PhD position in functional characterization of plant pathogen effector proteins

Are you interested in understanding the interaction between plants and pathogens on a molecular level? Do you want to be part of a passionate and curiosity-driven research team? Are you challenged by learning and applying cutting-edge molecular biology techniques to address your research questions? Then this job may be for you!

The Molecular Plant Pathology group is looking for a PhD candidate to investigate virulence strategies of plant pathogenic Xanthomonas bacteria. Black rot, a disease caused by the bacterial pathogen Xanthomonas campestris pv. campestris, is the most important disease for Brassica crops (e.g. cabbage) globally. Given the scarcity of natural resistance sources in Brassica germplasms against Xanthomonas, this project aims to provide the knowledge to enhance disease resistance genetically through identification and characterization of host susceptibility genes.

If you enjoy working in an interdisciplinary research team and are eager to contribute to elucidating Xanthomonas infection strategies, then the Molecular Plant Pathology group, which is part of the Swammerdam Institute for Life Sciences at the University of Amsterdam, is the place to be. Research in our group aims at advancing fundamental knowledge of the interactions between plants and their pathogens, using state-of-the-art molecular methods in genetics, plant biology, genomics, cell biology, biochemistry, and microbiology. Engaging in public-private partnership projects, we aim to translate novel insights into solutions for societal problems.

This project focusses on understanding molecular processes during host-pathogen interactions using model and non-model plant species, such as Arabidopsis thaliana and Brassica oleracea, respectively. Ultimately, the insights into these processes will provide novel leads for resistance breeding against black rot and other bacterial plant diseases. The project of this PhD position is funded by a Topsector T&U grant in collaboration with two plant breeding companies.

What are you going to do?

Vascular Xanthomonas pathogens have a distinct infection strategy compared to other bacterial pathogens, as they infect their host via hydathodes, which are water pores at the leaf margin that are connected to the xylem endings. This provides the pathogen access to the vasculature for systemic spreading through the leaf. During different stages of the infection process Xanthomonas injects effector proteins into host cells to interfere with plant physiology and immune signaling thereby promoting bacterial proliferation. The overall goal in this project is to identify and characterize key plant processes manipulated by Xanthomonas pathogens. The approach will be to uncover the interactions between pathogen effectors and their target host proteins. Identifying host targets will pinpoint the genes and/or pathways that function as susceptibility factors, as the pathogen relies on them for successful infection. We will then genetically engineer plants modifying those effector targets and test resistance against Xanthomonas.

First, you will screen for host proteins manipulated by Xanthomonas effectors using a readily available protein proximity labelling technique and mass spectrometry-guided protein identification. Subsequently, you will characterize the function of the identified plant proteins during infection. For this, we will make use of the molecular tools available in the model plant Arabidopsis thaliana, which belongs to the same family as Brassica crops. This involves engineering plant knockouts using established CRISPR-Cas technology and applying advanced transcriptomics experiments. In particular, you will investigate the effector function during early infection stages in hydathodes. Lastly, you will test the function of the identified gene in Brassica plants during Xanthomonas infection.

Tasks and responsibilities:

• complete a PhD thesis within the official appointment duration of four years;
• perform your experiments in a systematic and controlled manner and keep records by properly documenting and organizing your work;
• be an active member of the research group and take responsibility for shared tasks;
• discuss your work with group members and during company update meetings. Incorporate feedback and give input to others.
• take a leading role in writing manuscripts for publication in peer-reviewed journals;
• participate in the PhD training programme of the University of Amsterdam and the Dutch Experimental School of Plant Sciences;
• assist in teaching and supervising Bachelor and Master internships and tutoring students.

You will get the opportunity to:

• combine the advantages that a collaborative project offers, such as access to state-of-the art research facilities of both the academic and the private partner;
• present your results at (inter)national scientific conferences;
• expand you academic, professional, and personal skills;
• contribute to science communication and outreach activities;
• thrive in a team that values impactful research and mutual support.

Your profile:

You are passionate about science and have a particular interest in molecular plant pathology. You enjoy performing experimental lab work (e.g. molecular biology, plant transformations, disease assays), as well as data analysis and using bioinformatic tools. You have a creative mind and look forward to learning and applying your skills and knowhow. Finally, you are a team player and a pleasant colleague who enjoys being part of an international team of plant scientists.

Your experience and profile

• a recent MSc degree in molecular biology/biochemistry/plant biology;
• demonstrated hands-on experience with some of the following techniques and skills: DNA cloning, RNA extraction,
• Western blotting, plant disease assays, and data analysis;
• fluency in English, both written and spoken.

Our offer

We offer a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible but at the latest October 1st 2024. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2,770 in the first year to €3,539 in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:

• 232 holiday hours per year (based on fulltime)
• multiple courses to follow from our Teaching and Learning Centre;
• a complete educational program for PhD students;
• a pension at ABP for which UvA pays two third part of the contribution;
• the possibility to follow courses to learn Dutch;
• help with housing for a studio or small apartment when you’re moving from abroad.