Escherichia coli BW25113 (ΔaraBD) (Datsenko & Wanner, 2000) and BL21 (DE3) were grown in M9 medium supplemented with 0.2% casamino acids and 0.5% glycerol at 37 °C. The primers used in this study are summarized in Table 1. The coding sequences of ygfX alone or ygfYX were PCR-amplified using primers YGFX-F and YGFX-R1, or YGFY-F
and YGFX-R1, respectively. The fragments were cloned into pBAD24 vector (Guzman et al., 1995) and designated as pBAD24-ygfX and pBAD24-ygfYX, respectively. The coding sequence of YgfX in a fusion with His6-tag at the C-terminal (YgfX−His) was also cloned into pBAD24 using YGFX-F and YGFX-R2. A truncated protein of YgfX (YgfX(C); cloned from V49 to Z135) was cloned into buy Nutlin-3 pCold-Km (unpublished results, Inouye laboratory) using YGFXs-F and YGFX-R1. His6-tagged FtsZ and MreB were constructed previously (Tan et al., 2011). FLAG-tagged FtsZ and MreB
were also previously constructed in pET17b, having a tag at the C-terminal end (H. Masuda and M. Inouye, unpublished results). For examining the growth rate, 0.2% arabinose was added to the cultures during the early exponential phase. His6-tagged YgfX(C), FtsZ, and MreB were expressed in E. coli BL21(DE3). Protein expression was induced for 2 h by adding 1 mM IPTG when the OD600 nm reached 0.8. The cells were collected by brief centrifugation at 8000 g and lysed by French pressure press (Thermo Fisher Scientific, MA). FtsZ and MreB were purified as described before (Tan et al., 2011). YgfX(C)−HIS was purified from the insoluble materials after being dissolved learn more in 8 M urea (pH 8.0). Proteins were purified
using Ni-NTA agarose according to the manufacturer’s instructions (Qiagen, CA). Inner and outer membrane proteins were isolated following the method described previously (Hobb et al., 2009). Briefly, the total membrane proteins were collected from the lysate by ultracentrifugation at 100 000 g for 1 h. The pellet was washed, then resuspended in 1% (w/v) N-lauroylsarcosine in 10 mM HEPES, pH 7.4, and incubated at 25 °C for 30 min with gentle agitation. The inner and outer membrane fractions were further separated by ultracentrifugation. His6-tag pulldown assays were carried out by incubating the cell lysate containing YgfX−HIS and the cell lysate containing FsZ−FLAG or MreB−FLAG (lysis buffer: 50 mM HEPES-KOH, pH 7.5, 10 mM MgCl2, 200 mM KCl, 0.1 mM EDTA, and 10% ID-8 glycerol) overnight at 4 °C. Ni-NTA agarose (0.5 mL) was added to the lysate, and the mixture was incubated at room temperature for 1 h. The beads were washed three times with 20 mL of the same lysis buffer containing 20 mM imidazole. Protein complexes were then separated by 17.5% SDS-PAGE and visualized by Western blot using monoclonal anti-FLAG antibody conjugated with horseradish peroxidase (Sigma-Aldrich, MO). The effect of YgfX on FtsZ and MreB polymerization was determined by a sedimentation method as previously described (Anand et al., 2004) with a few modifications.