Effect of gene cluster relocation to the central chromosomal compartment on its expression in Streptomyces

Streptomyces bacteria are renowned for their intricate life cycle and prolific production of specialized metabolites, including antibiotics. Their linear chromosome is spatially compartmentalized: the central region contains highly conserved and expressed genes, while the terminal regions harbor less conserved, poorly expressed sequences, often rich in specialized metabolite biosynthetic gene clusters. To investigate the relationship between genome architecture and gene expression, we relocated the congocidine antibiotic biosynthetic gene cluster (CGC) from its native terminal position to the central compartment in Streptomyces ambofaciens. This relocation enhanced CGC transcription compared to its original terminal location, both in antisense orientation during exponential growth and in sense orientation after metabolic differentiation, resulting in 50% increase in congocidine production. At the 3D-level, transcription-induced domains formed at both the relocated and native CGC sites, creating sharp boundaries at a larger scale. Notably, the formation of such a boundary in the central compartment during the early stationary phase did not disrupt interarm contacts or affect neighboring gene expression. These results indicate that relocating a terminal cluster to the central chromosomal compartment provides a more favorable environment for transcription without altering chromosome compaction in the stationary phase, offering a promising strategy to enhance antibiotic production in the native host. Key points- Central relocation of a gene cluster enhanced its transcription while preserving chromosome compaction. - A transcription-induced domain formed at the new locus without altering neighboring gene expression. - This strategy increased antibiotic yield by 50% in the native host.