From fundamental understanding to engineering of carboxysomes for biotechnological applications

Carboxysomes are self-assembling proteinaceous microcompartments that encapsulate ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase within a semipermeable shell, thereby increasing local CO₂ concentrations around Rubisco to improve carbon fixation. Their inherent design principles, including programmable architecture, cargo encapsulation, semi-permeability, and modular assembly, position carboxysomes as powerful models in synthetic biology and bioengineering, offering unprecedented opportunities to increase carbon assimilation and unlock novel biotechnological functions. This review summarizes our current understanding of the molecular mechanisms underlying carboxysome structure, assembly, and function, highlighting recent breakthroughs and key challenges such as achieving precise control of shell permeability, efficient cargo encapsulation, and integration of carboxysomes into heterologous hosts. We also outline emerging strategies and future perspectives for engineering carboxysomes as enhanced CO₂-fixing engines and repurposing them as versatile nanomaterials for biotechnological applications. Together, these advances underscore the growing potential of carboxysome engineering to transform carbon-fixation pathways across diverse biological systems.