PhD position (M/F) in Plant Biology

Job Description

Thesis Subject

Aim and PhD Research Topic
In the model plant Arabidopsis thaliana, the ARGONAUTE1 (AGO1) protein plays a central role in microRNA- and small interfering RNA-mediated gene regulation, as well as in plant development and antiviral defence. Its subcellular localisation is dynamic: after being loaded with small RNAs in the nucleus, AGO1 is exported to the cytoplasm, where it associates notably with the endoplasmic reticulum and various ribonucleoprotein condensates. The host laboratory has shown that heat stress promotes AGO1 phase separation and its recruitment into stress granules.
This PhD project aims to determine how heat stress and phase separation influence the subcellular localisation, molecular interactions and functions of AGO1 in small RNA-mediated gene regulation. Particular attention will be paid to the mechanisms responsible for AGO1 recruitment into stress granules, the role of its glutamine-rich N-terminal domain in phase separation, and the functional consequences of this relocalisation for small RNAs and their target messenger RNAs.

Scientific Fields and Research Areas: Protein biochemistry, transcriptomics, proteomics and cell biology.

Detailed Presentation of the Research Project
What is the role of the Poly-Q domain in AGO1 phase separation?
Transgenic Arabidopsis lines expressing an AGO1 variant lacking the Poly-Q domain will be generated. The localisation of this mutant protein will be compared with that of wild-type AGO1 using confocal microscopy before, during and after heat stress to determine whether this domain is required for condensate formation.

What is the physiological function of AGO1 phase separation under stress conditions?
Lines expressing AGO1 without the Poly-Q domain will be used to assess how impaired phase separation affects AGO1 stability and activity, as well as plant growth, survival and recovery following different stresses. Different stress conditions will be compared to determine whether condensate formation represents a general mechanism for protecting AGO1.

How do the intensity and duration of heat stress affect small RNA-mediated gene regulation?
Post-transcriptional RNA silencing will be analysed at different temperatures (30, 37 and 42°C) and following different periods of stress exposure and recovery. AGO1 localisation, small RNA loading and cleavage activity, as well as the expression of its target messenger RNAs, will be investigated using imaging, biochemical and transcriptomic approaches.

Which molecular mechanisms control the formation and functions of AGO1 condensates?
The potential role of AGO1 post-translational modifications in phase separation will be investigated using proteomics and the analysis of proteins mutated at the identified sites. Condensate composition will also be characterised to determine whether they recruit deadenylation factors, ubiquitin ligases or other proteins involved in RNA regulation and protein quality control.

Collaborative Aspects
This interdisciplinary project brings together the Laboratoire Génome et Développement des Plantes (LGDP, UMR 5096 CNRS–UPVD) in Perpignan and the Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF, University of Seville–CSIC) in Seville. It draws on complementary expertise in biochemistry, protein-interaction analysis, thiol oxidoreductase systems and cell imaging. Bioinformatic approaches will also be used to identify the AGO1 residues or regions required for liquid–liquid phase separation. Finally, the Spanish partner's expertise in characterising key stress-granule components will contribute directly to the successful completion of the project.

Scientific, Material and Financial Conditions
The PhD position is funded through the ANR-PRC GRANULOX project. The funding allocated to the project will cover confocal microscopy experiments, LC-MS/MS proteomic analyses, RT-qPCR, RNA sequencing and analysis, as well as plant production and characterisation. It will also cover travel associated with national and international collaborations and participation in scientific conferences.

Research Valorisation Objectives
By elucidating the mechanisms governing the formation of AGO1-containing ribonucleoprotein granules in response to stress, this project will generate knowledge that could contribute to improving crop resilience and productivity in the context of climate change. Funding for participation in scientific conferences is also explicitly included in the project budget.

Your Work Environment

Scientific and institutional environment
The PhD project will be conducted at the CNRS Institute of Plant Molecular Biology in Strasbourg. The successful candidate will have opportunities to interact with another team involved in the project and based at the same institute, as well as with national and international collaborators. The institute is easily accessible by public transport, and the PhD candidate will have access to a nearby staff restaurant offering subsidized meals.

Doctoral school and specialization: The PhD candidate will be affiliated with the Doctoral School of Life and Health Sciences (ED 414).

Partners and collaborators: Rémy Merret, Institute of Plant Molecular Biology (UPR 2357 CNRS–University of Strasbourg); Jean-Philippe Reichheld, Laboratory of Plant Genome and Development (UMR 5096 CNRS–UPVD); and Emilio Gutierrez Beltran, Institute of Plant Biochemistry and Photosynthesis (IBVF, University of Seville–CSIC).

Working environment and interactions: The PhD candidate will be fully integrated into the project team and will participate in the scientific activities of UPR 2357 CNRS–University of Strasbourg, as well as in meetings and discussions organized within the project and the EUR IMCBio Graduate School (https://labex-netrna.cnrs.fr/training/imcbio-graduate-school/). The candidate will also benefit from the scientific environment of the research cluster and Laboratory of Excellence (https://labex-netrna.cnrs.fr/)) dedicated to the study of regulatory RNAs and their functions across the different kingdoms of life, in which the host team participates.

Available resources: The project benefits from dedicated operating funds and access to the technological platforms required for its implementation. Funding is also available for travel related to collaborations, participation in scientific conferences, and publication costs.

Constraints and risks

The project involves the standard constraints and risks associated with research in plant molecular biology. One or more research visits are planned, notably to the Laboratory of Plant Genome and Development (LGDP, UMR 5096 CNRS–UPVD) in Perpignan, to benefit from its expertise and research facilities.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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