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Investigating the epigenetic control of development and stress responses in plants

Principal Supervisor: Professor Daniel Gibbs

Secondary Supervisor(s): Dr Juliet Coates

University of Registration: University of Birmingham

BBSRC Research Themes:

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Deadline: 4 January, 2024


Project Outline

To survive and thrive in dynamic environments, plants must be able to continually sense their surroundings and modify gene expression to orchestrate appropriate growth and developmental responses. One way in which gene expression is controlled is through methylation of histones in the chromatin of target genes by a conserved eukaryotic protein complex called the polycomb repressive complex 2 (PRC2). This methylation leads to epigenetic repression of gene expression, which is important for regulating cell identity, developmental fate, and environmental memory. Although many agronomically relevant plant processes are regulated by the PRC2, fundamental knowledge about how the complex directly senses and transduces environmental signals into chromatin changes is still lacking.

We recently showed that the stability/abundance of a flowering plant specific subunit of the PRC2 - a protein called Vernalization 2 – is regulated by oxygen availability (Gibbs et al. 2018 Nature Communications; Labandera et al. 2021 New Phytologist). This post-translational regulation means that VRN2 is degraded when oxygen is plentiful, but stabilised under low oxygen conditions (e.g., in specific hypoxic tissues, such as root and shoot meristems, and in response to stresses such as floods, which are increasing in frequency as climate change takes hold). We now want to explore the consequence of this regulation further, to understand how VRN2 contributes to diverse aspects of plant development, stress tolerance and environmental memory. A PhD project in my lab would be focussed on one of several key areas of inquiry, including:

  1. Investigating a role for VRN2 and other histone modifying proteins in establishing stress tolerance and memory (especially during flooding stress), and exploring how manipulating their function can improve stress-resilience.
  2. Investigating how post-translational accumulation of VRN2 in hypoxic niches of the root and shoot meristems helps to co-ordinate plant development.
  3. Using synthetic biology approaches to rewire protein stability and function to create programmable plants that have desired developmental and stress-associated traits.

The exact focus of the project is flexible and can be tailored to specific interests. Most of our work is carried out in the genetic model plant Arabidopsis, with the eventual aim of this research being to translate key findings into crop species, such as barley or rice. As such, this project aligns with the BBSRC priority area of Sustainable Agriculture and Food. The research will be largely molecular based and will also include ‘omics’ approaches (such as ChIP-Seq and proteomics). The PhD candidate will therefore gain expertise in a wide range of cutting edge and transferable techniques.

References

Gibbs DJ, Tedds HM, Labandera A-M, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm Polycomb Repressive Complex 2 subunit VERNALIZATION2. Nature Communications. 9:5438 DOI:10.1038/s41467-018-07875-7

Labandera AM, Tedds H, Bailey M, Sprigg C, Etherington R, Akintewe O, Kalleechurn G, Holdsworth MJ and Gibbs DJ (2021) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. NEW PHYTOLOGIST. https://doi.org/10.1111/nph.16477

Techniques

This project will use a wide range of state-of-the-art molecular biology, genetic and protein biochemistry approaches to characterise a recently identified environment sensing histone modifier, and to link its function to important physiological and growth processes in plants. Depending on the specific project, candidates will gain experience in gene cloning and the generation of mutant and transgenic plants to assist in the dissection of gene function, gene expression analysis (e.g. qRT-PCR) and phenotypic assessment at the physiological and molecular level. This will also inclue transcriptomics and ChIP-seq approaches. Crucially, since this project is related to protein degradation, protein biochemical approaches (including western blotting, protein stability assays and immunoprecipitation/pull down techniques) will also be heavily utilised, as well as mass-spectrometry based proteomics methods for protein screening and assessing protein stability/modifications. Candidates will gain skills in confocal microscopy and image analysis. This project will therefore provide the candidate with training in a wide range of varied, important and highly transferable molecular laboratory-based skills.