Temporal Co-regulation of Pathogenesis in Phytophthora

How do plant pathogens, such as the potato late blight pathogen, Phytophthora infestans, regulate the timing of their different infection stages, and which genes are required at specific stages of plant infection? Despite the enormous cost and impact of Phytophthora diseases, we know little about how this group of pathogens regulate and coordinate specific stages of plant infection that culminate in disease development.
Late blight, caused by P. infestans, is the most devastating disease of potato, the third most important food crop globally. The very broad host range pathogen P. capsici is a major threat to vegetables, against which (durable) resistance is not available in most crops. Crop plant diseases caused by Phytophthora pathogens are thus a threat to global food security. The situation in Europe is compounded by legislation banning or restricting some chemicals that farmers rely on to prevent Phytophthora diseases. Changes in pathogen populations, coupled with the need to produce more food with a diminished environmental footprint, means that new avenues of disease control must be sought. In addition to P. infestans and P. capsici, more than 120 species of Phytophthora have been characterized, which collectively cause significant disease on almost all dicot crops. Some are limited in host range, and the resources for host genetics and genomics provide novel opportunities to identify and harness natural disease resistance. However, others, such as P. ramorum and P. kernoviae, are emerging as threats to natural ecosystems, infecting a broad range of tree and shrub species with which they have not co-evolved. To combat these, breeding for resistance is not a viable strategy. A deep understanding of Phytophthora infection biology is required to provide novel, next generation targets for highly specific and environmentally benign chemical control, and to identify new avenues that lead to disease resistance in plant hosts.
In order for it to be a successful pathogen, Phytophthora must grow within living plant tissue and then spread to new plants by producing spores. This requires the formation of different pathogen infection structures, which involves the action of many different genes, many of which are only active at these specific stages of infection. The DNA sequences of P. infestans and P. capsici have revealed hundreds (over 500) of candidate virulence factors that are transferred into plant cells to promote disease. These pathogens also have many other potential virulence proteins about which little is known. By identifying which of these candidate virulence genes are most active during specific infection of plants, this project will allow us, for example, to identify how Phytophthora coordinates its gene expression to form specialised infection structures, and what nutrients it obtains from its host plants.
However, the main focus of this project is to identify the 'switches' that initiate and regulate expression of the large numbers of genes required for infection. We will search for those regulatory switches that are common to P. infestans and P. capsici, as essential and conserved are likely to be more promising for later development of broadly applicable disease control strategies. As these are likely to be the central controls of Phytophthora disease development, it is likely that disruption of their function will also severely compromise the ability of Phytophthora to cause plant disease.
Gene expression underlying specific stages of disease development could be exploited through identification of crop plant traits that interfere with, or otherwise reduce, production of Phytophthora virulence factors. Alternatively, as we are seeking the regulatory components that are common to both narrow and broad host range Phytophthora species, these may be attractive targets for development of new chemical control agents that may also be active against other oomycete plant pathogens.

Driven by the availability of the Phytophthora genome sequences, recent years have seen the identification of vast collections of secreted effector proteins which suppress PAMP-triggered immunity. Much research focuses on the RXLR class of effectors, as these are delivered inside plant cells to directly manipulate host defences.
Many Phytophthora pathogenicity proteins and RXLR effectors show highly coordinated temporal changes in expression. Although the importance of both pathogen protein classes to epidemics is undisputed, we know little about how such tight regulation of expression is achieved. This project aims to combine next generation sequencing of Phytophthora-host interaction transcriptomes, bioinformatic and functional gene promoter analyses, DNA-protein interaction assays, and silencing and overexpression of transcription factors to identify and validate the protein 'switches' that specify Phytophthora gene expression changes during disease establishment.
Transcriptome sequencing will reveal the conserved groupings of genes that exhibit differential expression during infection, giving insight into the mechanisms of infection establishment. Identification of the transcription factors, conserved in narrow (P. infestans) and broad host range (P. capsici) Phytophthora species, that initiate expression of large groups of essential pathogenicity factors will provide next generation targets for the control of Phytophthora disease. That is, wide-ranging disruption of effector and other infection-related gene regulation in Phytophthora, though targeting of their regulators, forms an attractive strategy for disease control. This may be realised through development of novel chemical agents designed to generally inhibit infection processes conserved across Phytophthora species, or through traits present in crop plant germplasm. As such, this project will provide the basis for control solutions for new threats to crops and natural ecosystems.

More than 120 species of Phytophthora have been described, all of which cause diseases of dicot plants. Some, such as P. infestans, which is the major constraint to global potato production, are limited in host range, and the resources for host genetics and genomics provide novel opportunities to identify and harness natural disease resistance. However, others, such as P. capsici, infect a broad range of economically important crop hosts and strong resistance traits are often lacking. Furthermore, species such as P. ramorum and P. kernoviae are emerging as threats to natural ecosystems, infecting a broad range of tree and shrub species with which they have not co-evolved. To combat these, breeding for resistance is not a viable strategy. A deep understanding of Phytophthora infection biology is required to provide novel, next generation targets for highly specific and environmentally benign chemical control, and to identify new targets for disease resistance in crop plant hosts.

To date, all characterized host resistances to oomycetes have been found to detect RXLR effectors, which are delivered to the inside of plant cells, and exhibit elevated levels of transcript accumulation during infection. All other factors from Phytophthora found to be essential for infection also exhibit elevated expression during infection. This suggests that effective targets for control of Phytophthora disease may be identified from the interaction transcriptome. Although not the immediate focus of this project, it will deliver potential conserved pathogen targets that may encompass previously uncharacterized secreted effectors for detection by host R genes, conserved metabolic proteins to be targeted for chemical control, or the regulators of infection-specific gene expression themselves. An additional outcome that is outside the scope of this project will be the identification of plant genes that exhibit modified expression in the presence or absence of specific groups of pathogen effectors, and which may be involved in plant defence against disease. Each of these outcomes can potentially lead to next-generation targets for precise and oomycete-specific disease control.

Earlier Phytophthora gene expression studies have either lacked sensitivity (microarray) or systematic sampling (qRT-PCR) of early time points of infection. For example, 48 hours after infection has been the earliest infection time assessed by microarray, although much transcriptional activity has already occurred before this time. By combining sequencing of the interaction transcriptomes at a series of time points, combined with protein/DNA interaction assays, promoter functional assays in the pathogens, and silencing of transcription factors, this project will provide a fundamental understanding of coordinated gene expression and components of regulation during Phytophthora infection.

Exploitation of plant germplasm in breeding programmes of solanaceous crops are part of JHI's (potato) and Syngenta's (tomato, pepper) business. As we are working with a common solanaceous host plant in this project, findings will be directly translatable to the three major crop plants of interest to the project partners. With Syngenta as a partner in this project, there is scope for immediate dialogue with end users of the data produced from this project. Added value is also derived from knowledge transfer from the academic partners at UoD and JHI to Syngenta regarding action and targets of effectors, and essential pathogenicity factors in Phytophthora. This direct connection with industry will facilitate the conversion of academic knowledge to commercial outcome, with more rapid benefits to industry and agriculture.