Professor Isabelle Carre

Contact Details

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

Plants, like animals, possess a biological clock which enables them to fine-tune their physiology according to the time of the day. This timing mechanism, known as the circadian clock, drives rhythmic changes in gene expression which in turn impact on a broad range of processes, including for example photosynthesis, responses to cold, heat or drought stress, changes in leaf position, opening and closing of petals, and overall plant growth. Our current work focuses on how the plant circadian clock impacts on interactions with micro-organisms surrounding the root. This is important, because some of these microbes can cause disease, while others play essential roles to make soil nutrients available for the plant. Domestication of a number of crops has resulted in selection for specific alleles of circadian clock genes, and we need to understand how this impacted on plant-microbe interactions and the consequences for crop health and productivity.

Recent work with Gary Bending demonstrated that a substantial proportion of fungal and bacterial species exhibit daily changes in abundance in the rhizosphere of Arabidopsis plants. These rhythms persisted under constant environmental conditions, but free-running rhythms were disrupted in the rhizosphere of mutant plants with dysfunctional circadian clock, demonstrating a key role for the clock of the plant host to synchronise these microbial rhythms. Future research will investigate how this benefits the plant host.

Together with Miriam Gifford, we are also investigating how the circadian clock of the plant impacts on symbiotic interactions between the model legume, Medicago truncatula, and the nitrogen-fixing bacterium Sinorhizobium meliloti. Optimisation of circadian rhythms in legumes may result in enhanced nitrogen fixation, thereby reducing the need for nitrogen fertilisers and their negative impact on the environment.

Research Groups

Cells and Development

Environment and Ecology

Plant and Agricultural Biosciences

MIBTP Project Details

Current Projects (2025-26)

Joint primary supervisor (with Professor Lorenzo Frigerio) for:

Clock-watchER: Circadian coordination of the plant endoplasmic reticulum

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Clock-watchER: Circadian coordination of the plant endoplasmic reticulum

Secondary Supervisor(s): Dr Emily Breeze

University of Registration: University of Warwick

BBSRC Research Themes:

Sustainable Agriculture and Food (Plant and Crop Science)
Understanding the Rules of Life (Plant Science)

Project Outline

The rotation of the Earth creates periodic day-night changes in environmental conditions such as light and temperature. Organisms are able to adapt to these predictable diurnal cycles through their internal timekeeping system, the circadian clock, which has a periodicity of approximately 24 hours. The circadian clock enables plants to synchronise their metabolism and development with environmental rhythms to maximise fitness. This is reflected in the observation that at least 30% ofArabidopsis thalianatranscripts exhibit circadian rhythmicity and includes genes involved in flowering time, germination, photosynthesis, gas exchange, phytohormone synthesis and signalling, cellular redox status and plant immunity. Thus, circadian rhythmicity occurs at multiple levels from whole organs to individual organelles.

The endoplasmic reticulum (ER) is the gateway to the plant secretory pathway acting as the major platform for secretory protein production, transport, folding and quality control. The ER forms an architecturally intricate network of tubules and cisternae which is constantly remodelling in response to internal and external cues. Such ER reorganisation occurs through tubule extension and sliding and the concomitant formation and closure of polygonal regions; expansion and contraction of cisternae which also results in a shifting of the ratio of tubules to cisternae, and bulk ER streaming along actin filaments. Collaboration between the Frigerio lab (Warwick) and the Fricker lab (Oxford) has enabled us to develop and utilise a quantitative multivariate analysis tool (AnalyzER) (1) which extracts morphological, topological and dynamic features of the ER network and captures even subtle changes in ER structure or behaviour with statistical confidence.

Through our characterisation of the plant ER as part of a wider BBSRC-funded project on ER-mediated plant immunity, we have observed significant changes in the morphology and dynamics of the ER in Arabidopsis leaf epidermal cells associated with different times in the light-dark cycle. Alterations in ER form are likely intrinsically linked to changes in ER function, suggesting that protein secretion may also be rhythmic. Such behaviour would presumably enable the plant to prime the ER machinery for anticipated increases in protein demand thus avoiding ER stress.

Objectives/Biological Questions

1. Is the plant secretory pathway under the control of the circadian clock? Does protein flux through the ER exhibit diurnal behaviour?

2. Can we manipulate the morphology and/or dynamics of the ER to modulate protein secretion? This would have multiple potential beneficial impacts including biotechnological applications and breeding plants with increased resistance to plant pathogens and environmental stress.

Methods

1. Characterise further the diurnal changes in ER morphology and dynamics of both wild-type plants and known clock mutants using confocal microscopy with subsequent image analysis.

2. Identify which, if any, components of the ER machinery (eg chaperones, folding enzymes, heat shock proteins, redox regulators, unfolded protein response pathway) exhibit rhythmic changes in expression to support the hypothesis that ER activity is circadian regulated.

3. Perform functional analysis of known clock mutants to assess impact on secretory protein levels.

Project Management

This project will be a joint collaboration between the Frigerio/Breeze group who specialise in plant cell biology and plant pathology, and the Carre group who have extensive expertise in circadian biology. As such the successful candidate will have the opportunity to take the project in several different directions depending on their own biological interests and results. They will also receive training in a variety of cell biology and molecular biology techniques.

References

1. C. Pain, V. Kriechbaumer, M. Kittelmann, C. Hawes, M. Fricker, Quantitative analysis of plant ER architecture and dynamics. Nat Commun 10, 984 (2019).

Previous Projects (2024-25)

Joint primary supervisor (with Professor Lorenzo Frigerio) for:

Clock-watchER: Circadian coordination of the plant endoplasmic reticulum