentration was determined using the NanoDrop ND-1000 Spectrophotometer and an extinction coefficient of 7,575 M-1 cm-1.