Systems biology of photosynthetic organisms

A systems-level understanding of gene functions will open doors to rapid advances in agriculture, bioenergy and global ecology. While the genomes of thousands of photosynthetic organisms have been sequenced, the functions of most of the genes they encode remain unknown. We seek to develop new systems biology tools and resources that will reveal currently unknown cellular functions and will accelerate the community's ability to understand and ultimately engineer key genes.

The green alga Chlamydomonas reinhardtii ("Chlamy") is a powerful model photosynthetic organism. The green plant photosynthetic apparatus is highly conserved and thus can be studied in Chlamy. Chlamy can grow as a haploid and in the absence of a functional photosynthetic apparatus, allowing rapid isolation of mutants of interest. Its unicellular nature and short doubling time enable higher throughput experiments than multicellular systems, making it complementary to higher plant models. Importantly, Chlamy benefits from a highly collaborative and very friendly community of researchers.

We are developing transformative tools to enable high-throughput studies of gene function in Chlamy. We have developed a genome-wide collection of 60,000 Chlamy insertion mutants as a powerful resource for the research community. We have developed pipelines for high-throughput characterization of protein localization and protein-protein interactions that reveal key clues to the functions of uncharacterized proteins. We now seek to enable the systematic placement of genes into pathways and the discovery of new pathways by leveraging high-throughput genetics, protein localization and protein-protein interactions.

Understanding and engineering the algal pyrenoid

The pyrenoid is a poorly characterized structure that allows algae to assimilate CO2 more efficiently than C3 crop plants. The pyrenoid consists of a ball of the CO2-fixing enzyme Rubisco, traversed by membrane tubules that feed the Rubisco with concentrated CO2 to make it run faster. Nearly all eukaryotic algae in the oceans use a pyrenoid to assimilate CO2. Despite its importance to the global carbon cycle, until very recently, the pyrenoid has remained almost completely uncharacterized at a molecular level.

If we understood how a pyrenoid works, we could engineer it into crop plants to increase their growth rates and reduce their need for water and fertilizer. We are working with our collaborators in the NSF project 
Combining Algal and Plant Photosynthesis to identify and transfer pyrenoid components into the model C3 plant Arabidopsis, as a first step towards ultimately improving yields by enhancing CO2 uptake in wheat and rice.

We aim to transform our understanding of pyrenoid protein composition, structure and function. We recently discovered ~90 protein components of the pyrenoid, and determined their sub-pyrenoid localization and physical interactions. Among them, we identified 
a key protein that we think holds the carbon-fixing enzyme Rubisco together in the pyrenoid. We also discovered that the Chlamy pyrenoid behaves as a phase-separated, liquid-like organelle, not as a crystalline solid as it has long been thought to be. We now seek to understand the fundamental principles of pyrenoid biogenesis and function at a level that enables the functional engineering of this structure into higher plants.