Differential translation of mRNA isoforms transcribed with distinct sigma factors

σ^A-dependent mRNA isoforms have extended secondary structures in vivo. (A) Minimum free energy (MFE) structures of the σ^A-dependent isoforms of ctc and yvrE near the ribosome binding site. 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. (B) DMS-MaPseq workflow for in vivo RNA structure determination of σ^A-dependent isoforms. (C) Cumulative distributions of the per-base mutational fractions for the σ^A-dependent isoforms of ctc and yvrE. Solid and dashed lines indicate conditions with and without DMS treatment. (D) DMS-constrained MFE structures of representative transcripts for σ^A-dependent isoforms of ctc and yvrE colored by normalized DMS-MaPseq mutation rate (DMS signal), where values correspond to increased base accessibility. Structured regions containing putative SD sequences are magnified.