Hence, in order to overexpress and purify pneumococcal SmpB, its coding region was cloned in fusion with pneumococcal ssrA (the gene encoding tmRNA) to allow co-expression of both. smpB was amplified by PCR with primers rnm010 and rnm011, which contains a 3’ extension complementary to the 5’-end of ssrA. ssrA was amplified using the primer pair smd057/smd058. The two PCR fragments were then mixed and used as template in a PCR with primers LY333531 mouse rnm010 and smd058. The resulting PCR product was digested with NdeI and BamHI (Fermentas), and cloned into the pET-15b vector (Novagen) previously cleaved with the same restriction enzymes. This construction, named pSDA-02, was first obtained in E. coli DH5α and

then transferred to E. coli BL21(DE3) to allow the expression of His-SmpB. This construct was confirmed by DNA sequencing. Overexpression and purification of proteins RNase R from S. pneumoniae was purified as previously described [30]. For purification of SmpB, BL21(DE3) cells containing pSDA-02

plasmid were grown at 37°C in 250 ml of LB medium supplemented with 100 μg/ml Amp to an OD600 of 0.5. Overexpression Protein Tyrosine Kinase inhibitor of SmpB was then induced by addition of 1 mM IPTG; induction proceeded for 3 hours at 37°C. Cells were harvested by centrifugation and stored at −80°C. Purification was performed by histidine affinity chromatography using HisTrap Chelating HP columns (GE Healthcare) and AKTA HPLC system (GE Healthcare) as follows. Frozen cells were thawed and resuspended in lysis buffer (50 mM HEPES pH 7.5, 1 M NH4Cl, 5 mM MgCl2, 2 mM β-mercaptoethanol, 10 mM imidazole). Cell suspensions were lysed using a French Press at 9000 psi in the presence of 1 mM PMSF. The crude extracts were treated with Benzonase (Sigma) to degrade the nucleic acids and clarified by a 30 min centrifugation

at 10000 xg. The clarified extracts were then loaded onto a HisTrap Chelating Sepharose 1 ml Farnesyltransferase column equilibrated with buffer A (20 mM sodium phosphate pH 7.4, 0,5 M NaCl, 20 mM imidazole). Protein elution was achieved by a continuous imidazole gradient (from 20 mM to 500 mM) in buffer A. The fractions containing the purified protein were pooled together and concentrated by centrifugation at 4°C in an Amicon Ultra Centrifugal Filter Device with a molecular mass cutoff of 10 kDa (Millipore). Protein concentration was determined using the Bradford method [59]. SmpB and RNase R purified proteins were loaded in a SDS-PAGE gel and Coomassie blue stained for band excision (data not shown). Bands corresponding to a total of 500 μg of each protein were used to raise antibodies against the respective pneumococcal proteins (Eurogentec). RNA extraction and northern blotting Overnight cultures of S. pneumoniae TIGR4 wild type and mutant AZD6244 nmr derivatives were diluted in pre-warmed THY to a final OD600 of 0.1, and incubated at 37°C until OD600 ~ 0.3. At this point, cultures were split in two aliquots and each aliquot was further incubated at 15°C or 37°C for 2 h.