Biosynthesis and mode of action of a new antifungal antibiotic produced by bacterial plant pathogens and rhizosphere bacteria

Lead Research Organisation: University of Cambridge
Department Name: Biochemistry

Abstract

The global human population is increasing and it is estimated to reach around 9 Billion by mid-century. Demand for human and animal food crops will increase in line with this growth rate and our food security will be compromised unless we can significantly increase crop productivity, decrease crop losses due to disease and spoilage - or, preferably, both. Recent research has shown that fungal (and oomycete) plant pathogens play increasingly important roles in causing plant diseases that reduce crop production or lead to spoilage of harvested food crops. Current crop protection methods involve various approaches, including the use of some pesticides made by polluting chemistry that can have undesirable environmental impacts.

This project will involve a study of a novel antifungal molecule(s) that is made naturally by some species of bacteria that live in close association with plants. This naturally-made antifungal antibiotic is lethal to a range of fungi that kill pants, including crop plants, and so it might be useful in preventing or limiting crop diseases without recourse to synthetic toxic pesticides. The genes responsible for the formation of this new natural antifungal molecule have been discovered in a range of bacteria isolated from the environment and a hypothetical pathway to biosynthesis of the active molecule has been suggested.

We will overproduce this new molecule using bacterial genetics and physiology methods and then purify the antifungal to try to determine the chemical structure of the antibiotic using a range of chemical and physical methods. We will study how the new antibiotic is assembled in the bacteria that produce it. We have shown that the antifungal antibiotic can also kill simple yeast (fission yeast) in addition to fungi that cause plant disease. The simple yeast is easy to study using genetics and molecular biology methods and so we intend to exploit this by investigating the cellular target of the new antifungal in yeast cells. We expect this information will be also directly relevant to identifying the nature of the molecular target in the plant pathogenic fungi and this will help us in future to develop different natural and semi-synthetic molecules that may protect crop plants from disease and spoilage - and thereby enhance our food security.

Technical Summary

Fungi and oomycetes are major pathogens of crop plants and agents of post harvest decay that directly challenge our food security while causing tremendous economic losses. Crop protection processes can depend on man-made agrochemicals, but some of these are under threat through legislative changes because of environmental and toxicity concerns. There is therefore a growing need for new antifungals that might be useful in controlling disease and decay in important crops.

We have been investigating production of natural antifungal molecules made by Gram-negative, plant-associated bacteria. We have investigated a new broad spectrum antifungal activity ("matillamide") in strains of Serratia and the bacterial phytopathogen, Dickeya solani. Through a transposon mutagenesis programme coupled with bioassays on various hosts we have defined the gene cluster responsible for this new bioactivity and assessed its distribution in taxonomically related bacteria. In this project we will clone the matillamide production gene cluster in E. coli and overproduce the molecule (either in the heterologous host or by forced overproduction/deregulation in natural producers). Overproduction of the antifungal will enable isolation and purification of the new antifungal antibiotic and assist definition of its chemical structure. We will investigate the biosynthetic cluster in detail and will dissect its organization and the functionality of each gene in the putative biosynthetic operon using engineered in-frame deletion mutants and corresponding genetic complementation assays, to try to define the product assembly pathway. The antibiotic has a broad host range but it does not affect bacteria or nematodes. Its lethality in fission yeast will be exploited to try to define the eukaryotic target for the new molecule. We will make use of the genetics and molecular biology of the experimentally tractable Schizosaccharomyces pombe to identify the mode of action of the new antifungal.

Planned Impact

Who will benefit from this research?
There could be diverse beneficiaries from a productive research project of this nature. These could include crop producers (agriculture), the manufacturers and processors of food and, ultimately, consumers. If successful, this research work could have implications for food security through enhanced crop productivity and reduction in spoilage. The work will also impact on ecosystem health and food sustainability, and, consequently our nutrition and health. The project aspires ultimately to have impacts on food crop productivity (for man and animals) but of course it could have beneficial impacts on non-food crops and environmental/leisure lifestyle aesthetics where plants and trees are also susceptible to seriously impactful fungal pathogens. The research may also have impacts in biofuel and fibre production.

The project involves the analysis of genes encoding production of a new antifungal antibiotic; how this is made in the producer and how this acts to kill fungal plant pathogens. The relevant genes, enzymes and molecules may be potentially exploitable in the manufacture of novel natural products, by semi-synthesis, with agricultural or other value. The research could ultimately create new molecules for more natural control of plant diseases using regimes that may be less ecologically damaging, more sustainable and more eco-friendly than the currently used industrial agrochemicals (increasing numbers of which are under threat now due to restrictive EU legislation). The biosynthetic enzymes investigated in this study could have utility in translational process technologies in chemical and synthetic biology applications e.g. in specific bioconversions or for use in bacterial biorefineries.

How will they benefit from this research?
Crop losses due to fungal pathogens and post harvest decay processes are massive, on a global scale, and they can account for losses of around 10-30% of production - ecologically and agriculturally devastating in some locations. These losses may be significantly exacerbated through climate change at the worst possible time, when we have an increasing global demand for crops to feed a rapidly expanding human population. Our research could underpin better disease control technologies that may decrease crop losses and thereby increase profitability in food production and distribution. Cutting our dependence on potentially toxic xenobiotic agrochemicals is now legislatively pertinent, ecologically sensible and perhaps even beneficial in human and animal health terms. Any possibility of improving UK food security and decreasing use of xenobiotic agrochemicals must be a good impact target. Furthermore, crop disease control in emerging nations would enhance food production and nutritional health and both of these could have considerable impacts on human health and longevity. To realise such translational benefits, this work would eventually need industrial sector partnership and commercial exploitation over a long time scale.

