In photosynthesis, sunlight interacts with colorful photosynthetic pigments like the chlorophylls, carotenoids and phycobilines. The first two of these pigments can be bound by members of the extended light-harvesting complex (LHC) protein superfamily and are organised in order to take on functions in the collection of or in the defense against sunlight. The extended LHC superfamily comprises several protein families, like the LHCs, the photosystem II subunit S (PSBS), the red algal lineage chlorophyll a/b-binding (CAB)-like proteins (RedCAP), and several LHC-like proteins. Some of these groups are very old, likely over two billions of years, and they show a characteristic distribution across different groups of photosynthetic organisms, like cyanobacteria, red algae, algae with secondary plastids, green algae or plants.In this work we aim to distangle the evolutionary history of this complex protein superfamily and to use the results to inform functional studies of different LHC-like proteins in plants and diatoms. After careful searches of homologous protein sequences in public sequence databases, we developed a coherent classification system of the different protein families in part based on hidden Markov model analyses. With this approach, we identified many new LHC-like proteins including several from the model plant species Arabidopsis thaliana and described new families, like the RedCAP from red algae and complex algae with red plastids, and new subfamilies of two-helix proteins from glaucophytes, red algae, diatoms and plants. A group of newly found RedCAP and LHC-like proteins from the diatom Phaeodactylum tricornutum was of sufficient interest for functional follow-up experiments, done by collaborators. The results of these mRNA expression and cellular targeting experiments in combination with evolutionary analyses were used to make inferences about possible functions of these proteins.Results from reverse genetics experiments on the LHC-like one-helix proteins (OHP) 1 and 2 done by others in the Adamska lab were interpreted in an evolutionary framework. Specifically, ohp1 and ohp2 knock out mutants of A. thaliana were extremely sensitive to light so that they had to be grown under very low light conditions and on sugar-supplemented medium. This pointed to fundamentally important functions of these proteins in photoprotection of photosystem I, a point that could be supported by their taxononomic distributions and conservation patterns across algae and plants.The main result of this work was an improved model for the evolution of the extended LHC protein family. By adjusting different phylogenetic methods to our questions, we showed that LHC and PSBS, as well as other eukaryotic three-helix proteins, have evolved independently, contrary to previous suggestions. Likely, they were derived from a pool of two-helix stressenhanced proteins (SEPs). Over the last billions of years and in an still ongoing process, adaptational processes including the evolution of new protein functions, origin of novel proteinfamilies and secondary losses of others, as well as lineage-specific family expansions have shaped this protein superfamily. This has allowed algae and plants to survive and thrive in a multitude of environments, hereby changing our planet forever
