Differential translation of mRNA isoforms transcribed with distinct sigma factors

Translationally activated σ^B regulon genes display alternative mRNA isoforms. Rend-seq and ribosome profiling data from conditions with inactive/active σ^B for the operons containing (A) ctc and (B) yvrE (σ^B regulon genes are highlighted in red). Orange and blue bars represent 5′- and 3′-mapped read counts, respectively, and the black scale bars correspond to 0.5 kb. Fold changes (FC) for Rend-seq and ribosome profiling between σ^B active and σ^B inactive conditions are shown. Rend-seq 5′ ends corresponding to the σ^B-dependent transcription start sites are marked by red arrows. Putative σ^B-dependent promoter sequences are listed for each gene (+1 corresponds to the 5′ end of the σ^B-dependent isoform mapped by Rend-seq). The consensus sequences for the −10 and −35 regions of σ^B-dependent promoters are GTTTaa and GGG(A/T)A(A/T) (Petersohn et al. 1999). For ctc specifically, the additional 5′/3′ peak pair (*) in the σ^B active condition corresponds to a spurious RNase A cleavage site that likely occurred post-lysis. See also Supplemental Figures S1, S2.