Investigating RNA polymerase regulation in antibiotic producing streptomyces bacteria

Organisms belonging to the Streptomyces genus produce a vast number of useful secondary metabolites, including over half of all clinically relevant antibiotics. Recent genome sequencing, however, has revealed large clusters of genes in Streptomyces that are not expressed under standard growth conditions and that hold potential for the discovery of novel antibiotics. Several studies have shown that certain RNA polymerase mutations can increase antibiotic production, as well as stimulate the synthesis of previously undetected secondary metabolites. However, the basis of this is not understood and little is known about how RNA polymerase levels are controlled in Streptomyces. The analysis of RNA-seq data from S. coelicolor and S. venezuelae revealed that the rpoBC operon, encoding the large ß and ß’ subunits of RNA polymerase, is subjected to a largely unstudied form of gene regulation known as reiterative transcription (RT) at the transcriptional start site. This is the first identified case of RT in Streptomyces, with this study focussing on further understanding this nucleotide based control of gene expression. Mutagenesis of this TSS was carried out revealing RT has a detrimental effect on the expression of rpoBC. Further use of reporter-based transcriptional fusions also revealed several regulatory elements are present within the 5’ UTR region of rpoB also affecting expression of these large RNA polymerase subunits. This contribution to a greater understanding of how RNA polymerase levels are controlled in Streptomyces, might enable novel approaches towards the synthesis of novel inhibitory compounds and therefore contribute to overcoming the current antimicrobial resistance crisis.