Differential translation of mRNA isoforms transcribed with distinct sigma factors

Long-range mRNA secondary structures in σ^A-dependent isoforms sequester sequence elements necessary for translation. MFE structures of transcripts for σ^A-dependent isoforms of other translationally activated σ^B regulon genes. The transcription start sites of σ^B-dependent isoforms (indicated with arrows), putative Shine–Dalgarno (SD) sequences, and start codons are highlighted in magenta, blue, and green, respectively. The stop codon of the upstream gene in the operon is indicated with an orange box. Computationally determined base-pairing probabilities for individual bases in the SD sequences are shown beside each structure.