Principal Supervisor name, department, University:
Dr Lorenzo Frigerio, School of Life Sciences, University of Warwick
Second Supervisor name, department, University:
Dr Till Bretschneider, Warwick Systems Biology Centre, University of Warwick
Where will the student be based?
School of Life Sciences/Warwick Systems Biology
PhD project title: Towards a quantitative understanding of plant endoplasmic reticulum dynamics
Project description:
The plant endoplasmic reticulum (ER) is a very dynamic organelle, which serves as both the port of
entry and storage site for many major proteins and lipids necessary for human and animal nutrition
(Sparkes et al, 2011). How the shape and dynamics of the ER influence its biosynthetic capacity is
therefore a key research question for the improvement of protein yield in food and oil crops.
The ER is a complex, very mobile network of membrane sheets and tubules (Sparkes et al, 2011). We
have recently identified proteins responsible for conferring the ER its tubular structure (Tolley et al,
2008, 2010) and proteins that are potentially involved in the fusion of ER membrane tubules (Lee et
al., 2012). Perturbation of these proteins leads to major changes in the architecture of the ER, but
also indicates that other, as yet unknown factors, are also needed to determine overall ER shape and
movement. The time is right to undertake a forward genetic screen for ER morphology mutants, and
also a small molecule (chemical genomic) screen to identify new compounds that affect ER shape,
and their targets. In order to achieve this, we first need to develop robust, quantitative methods
that will allow us to measure and compare the ER morphology in different mutants or treatments.
We have several transgenic Arabidopsis lines expressing XFP-tagged markers of the ER lumen and the
ER membrane. These can be used to generate 4D image datasets of ER movement, and 3D datasets
of the overall structure of the peripheral ER in different tissue/cell types and during developmental
transitions (ie seed germination).
To obtain a quantitative understanding of ER dynamics we will develop tools for morphometric
analyses, which allow screening for alterations in ER architecture. These methods will employ
advanced segmentation methods recently developed by us (Du et al, 2010). The obtained structures
will then be subject to harmonic and fractal analysis to determine generic structural features of the
overall ER topology. Principal component analysis will be used to determine suitable features for
morphometric classification. Using image analysis to extract particular structures such as line
segments, vacuolar structures and polygonal structures will help to identify ER remodelling observed
under different experimental conditions. Validation of the novel tools will make use of synthetic
data.
The project will be jointly supervised by Lorenzo Frigerio (Warwick School of Life Sciences), expert in
the biology and imaging of the plant endoplasmic reticulum, and Till Bretschneider (Warwick Systems
Biology Centre) with expertise in quantitative image analysis of cellular dynamics. The nature of the
project is genuinely interdisciplinary, but depending on the student’s background there can be more
emphasis on either the wet or dry side.
Key experimental skills involved:
Plant molecular biology
In vivo light microscopy (confocal, spinning disc, TIRF)
Image and data analysis, computational modelling
References:
C.-J. Du, M. Marcello, D.G. Spiller, M.R.H. White, T. Bretschneider. Interactive Segmentation of
Clustered Cells via Geodesic Commute Distance and Constrained Density Weighted Nyström
Method. Cytometry A, 77(12):1137-1147, 2010.
Lee H, Sparkes I, Gattolin S, Dzimitrowicz N, Roberts LM, Hawes C, Frigerio L (2012). An Arabidopsis
reticulon and the atlastin homologue RHD3-like2 act together in shaping the tubular endoplasmic
reticulum. New Phytol. doi:10.1111/nph.12038.
Sparkes I, Hawes C, Frigerio L (2011). FrontiERs: movers and shapers of the higher plant cortical ER.
Curr Opin Plant Biol 14:658-665.
Tolley N, Sparkes IA, Hunter PR, Craddock CP, Nuttall J, Roberts LM, Hawes C, Pedrazzini E, Frigerio L
(2008). Overexpression of a Plant Reticulon Remodels the Lumen of the Cortical Endoplasmic
Reticulum but Does not Perturb Protein Transport. Traffic 9:94-102.
Tolley N, Sparkes I, Craddock C, Eastmond P, Runions J, Hawes C, Frigerio L (2010). Transmembrane
domain length is responsible for the ability of a plant reticulon to shape endoplasmic reticulum
tubules in vivo. Plant J 64:411-418.
Contact details for application enquiries:
l.frigerio@warwick.ac.uk
Keywords:
Plant cell biology, Endoplasmic reticulum, organelle structure, in vivo imaging, image analysis.