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A green switch? A quest for regulators of chloroplast biogenesis through parallel cellular and transcriptional analysis of wheat leaf development.

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  • Full or part time
    Dr E Lopez-Juez
    Dr P J Nixon
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

A long term goal of our lab is to improve crop yields through enhancement of photosynthesis at the level of increasing or adjusting the volume of chloroplasts in leaf cells. Like mitochondria in mammals, chloroplasts develop differently and to different extents in various cell types (Jarvis and Lopez-Juez 2013). An ability to alter the “chloroplast compartment size” would require the identification of regulators of chloroplast development, and would open the door towards interventions which would alter crop photosynthetic capacity (Long et al. 2015). This project will seek such regulators. We will exploit the long-recognised gradient of chloroplast biogenesis along developing cereal leaves, with meristematic, undifferentiated cells at the base and mature ones at the tip (Dean et al. 1982, Jarvis and Lopez-Juez 2013). Wheat is one of the world’s three leading crops, the leading one by cultivated area. Its hexaploid nature has led to large cell sizes which make it particularly amenable to microscopy-based analyses (Boffei et al. 1982). While its genetic make-up also makes it challenging from a molecular-biological point of view, great strides have been made in the unravelling of its genome and the analysis of global gene expression (IWGSC 2014). The Lopez-Juez lab (http://pure.rhul.ac.uk/portal/person/e.lopez/) has carried out microscopy-based analyses of the chloroplast compartment in cells of fruit pericarp (Enfissi et al. 2010) and has extended them to leaves of dicot and monocot plants. Chloroplast possess their own genetic machinery, carrying their own genome and prokaryotic-type ribosomes. The lab has established quantitative PCR-based analyses of the copy number of the organellar and nuclear genomes. The Nixon lab (http://www.imperial.ac.uk/people/p.nixon/research.html ) has extensive experience in the manipulation of the chloroplast genome of tobacco (Ahmad et al. 2016), and recently in the quantitation of the genome of cyanobacteria. This project will use microscopy, quantitative PCR, Western blots and flow cytometry to monitor at high resolution activities of cells (division) and chloroplasts (division, growth), as well as physiological (photosynthesis) and biochemical (photosystem assembly) processes along the leaf. The Mochida lab (http://www.riken.jp/bmep/teams/biomass_research_platform/member_mochida_en.html ) has expertise in the use of global gene expression analysis (transcriptomics) in wheat and closely related species (Mochida and Shinozaki 2013). This project will then profile gene expression (using RNAseq) along the same wheat leaf developmental gradient, using a strategy first employed (without a chloroplast focus) in maize (Li et al. 2010). The combined data, both of a quantitative nature, will then be explored by a variety of correlation and mutual-information techniques to identify candidate chloroplast regulators. Such regulators will in a first stage be tested for function through the examination of Arabidopsis orthologue knock-outs.
The student will become trained in cell biological, biochemical and high-throughput data analysis approaches. Should this be required, the project, and the student, will benefit from shared funded work with world-class specialists in leaf development and the biogenesis of the photosynthetic apparatus (See Hibberd et al. 2008).

Funding Notes

Applicants should already have or be expected to obtain a First or upper Second Class degree in a relevant discipline. This BBSRC DTP studentship is fully funded for four years. It includes a stipend at the standard Research Council rate (currently £16,296 per annum), covers research costs and tuition fees at the UK/EU rate, and is available for UK and EU students who meet the UK residency requirements http://www.bbsrc.ac.uk/documents/studentship-eligibility-pdf/

A DTP Studentship is available on either a full-time or part-time basis. A student in part-time employment may be eligible for a part-time award. Students employed full-time are not eligible.


Jarvis, P and Lopez-Juez E (2013) Chlroplast biogenesis and homeostasis. Nat. Revs. Mol. Cell Biol. (December issue)
Enfissi, E.et al. (2010) Integrative transcript and metabolite analysis of DE-ETIOLATED1 down-regulated tomato fruit reveals the underlying metabolic and cellular events associated with their nutritionally enhanced chemotype. Plant Cell 22: 1190-1215
Bögre L, Magyar Z, López-Juez E (2008) New clues to organ size control in plants. Genome Biol. 9:226.
López-Juez E, et al. (2008) Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis. Plant Cell 20: 947-968.
López-Juez E, Bowyer JR, Sakai T (2007) Distinct leaf developmental and gene expression responses to light quantity depend on blue-photoreceptor or plastid-derived signals, and can occur in the absence of phototropins. Planta 227: 113-123.

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