FIGURE 5.

Transcriptional organization of the btm gene cluster. (A) RT-PCR cotranscription analysis of the intergenic regions with no overlapping genes in the btm cluster (highlighted with blue squares in the schematic representation of the btm gene cluster below the gel images; loop symbols in this diagram indicate the location of predicted transcription terminators -solid line- and attenuators -dashed line- in the cluster). (B) Transcription start site mapping of the btm cluster using 5′-tag-RNA-seq. The plots (generated in IGB) show the mapping of reads with TSS tags in the btm cluster in the WT (top) and ΔbtmL (bottom) strains. Sharp peaks corresponding to mapped reads precede btmB, btmC, and btmD, along with some non-specific transcription initiation in the btmD region. The vertical axis in the plots represents read counts and the horizontal axis maps to the gene cluster shown in (A). The direction of transcription from the identified TSSs is represented with black arrows in the cluster. (C) Precise mapping of TSS and potential promoter regions in the btmB-C intergenic region. btmB and btmC start codons are marked in green, and the TSSs identified for btmB and btmC using both 5′tag-RNA-seq and 5′-RACE are labeled in red. −10 and −35 promoter regions for btmC (predicted with BPROM) and btmB (annotated manually) are represented in light blue. (D) Mapping of btmD TSS (red) within the coding sequence of btmC (shadowed in gray, with its stop codon highlighted in bold).