2. The cultures were then incubated at 30 °C for 12 h. For qRT-PCR analysis of SYK-6 and ferC mutant, the cells prepared, as described earlier, were used as induced cells, while the cells incubated in LB medium for 12 h, were employed

as uninduced cells. For identification of an inducer, cells of SYK-6, FAK, and FBK were incubated in Wx-SEMP medium at 30 °C for 4 h. After the addition of 5 mM ferulate, 5 mM vanillin, or 10 mM vanillate, the cells were further incubated for 6 h. Total RNAs were isolated as described previously (Kamimura et al., 2010) and then treated with RNase-free DNase I (Takara Bio Inc.) to remove contaminating DNA. RT-PCR and qRT-PCR analyses were carried out according to the previous reports (Kamimura et al., 2010; Kasai et al., 2010). A Beckman H 89 mouse dye D4 (D4)-labeled primer, PEferB, complementary to the ferB mRNA from 91 to 111 nucleotides downstream from the

ferB start codon, was used to INK-128 detect the start site of the ferB mRNA (Table S3). Primer extension reactions were performed as described previously (Kasai et al., 2010). The reporter plasmids carrying the ferB promoter-lacZ fusion with or without ferC were introduced into SME043 cells. The resulting transformants were grown in Wx medium containing 5 mM ferulate or grown in LB medium at 30 °C for 12 h. Preparation of cell extracts and β-galactosidase assays were performed as described previously (Kasai et al., 2010). The coding region of ferC was amplified by PCR using Ex Taq DNA polymerase (Takara Bio Inc.) together with NdeferC-F and R primer pair (Table S3). The 0.6-kb NdeI-XhoI fragment of the PCR product was inserted into pET-16b to generate pETRR1. E. coli BL21(DE3) cells harboring pETRR1 were grown in 100 mL of LB medium at 30 °C. When A600 nm of the culture reached 0.5, expression of ferC with an N-terminal His tag was induced for 6 h by adding 1 mM isopropyl-β-d-thiogalactopyranoside. After the incubation, cells were resuspended in 50 mM Tris–HCl buffer (pH 7.5) and broken by an ultrasonic disintegrator (UD-201; Tomy Seiko Co.). The supernatant obtained by centrifugation (19 000 g, 20 min) was applied to a His Spin Trap (GE Healthcare) previously equilibrated

with buffer A, consisting of 50 mM Tris–HCl (pH 7.5), 500 mM NaCl, and 100 mM imidazole. After the centrifugation at 100 g for 30 s, samples were washed twice with 500 μL of buffer Fossariinae A. His-tagged FerC (ht-FerC) was eluted with 400 μL of buffer B, consisting of 50 mM Tris–HCl (pH 7.5), 500 mM NaCl, and 500 mM imidazole, and resultant fractions were subjected to desalting and concentration by centrifugal filtration with an Amicon Ultra-0.5 10k filter unit (Millipore). The purity of the enzyme preparation was examined by sodium dodecyl sulfate-12% polyacrylamide gel electrophoresis (SDS-PAGE). In vitro cross-linking of ht-FerC was performed as descried in a previous study (Kamimura et al., 2012). EMSAs for ht-FerC were performed with a DIG gel shift kit 2nd generation (Roche).