3). Notably, Compound Library molecular weight qChIP experiments revealed that CtrA occupied the fliF promoter at similar levels in ΔfliG and ΔtipF (99 ± 4% and 80 ± 6% relative to WT, respectively) (Fig. 3), indicating that the increase in class II flagellar gene transcription

in ΔfliG and ΔtipF mutants is not due to an elevated occupancy of CtrA at the promoter(s). Consistent with fliF upregulation seen in ΔfliG and ΔtipF by the β-galactosidase assay, qChIP revealed that the occupancy of FlbD (repressing class II genes) was decreased at the fliF promoter in the ΔfliG (45 ± 1%) and ΔtipF (51 ± 8%) strains (Fig. 4a). FliX, the regulatory factor that links the status of flagellar assembly to FlbD activity (Muir & Gober, 2005), was present at the class II promoters, at higher levels than WT, in ΔfliG (170

± 7%) and ΔtipF (144 ± 4%), consistent with the decreased levels of FlbD at the fliF promoter (Fig. 4a). FliX has been shown to interact with FlbD and block its access to enhancer DNA sequences in vitro (Dutton et al., 2005), and this new qChIP-based approach further suggests that FliX occupies the promoters to modulate FlbD activity at the class II-fliF promoter in vivo. Next, we determined the presence of FlbD and FliX at the class III-flgE and class IV-fljL promoters. qChIP showed that FlbD occupancy at the class III-flgE promoter was reduced in ΔfliG (68 ± 5%) and ΔtipF strains (75 ± 10%) (Fig. 4b), while that of FliX was elevated (155 ± 5% in ΔfliG and 227 ± 9% in ΔtipF) (Fig. 4b). These data demonstrate that the ΔtipF

strain is similar to the ΔfliG mutant strain with regard to the occurrence of FlbD LEE011 nmr and FliX at the flgE promoter. It is further consistent with the view that FliX is also present at class III promoters to block FlbD access. The class IV-fljL promoter, however, had an abundance of FlbD similar to WT (123 ± 8%) and decreased levels of FliX (64 ± 7%) in ΔtipF, while the ΔfliG mutant had decreased FlbD (20 ± 2%) and increased FliX (200 ± 9%) (Fig. 4c). These results, also supported by the β-galactosidase promoter-probe assays (Fig. 2), suggest that, unlike FliG, TipF is not necessary to confer the transcription of class IV flagellar genes. Both flbD∷Tn5 and fliX∷Tn5 mutant strains were included as controls. Accordingly, FlbD was considerably Epigenetics inhibitor decreased at the fliF (7 ± 1%), flgE (22 ± 3%), and fljL (7 ± 1%) promoters in the flbD∷Tn5 mutant compared with WT (Fig. 4a–c). Similarly, the fliX∷Tn5 mutant had decreased levels of FliX at the fliF (8 ± 2%), flgE (15 ± 1%), and fljL (15 ± 1%) promoters (Fig. 4a–c). The ΔtipN mutant possessed lowered levels of FlbD at the fliF (69 ± 5%) and flgE (57 ± 3%) promoters, while fljL (103 ± 9%) was near WT levels (Fig. 4a–c). FliX was present at the fliF (109 ± 8%), flgE (166 ± 9%), and fljL (129 ± 25%) promoters in the ΔtipN mutant relative to WT. Because the ΔtipN mutant frequently possesses multiple flagella that are often misplaced (Huitema et al., 2006; Lam et al.