Exploiting natural product assembly line genomics and synthetic biology for discovery and optimisation of novel agrochemicals

Lead Research Organisation: University of Warwick
Department Name: Chemistry

Abstract

Microorganisms including bacteria and fungi are everywhere in the environment. Although a few microorganisms have roles in causing disease, most microorganisms are harmless, and many of them actually produce medicines and chemicals useful to man. A good example is penicillin which is produced by a fungus and used as an effective antibiotic in human and animal medicine. Other compounds include anticancer drugs, drugs which allow organ transplants by suppressing the immune system and anticholesterol drugs. Many microbes also produce compounds of huge importance in agriculture which can be used as insecticides, herbicides and fungicides. It is estimated that around 40% of current world food productivity would be lost without these. As the world population grows and as climate change takes hold efficient food production and food security will become more important and the roles of these naturally occurring compounds will increase yet further.
Penicillins came into use during the 1940s, and for around half a century research provided a steady stream of newly discovered natural products. However, traditional approaches began to fail as more and more compounds were discovered because the available methods kept finding the same known compounds. This led companies to try other avenues to provide new compounds for use as medicines and agrochemicals - however fully synthetic compounds have not proven as successful as natural products.
Over the past decade academic research, much funded in the UK by BBSRC, but also an international effort, has led to the understanding that most microbes have the capacity to produce very many more compounds than observed - perhaps only 10% of a given organism's potential has been collected to-date. Genome sequencing has revealed that the biosynthetic potential of known organisms is huge - and new organisms are continually being found. If the 90% of unused genes in just the known organisms could be activated there could be a strong flow of new compounds for testing as medicines and agrochemicals - this flow could be increased to a flood if a generic technology could exploit all the as-yet undiscovered microbes.
In parallel with the genome sequencing efforts huge progress has also been made in understanding the genes, enzymes and chemistry involved in the microbial synthesis of secondary metabolites. This now allows the pathways responsible for the synthesis of secondary metabolites in microbes to be engineered to produce yet more compounds. The confluence of cheap whole genome sequencing and the ability to engineer microbial pathways underpins this research proposal.
The project will be a collaboration between 6 partners: the Challis group at Warwick, expert in microbial genome analysis; the Leadlay group at Cambridge, expert in bacterial polyketide biosynthesis; the Micklefield group in Manchester, expert in bacterial peptide production; the Cox group in Bristol expert in fungal biosynthesis; and Syngenta and Biotica, UK companies with major interest in secondary metabolites. We will obtain the genome sequences of bacteria and fungi known to produce agrochemically useful compounds. We will find the genes responsible for their production and recombine and engineer them to make higher amounts of these compounds, and then libraries of related compounds for testing. We will work with partners in the international agrochemical company Syngenta to develop these as new herbicides, insecticides and fungicides, while partners at the Biotechnology company Biotica will focus on compounds with use in human medicine. Overall we aim to develop a platform technology which can exploit the potential of microbes for the production of useful compounds for use in agriculture and medicine. We will also disseminate our results widely and undertake outreach activities to increase public awareness of industrial biotechnology and the role of genetic engineering and microbiology in ensuring future food security.

Technical Summary

This project will exploit a major opportunity which has arisen due to three factors: the dramatic lowering in cost of microbial full genome sequencing; the recent advances in rational engineering of microbial metabolic pathways; and the re-emergence of interest in natural products as new agrochemicals and drugs by international companies. The project will bring together 6 partners: the Challis group at Warwick, expert in genomics-based natural product discovery; the Leadlay group at Cambridge, expert in bacterial polyketide biosynthesis; the Micklefield group in Manchester, expert in bacterial nonribosomal peptide bioengineering; the Cox group in Bristol expert in fungal biosynthesis; and Syngenta and Biotica, UK companies with major interest in secondary metabolites. The collaboration will allow the 6 partners to embark on an ambitious programme to rapidly sequence the genomes of 40 microorganisms with the known ability to produce compounds with potential in the agrochemical arena. New bioinformatic methods will be used to rapidly identify biosynthetic gene clusters and link them to the synthesis of particular compounds. Engineering will then be employed to increase titres and activate 'silent' gene clusters with potential to produce bioactive compounds. Focussed libraries of target compounds will be made by biosynthetic engineering and the libraries used for SAR by Syngenta. Compound activity will then be maximised by a combination of biosynthetic engineering and synthetic chemistry. The partners will also engage in dissemination, training and outreach activities designed to maximise the impact of the project in the academic, industrial and public communities.

Planned Impact

Short term: The project will have high impact with the directly involved partners. For the companies involved it will allow them to gain access to and exploit the significant pool of knowledge and experience within the UK academic community in the area of biosynthetic engineering and synthetic biology. In particular this will help give Syngenta a competitive advantage and maintain their significant research and employment base in the UK. It will have a significant impact for the 4 academic groups involved because it will allow them to collaborate and disseminate best practice in complementary areas of research - this is likely to lead to more publications and publications of higher impact and thus help maintain the UK's competitivity in this area. It will help the academic groups focus their efforts on the development of new products and bring knowledge and experience from commerce into the academic arena. This in turn will enable the academic groups to form new and effective collaborations.

Medium term: The research has a good likelihood of leading to the development of new products with utility in the agrochemicals sphere which will underpin improvements in food security internationally. The project will train at least 8 PDRAs and up to 4 students in the area of synthetic biology as applied to industrial biotechnology. These people will form a core of expertise which will benefit both academia and industry.

Long term: The development of a platform technology for the systematic exploitation of microbes for the development of new medicines and agrochemicals will form the basis for the development of new technologies using synthetic biology. For example it is likely that similar methodology will underpin the development of new materials, new fine chemicals and processes, new methods to access biofuels and new methods to access foodstuffs.

