Anti-infective discovery from competitive ecosystems

One of the biggest threats to global health and food security of our time is antibiotic resistance (AMR) causing existing antibiotics to become ineffective as a treatment for humans and livestock. AMR is a natural evolutionary process but misuse of antibiotics (for example, through inappropriate prescription) is causing it to develop at a much faster rate. In order to tackle the AMR crisis, new antibiotics need to be discovered and a large proportion of antibiotics originate from fungi, bacteria and plants as natural products. These, also called secondary metabolites (SMs), are produced by organisms as they provide an ecological and physical advantage to better survive in their habitat.

A relatively understudied organism is the filamentous fungus Escovopsis weberi which has been isolated from leaf-cutter ants. E. weberi has adapted to grow in a very competitive environment, and SMs play a key role in its ability to cause disease (pathogenicity). Recent work has identified that this fungus produces a range of SMs with antifungal and antibacterial properties in order to compete with other microbes. Analysis of the E. weberi genome has identified that this fungus could produce many new and potentially bioactive SMs. At present, their discovery is halted by the lack of genetic tools and thorough chemical investigation.

This research program will aim to address the current AMR crisis by developing different tools that can be used to discover new natural products from E. weberi. The project will use microbiological, chemical and genetic techniques to culture E. weberi under a wide range of growth conditions with the aim of stimulating the production of new SMs. These cultures will be chemically extracted and thoroughly investigated with a very sensitive technique called liquid chromatography coupled with mass spectrometry. Any SMs will be isolated and later screened for antibacterial and antifungal activities. The SMs will also be investigated for their ecological role in the context of the leaf-cutter ant ecosystem.

The research will also develop the first genetic tools to manipulate the genome of E. weberi. This will allow targeting of specific genes required to synthesise new SMs, which in fungi are usually arranged in what is known as a multigene biosynthetic gene cluster. Genetic manipulation will also aim to engineer new strains that can produce valuable SMs in high quantities.

This project will be a step towards identifying new and effective antibiotics and further demonstrate the importance of natural product research using fungi isolated from complex ecosystems. Results will also yield a better understanding of the leaf-cutter ant ecosystem and provide chemical and genetic tools that could also be applied to other microbiomes.

Many important and economically valuable drugs are derived from fungal natural products. Recent advances in sequencing and bioinformatics analysis have revealed that fungal genomes encode for a high number of biosynthetic gene clusters (BGCs) with the potential of producing many new compounds. There are an estimated 5.1 M species of fungi but only a small portion (~3%) has been investigated.

Escovopsis weberi is a fungal pathogen of leaf-cutter ants which has co-evolved with other microbes. Recent work has isolated some known secondary metabolites (SMs) with antifungal and antibacterial properties and defined their ecological roles. Bioinformatics analysis revealed that several unique BGCs are encoded in the genomes of seven E. weberi strains and preliminary work has resulted in the isolation of the first fungal aminonucleoside SMs.
This project will use a combination of chemistry, genetics, microbiology and bioinformatics to develop a platform tailored to mine new bioactive compounds from E. weberi, to investigate their biosynthesis and to yield a better understanding of the complex ecosystem of the leaf-cutter ants.

The research program has three main objectives:
Firstly, investigate the biosynthesis of fungal aminonucleoside SMs using bioinformatics, endogenous transformation and heterologous expression.
The second objective is to induce the production of new SMs by screening several growth conditions, co-cultivation with other microbes and using chemical epigenetic modifiers. The cultures will be chemically extracted, and metabolomics analysis will be used to identify new SMs. These will be screened for biological and ecological activities.
The final objective will aim to develop a transformation system and optimise the Aspergillus oryzae heterologous platform for E. weberi. These genetics tools will be used to investigate the biosynthesis of new SMs, activate silent BGCs and target chromatin remodelling proteins to modify secondary metabolism.