The MtrAB-LpqB two component system links development with secondary metabolite production in Streptomyces species and can be manipulated to switch on silent secondary metabolite clusters

Streptomyces species are important producers of bioactive compounds such as antibiotics, antitumor and immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria and antibiotic production is linked to sporulation. The discovery of new bioactive compounds has declined since the 1960s but genome sequencing has revealed the potential to identify many more bioactive compounds. They are many secondary metabolite gene clusters which are inactive (silent) under laboratory conditions. We characterize the highly conserved actinobacterial two component system MtrAB which coordinates sporulation with secondary metabolite production in the two model organisms Streptomyces venezuelae and S. coelicolor. Deletion of the histidine kinase gene mtrB resulted in increased production of the antibiotic chloramphenicol in S. venezuelae and actinorhodin and undecylprodigiosin in S. coelicolor. Chloramphenicol is not usually produced under laboratory condition which suggests that deleting mtrB can activate silent antibiotic clusters. Additionally, we introduced point mutations at the D56 phosphorylation site of MtrA by CRISPR-Cas9 to abolish phosphorylation. This mutant shows the same phenotype as the ΔmtrA strain and chloramphenicol production is increased. Chromatin immunoprecipitation and sequencing (ChIP-seq) was used to identify MtrA targets and revealed that MtrA likely controls secondary metabolite production by binding to the promoter regions of cluster situated regulators in both model organisms. Additionally, MtrA binds upstream of genes involved in DNA replication and cell division. To our knowledge this is the first evidence of the connection of development and secondary metabolite production by a two component system.