, 2008). Besides being implicated in dimer formation, the conserved cysteine residue is of interest because a mutational analysis of certain motif residues in E. coli Ygf Z implicated C228 as a determinant of plumbagin

sensitivity (Lin et al., 2010). To gain further insight into the function of the Ygf Z motif, this study analysed the criticality of each of its conserved residues to growth and to MiaB activity. Only C228 was found to be indispensable. Complementation studies were carried out using the ΔygfZ strain described previously (Waller et al., 2010). This strain was transformed with pBAD24 GSK2118436 mw containing the wild-type E. coli ygfZ gene (EcYgfZ∷pBAD24; Waller et al., 2010) or mutants thereof, in which one of the conserved residues in the Ygf Z motif had been replaced by alanine by site-directed mutagenesis (Cormack, 2008). Cells were grown at 37 °C in Antibiotic Medium 3 (Difco), LB medium with or without 30 μM plumbagin, or M9 minimal medium plus 2 g L−1 glycerol as indicated. Media were solidified with 15 g L−1 agar; ampicillin and kanamycin were used at 50 and 50 μg mL−1, respectively. Gene expression was induced with 0.2 g L−1 l-arabinose. Growth kinetics were followed in a Bioscreen-C Automated Growth Curve Analysis System (Growth Curves Selleck MS-275 USA, MA) using the following parameters: continuous shaking; reading every 30 min; culture volume, 200 μL. As inoculum, overnight cultures in LB plus ampicillin

and kanamycin (washed three times with M9 Janus kinase (JAK) medium plus glycerol before dilution) were diluted to give a final OD600 nm of 0.005. Bioscreen experiments used triplicate cultures of three independent strains. Bulk nucleic acids were isolated from stationary phase cells cultured in Antibiotic Medium 3 and enriched for tRNA (Bailly et al., 2008) before Nucleobond AXR 400 column purification (Machery-Nagel). Purified tRNA was hydrolysed and analysed by liquid chromatography–tandem mass spectrometry (LC–MS) (Phillips et al., 2008). For immunoblot analysis, cells grown in LB medium to an OD600 nm of 1.0 were harvested

by centrifugation, washed once in ice-cold phosphate-buffered saline and sonicated in 50 mM Tris–HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA and 1 mM phenylmethylsulfonyl fluoride. Extracts were centrifuged to clear. Electrophoresis and immunoblotting were as described (Turner et al., 2005); the primary antibody was anti-pentahistidine mouse monoclonal IgG (Qiagen), dilution 1 : 1000, and the secondary antibody was goat anti-mouse IgG (H + L) alkaline phosphatase conjugate (Bio-Rad), dilution 1 : 3000. Protein was estimated by the Bradford (1976) dye-binding method using bovine serum albumin as standard. The functional importance of the eight conserved residues in the Ygf Z motif was assessed by expressing mutant YgfZ proteins from a plasmid and testing their ability to complement various phenotypes of the ΔygfZ strain.