Identification of the negamycin split biosynthetic gene cluster in Kitasatospora purpeofusca ATCC21470

Strueder, A.; Touzi, S.; Long, M.; Mingyar, E.; Schwitalla, C.; Berscheid, A.; Bourcier, S.; Broetz-Oesterhelt, H.; Darbon, E.; Frankenreiter, P.; Franz-Wachtel, M.; Geibel, C.; Harbig, T.; Hughes, C. C.; Macek, B.; Nieselt, K.; Sales-Ortells, H.; Touboul, D.; Lautru, S.; Stegmann, E.

doi:10.1101/2025.07.31.667836

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bioRxiv · 10.1101/2025.07.31.667836

Identification of the negamycin split biosynthetic gene cluster in Kitasatospora purpeofusca ATCC21470

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Abstract

Negamycin is a ribosome-targeting antibiotic with activity against Gram-positive and Gram-negative bacteria including ESKAPE pathogens. Furthermore, it promotes premature stop codon readthrough. Its therapeutic potential is limited by low natural production and synthetic complexity. To enable scalable biosynthesis, we identified and characterized its genetic basis in Kitasatospora purpeofusca ATCC 21470. Two distant chromosomal regions, neg1 and neg2, were found to be essential. Deletion of neg1, involved in nitrite provision for N-N bond formation, reduced production to [~]10%, while deletion of neg2, which directs {beta}-lysine generation and scaffold assembly, abolished it completely. Isotope-labeling experiments confirmed nitrite incorporation. Transcriptomic and proteomic analyses further supported the involvement of both regions. The heterologous expression of neg1 along with the neg2 region in Streptomyces albidoflavus reconstituted negamycin biosynthesis, confirming the unusual involvement of two distant gene clusters in the biosynthesis, and provides a foundation for biotechnological production and further development of this promising antibiotic. SIGNIFICANCEThe rapid rise of antimicrobial resistance (AMR), particularly among Gram-negative ESKAPE pathogens, represents one of the most urgent global health threats. Despite this, the discovery and development of new antibiotics have stagnated. Addressing this challenge requires the exploration of natural products with novel mechanisms of action, alongside the development of scalable production strategies. Negamycin has emerged as a compelling candidate in this regard, characterized by an unusual mechanism of action and therapeutic potential extending beyond traditional antibacterial use. However, its development has been constrained by low production yields in the native producer. In this study, we identify and characterize the biosynthetic genes responsible for negamycin production, providing a foundation for pathway engineering, yield optimization, and the rational design of new analogs.

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Strueder, A., Touzi, S., Long, M., Mingyar, E., Schwitalla, C., Berscheid, A., Bourcier, S., Broetz-Oesterhelt, H., Darbon, E., Frankenreiter, P., Franz-Wachtel, M., Geibel, C., Harbig, T., Hughes, C. C., Macek, B., Nieselt, K., Sales-Ortells, H., Touboul, D., Lautru, S., Stegmann, E.. 2025-07-31. Identification of the negamycin split biosynthetic gene cluster in Kitasatospora purpeofusca ATCC21470. https://doi.org/10.1101/2025.07.31.667836

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