Computational Modeling and Evolutionary Implications of Biochemical Reactions in Bacterial Microcompartments

Abstract

Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.

Role of carboxysomes in cyanobacterial CO2 assimilation: CO2 concentrating mechanisms and metabolon implications

“…A protein‐encased bacterial microcompartment (BMC) called a carboxysome (Figure 1D) is a central component of all cyanobacterial CCMs (Huffine et al, 2022). The carboxysome is a prototypical representative within an array of diverse BMCs widely defined by a conserved shell architecture but encapsulating different metabolic pathways.…”

“…The impact of O 2 in the evolution of CCM systems is an active and relevant area of study, especially given the sensitivity of CCMs to environmental O 2 concentration (Neofotis et al, 2021), dictating CCM formation and function. It remains unclear if CCMs evolved initially for the purpose of CO 2 containment or O 2 exclusion (Huffine et al, 2022; Hurley et al, 2021). Nevertheless, it is clear that extant CCMs reduce photorespiration and enhance CO 2 ‐fixation.…”