Figure 6: Translational landscape of secondary metabolic genes.

(a) Ribosome-protected fragment (RPF) levels and translation efficiency (TE) fold-changes of the 221 known secondary metabolic genes in S. coelicolor. Leftmost numbers are the SCO gene numbers for each gene cluster. The respective known chemical structures are indicated for each secondary metabolite structure. 1, Mid-exponential phase; 2, transition phase; 3, late exponential phase; 4, stationary phase; T, fold-change between mid-exponential and transition phases; L, fold-change between mid- and late exponential phases; S, fold-change between mid-exponential and stationary phases. (b) mRNA and RPF levels of cluster-situated regulator-encoding transcripts for SCO3217 (CdaR), SCO5085 (ActΙΙ-ORF4), SCO5877 (RedD) and SCO5881 (RedZ) across the four growth phases. (c) mRNA and RPF levels of transcripts for SCO5803 (LexA), SCO3226 (AbsA2), SCO6265 (ScbR) and SCO4230, which represent other regulators of secondary metabolism. (d) Changes in mRNA level and TE. Red dots indicate genes encoding the cluster-situated regulators CdaR, ActΙΙ-ORF4, RedD and RedZ. Blue dots indicate other known regulators of secondary metabolism: SCO2792 (AdpA), SCO5803 (LexA), SCO3226 (AbsA2), SCO5231, SCO3063, SCO4907 (AfsQ1), SCO5260 (AtrA), SCO6008, SCO4159 (GlnR), SCO0310, SCO3932, SCO5405, SCO6265 (ScbR) and SCO4230 (PhoP). Grey dots and dark grey dots indicate, respectively, all genes and secondary metabolic genes. T, fold-change between mid-exponential and transition phases; L, fold-change between mid- and late exponential phases; S, fold-change between mid-exponential and stationary phases.