A synthetic biology approach to develop durable disease resistance in crops

A billion people alive today are undernourished. Crop losses due to pests and diseases are a major obstacle towards achieving global food security. In developing countries, pests and diseases account for up to half of crop losses. In developed countries, the use of pesticides, fungicides, and other chemicals for agriculture are heavily restricted due to EU directives. New, durable, sustainable, 'green' control measures are urgently needed.
Plants in the field are often under simultaneous attack from many different types of pathogens. Some of these are from above ground (i.e. the potato late blight pathogen Phytophthora infestans), and some are from below ground (i.e. microscopic nematode worms that parasitise plant roots). Both types of pathogens 'inject' proteins into the plant to hi-jack plant machinery to benefit themselves and help spread infection. These proteins (known as effectors) often interact with normal crop proteins, and in some way modify them to help the pathogen. The key research questions remain:

1) How do effectors modify host proteins to promote infection?
2) Do different types of pathogens target the same host proteins?
3) Can our understanding of the molecular interaction allow us to disrupt it, favouring plant immunity?

I aim to determine how pathogen effectors physically interact with plant proteins in order to direct changes to the latter so that the pathogens can no-longer manipulate them. To accomplish this I propose a collaboration between the University of Dundee in Scotland and the John Innes Centre in Norwich. The University of Dundee Division of Plant sciences, together with the James Hutton Institute, aim to apply aspects of plant breeding, pathology and ecology to allow fundamental research to be readily translated to end-users. The John Innes Centre has extensive experience of structural biology, in particular in the area of plant-pathogen interactions. Bringing together these complementary institutes is vital to achieve the aims.

Potential applications and benefits:
The proposed work will provide a new understanding of how pathogens can manipulate and infect their host. With this understanding, the informed re-design of specific plant proteins so they can no-longer be targeted by pathogens will undermine and prevent infection. Proteins targeted by multiple pathogens are likely to be very important to successful infection. Modifying these by editing the plant DNA will help to create a durable 'green' solution to the use of pesticides against multiple different pathogens. This could help to ensure food production and security in developing and developed countries.

Multiple phylogenetically diverse pathogens that have co-evolved with the same host, and that require similar manipulations of that host, are likely to have targeted the same pathways and proteins. This proposal will analyse the structural basis of the interactions between effectors and host targets with the aim of using synthetic biology to design modified targets that evade disruption by effectors. The main aims will be:

1. Identification of potato host proteins that are common targets of Phytophthora infestans and potato cyst nematode effectors by Y2H, using known P. infestans effector targets to identify corresponding nematode effectors. Subsequent validation in planta by Bimolecular fluorescence complementation and co-immunoprecipitation will be performed.

2. Determine the three-dimensional structures of host targets in effector-bound and effector-unbound states.

3. Elucidate the biology of effector-target interactions using a combination of biophysical and molecular biological analytical techniques. Provide high-throughput bioassays that will monitor the effectiveness of perturbing these molecular interactions.

4. Use knowledge of structure-function relationships between effectors and their targets to re-design target proteins to undermine effector binding/activity yet retain endogenous function.
Understanding the structural basis of how an effector-bound target functions differently to promote pathogen success, with sufficient detail to undermine the interaction, can be applied directly to crop species using synthetic biology genome editing tools.

In addition to the numerous and diverse academic beneficiaries detailed in the appropriate section, the proposed work will generate data with strong translational potential that meets societal needs of relevance to the Food Security Strategic Priority area of the BBSRC.

Although a challenging aim, the long-term goal of the research is to develop approaches with the potential to reduce pesticide use and increase agricultural stability. This may benefit commercial farmers by limiting the need for repeated spraying of pesticides, as well as subsistence farming where growers do not have access to means of chemical disease control. Consistent agricultural production in the UK is critical to maintain a position of economic competitiveness, particularly in light of recent reductions of pesticide use by EU legislation (91/414/EEC). In addition, the substantial gross value added to the economy for every pound invested in JIC science represents the wide indirect benefit of the research.

The economic and farming impact will need to be realised through industry. Biotechnology industry will benefit from the research, and the UK is well positioned to ensure effective exploitation. This will be carried out through the extensive network of industrial partners associated with the host institution and group.
Realising the potential impact of the proposal will rely on the extensive public engagement activities detailed in the pathways to impact. In summary, taking advantage of the resources available at two geographically distinct locations, with exceptional track records of public engagement, will ensure the broadest possible impact. Through engagement with schools, the education sector has the potential to benefit from the research through knowledge exchange. Especially relevant is the long-term potential of the research to contribute to food security, global sustainability (limiting potentially damaging chemical inputs into the environment) and to enthusing the next generation of scientists. Synthetic biology in particular is in its infancy. Promoting this discipline to the public, starting at a young age, will allow the UK to make the most of the opportunities it provides. Promoting doctors in science in local schools, with an emphasis on gender equality, will aim to address some of the general issues in science.