A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach

Abstract

Cyanobacteria and red algae represent some of the oldest lifeforms on the planet. During billions of years of evolution, they have fine-tuned the structural details of their light-harvesting antenna, called phycobilisomes, which represents one of the most efficient systems for light harvesting and energy transfer. Yet, the exact details of phycobilisome assembly and energy transfer are still under investigation. Here, we employed a multi-modal mass spectrometric approach to unravel the molecular heterogeneity within B-phycoerythrin, the major phycobiliprotein in the red algae P. cruentum. B-phycoerythrin consists of 12 subunits (αβ) 12 arranged in a ring with the central cavity housing a linker (γ) subunit, which is crucial for stabilizing B-phycoerythrin within the phycobilisome. Using top-down MS, we unravel the heterogeneity in the γ proteoforms, characterizing the distinct γ chains and multiple isobaric chromophores they harbor. Our data highlight the key role γ plays in phycobilisome organization that enables optimal light transmission. Some of the most efficient light-harvesting machineries present on earth are found in red algae and cyanobacteria. These systems, termed phycobilisomes, comprise numerous proteins decorated with a plethora of chromophores. The precise arrangement of all proteins and chromophores in the phycobilisome assembly form the basis for extremely efficient energy transfer. Here, we combine different mass spectrometric methods, enabling the structural investigation of all components of the B-phycoerythrin sub-complex in a highly detailed manner. This includes identifying all proteoforms present in the assembly, as well as distinguishing the various (isobaric) chromophores they harbor. Together, this information leads to fundamental insights into the arrangement and chemical heterogeneity of the phycobilisome. Better understanding of the architecture of this complex is essential for the future design of even more efficient light-harvesting machineries. B-phycoerythrin is an extremely heterogeneous protein assembly comprising 13 subunits, all decorated with numerous chromophores. By combining different tiers of mass spectrometric analysis, native MS, top-down MS, and bottom-up MS, Tamara et al. characterize B-phycoerythrin in great detail. Integrating the data allowed them to identify all co-occurring proteoforms within B-phycoerythrin and identify the chemical nature and exact localization of all chromophores they harbor. Knowledge of these structural heterogeneities will be beneficial for the future design of even more efficient light-harvesting systems.