Analysis of the deduced amino acid Lumacaftor mw sequence of the PhaR protein revealed the presence of a helix–turn–helix motif, which is a feature of a DNA-binding domain. We have determined that this protein can bind to the promoters of phaP, phaR, phaC, or phaZ of Rhodobacter sphaeroides

FJ1. We also found the sequences CTGCGGCGCAG located at nucleotides −69 to −59 and CTGCGGCTGCAG located at −97 to −87 relative to the translation start site of the phaP gene capable of forming a palindrome, which is a characteristic feature of a repressor-binding site. Therefore, we examined its ability to bind the PhaR protein and to function as a regulatory sequence in vitro and in vivo. Rhodobacter sphaeroides wild-type strain FJ1 was described previously Gefitinib in vitro (Yang et al., 2006). Plasmids were replicated in Escherichia coli strain DH5α (Invitrogen, Carlsbad, CA). Rhodobacter sphaeroides cells were grown in TSB medium (10 g of Bacto tryptone, 5 g of Bacto soytone, 5 g of NaCl, and 2 g of glucose per liter) at 28 °C in an incubator (100 × 40 × 50 cm3 in size) illuminated with two 60 W incandescent light bulbs, and E. coli cells were grown at 37 °C in Luria–Bertani medium. PCR was performed using Taq DNA polymerase (Invitrogen). Southern hybridization was performed using DNA probes labeled with digoxigenin by random priming. DNA sequences were determined using

the dideoxy chain termination method (Sanger et al., 1977) using Pfu DNA polymerase (Stratagene, La Jolla, CA). The PhaR protein was purified from the cell

lysate of E. coli strain ER2566 harboring pHbR1E as described previously (Chou et al., 2009). The DNA fragments 187-bp FP1 and 134-bp FP2, consisting of nucleotides −71 to +116 and −216 to −83 relative to the translation start site of phaP, respectively, were used as the probes for EMSA. To identify the PhaR-binding sequence, mutagenesis was performed on fragment HSP90 FP1 by PCR with various primers (Table 1). All mutations generated were confirmed by DNA sequencing. EMSA was performed using a DIG gel shift kit (Roche Applied Science, Indianapolis, IN). The DNA probes were labeled at their 3′-ends with DIG-11-ddUTP using terminal transferase. The EMSA reaction mixture (10 μL), which contained 0.75 ng of a DIG-labeled probe and various amounts of the PhaR protein in binding buffer [50 mM NaCl, 20 mM Tris-HCl (pH 7.5), 1 mM dithiothreitol, and bovine serum albumin (100 μg mL−1)], was incubated at room temperature for 15 min and then mixed with 2.5 μL of a loading buffer (0.25 × TBE buffer, 40% glycerol, and 0.2% w/v bromophenol blue). The entire mixture was loaded on a native 5% polyacrylamide gel (acrylamide : bisacrylamide=29 : 1 w/w). The Mini-PROTEAN II Dual Slab Cell (Bio-Rad, Hercules, CA) electrophoresis apparatus was used. Electrophoresis was carried out with 0.5 × TBE buffer (pH 8) at 64 V at room temperature for 2 h. The gel was then blotted onto a positively charged nylon membrane using the Mini Trans-Blot (Bio-Rad) apparatus at 30 V for 30 min.