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Exploring the diversity of mechanisms used by microbial organisms to reprogram host behaviour

Principal Supervisor: Dr Patrick Schäfer, School of Life Sciences

Co-supervisor: Dr Sascha Ott, Computer Science, Dr Alex Jones, School of Life Sciences

PhD project title: Exploring the diversity of mechanisms used by microbial organisms to reprogram host behaviour

University of Registration: University of Warwick

Project outline:

This projects combines RNAseq (transcriptomics), bioinformatic gene network analyses, protein biochemistry (mass spectrometry) and non-invasive live cell imaging to study most ancient mechanisms employed by microbial organisms to reprogram their hosts.

More than 400 million years of co-evolution established microbial organisms as indispensable protectors of plants, and allowed plants to colonise land in the hostile Mid-Palaeozoic era. Having protected plants throughout plant evolution suggests that microbes activate protection mechanisms that are fundamental and presumably conserved in plants. Identifying these mechanisms can equip us with novel and sustainable plant protection strategies. However, it is unknown how microbes protect other organisms, including plants.

In this project you will explore the sophisticated mechanisms developed by microbes to manipulate plant signalling. We found that plant microbes deliver proteins, termed effectors, into plant cells. These effectors interact with plant proteins in order to specifically change their activities in respective plant signalling pathways. An understanding of the molecular mechanisms of this effector-mediated plant protection is of high scientific relevance towards our aim to develop new crops that can help to overcome hunger.

The approach followed in this project applies a novel concept – exploiting effectors as highly precise tools to improve stress protection in plants. Evolved over millions of years, effectors activate (regulate) most fundamental mechanisms in plants. The project will be “mind-changing” and is of significance beyond stress protection. We can develop synthetic effectors with new activities that enable us studying, understanding and applying key mechanisms in pathway regulation in plants in a yet unprecedented way. This project is based on a profound set of preliminary data and will allow you to identify fundamental functions of effectors to activate protective plant signalling pathways. Your main working packages will include:

1) Using the currently most efficient proteome platform to create a high resolution map of all plant protein-effector interactions. This high resolution interactome map allows you to identify plant proteins that upon their interaction with effectors participate in plant protection.

2) RNAseq-based transcriptomics and bioinformatics of plants overexpressing effectors with a confirmed function in activating plant stress protection pathways to identify key regulatory principles in plant stress protection networks.

3) Biochemical and non-invasive cell biological techniques (e.g. confocal laser-scanning microscopy) analyses to validate the function of identified of effectors and their targeted plant proteins.

BBSRC Strategic Research Priority: Food Security and Molecules, cells and systems

Techniques that will be undertaken during the project:

Supervised by internationally recognised scientists, the PhD student will apply:

  • yeast two-hybrid
  • tandem mass spectrometry
  • protein immunoprecipitation
  • non-invasive live cell imaging (e.g. confocal laser-scanning microscopy)
  • in silico prediction of gene/protein functions
  • systems biology-based techniques for network modelling

Contact: Dr Patrick Schäfer, University of Warwick