The function, evolution, and future of carboxysomes

Since their discovery as Rubisco-containing compartments >50 years ago, significant breakthroughs have advanced our understanding of carboxysome structure and function, and their centrality to cyanobacterial CO₂-concentrating mechanisms (CCMs). Within CCMs, cellular bicarbonate (HCO₃^-) is actively accumulated and maintained by a suite of HCO₃^- transporters and CO₂-to-HCO₃^- conversion pumps to support carboxysome function. This elevation of cellular HCO₃^- is indispensable for the action of carboxysomes, as they rely entirely on concentrated HCO₃^- to generate internal CO₂ for Rubisco. This review traces the historical progression of carboxysome research, from early structural observations to modern insights into their biogenesis, internal organization, and function. We explore the evolutionary trajectory of carboxysomes, hypothesizing why terrestrial plants, despite sharing a common ancestor with cyanobacteria, lack these microcompartments. Despite their absence from plants, carboxysomes are now being engineered into plant chloroplasts as part of efforts to improve photosynthetic performance. We also address the physiological implications of carboxysome gas permeability, the role of oxygenation, and the need for in vitro assays to assess carboxysome functionality in engineered systems. We discuss the challenges of reconstructing functional carboxysomes in heterologous systems, particularly the need for HCO₃^- accumulation. Finally, we consider the future of carboxysomes, including their use as modular platforms for carbon fixation and novel catalytic functions, and their potential forward evolutionary trajectories. By synthesizing historical, mechanistic, and applied perspectives, this review highlights both the possibilities and limitations of Rubisco encapsulation in heterologous systems.