To explore the chloroplast proteome of dinoflagellates, we are using the model species Amphidinium, whose chloroplast genome is directly transformable. We aim to generate synthetic Amphidinium lines in which we can either tag and sequence unknown chloroplast proteins, or suppress their expression and measure defects in dinoflagellate physiology. Alongside this, we are assembling a compendium of dinoflagellate chloroplast proteins from genome data, focussing in particular on the group Kareniaceae, which are a model for understanding how secondary red chloroplasts evolve. An important early result from ChloroMosaic is that Kareniaceae have repeatedly acquired their chloroplasts from one single algal group, the haptophytes, with different proteins evolving to support this symbiosis in each case.
To understand novel chloroplast proteins in diatoms, we are using combined environmental data from the Tara Oceans expedition and the model transformable species Phaeodactylum, testing carbon metabolism, transporter proteins, and a novel protein related to ATP synthase. We are particularly interested to make convergent predictions on protein function using environmental and experimental techniques. In one early project we show, for example, that diatom chloroplast lower-half glycolysis is most highly expressed in subpolar oceans, characterised by long days and low temperatures, and Phaeodactylum mutant lines for these proteins show perturbed physiology in response both to illumination and cold stress. We are now moving beyond working strictly on diatoms, testing some of our proteins in the model green alga Chlamydomonas and in heterotrophic eukaryotes.
Finally, to understand how mosaic evolution connects to the environment, we are sequencing nearly 50 new algal genomes, with a particular concentration on the Arctic Ocean. Early in ChloroMosaic, we showed that a non-chloroplast protein family, ice-binding proteins, shows as a geographically structured mosaic history, with Arctic species possessing distinct isoforms to closely related species from the Antarctic Southern Ocean. We are now exploring how these proteins, and algal chloroplast metabolism in general, respond to heating and salinity stress, as will become increasingly prevalent in a global ocean impacted by anthropogenic climate change.
