Fig. 4: Regulation of several genes under the control of TrcR.

a EMSA showing the binding of TrcR to the promoter regions of trn and other potential target genes (with more than 8-folds upregulation in ΔtrcR). b Purification and quantification of TrcR and TrcR-L44P (TrcR bearing a mutation with replacement of L44 by P) used for EMSA by SDS-Polyacrylamide Gel Electrophoresis following Coomassie blue staining. c Binding assay of TrcR-L44P to the promoters of trn, alr3301, all3526, alr8077 and all8564 tested by EMSA. No binding to any promoter was detected. d Transcription levels of all3526, alr8077 and alr3303 quantified by qRT-PCR in WT, ΔtrcR and C-trcR. n = 3 biologically independent samples. The experiment was repeated three times for each sample. Data shown are the mean values ± S.D. e The consensus binding motif of TrcR based on the DNA region protected by TrcR in footprint experiments. Analysis was performed by using MEME on website (https://meme-suite.org/meme/tools/meme). f Relative positions of the identified TrcR binding motif (shaded background) and the −10 boxes (red letters) are shown in the promoter regions of trcR, alr1537, alr3301, all3526, alr3077, all8564 and trn. The positions of −10 boxes were deduced based on the RNA-Seq data from Mitschke et al.²⁶.