Publications

10 25 50
 
Description 44 Streptomyces and 10 fungal genomes have been sequenced. Numerous novel specialised metabolite biosynthetic pathways have been discovered by analysing the genome sequences. The metabolic products of numerous pathways have been isolated and sent to Syngenta for biological testing. Several pathways of interest have been experimentally elucidated. Examples include: thaxtomin A, TMC-86A, malonomycin, cycloaspeptide, strobilurin and marginolactones. The thaxtomin and cycloaspeptide pathways have also been manipulated, providing access to novel derivatives of the natural products. A wide range of methods for activating biosynthetic gene clusters in Actinobacteria that are poorly expressed in laboratory cultures have been explored, leading to the identification of a method that appears to have general applicability. This method has been applied to the discovery of a range of novel metabolites, the structures and biological activities of which are being elucidated through follow-on funding.
Exploitation Route Syngenta will take our findings forward to help develop novel crop protection chemicals. Our results also have potential to be used by the pharmaceutical and animal health industries. The novel insights into molecular mechanisms of natural product biosynthesis we have generated can be exploited to develop new biocatalysts with a range of potential applications. They can also be harnessed to develop new biosynthetic engineering strategies able to create novel natural product analogues with improved application potential. The broadly applicable method we have developed for activation of "silent" biosynthetic gene clusters offers significant potential for the generation of novel natural product libraries. We are currently exploring the possibility of commercializing this with support from the Warwick Impact Fund.
Sectors Agriculture, Food and Drink,Chemicals,Education,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Our findings are being used by Syngenta in agrochemical discovery programs. To date we have supplied them with more than 70 natural products for pesticidal screening, of which 24% showed activity. We have also received financial support from the Warwick Impact Fund to further develop some of the methods we established during the course of the project and explore their commercial potential. We are currently in the putting together an application for the next round of ICURe, through which we aim to establish a spin out company.
First Year Of Impact 2013
Sector Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description BBSRC-IAA
Amount £1,000 (GBP)
Funding ID BB/IAA/Warwick/15 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 07/2016
 
Description BBSRC/EPSRC Multidisciplinary Research Centres in Synthetic Biology
Amount £10,521,613 (GBP)
Funding ID BB/M017982/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2015 
End 05/2020
 
Description IPC CASE
Amount £96,696 (GBP)
Funding ID BB/P504804/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2020
 
Description Industrial Contract
Amount £121,493 (GBP)
Organisation Achaogen 
Start 10/2017 
End 09/2018
 
Description Newton International Links
Amount £113,573 (GBP)
Funding ID 261846416 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2017 
End 09/2019
 
Description Warwick Impact Fund
Amount £51,903 (GBP)
Organisation University of Warwick 
Sector Academic/University
Country United Kingdom
Start 08/2018 
End 04/2019
 
Description Syngenta matched funding 
Organisation Syngenta International AG
Department Syngenta Ltd (Bracknell)
Country United Kingdom 
Sector Private 
PI Contribution We have isolated and structurally characterized several tens of natural products from Actinobacteria and filamentous fungi.
Collaborator Contribution Our collaborators have have investigated the pesticidal activity of the natural products we have isolated.
Impact The pesticidal activity has been determined of several natural products and derivatives that have hitherto never been tested by Syngenta. In some cases potent agrochemically-relevant biological activity has been observed. Discussions with Syngenta about how to further develop these compounds are ongoing. In addition, Syngenta have increased their activity in the area of natural product discovery and development, in particular through recruiting to specialist in this field who received postdoctoral and or PhD training in our group at the University of Warwick.
Start Year 2013
 
Title A genomics-driven platform for novel bioactive natural product discovery 
Description This project has allowed us to build on earlier work to develop what appears to be a widely applicable strategy for the activation of silent biosynthetic gene clusters. 
IP Reference  
Protection Protection not required
Year Protection Granted
Licensed No
Impact In December 2017 we received funding form the Warwick Impact Fund to explore the commercial prospects for this strategy with a view to establishing a spin-out company.
 
Description Schools mini-project 
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 Schools
Results and Impact "Discovery of Agrochemical Natural Products" practical science projects were run with groups of GCSE and A-level students from local schools in economically disadvantaged areas. This involved the students in a series of visits to our laboratories on Wednesday afternoons to carry out practical laboratory tasks and data interpretation exercises, which guided them through the steps from isolating and characterizing a new microbial strain, through assessing its potential to produce novel bioactive metabolites, to elucidating the structures of the metabolites. At the end of one of the projects, the students were accompanied by the PI/researchers/school teachers on a visit to Syngenta where the students gave a presentation on their project to colleagues in the company. The participants were also given a tour of the company's facilities. Postgraduate students from the lab were involved in the preparation and delivery of the project, in addition to the researchers employed on the project. At our grant partner Manchester, several groups of year 12 students visited for a day. Their studies and interests, as well as their future plans, were discussed. They were provided with an introduction to Streptomyces and biosynthesis of secondary metabolites with a particular focus on the wide variety of antimicrobials and agrochemicals that are of Streptomyces origin. The process of how early stage drug discovery has changed from screening to the development of genome sequencing and synthetic biology and how modern techniques are used in the lab to create bespoke compounds of interest was discussed. The students had plenty of opportunity to ask questions in an informal setting and engage with a variety of researchers from at different levels (masters students, PhD students and postdoctoral research fellows). The overall goal was to develop understanding of how life in a research lab actually operates and the exciting technologies that are driving innovation.
Year(s) Of Engagement Activity 2013,2015,2016