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.

Apparent size and morphology of bacterial microcompartments varies with technique

“…Metabolic engineers have sought to increase flux through target pathways of interest by increasing local concentrations of enzymes and their substrates [28]. MCPs can accomplish this task and offer the potential added benefit of sequestering toxic or volatile intermediates from damaging or escaping the cell [29,30]. They also have the potential to reduce unwanted side reactions and provide private cofactor pools separate from central metabolism [31].…”

Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory

“…A key result of this analysis is that microcompartments significantly enhance pathway flux for a range of external substrate concentrations. We predict that the natively encapsulated system enjoys a four-order of magnitude enhancement in flux upon encapsulation, as compared to free diffusion of the enzymes in the cytosol 43 . Appropriately chosen heterologous pathways might also accrue such flux enhancements, as well as potentially reduce the loss of pathway intermediates to the extracellular space.…”

“…To address the kinetic consequences of encapsulation in Pdu microcompartments, we make use of a model 43 developed to analyze the native function of the microcompartment organelles. A key result of this analysis is that microcompartments significantly enhance pathway flux for a range of external substrate concentrations.…”

“…In the case of organelle- or scaffold-based organization, a closed-form analytical solution to the governing equations can be found, provided we assume that the metabolite concentration inside the organelle or scaffold region is constant. This solution is used to generate the various figures comparing organization strategies; see 43 for the derivation and complete analytical solutions. A scaffold-like behavior is created by setting the permeability at the organelle boundary to approximate free diffusion (that is, k c S1 = k c S2 ~ 10 3 ).…”

“…Due to their relative simplicity and ease of manipulation, these various protein-based compartments make excellent model systems for exploring the role of spatial organization on metabolism. It is thought that they function both by protecting the cellular contents from toxic intermediates 42 and by increasing the local concentration of the kinetically relevant intermediate inside the organelle 43 .…”