Understanding how plant antimicrobial "hot zones" can accelerate pathogen evolution

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This project will focus on understanding the mechanistic basis of bacterial pathogen evolution during the colonisation of resistant plant hosts, using the interaction of Pseudomonas syringae pv. phaseolicola (Pph) with bean as a model system. We hypothesise that identifiable factors from the plant apoplast trigger genomic island excision from the chromosome of Pph, and uptake of naked DNA through natural transformation competence, and that specific genes for competence are present in Pph. We thus aim to identify the signals that induce gene loss and gene gain in Pph, and to characterise the mechanism used by Pph to acquire DNA. This will be achieved through the following objectives:

Objective 1. Investigate the impact of host cultivar, pathogen genotype and environment on the excision and transformation competence-inducing activity of apoplast extracts.
Objective 2. Identify components present in apoplast extracts that induce excision and competence in Pph.
Objective 3. Identify genes required for competence in Pph.
Objective 4. Profile the transcriptional response of Pph to apoplast extracts and determine whether competence genes are expressed at a higher level from resistant plants.

We will first investigate the impact of host, pathogen and environment on the excision and competence-inducing activity of apoplastic extract. We will use this information to compare the composition of apoplast extracts with high or low levels of inducing activity and to identify components present in apoplastic extracts that induce excision and competence. Competence gene identification will be achieved using a variety of methods ranging from a targeted bioinformatics approach to a random gene knock-out method. Global RNA sequencing and targeted gene expression analyses will be used to study the expression of competence genes in response to environmental factors and to understand the physiological context of competence induction in Pph.

The long term aim of our research is to understand the interaction between plant pathogens and plants with the goal of being able to use this information to develop control strategies in the field or glasshouse. This project specifically aims to understand how antimicrobial "hot zones" formed in response to pathogen attack trigger genetic changes within the pathogen and provide a foundation for selection of more virulent pathogens. We also aim to uncover the mechanisms by which pathogens can acquire DNA to evolve enhanced virulence. This proposal fits within the BBSRC strategic priority of Crop Science as it focuses on a serious problem for crop performance i.e. loss of crop yield or quality though plant disease, and therefore has relevance to Global Food Security. A number of groups aside from academics will also benefit from this work, although it should be stressed that further research may be required to realise the benefits to some of these users.
1. Agriculture and the private sector will benefit because this work will lead to a better understanding of the plant factors that promote pathogen evolution and the breakdown of disease resistance. Ultimately, an understanding of the causes of pathogen evolution could lead to directed breeding for plants that do not trigger pathogen change as rapidly. For example, breeders may be able to breed plants that fail to produce a specific molecule that accelerates pathogen evolution. Alternatively, farmers and horticulturalists may be able to alter growth management practices to modify plant chemical composition to reduce the levels of inducing factors. A direct benefit of this project will be the development of quantitative bioassays for studying the impact of specific factors on pathogen evolution, which can be used by plant breeders and government research institutes, and which may also have broad applications in other fields of research such as drug discovery and clinical microbiology. Our long term goal of developing models of the loss and transfer of DNA in pathogen populations on plants will also have an impact by allowing researchers to make predictions regarding plant pathogen evolution and disease management, which can be experimentally tested in greenhouse and field trials.
2. Government organisations and policy makers will benefit by having more detailed information on the drivers of pathogen evolution and understanding how pathogens evolve. This will not only benefit the national agenda for food security, but can be disseminated through a variety of agencies to the international agriculture arena.
3. The public will ultimately benefit through increased food supply, and improved economics resulting from it, thus directly addressing Food Security, which goes to the heart of BBSRC's priorities. The public will also benefit from our outreach programmes, which will present the data that we generate, and highlight the impact of plant disease on food security and the research that is on-going to protect our crops.
4. Undergraduate and postgraduate students will benefit from progressive developments in teaching curricula that will be underpinned by the research outputs from the investigators: all the investigators associated with the project teach aspects of bacterial pathogen evolution. Students will also be able to participate directly in this research area by undertaking undergraduate and graduate research projects in our research groups.
5. The staff who are involved in the project, both investigators and research associates, will benefit from the research through learning new research skills and techniques. The RAs will also benefit from the research in terms of developing generic career skills. For example through attendance of the BBSRC media training workshop, presentations to both the scientific community and the public, preparation of manuscripts and grant applications, student supervi