, 1994; Mullin et al., 1994;
Wingrove & Gober, 1994; Dutton et al., 2005). Direct evidence of FlbD binding to flagellar promoters in vivo has not been shown. FlbD activity is modulated by the trans-acting factor FliX that links class II flagellar assembly to class III/IV flagellar gene transcription in two ways (Wingrove & Gober, 1994; Muir et al., 2001; Muir & Gober, 2004). First, FliX stimulates the activation of class III genes by FlbD during the assembly of the basal body. Second, when flagellar assembly is blocked, FliX prevents the activation of the class III gene pathway by FlbD (Muir & Gober, 2002, 2004). Genetic and biochemical studies provide evidence for FliX binding directly to FlbD (Muir & Gober, Mitomycin C in vivo 2002, 2004) to prevent binding to ftr (Dutton et al., 2005); yet, whether FliX associates with FlbD-dependent promoters in vivo remains to be determined. TipF, a predicted 50-kDa protein with two N-terminal transmembrane domains, a coiled-coil region, and a C-terminal EAL domain, is required for flagellum biogenesis (Huitema et al., 2006). TipN, a membrane-embedded landmark protein,
dictates the proper localization of TipF and the flagellar structure (Huitema et al., 2006; Lam et al., 2006). Little is known about how TipF and TipN affect flagellar gene expression. Here, we use β-galactosidase promoter probe assays and quantitative chromatin immunoprecipitation (qChIP) analyses to explore how a ΔtipF mutation Ku-0059436 affects the activity of flagellar promoters when compared with WT, a flagellar assembly (ΔfliG) mutant, positioning
(ΔtipN), and regulatory (fliX∷Tn5 and flbD∷Tn5) mutants. These experiments reveal, for the first time, the direct quantification of the occupancy of flagellar promoters by their cognate transcriptional regulators in vivo. Caulobacter crescentus NA1000, a synchronizable derivative of the CB15 wild-type strain (Evinger & Agabian, 1977), and derivatives were grown at 30 °C in peptone yeast extract (PYE) [2 g peptone, 1 g yeast extract, 0.2 g MgSO4, and 1 mL CaCl2 (0.5 M) per liter] (Poindexter, 1964; Johnson & Ely, 1977). β-Galactosidase activity (Miller, 1972) was measured at 30 °C with log-phase cultures grown in PYE–tetracycline (0.5 μg mL−1). Assays were performed in triplicate, with a minimum of two independent cultures for each promoter construct. For the generation of anti-FlbD antibodies, FlbD was overexpressed Sitaxentan in Escherichia coli Rosetta (DE3)/pLysS using pET28a (Novagen) as an N-terminal His6-tagged variant and purified using Ni-NTA agarose (Qiagen). Purified proteins were cut out from a 12.5% sodium dodecyl sulfate (SDS) polyacrylamide gel and used to immunize rabbits (Josman LLC). Cells (20 mL) were grown to the mid-log phase and cross-linked in 10 mM sodium phosphate (pH 7.6) and 1% formaldehyde for 10 min at room temperature and on ice for 30 min thereafter. Cells were then washed three times in phosphate-buffered saline (pH 7.4), resuspended in 500 μL of TES buffer [10 mM Tris-HCl (pH 7.