CRISPR/Cas9-mediated genome editing to discover new antibiotics in Streptomyces bacteria

HUTCHINGS_J23DTP2

The continued evolution of antimicrobial resistance presents a significant threat to global health and new antibiotics with novel mechanisms of action are urgently needed. Most antibiotics currently used in the clinic are derived from the specialised metabolites of Streptomyces strains isolated more than 50 years ago.
On average, a single Streptomyces strain encodes between 25 and 50 specialised metabolite biosynthetic gene clusters (BGCs), many of which will produce compounds with clinically relevant bioactivity, however, around 90% of these molecules are not produced under standard laboratory conditions, meaning many new compounds remain to be discovered.

To access the full biosynthetic potential of Streptomyces species, cryptic pathways encoding new molecules need to be switched on under laboratory conditions.
The aim of this project is to discover new molecules from Streptomyces formicae, a strain isolated from Tetraponera penzigi plant-ants. Currently, only one antibiotic biosynthesis pathway has been studied in S. formicae, the formicamycin biosynthetic gene cluster (for BCG), however, genome sequencing shows the strain encodes as many as 45 BGCs, most of which are novel.

Recent work in the Hutchings laboratory has used CRISPR genome editing to delete the well studied formicamycin pathway and induce the expression of two previously-cryptic BGCs in S. formicae which have been shown to produce antibiotics.

In this project, the bioactivity of these antibiotics will be characterised in detail to determine their clinical potential. In addition, their biosynthetic pathways will be elucidated, including assigning functions to new genes and defining the transcriptional regulation to gain more understanding of how antibiotics are made in S. formicae. The knowledge gained will inform future natural products and drug discovery projects.

References

Devine R, McDonald H, Qin X, Arnold C, Noble K, Chandra G, Wilkinson B* and Hutchings MI* (2021). Re-wiring the regulation of the formicamycin biosynthetic gene cluster to enable the development of promising antibacterial compounds. Cell Chem Biol. 28:515-23.

Qin Z, Devine R, Booth TJ, Farrar EHE, Grayson MN, Hutchings MI* and Wilkinson B* (2020). Formicamycin biosynthesis involves a unique reductive ring contraction. Chem Sci. https://doi.org/10.1039/D0SC01712D.

Qin Z, Devine R, Hutchings MI* and Wilkinson B* (2019). A role for ABM domain proteins in fidelity control during aromatic polyketide biosynthesis. Nature Comms. 10:3611.

Hutchings MI, Truman A and Wilkinson B (2019). Antibiotics: past, present and future. Curr Op Microbiol. 51:72-80.

Qin Z, Munnoch, JT, Devine R, Holmes N, Seipke RF, Wilkinson B* and Hutchings MI* (2017). Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci. 8:3218-27.