Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments

• Published in: Current opinion in microbiology Vol. 65; pp. 15 - 23
• Main Authors: Huffine, Clair A, Wheeler, Lucas C, Wing, Boswell, Cameron, Jeffrey C
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01-02-2022
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Computer Simulation; Cyanobacteria; Organelles - metabolism
• ISSN: 1369-5274; 1879-0364
• DOI: 10.1016/j.mib.2021.10.001

•Computational modeling of BMCs enlightens experimentally hard-to-measure features.•Significant exploration remains of catabolic BMC capabilities.•Oxygen sensitivity is relatively common across BMC-contained enzymes.•BMC shell proteins are selectively permeable to negatively charged metabolites.
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.