DC6 - Characterisation of putative effectors of protist parasites of brown algae

Advisors: Sigrid Neuhauser, Claire Gachon, Wolfgang Lechner

How to apply for this position
The submission deadline for this project was May 15th, 2024 and we are currently not accepting any new application. 

Location: The research will be performed at the University of Innsbruck and the student will graduate with a PhD of this institution. The University of Innsbruck was founded in 1669 and is one of Austria‘s oldest universities. Today, with over 28.000 students and 5.000 staff, it is western Austria‘s largest institution of higher education and research. The University of Innsbruck offers access to a wide range of experimental and analytical facilities.

Scientific context:
While the effects of pathogen effectors and other processes on animals and land plants have been extensively studied, there is a notable scarcity of information regarding how parasites communicate and compete with brown algae for nutrients and space.  
The aim of this study is to identify candidate proteins that play a role in the successful colonization of brown algae strains (e.g. Ectocarpus spp., Macrocystis spp.) by the phytomyxean pathogen Maullinia ectocarpii. Phytomyxea are obligate biotrophic pathogens of plants, brown algae and stramenopiles, which means they cannot be cultured in pure culture, but that they need to maintained with their host (see life cycle in the illustration below). Stable dual-culture pathosystems are available in the hosting lab along with several RNAseq datasets of the dual cultures. These data will form the starting ground for this project along with existing qPCR, RNA-FISH and physiological methods.

Objectives and candidate profile: 
Employ existing and novel RNAseq datasets to identify potential effectors of Maullinia ectocarpii. Construct a heterologous expression system in yeast and/or E. coli for the purpose of characterizing these effector proteins. 

1. Confirm the role in the infection by localizing the associated mRNAs using smFISH and quantifying their expression over the course of the pathogen life cycle using qPCR and ddPCR. 
2. To determine the response of different hosts, phenotyping and RNAseq phenotypes can be used with heterologously expressed proteins on host cultures from a wide taxonomic range of seaweeds. 
3. Test the transferability of the 3D structural predictions to Quantum Computing Systems.

Hence, this ambitious doctoral program is structured around three primary pillars, which include (1) traditional culture-based approaches, (2) comparative bioinformatics, and (3) imaging techniques. The preferred candidate should possess proficient microbiology skills and a strong foundation in phytopathology or plant-microbe interactions. Candidates with a background in data analysis and bioinformatics are preferred, but those without experience can still be considered as training can be provided during the PhD program.

Expected Results: 
1) The primary objective is to investigate parasite-host interactions by characterizing putative effector molecules, with a specific emphasis on understanding the functions of previously unexplored effectors. 
2) By conducting tests and validations on the function of putative pathogen effector molecules, it is possible to identify previously unknown response mechanisms in algae towards biotrophic pathogens.
3) Exploring and evaluating novel methods for computational analysis of predicted proteins. 

Planned secondment(s): 
At CNRS-Roscoff with Yacine Badis to use an existing yeast two hybrid system to screen brown algal proteins for interaction with effectors 
At MNHN with Claire Gachon to screen the elicitation of a defence response on a taxonomically diverse range of red and brown seaweeds with heterologously expressed effectors 
At Parityqc to pilot quantum computation algorithms for the modelling of 3D Protein structure of selected effectors.