Discovery of natural products that are critical for controlling plant pathogens (TRUMAN_J17DTP)
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
Plant diseases are a huge problem for many crops, and can cause a vast amount of ecological and economic damage. In many cases, it is difficult to control these diseases as current treatments are ineffective, expensive or environmentally damaging. A promising route to disease control is the use of bacterial biocontrol strains that naturally inhibit pathogen growth, and there is significant evidence to show that bacterial natural products are critical for the suppression of various pathogens. This is consistent with the crucial role that natural products have across medicine (e.g. antibiotics) and agriculture (e.g. insecticides).
This project will investigate a novel family of Pseudomonas natural products that were discovered using a pathogen suppression screen using common scab, an economically important bacterial disease that affects potatoes. These compounds will be structurally characterised, and their bioactivities, regulation and biosynthesis will be determined. The project will also employ our genome-based screening approach to identify natural products that contribute to the suppression of other plant diseases, with the ultimate aim of developing compounds or strains that can be used to control plant disease.
This project will investigate a novel family of Pseudomonas natural products that were discovered using a pathogen suppression screen using common scab, an economically important bacterial disease that affects potatoes. These compounds will be structurally characterised, and their bioactivities, regulation and biosynthesis will be determined. The project will also employ our genome-based screening approach to identify natural products that contribute to the suppression of other plant diseases, with the ultimate aim of developing compounds or strains that can be used to control plant disease.
People |
ORCID iD |
| Andrew Truman (Primary Supervisor) | |
| Alaster Moffat (Student) |
Publications
Moffat AD
(2021)
A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition.
in Synthetic biology (Oxford, England)
Moffat AD
(2021)
A User Guide for the Identification of New RiPP Biosynthetic Gene Clusters Using a RiPPER-Based Workflow.
in Methods in molecular biology (Clifton, N.J.)
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 1937478 | Studentship | BB/M011216/1 | 01/10/2017 | 30/09/2021 | Alaster Moffat |
| Description | Through development of an automated screening workflow, in collaboration with the Earlham Institute (Norwich, U.K.), we were able to discover a gene cluster in parallel with another research group, that was previously unknown. This worked has linked the biosynthesis of tropolone natural products in Proteobacteria to the inhibition of the economically important plant pathogen Streptomyces scabies. However, the biosynthetic pathway of the tropolone natural product, and indeed the identity of the final products of the pathway, are not yet known. Our data suggests possible additional uncharacterised molecules arising from this pathway, which we are in the process of investigating. |
| Exploitation Route | If the compound proves to be of relevance to agriculture, there is the possibility of collaborating with non-academic industrial partners to explore a broader range of assays, and evaluate the feasibility for commercial production. If a novel biosynthetic mechanism is discovered, there is the potential to search bacteria for related compounds in other species, and to investigate its relevance to interspecies interactions in the soil environment by our research group and others in the field. |
| Sectors | Agriculture, Food and Drink,Environment |
| Description | Given the promise of certain strains for development as biocontrol agents, I was involved in the formulation of strains for field trials. The trials involved prophylactic application of candidate biocontrol strains to potato crops, and comparing the efficacy of this treatment to the current gold-standard chemical treatments against potato late blight caused by Phytophthora infestans. This work was carried out with VCS Potatoes in Norfolk, UK. There is the potential for future field trials using similar inocula, looking for efficacy against potato common scab caused by Streptomyces species. |
| First Year Of Impact | 2020 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Title | Development of a automated screening platform to investigate genes involved in pathogen inhibition in bacteria |
| Description | The method involved automating a process usually performed by hand, by making use of the Biofoundry at the Earlham Institute (Norwich, UK). We used a liquid handling robot to perform curation and screening of a transposon mutant library that we had generated using standard methods. The improvements were in reproducibility, time saving, and allowing the workflow to be performed under conditions that would have been prohibitively time-intensive if performed by hand. In short, the colony-picking functionality of the liquid handling robot created a library of 2,880 bacterial mutants in a standard 96-well format. The platform was then used to automatically apply an indicator strain to 2,880 wells in 24-well plates (a conversion that would be error prone and time intensive by hand), then inoculate these wells with the mutants to be tested. After some days of incubation, the 24-well plates could then rapidly be investigated visually. This workflow was estimated to save a number of weeks, massively aid reproducibility and accuracy, and reduce repetitive strain injury. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Developing and using this approach allowed us to discover a previously unannotated gene cluster in the bacterial strain under investigation, and link it for the first time to inhibition of a commercially relevant crop pathogen, Streptomyces scabies. |
| URL | https://academic.oup.com/synbio/article/6/1/ysab004/6122745 |
| Description | Collaboration with DNA Foundry at Earlham Institute on a high throughput assay for bacterial phenotyping |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Use of the experience and facilities at the Earlham institute facilitated a particularly troublesome assay that was important to the research, enabling high throughput assay of many bacterial mutants in an error-free way. This work is helping us to identify the genetic basis for an antimicrobial phenotype in an environmental bacterial isolate. |
| Collaborator Contribution | Our collaborators enabled access to specialist equipment at a lower rate, charging only for equipment time and consumables. The expertise provided by our collaborators was indispensable for this experiment. |
| Impact | A poster presentation at the John Innes Centre annual science meeting (2019). This work has now been published in Synthetic Biology as an open access article entitled A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition. |
| Start Year | 2019 |
| Description | Earlham Institute Biofoundry |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Development of an assay for strains that inhibit the growth of the plant pathogen Streptomyces scabies |
| Collaborator Contribution | Technical insight and method development relating to the use of a robotic system for the high-throughput screening of Streptomyces inhibition. |
| Impact | A paper is currently in preparation for this work. |
| Start Year | 2018 |
| Description | Invited talk at Plant-Microbe Interactions Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar provided on Streptomyces-Pseudomonas interactions at a Plant-Microbe Interactions Workshop organised at the John Innes Centre. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation at John Innes Centre ASM 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster detailing the current progress of the research funded by the award was presented to fellow postgraduate students at the same institute. Postdoctoral researchers and principal investigators were also present at the event. Interesting comments on how best to direct future research efforts on the project were received. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation at John Innes Centre ASM 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | A poster was presented on a specific workflow generated through collaboration with an adjacent institute (Earlham Institute, Norwich, UK). |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation at Microbes in Norwich |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation of a research poster detailing the progress of the research funded by the award, at a conference showcasing the work in microbiology across the Norwich Research Park and University of East Anglia. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation to Bayer Agronomy team |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation and discussion with the agronomy team at Bayer about biocontrol products |
| Year(s) Of Engagement Activity | 2019 |
| Description | UEA student symposium for final year Undergraduate students (talk) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | A presentation on my work to final year undergraduate students in the school of biological sciences at UEA. The aim was to provide a glimpse into the world of research and the life of a PhD student. The students showed great engagement with the work, as attendance was optional, and were keen to gain insight into the life of a postgraduate researcher. |
| Year(s) Of Engagement Activity | 2019,2020 |