Mass spectrometry raw data files and purification traces to support the publication: Heterogeneity within Phycobilisomes is Highly Orchestrated.

Abstract: The phycobilisome (PBS) is one of the oldest and most efficient light-harvesting protein complexes known. Throughout billions of years of evolution, the PBS has readily adapted to its environment through differential gene expression alongside controlled assembly/disassembly of its components. How hundreds of protein subunits assemble in a controlled manner into different PBS structures within different cyanobacterial species is unknown. Moreover, PBSs are not static entities, and can have different compositions that enables them to modulate their overall function in response to changes in their environment. Here, we utilised high resolving native mass spectrometry (MS) to probe the heterogeneity within PBSs and determine factors that govern its self-assembly. By monitoring PBSs stable sub-complexes, we were able to detect low abundant allophycocyanin variants ApcD and ApcF, in addition to the core linker protein ApcC, and determine their complex stoichiometry. Furthermore, native MS revealed the phycobiliproteins, phycocyanin and allophycocyanin, are unable to form mixed rings within the PBS structure, and instead can only stack, one on of top of another, for efficient energy transfer. Finally, we show that in strains such as A. marina where no allophycocyanin core is present, phycocyanin variants acts as distinct entities to ensure highly orchestrated PBS assembly. Together, the methodology and data obtained open up new avenues for future exploration into how the PBS adapts for effective function.