Characterization of the sequence motifs for MtrA in the M. tuberculosis dnaA gene promoter region. The DNA-binding assays of M. tuberculosis MtrA were performed using modified EMSA and SPR assays, as described in "Materials and Methods". (A) Several short DNA fragments were synthesized and used as DNA substrates, which covered a different dnaA gene promoter region. The sequences of their positive strands are indicated, and two 7 bp motifs are underlined. (B) The DNA-binding assays for MtrA on different DNA substrates. The EMSA reactions (10 μl) for measuring the mobility shift contained 200 fmol 32P-labeled DNA and increasing amounts of MtrA proteins (100 nM-600 nM). The protein/DNA complex is indicated by arrows on the right of the panels. (C) Schematic representation of conserved motifs located downstream of two dnaA promoters. The base-pair numbers far from the start codon of the dnaA gene are indicated.