Fig. 5
Examples of gene loci and operon predictions. The double-lines indicate the genomic DNA. rTSSs are indicated as bent black arrows, with genomic positions, and RNA as thin black arrows. ORFs are shown as light grey arrows. Transcriptional terminators predicted by TransTermHP [39] are indicated by stylised hairpins. The nucleotide position of each key element is also shown. a Layout of the spx and trfA locus, with multiple TSSs for each ORF (the use of the names trfA and mecA depend on which S. aureus genome annotation is used). b The valS-folC operon. Expression of the valine-tRNA ligase (valS) is tightly controlled by a T-box riboswitch in its 5’-UTR (thick dark grey line) that is transcribed from a position 350 nt upstream of the ORF [23]. The transcript continues into the downstream folC gene, which seems to be dually controlled by both the T-box riboswitch and by its own promoters at positions 1734661 and 1734683. c An example of the beginning of ribosomal RNA operon, where multiple promoters (and TSSs) permit high transcription. Only the first gene of the operon (16S rRNA) is shown as a dark grey line. d Example of an operon where separate σA and σBpromoters contribute to expression (indicated underneath their respective bent arrows)