A synthetic genomics platform for antibiotic discovery

Antibiotic resistance is the "slow pandemic". A recent UN report estimates that by 2050 it will be responsible for 10 million deaths a year globally, with an economic impact comparable to the 2008 financial crisis. Development of tools to tackle resistance to antimicrobial compounds is of pressing importance and has been identified as a key objective in the BBSRC's Forward Look for UK Bioscience.
Nonribosomal peptides (NRPs) represent a diverse class of secondary metabolites and include many antibiotics and antibiotic precursors. They typically consist of amino acids that are assembled enzymatically and then modified by an array of tailoring enzymes. In this way, a core antibiotic molecule can be modified in many ways, potentially circumventing antibiotic resistance mechanisms.
We have shown that NRP antibiotic production can be achieved in yeast using a synthetic biology approach. Yeast has an unparalleled genetic toolbox available, opening up new possibilities for discovering novel NRP-derived antibiotics
In this project, the student will establish a synthetic yeast platform for production and screening of novel NRP molecules for antibiotic properties. The bacterial co-culture system established in the rotation project will be used to select a strain that is enhanced for penicillin production through SCRaMbLE genome evolution. This strain will then act as the base NRP-production strain for combinatorial prototyping of tailoring enzyme combinations.
Bioinformatics tools will be used to identify candidate tailoring enzyme genes from genomic datasets to be tested in our system. Genes will be cloned into a Golden Gate library with SCRaMbLE-compatible formatting. Libraries of different gene combinations will be introduced to the NRP-production strain and SCRaMbLE will be used to further increase host genome and library diversity. These massively diversified libraries will be co-cultured with bacterial strains with different antibiotic resistance profiles. Survival of the yeast cells in these conditions will be reliant on the inhibition of bacterial growth in a way that evades the respective antibiotic resistance mechanism. Strains surviving the assays will be isolated and fully characterised to identify any novel compounds that act as antibiotics or that inhibit antibiotic resistance mechanisms.
This work will establish the feasibility of a synthetic yeast approach to antibiotic discovery and may yield novel antimicrobial compounds. The system could subsequently be expanded to include a wider range of candidate tailoring enzymes and additional NRP molecules.
Supervision Team - Benjamin Blount is an expert in synthetic genomics and a member of the International Synthetic Yeast Genome Project. He was part of the first team to successfully engineer NRP antibiotic production into S. cerevisiae yeast and was the first to demonstrate that SCRaMbLE can be used to improve production from engineered pathways, including penicillin. John Heap is an expert in combinatorial approaches to metabolic engineering and the application of synthetic biology techniques to the improvement of strains for biotechnology.