Systems biology to discover novel photosynthesis components in eukaryotic green algae

One of the greatest challenges facing civilization is the sustainable production of food to feed a rapid growing global population. To meet this ever-increasing demand novel technologies and ingenious engineering approaches are necessary to enhance crop production. One exciting approach is the improvement of crop photosynthesis by introducing a mechanism that concentrates CO2 in the proximity of Rubisco, the principal carbon-fixing enzyme (Long et al., 2015). The Mackinder Lab at the University of York is looking to recruit a highly motivated and dedicated student to undertake a PhD in understanding the efficient CO2 concentrating mechanism (CCM) in green algae, with an ultimate goal to transfer components to higher plants to improve photosynthesis.

At the center of the eukaryotic algal CCM is an organelle called the pyrenoid where the cell releases CO2 in the presence of tightly packaged Rubisco. We recently discovered a key protein component of the pyrenoid (Mackinder et al., 2016) that along with other CCM components are currently being expressed in higher plants to see if they improve photosynthetic performance (Atkinson et al., 2015). However, we believe we are still missing several key components necessary for the successful engineering of a pyrenoid and CCM in higher plants.

The successful PhD candidate will use systems biology in combination with cell physiology approaches to identify new CCM and pyrenoid components. The PhD will have 3 core parts: 1) Identify new pyrenoid components by high-throughput tagging and protein-protein interaction studies. We have recently developed a high-throughput fluorescence protein tagging and protein-protein interaction pipeline to identify new pyrenoid proteins. The prospective student will further expand this dataset to saturate the pyrenoid interactome. Proteins of interest will be fluorescently tagged and localized using confocal microscopy and their interaction partners will be identified by co-immunoprecipitation mass spectrometry. 2) Characterise newly identified pyrenoid components. A set of recently identified pyrenoid proteins in addition to those newly discovered in part 1 will be further characterised. Mutants in these proteins will be screened for CCM defects and the proteins characterised biochemically. The PhD candidate will use a wide range of molecular and cell physiology techniques, including PCR, cloning, western blotting, O2 evolution, confocal and electron microscopy and protein biochemistry. 3) Screen for mutants in the CCM using a barcoded mutant library. The Jonikas Lab based at Princeton has developed a methodology to screen >100,000 mutants simultaneously for a phenotypic defect. In collaboration with the Jonikas Lab we will perform screens to identify additional CCM mutants.

The successful candidate will have the potential opportunity to work with and visit collaborators at Princeton University and the University of Edinburgh.