yfmHG promoter and leader region. (A) Sequence of the yfmHG promoter and leader region. The −35 and extended (ext) −10 promoter elements and the transcription start site (+1) are in bold. The yfmH Shine-Dalgarno (SD) sequence and the YfmH protein-coding sequence including start (ATG) and stop (TAA) codons are shown. The yfmG SD sequence and TTG start codon are also shown. The anti-antiterminator (AAT), antiterminator (AT), and terminator (T) hairpins are indicated by pairs of inverted arrows. The termination site (term) identified in vivo by Term-seq is also marked (Mondal et al. 2016). The overlap between the AAT and AT structures are shown in cyan, while the overlap between the AT and T structures are in red. Numbering is with respect to the start of transcription. (B) Primer extension mapping of the yfmHG transcription start site. Primer extension analysis was performed on total cellular RNA extracted from a wild-type strain of B. subtilis grown in minimal + glutamine medium (M) and minimal medium containing all amino acids (AA). The primer extension product identifying the transcription start site is marked (+1). Sequencing lanes (A, C, G, T) are shown. (C) Transcription attenuation model. Predicted structures of the anti-antiterminator and terminator structures (left) or the antiterminator structure (right) are shown. Overlaps and color coding between the competing structures are as described in A. The yfmH SD sequence, start (met) and stop codons are indicated. Numbering is with respect to the start of transcription.
