Mass spectrometry reveals the evolutionary conservation of phycobiliprotein complexes

Cyanobacteria are a highly taxonomically and ecologically diverse group of oxygenic phototrophs that have colonized many different environments on our planet. Despite their differences, almost all cyanobacteria rely on highly efficient light-harvesting protein complexes, termed phycobilisomes, for effective photosynthesis. Phycobilisomes, along with the phycobiliproteins that make them up, have maintained their function throughout evolutionary history while also diversifying to optimize energy capture and transfer in different conditions. Here, we use a combination of evolutionary proteomics, phylogenomics, and structural bioinformatics to probe how phycobiliproteins have maintained their function while adapting to different habitats. Using high-resolution native mass spectrometry, we show that the two most abundant phycobiliprotein complexes, phycocyanin and allophycocyanin, are highly dynamic. Moreover, upon mixing phycobiliproteins from cyanobacterial strains representing diverse environments and evolutionary lineages, heterologous phycobiliprotein complexes rapidly form, comprising building blocks from different cyanobacterial strains. Bioinformatics and structural prediction methods allow us to identify critical residues involved in these interactions. We thus demonstrate that key structural features within the phycobiliprotein components have remained conserved over three billion years of cyanobacterial evolution, ensuring effective photosynthesis across a wide variety of natural environments.