Figure 3. Putative σ⁵⁴ promoters are found in the majority of polyketide and non-ribosomal peptide biosynthetic gene clusters.

(a) The oxyABCDEF operon from the S. rimosus oxytetracycline biosynthetic pathways contains a putative σ⁵⁴ promoter. The promoter shows high homology to the σ⁵⁴ promoter consensus sequence especially at the key −12 and −24 positions. A mutation of the highly conserved GG residues at −24 (−24*) and 5′ RACE were used to confirm that this promoter is responsible for direct, positive transcriptional regulation of the oxyB gene by σ⁵⁴ over-expression. (b) Transcription of the oxyABCDEF operon is directly controlled by the σ⁵⁴ promoter upstream of oxyA. Mutation of the highly conserved GG residues −24 from the transcriptional start site to TT leads to a greater than 40 fold decrease in oxyB transcript levels as determined by qPCR. qPCR data was obtained from BAP1 transformed with pDCS11 and either pDCS61 or pDCS62. (c) Results of a bioinformatics analysis of 58 bacterial genomes containing 180 polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) biosynthetic gene clusters show that the majority of gene clusters contain putative σ⁵⁴ promoters. It is particularly intriguing that Actinobacteria possess gene clusters with σ⁵⁴ promoters since they lack the gene encoding σ⁵⁴. See also Tables S2, S3, S4.