σB can activate both transcription and translation. (A) Models of transcriptional and translational induction for a transcriptional unit consisting of a promoter, coding sequence, and terminator. Stimuli are indicated with lightning bolts and ribosomes are colored in yellow. (B) RNA-seq, (C) ribosome profiling, and (D) apparent translation efficiency measurements from σB active and inactive conditions. σB regulon genes are indicated with black crosses (+), and subsets that are translationally activated or translationally repressed are highlighted in red and yellow, respectively (Rend-seq/ribosome profiling traces shown in Supplemental Fig. S4). Induced σB regulon genes without complex isoform architecture (Materials and Methods) are highlighted in cyan (Rend-seq/ribosome profiling traces for a subset shown in Supplemental Fig. S5). The dashed blue lines mark a 3.7-fold change in expression for visual reference. The dashed red line is an approximate threshold (2.7-fold) separating the population of translationally activated genes from those whose apparent TE does not markedly change. The insets show the cumulative distribution function (CDF) of fold change (FC) across the two conditions in each measurement, with separate CDFs for all genes (gray) and σB regulon genes (black). The percentage of genes in each group exceeding the chosen thresholds are listed on the right. Contributions of mRNA levels and translation to changes in protein synthesis rate among (E) translationally activated σB regulon genes and (F) a representative subset of induced σB regulon genes without complex isoform architecture. The fold change in protein synthesis rate is indicated by the height of the bars up to the arrows (arrows pointing down correspond to decreased translation efficiency). The light and dark gray regions denote the respective contributions of mRNA levels and translation, that is, fold-change in protein synthesis = (fold-change in mRNA level) × (fold-change in translation efficiency).
