Temporal Co-regulation of Pathogenesis in Phytophthora
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
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Technical Summary
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.
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.
Planned Impact
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.
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.
People |
ORCID iD |
Edgar Huitema (Principal Investigator) | |
Paul Birch (Co-Investigator) |
Publications
Stam R
(2013)
Characterization of cell death inducing Phytophthora capsici CRN effectors suggests diverse activities in the host nucleus.
in Frontiers in plant science
Description | So far, we have 1. Identified motifs that may underpin gene regulation in P. capsici (and possibly P. infestans). we are about to start screening for the TFs that may bind these elements 2. We have analysed a large RNAseq experiment to further refine motif predictions. we are able to quantify P. capsici gene expression at the very early stages, a capability that we will seek to exploit for further motif identification. 3. We have identified a candidate TF in P. capsici that when over expressed, gives a phenotype during infection. We are currently characterising this protein further (Co-IP, Y2H) and have completed microarray analyses on over expression lines to identify candidate target genes. we are currently preparing an MS that describe these results. 4. We have identified TFs that appear to be differentially expressed in P. capsici. We are currently studying their function in vivo by means of OE and by attempting knock-down/outs. We have demonstrated that PcNMRAL1 may regulate the transition from biotrophy to necrotrophy in P. capsici. This work has now been published (Pham et al., 2018) |
Exploitation Route | We may be able to target NMRA like proteins in P. capsici (chemically) to disable pathogenesis. |
Sectors | Agriculture Food and Drink Chemicals Creative Economy |
URL | https://www.ncbi.nlm.nih.gov/pubmed/?term=29419371 |
Description | We have communicated our results to Syngenta, our industrial partner. We will send the Y1H materials to this company as well as the sequences and expression data of all genes differentially expressed during infection. Since this is an industrial collaboration, the intent on data use has not been disclosed to me. I therefore cannot fully comment on future use by our partners. |
First Year Of Impact | 2016 |
Sector | Agriculture, Food and Drink,Creative Economy,Other |
Impact Types | Economic |
Description | EASTBIO DTP3 |
Amount | £96,000 (GBP) |
Organisation | East of Scotland BioScience (EastBio) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 08/2021 |
End | 09/2025 |
Description | James Hutton Institute collaboration on project |
Organisation | James Hutton Institute |
Department | Cell and Molecular Sciences |
Country | United Kingdom |
Sector | Public |
PI Contribution | We have held regular meetings to discuss projects on our understanding of Phytophthora gene expression during infection of plants. we have generated a combined P. infestans and P. capsici Y1H library for our collaborators and screened motifs (present in both organisms) for interactors (transcription factors). in addition, we have tried to over-express P. infestans TFs in P. capsici to get to grips with possible roles in infection. |
Collaborator Contribution | Complementary efforts toward understanding these processes allowed us to test the possible roles of regulators in two distinct Phytophthora species. these efforts include expression profiling of P. infestans and P. capsici candidate transcriptional regulators and comparative analyses. |
Impact | Comparative gene expression analyses and datasets for candidate TFs. Candidate DNA motifs present in either P. capsici, P. infestans or both |
Start Year | 2013 |
Description | Syngenta (Industrial Partner) |
Organisation | Syngenta International AG |
Country | Switzerland |
Sector | Private |
PI Contribution | We have contributed gene expression data, expertise and our latest results of our research to Syngenta in the form of reports and meetings. |
Collaborator Contribution | Syngenta made a £35,000 contribution as they are part of this IPA award. |
Impact | Gene expression information on P. capsici-host interactions. Annotation and characterisation of candidate transcriptional regulators. Site visits and exchange of ideas, expertise and information (knowledge exchange). |
Start Year | 2013 |
Description | Cafe Science Talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Cafe Science to the public about my research. included research funded by BBSRC |
Year(s) Of Engagement Activity | 2015 |
Description | Collaborator event Syngenta |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | paper presentation |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | This was an annual event that is organised at Syngenta to present work on projects that are sponsored by Syngenta. Dr. Jasmine Pham presented the work of the project (in collaboration with project lead Dr. Steve Whisson) to a mostly academic audience. None known to us |
Year(s) Of Engagement Activity | 2014 |
Description | Invited speaker LFC workshop in Hohhot (Inner Mongolia, China) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation to the LFC workshop focussed on Molecular plant-microbe interactions |
Year(s) Of Engagement Activity | 2017 |
Description | Invited speaker Nanjing Agricultural University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Presentation to the faculty of NAU, dept of plant pathology. |
Year(s) Of Engagement Activity | 2017 |
Description | Phytophthora capsici effectors target the host nucleus to promote virulence |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | Yes |
Type Of Presentation | Keynote/Invited Speaker |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Scientific talk at COST meeting: Workshop on cellular dynamics of effector action and recognition Presentation and Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2014 |
Description | Presentation at the Oomycete Genomics Network Meeting, Asilomar (CA, USA) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation given by Dr. Jasmine Pham (PDRA employed on grant) at a scientific meeting. |
Year(s) Of Engagement Activity | 2015 |
Description | Research Collaboration Event, Syngenta |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | Yes |
Type Of Presentation | Poster Presentation |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Jasmine Pham, PDRA employed on this grant, attended a Research Collaboration Event at Syngenta, on the 2nd and 3rd of Sept 2013. At this event, a poster was presented on her most recent work on this project. None Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Scientific Talk at Enza Zaden |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Presentation of work towards understanding P. capsici biology to a breeder audience (Enza Zaden Company) in the Netherlands |
Year(s) Of Engagement Activity | 2018 |
Description | Visit to Syngenta |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Visit to Syngenta where a research talk was given. presentation was broadcasted to Syngenta research sites world wide. |
Year(s) Of Engagement Activity | 2015 |