A Systems-Level Model Reveals That 1,2-Propanediol Utilization Microcompartments Enhance Pathway Flux Through Intermediate Sequestration

Abstract

The spatial organization of metabolism is common to all domains of life. Enteric and other bacteria use subcellular organelles known as bacterial microcompartments to spatially organize the metabolism of pathogenicity-relevant carbon sources, such as 1,2-propanediol. The organelles are thought to sequester a private cofactor pool, minimize the effects of toxic intermediates, and enhance flux through the encapsulated metabolic pathways. We develop a mathematical model of the function of the 1,2-propanediol utilization microcompartment of Salmonella enterica and use it to analyze the function of the microcompartment organelles in detail. Our model makes accurate estimates of doubling times based on an optimized compartment shell permeability determined by maximizing metabolic flux in the model. The compartments function primarily to decouple cytosolic intermediate concentrations from the concentrations in the microcompartment, allowing significant enhancement in pathway flux by the generation of large concentration gradients across the microcompartment shell. We find that selective permeability of the microcompartment shell is not absolutely necessary, but is often beneficial in establishing this intermediate-trapping function. Our findings also implicate active transport of the 1,2-propanediol substrate under conditions of low external substrate concentration, and we present a mathematical bound, in terms of external 1,2-propanediol substrate concentration and diffusive rates, on when active transport of the substrate is advantageous. By allowing us to predict experimentally inaccessible aspects of microcompartment function, such as intra-microcompartment metabolite concentrations, our model presents avenues for future research and underscores the importance of carefully considering changes in external metabolite concentrations and other conditions during batch cultures. Our results also suggest that the encapsulation of heterologous pathways in bacterial microcompartments might yield significant benefits for pathway flux, as well as for toxicity mitigation. Funding: This work was supported by the National Science Foundation (award MCB1150567 to DTE) https://www.nsf.gov. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author SummaryMany bacterial species, such as Salmonella enterica (responsible for over 1 million illnesses per year in the United States) and Yersinia pestis (the causative agent of bubonic plague), have a suite of unique metabolic capabilities allowing them to proliferate in the hostile environment of the host gut. Bacterial microcompartments are the subcellular organelles that contain the enzymes responsible for these special metabolic pathways. In this study, we use a mathematical model to explore the possible reasons why Salmonella enclose the 1,2-propanediol utilization metabolic pathway within these sophisticated organelle structures. Using our model, we can examine experimentally inaccessible aspects of the...

Bacterial microcompartments

“…The separation of the encapsulated enzymatic core from the cytosol is thought to protect the cell from toxic metabolic intermediates and prevent unwanted side reactions. Moreover, the co-localization of the encapsulated enzymes enhances flux through multi-step pathways 9 and may increase enzyme stability.…”

De novo design of signal sequences to localize cargo to the 1,2‐propanediol utilization microcompartment

“…[10][11][12] The organelles are thought to function by sequestering toxic intermediates, 13 providing a private pool of cofactors, 14,15 and enhancing pathway flux. 16 Synthetic biologists and metabolic engineers hope to manipulate microcompartment systems to gain these benefits for heterologous pathways of interest. A central aspect of these engineering efforts is the controlled encapsulation of heterologous cargo in the microcompartment lumen.…”

“…Native microcompartment systems are known to metabolize 1,2‐propanediol, ethanolamine, and plant saccharides . The organelles are thought to function by sequestering toxic intermediates, providing a private pool of cofactors, and enhancing pathway flux . Synthetic biologists and metabolic engineers hope to manipulate microcompartment systems to gain these benefits for heterologous pathways of interest.…”

Biotechnological Advances in Bacterial Microcompartment Technology

“…There are two main trains of thought as to why bacteria require these elaborate structures. The first centres around the idea that the compartment, with its high internal concentration of enzymes, enhances metabolic flux utilising proximity and channelling effects [15], thereby providing a competitive growth advantage over other organisms [15][16][17]. The second theory revolves around the idea that the compartment, and specifically its outer shell, provides a diffusion barrier for toxic or volatile intermediates such as aldehydes or CO 2 [12,18].…”