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Department of Plant Sciences

 

UF / OTHER

 

Supervisor: Julian Hibberd

 

Importance of the area of research:

Photosynthesis is the basis of life on our planet, and is identified as a key target for crop improvement. This is because photosynthesis in natural vegetation has been under very different selection pressures compared with the conditions in which our crops are now grown. The consequence is that many aspects of the photosynthetic process act sub-optimally for agriculture. However, there is significant natural variation in photosynthetic efficiency between species, such that some forms of photosynthesis are more efficient than others. One striking example is the C4 pathway that allows about 50% more productivity than the ancestral C3 state (Hibberd, Sheehy and Langdale 2008). The project aims to better understand a key phenomenon associated with the C4 pathway – the ability to restrict photosynthesis gene expression to either mesophyll of bundle sheath cells in the leaf.

 

What the project will involve:

In the vast majority of lineages, the C4 pathway involves restricting the expression of some photosynthesis genes to either mesophyll or bundle sheath cells (Hibberd and Covshoff, 2010). Although various DNA motifs (cis-elements) have been identified and shown to be necessary for expression either in mesophyll or bundle sheath cells (Brown et al 2020; Williams, Burgess et al 2018; Reyna-Llorens et al 2018), their cognate transcription factors have remained elusive. Using the C3 model A. thaliana we recently identified a pair of transcription factors that determine expression in bundle sheath cells (Dickinson, Knerova et al. 2020). Moreover, we have also identified other DNA regions that specify either mesophyll of bundle sheath expression in A. thaliana, and have established a computational pipeline that defines the most likely transcription factors responsible for generating cell specificity. We now wish to build on these breakthroughs to uncover additional transcription factors governing cell specific expression in leaves.

 

What the student will be doing:

We are seeking a highly motivated PhD student to identify the transcription factor networks that govern cell specificity of gene expression in the leaf. The work will involve both wet-lab and in silico analysis.

 

Training that will be provided:

The student will gain experience in molecular biology and genetics using the model A. thaliana. They will also gain training in cutting-edge use of cloning technologies, reporter genes, and approaches to understand gene expression in specific cell types. Transcription factor binding assays as well as bioinformatics analysis will be used. Overall, an advanced training in molecular biology, genomics and computational biology will be provided.

 

References:

Hibberd, J.M., Sheehy, J.E., Langdale, J.A. (2008) Using C4 photosynthesis to increase the yield of rice -rationale and feasibility. Current Opinion in Plant Biology, 11: 228-31.

Hibberd, J.M. & Covshoff, S. (2010) The regulation of gene expression required for C4 photosynthesis. Annual Review of Plant Biology, 61: 181-207.

Brown, N.J., Newell, C.A., Stanley, S., Chen, J.E, Perrin, A.J., Kajala, K., Hibberd, J.M. (2011) Independent and parallel recruitment of pre-existing mechanisms underlying C4 photosynthesis. Science, 331: 1436-1439.

Williams, B., Burgess, S.J., Reyna-Llorens, I., Knerova, J., Aubry, S., Stanley, S., Hibberd, J.M. (2016) An untranslated cis-element regulates the accumulation of multiple C4 enzymes in Gynandropsis gynandra mesophyll cells. The Plant Cell. doi:10.1105/tpc.15.00570

Reyna-Llorens I, Burgess S.J., Reeves G., Singh P., Stevenson S.R., Williams B.P., Stanley S. and Hibberd J.M. (2018) Ancient duons may underpin spatial patterning of gene expression in C4 leaves. Proceedings of the National Academy of Sciences, USA. doi/10.1073/pnas.1720576115.

Burgess, S.J. Reyna-Llorens, I., Stevenson, S.R., Singh, P., Jaeger, K.., Hibberd, J.M. (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses. The Plant Cell doi.org/10.1105/tpc.19.00078.

Dickinson, P., Kneřová, J., Szecówka, M., Stevenson, S.R., Burgess, S.J., Mulvey, H., Bågman, A-M., Gaudinier, A., Brady, S.M., Hibberd, J.M. (2020) A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana. Nature Plants doi10.1038/s41477-020-00805-w.