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Our work on understanding the C4 pathway makes use of model organisms as well as natural variation, and classical molecular biology approaches as well as emerging technologies in bioinformatics and computational processing.
We are extending the phylogenetic breadth of RNAseq on closely related C3 and C4 species. This includes cell specific transcriptomes and will form the foundation for an understanding of the extent to which the M and BS transcriptomes of independent C4 lineages are convergent.
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The model C3 plant A. thaliana contains all the proteins used in the C4 pathway. We are using Arabidopsis to define the ancestral role of these proteins in C3 species prior to their recruitment into the C4 pathway.
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We are involved in building the basic biochemistry required for the C4 pathway in leaves of rice, this is done in collaboration with IRRI. In addition, in we have identified candidate regulators of the patterns of C4 gene expression and with Bob Furbank (CSIRO) are testing the role of these proteins in Setaria italica.
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In collaboration with Mike Blatt, Nigel Burroughs, Cheryl Kerfield, Nick Smirnoff and John Golbeck we are investigating whether photosynthesis can be enhanced using artificial protein scaffolds and light driven HCO3- pumps.
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As with all major crops, rice went through a series of domestication bottlenecks that reduced allelic variation compared with its ancestors and current wild species. With IRRI we are using wild species of rice and Multi Advanced Generation Inter-Crossing to re-introduce tolerance to biotic and abiotic stresses.
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<p>With Andreas Weber’s lab we initially conducted analysis of RNA populations in whole leaves of C<sub>3</sub> and C<sub>4</sub> <i>Cleome</i> species. We are extending this to undertake large-scale analysis of many more lineages, of leaf maturation, and of mesophyll and bundle sheath transcriptomes. To fully understand these large dataset, significant investment in development of computational approaches is required!</p>
Images: top and left: traced leaf venation patterns of C3 vs. C4 plants.
<p>Despite having well-characterised functions in C<sub>4</sub> species, many of the core enzymes of the C<sub>4</sub> pathway have poorly understood roles in C3 plants. We are analyzing the roles that they play through analysis of when and where they are expressed, as well as the use of insertional mutants and overexpression, followed by in depth photosynthetic and metabolic phenotyping. Many of these proteins are members of multi-gene families, and belong to redundant networks, and so the analysis is often intellectually challenging.</p>
<p><i>Images: top and left: developing Arabidopsis seedlings expressing a marker</i></p>
<p>Our focus has been generating resources that allow us to test the extent to which the basic C<sub>4</sub> cycle can be installed in rice. This has involved analysis of the extent to which C<sub>4</sub> genes from maize are expressed in a cell specific manner in rice, and also investigating potential regulators of these genes. Clearly, this is a long-term, incredibly challenging project, but we are finding that we learn a lot about the fundamentals of C<sub>4</sub> photosynthesis along the way.</p>
Images: top: C3 rice (foreground) growing alongside C4 Echinochloa glabrescens (mid) and maize (rear). The increased efficiency of C4 enables the C4 plants to grow faster with the same resources. left: rice growing in paddy conditions.
<p>For many decades, work has been conducted that aims to increase the efficiency of RuBisCO by modifying its catalytic characteristics. We are taking an alternate approach inspired by Synthetic Biology in order to investigate whether artificial protein scaffolds can be used to improve the efficiency of photosynthesis. We hope that we can use this as proof of concept for engineering plant metabolism in general.</p>
<p><i>Images: top: structure of RuBisCO complex consisting of 8 large and and 8 small subunits. left: RuBP binding the active site of the RuBisCO large subunit.</i></p>
<p>A significant amount of work has been undertaken in which individual wild relatives of rice have been used as sources for useful traits in domesticated rice. In this project we are broadening this concept to source variation present in all the AA rice genomes, and increase it further using the multi advance generation intercrossing approach. Back crossing into <i>O. sativa</i> allows useful traits to transferred into elite germplasm. The wide crossing, and the subsequent analysis of gene expression and genomic structures represent significant technical and computational challenges.</p>
<p><i>Images: top and left: wild relatives of rice showing the broad morphological spectrum in the genus. This project aims to harness that diversity to improve cultivated rice.</i></p>
- Cleome as a model for C4 photosynthesis (The Leverhulme Trust)
- The role and regulation of PPDK in C3 species (BBSRC Responsive mode)
- The role of C4 acid decarboxylases in Arabidopsis (BBSRC Responsive mode)
- Photosynthesis in discrete cell types. (BBSRC Sir David Phillips Research Fellowship)
Collaborations:
- With Dr Alex Webb. The circadian clock and photosynthesis. (BBSRC Responsive mode)
- With Dr Mark Tester and Emmanuel Guiderdoni. Rice enhancer traps (BBSRC Responsive mode)