Periodic Reporting for period 1 - ChloroMosaic (Environmentally-informed functional characterisation of the secondary red chloroplast proteome)
Reporting period: 2023-01-01 to 2025-06-30
Half of the oxygen that we breathe is produced by aquatic algae. These organisms are evolutionarily diverse, ranging from tiny single-celled cyanobacteria to giant multicellular seaweeds, and are spread across all marine and freshwater habitats, ranging from the polar ice-caps threatened by melting to tropical oceans impacted by increasingly recurrent heatwaves as a result of anthropogenic climate change. The most abundant algae within these envieonments come from groups diatoms, haptophytes, dinoflagellates) that possess chloroplasts derived from the secondary or higher endosymbiotic uptake of a red alga, itself possessing a nucleus and chloroplasts. These algae and their chloroplasts are very distantly related to plants, and are supported by novel proteins that come from a « mosaic » of different sources but may be essential to their functions in the wild.
ChloroMosaic seeks to understand the dark matter of the secondary red chloroplast proteome, its evolutionary origins, its cellular functions, and its environmental relevance to a heating global ocean. First, we are profiling the chloroplast proteome of dinoflagellate algae, essential symbionts of coral reefs, with distinctive cell biology very different from that of other algal groups. Next, we are using combined evolutionary and cell biology techniques to characterise individual chloroplast proteins found across secondary red algal plastids but not associated with plants, focussing in particular on diatoms, the single most abundant of these algal groups. Finally, we are considering at a more conceptual level how mosaic algal genomes form and function, focussing in particular on the distantly related algae native to the Arctic, and to one algal group, haptophytes, who are spread across a heating global ocean.
ChloroMosaic seeks to understand the dark matter of the secondary red chloroplast proteome, its evolutionary origins, its cellular functions, and its environmental relevance to a heating global ocean. First, we are profiling the chloroplast proteome of dinoflagellate algae, essential symbionts of coral reefs, with distinctive cell biology very different from that of other algal groups. Next, we are using combined evolutionary and cell biology techniques to characterise individual chloroplast proteins found across secondary red algal plastids but not associated with plants, focussing in particular on diatoms, the single most abundant of these algal groups. Finally, we are considering at a more conceptual level how mosaic algal genomes form and function, focussing in particular on the distantly related algae native to the Arctic, and to one algal group, haptophytes, who are spread across a heating global ocean.
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.
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.
ChloroMosaic seeks to give new insights into the dark matter of algal chloroplasts, provide fundamental mechanistics for the evolutionary complexification of algal life, and help calibrate predictive models of algal resilience and fragility to anthropogenic climate change. Resolving the chloroplast proteome of dinoflagellates, which remain due to their unusual cell structure and internal biology by far the least understood of the major eukaryotic algal groups, will provide important insights into their functions in the world ocean, including as essential photosynthetic symbionts of coral reefs, and as toxic agents of harmful red tides. The elaboration of Kareniaceae, as a model for the endosymbiotic acquisition of chloroplasts, gives us a new window into what cellular and ecological factors underpin the repeated evolution of photosynthetic capacity across the algal tree of life.
Characterising novel diatom chloroplast proteins may provide us with explanations for their striking success in the world ocean, and identify new gene targets for synthetic engineering of increased primary production and metabolic activity in transformable model algal species. In particular, the complementary use of experimental and environmental data allows us to develop new strategies for inferring protein function, insofar as we can now use meta-genomics to « predict » protein phenotypes that can be validated at the bench. We are now using these techniques to identify protein functions that have never previously been associated with chloroplasts, e.g the probable transport of novel metal substrates, and use of a novel strategy for ATP management in algal chloroplasts.
Finally, by sequencing and understanding the mosaic fomration of Arctic algal genomes will provide us with unprecedented insight into this biologically unique and fragile ocean biome, alongside providing us with clues about how algal chloroplast metabolism underpins species responses to ocean heating. We are now using these data with globally distributed haptophyte algae to develop whole-cell models of how haptophyte chloropalst activity changes with temperature, which aim to use these to refine our predictions of algal fitness and chloroplast function in the future ocean.
Characterising novel diatom chloroplast proteins may provide us with explanations for their striking success in the world ocean, and identify new gene targets for synthetic engineering of increased primary production and metabolic activity in transformable model algal species. In particular, the complementary use of experimental and environmental data allows us to develop new strategies for inferring protein function, insofar as we can now use meta-genomics to « predict » protein phenotypes that can be validated at the bench. We are now using these techniques to identify protein functions that have never previously been associated with chloroplasts, e.g the probable transport of novel metal substrates, and use of a novel strategy for ATP management in algal chloroplasts.
Finally, by sequencing and understanding the mosaic fomration of Arctic algal genomes will provide us with unprecedented insight into this biologically unique and fragile ocean biome, alongside providing us with clues about how algal chloroplast metabolism underpins species responses to ocean heating. We are now using these data with globally distributed haptophyte algae to develop whole-cell models of how haptophyte chloropalst activity changes with temperature, which aim to use these to refine our predictions of algal fitness and chloroplast function in the future ocean.