Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.

Faculty of Science Department of Molecular Biology and Genetics University of South Bohemia České Budějovice Czech Republic Department of Evolutionary Protistology Institute of Parasitology Biology Centre CAS České Budějovice Czech Republic

Faculty of Science Department of Molecular Biology and Genetics University of South Bohemia České Budějovice Czech Republic Department of Evolutionary Protistology Institute of Parasitology Biology Centre CAS České Budějovice Czech Republic Faculty of Engineering and Natural Sciences Department of Computer Science Johannes Kepler University Linz Austria

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