Another area of impact, of course, will be in the training of research personnel employed in the project. The PDRAs will benefit from the development of diverse skills in bacteriology, genetics, chemistry and chemical biology, bioinformatics, and yeast molecular biology - coupled with experience in teaching, science communication and other career enhancing skills through personal development courses.

What will be done to ensure that they have the opportunity to benefit from this research?
As taxpayer-funded research work, our research outcomes will be disseminated to scientists in the public domain by peer-reviewed publications, lectures and posters presented in UK and international meetings. We will publish in open access journals, in line with BBSRC directives to ensure global access to the knowledge outputs we generate. We are very positive about industrial, and other stakeholder, collaborations, wherever possible.

Publications

10 25 50

 
Description We defined the genes involved in antifungal biosynthesis and examined their genomic distribution in other bacterial pathogens and bacterial saprophytes. In-frame deletion mutants were engineered for all biosynthetic genes and biochemical/chemical characterisation of mutants and wild type was conducted. We have gone a long way towards solving the final structure for the bioactive molecule (although that is proving to be less straightforward than we had hoped because of the novel chemistry involved). Approaches towards defining the susceptible eukaryotic functions in yeast revealed possible targets. We defined multiple new bacterial genes involved in antibiotic regulation. Mutants were made that exhibited enhanced antibiotic production and these were used to enable elevated production of the bioactive molecule for chemical analysis. We exploited new bacteriophages that infect the antifungal producer strain (and some other hosts) for strain engineering and constructed reporter gene fusions in the biosynthetic cluster to enable transcriptional control analysis on the antifungal production genes. Since the end of the funding period we have now identified the presence of the antifungal biosynthetic genes in a wider array of bacterial strains which are candidates for production of the molecule.
Exploitation Route We are not yet in a position to file a patent on the new antifungal antibiotic, because of some uncertainty about the final chemical structure of the bioactive molecule(s). Were we to have that unequivocal final structure we would progress with IP protection through the university enterprise support system.
Sectors Agriculture

Food and Drink

Education

Environment

Pharmaceuticals and Medical Biotechnology

 
Description BB/SCA/Cambridge/17 (Agri-Tech Seeding Catalyst) - Cambridge University internal reference RG92070
Amount £19,850 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 02/2018
 
Description Developing new bacteriophage banks for Pseudomonas tolaasii: route to biocontrol of mushroom brown blotch. Cambridge University IAA Internal Reference RG96069
Amount £14,250 (GBP)
Funding ID BB/S506710/1 (Internal Ref RG96069) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2019 
End 04/2019
 
Title Transducing phage for antibiotic producing Dickeya and Serratia strains from the rhizosphere 
Description Isolation of the phage phiMAM1 that is a generalised transducer for environmental and clinical strains of Serratia and Kluyvera. This allows strain engineering. We isolated further phages for Dickeya and Serratia strains that proved useful in genetic engineering of antibiotic producing enterobacteria. 
Type Of Material Biological samples 
Year Produced 2016 
Provided To Others? Yes  
Impact The phages have a wide host range (in terms of susceptible strains) and, as transducers, therefore enables strain engineering. This has been useful to study virulence and antibiotic production by some Serratia strains and particularly powerful for the genetic engineering of mutants and reporter strains of Dickeya for the study of regulation of antifungal antibiotic control. 
 
Description Open Days 2016-19 - assorted 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Examples of most recent events:
March 2019 - Science Week, Barnabus Oley School, 1pm - 3.30pm - PDRA Taught year three students about what types of bacteria that they might find on their hands and on fruit. Conducted an 'experiment' with students to test whether they were effective at washing their fruit.

July 2019 - Lumina Oxbridge Program, Harrow Borough - PDRA contributed to an outreach session for 100 students selected from Harrow borough as potential high achieving students from disadvantaged backgrounds. Led afternoon session on extension learning and help students with advanced problem solving.

PDRA also had role of Community Governor at Melbourn Village College and was the Science Link Governor for the School.
Year(s) Of Engagement Activity 2016,2017,2018,2019
 
Description PDRA School Governor Board member 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact PDRA role as member of Governing Board of Melbourn Village College and as the link Science Governor for the school
Year(s) Of Engagement Activity 2020,2021
 
Description PDRA contribution to Cambridge University Science Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact University Science Open Day in July 2019 (and virtually in July 2020 & September 2020)
Year(s) Of Engagement Activity 2019,2020
 
Description Participation of PDRA in Harrow Council Lumina Program July 2019 (and July 2020) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The Harrow Council Lumina Program is for students who are hoping to apply to university from underpriviledged backgrounds see: http://luminacourse.org.uk
Year(s) Of Engagement Activity 2019,2020
URL http://luminacourse.org.uk/
 
Description Volunteer worker as Data Analyst at Covid University Testing Centre 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact PDRA worker as a volunteer Data Analyst in the Cambridge Covid University Testing Centre (April 2020-August 2020) in a shift system with Staff Scientists from Astra Zeneca and GSK. This was a significant contribution to the monitoring of Covid-19 infection diagnostics and was recognised by the Vice Chancellor through a Professional Recognition Award for cross university collaboration.
Year(s) Of Engagement Activity 2020