Biosynthetic Origins and Utility of the Natural Product Antibiotic Nybomycin
Lead Research Organisation:
John Innes Centre
Department Name: UNLISTED
Abstract
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Technical Summary
The bacterial natural product nybomycin was first reported in 1955 but did not find clinical utility. Nybomycin was rediscovered during a screen for substances active against multidrug-resistant Staphylococcus aureus M50 which identified an actinomycete fermentation extract with a curious activity profile. Specifically, nybomycin is inactive against strains carrying intact type-II topoisomerase genes and active against those with mutated genes. Unexpectedly, rather than select for further additional mutations to generate dual resistance, quinolone resistant strains treated with nybomycin reverted to quinolone sensitivity by reversion of the relevant mutation, albeit at a low rate. Due to these phenomena nybomycin was termed a ‘reverse antibiotic’. Nybomycin’s biogenesis has remained elusive and this research project will utilise chemical and genetic studies (genome sequencing, mutational analysis) to elucidate the biosynthetic pathway and enable bioengineering studies to access increased titres and novel analogs in order to provide starting materials for the semi-synthesis of second generation nybomycins.
Planned Impact
unavailable
| Description | Directly related to the project: We have identified the nybomycin biosynthetic gene cluster via bioinformatics means. This involved generating a bespoke script to search the genome of the producing organism in order to find a cluster of genes encoding the key enzymes we anticipated would be required. We will use this data to probe the biosynthetic pathway in a follow on grant. 2020: We have now cloned the gene cluster using a new Cas9 mediated technique and overexpressed it in a new heterologous host when all standard hosts failed - this represents a significant advance technology wise; we are investigating how broadly the host may be useful. Heterologous expression led to the production of a new, more soluble analogue and we are scaling up production. In biochemical assays we have preliminary data that suggests the 'reverse' antibiotic nature of nybomycin may not be correct and a manifestation of pleotropic in vivo effects. Further analysis of this and of biosynthesis are underway. Indirectly related: We identified a new genetic architecture for a Streptomyces strain with a 4.2 Mb second genetic element, possibly a second chromosome (not observed before). A publication in in preparation on this work. |
| Exploitation Route | The core project has not developed to a stage where it would be of use to external researchers yet. However, the approach of generating a bespoke script to identify a specific biosynthetic gene cluster will be of significant interest to the biosynthesis community once published. 2020: the BGC cloning method and heterologous host may be useful generally. |
| Sectors | Manufacturing including Industrial Biotechology |
| Description | Nybomycin responsive mode follow on |
| Amount | £517,000 (GBP) |
| Funding ID | BB/P021506/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2020 |
| Description | Biosynthesis of natural products from an Australian actinomycete strain library |
| Organisation | BioAustralis |
| Country | Australia |
| Sector | Private |
| PI Contribution | Biosynthesis; genome mining; natural products chemistry |
| Collaborator Contribution | Strain and compound provision; data on metabolite profiles; fermentation data |
| Impact | Successful grant applciations |
| Start Year | 2014 |
| Description | School visit (Cambourne Cambs) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Spent two days presenting a cross curriculum presentation to two classes of Year 6 pupils at a primary school in collaboration with the SAW Trust (http://sawtrust.org/ ). Much debate and discussion about the topics of microbes, antibiotics, ecology and antimicrobial resistance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://sawtrust.org/buy-the-books/saw-antibiotics/ |