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Functional characterisation of a novel effector gene family from a plant pathogen

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  • Full or part time
    Prof P. Urwin
    Prof J Jones
    Prof J P Knox
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Plant pathogens cause catastrophic losses to crops worldwide. Many of these pathogens produce effector proteins that facilitate infection and a better understanding of how they function has the potential to make a significant contribution to global food security. This project will focus on effectors of potato cyst nematodes, commonly known as eel worms, which are important soil pathogens causing economic losses to potato growers. Globodera pallida is the most prevalent species of potato cyst nematode in the UK and its control is the most problematic. A lack of resistant potato varieties and concerns surrounding the use of chemical control measures have resulted in G. pallida being an intractable problem to farmers both in the UK and in many other countries.
G. pallida lives as a parasite and must complete the majority of its life-cycle in potato roots. It has a complex interaction with its plant host. Juvenile nematodes are microscopic worms that hatch from eggs in the soil upon detecting a host plant, then locate and subsequently invade the roots of the host. The nematode migrates inside the root and selects a single cell that it transforms into a large specialised, multi-nucleate feeding cell. Profound changes in plant cell structure and gene expression are induced by the nematode in establishing the feeding cell. These changes are mediated by proteins from the nematode, called ‘effectors’ that are secreted into the root via a stylet. Once the feeding site is induced the nematode becomes sedentary, losing the ability to move. Female nematodes feed for a period of 4-6 weeks while they develop and swell into mature, egg-producing adults. If at any time the feeding site is compromised the nematode cannot survive. Nematodes, like other biotrophic plant pathogens, have therefore evolved the ability to suppress host defences.
We recently identified a novel, hyper-variable effector family from plant parasitic nematodes. These effectors, termed HYPs, are secreted into host roots and are essential for successful parasitism but their specific role is unknown. HYP effectors are unique among plant pathogens; in G. pallida this family consists of at least 75 genomic sequences, split across three subfamilies. All sequences, irrespective of subfamily, share stretches of highly conserved nucleotides at the 5’ and 3’ ends and are distinguished primarily by subfamily-specific, variable-number tandem repeats. Most strikingly, HYP effectors display unprecedented copy-number variation between individual nematodes.
The project will benefit from the close involvement of Dr Sebastian Eves-van den Akker and Prof. John Jones, both based at the James Hutton Institute in Dundee. This extended supervisory team will provide specific expertise in aspects of the project, and will afford the student the opportunity to broaden their scientific network, experience and skill base.

Objectives
1) Determine the extent of HYP effector variability in different cyst nematode species and populations.
HYP effectors show unparalleled variation between individuals of the ‘Lindley’ population of G. pallida. Next generation sequencing will be used to investigate how common such HYP effector variability is in other populations of G. pallida and other species of cyst nematodes.
2) Investigate the role of HYP effectors in facilitating plant parasitism.
We have shown that HYP effectors are necessary for successful infection. This project will explore if they have a role in the suppression of plant defence responses required for completion of the cyst nematode lifecycle. Both stable and transient in planta over-expression of HYPs will be used to investigate enhanced susceptibility to potato cyst nematodes and other plant-pathogens or suppression of host defences in response to a range of known elicitors.
3) Identify plant binding partners of HYP effectors and determine the binding kinetics.
HYP effectors most likely exert their activity through binding to plant targets in the apoplast. Host binding partners of HYPs, which may be either proteins or cell wall glycans, will be investigated and the interactions characterised with respect to the variation in HYP sequence. This will provide important insights into the role of HYP effectors.
4) Investigate the structural characteristics of HYP effectors
There is scope for the project to encompass some in vitro structural analysis of HYP effector proteins using a range of biophysical techniques. This will inform understanding of how the sequence variation might affect molecular interactions and impact on function.

Funding Notes

BBSRC White Rose Mechanistic Biology DTP 4 year studentship.
Studentships covers UK/EU fees and stipend (c.£14,296) for 4 years to start in Oct 2017. Applicants should have/be expecting at least a 2.1 Hons. degree in a relevant subject. EU candidates require 3 years of UK residency in order to receive full studentship.
Not all projects advertised will be funded; the DTP will appoint a limited number of candidates via a competitive process and the projects selected by the successful candidates will be funded.
There are 2 stages to the application process. Please see our website for more information: http://www.fbs.leeds.ac.uk/postgraduate/phdopportunities.php

References

Eves-van den Akker, S., Lilley, C.J. Jones J.T. and P. E. Urwin. (2014) Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes. PLoS Pathogens 10(9): e1004391

Thorpe, P., Mantelin, S., Cock, P.J.A., Blok, V.C., Coke, M.C., Cotton, J.A., Eves van den Akker, S., Guzeeva, E., Lilley, C.J., Reid, A.J., Wright, K.M., Urwin, P.E & Jones, J.T. (2014) Characterisation of the full effector complement of the potato cyst nematode Globodera pallida. BMC Genomics 15:923

Cotton, J.A., Lilley, C.J., Jones, L.M., Kikuchi, T., Reid, A.J., Thorpe, P., Tsai, I.J., Beasley, H., Blok, V., Cock, P.J.A., Eves-van den Akker, S., Holroyd, N., Hunt, M., Mantelin, S., Naghra, H., Pain, A., Palomares-Rius, J.E., Zarowiecki, M., Berriman, M., Jones, J.T. &. Urwin, P.E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15:R43

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