Uncertainty Quantification of Bacterial Microcompartment Permeability
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| Formato: | Preprint |
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2025
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| author | Archer, Andre Palmero, Brett J. Abrahamson, Charlotte Mills, Carolyn E. Kennedy, Nolan W. Tullman-Ercek, Danielle Mangan, Niall M. |
| author_facet | Archer, Andre Palmero, Brett J. Abrahamson, Charlotte Mills, Carolyn E. Kennedy, Nolan W. Tullman-Ercek, Danielle Mangan, Niall M. |
| contents | Salmonella expresses bacterial microcompartments (MCPs) upon 1,2-propanediol exposure. MCPs are nanoscale protein-bound shells that encase enzymes for the cofactor-dependent 1,2-propanediol metabolism. They are hypothesized to limit exposure to the toxic intermediate, propionaldehyde, decrease cofactor involvement in competing reactions, and enhance flux. We construct a mass-action mathematical model of purified MCPs and calibrate parameters to measured metabolite concentrations. We constrain mass-action kinetic parameters to previously estimated Michaelis-Menten parameters. We identified two distinct fits with different dynamics in the pathway product, propionate, but similar goodness of fit. Across fits, we inferred that the MCP 1,2-propanediol and propionaldehyde permeability should be greater than 10^{-6} and 10^{-8} m/s, respectively. Our results identify parameter ranges consistent with prevailing theories that MCPs impose preferential diffusion to 1,2-propanediol over propionaldehyde, and sequester toxic propionaldehyde away from the cell cytosol. The bimodality of the posterior distribution arises from bimodality in the estimated coenzyme-A (CoA) permeability and inhibition rates. The MCP permeability to CoA was inferred to be either less than 10^{-8.8} m/s or greater than 10^{-7.3} m/s. In a high CoA permeability environment with low rates of CoA inhibition, enzymes produced metabolites by recycling (NAD+)/(NADH). In a low CoA permeability environment with high rates of CoA inhibition, enzymes required external NAD+/H to produce metabolites. Dynamics are consistent with prevailing hypotheses about MCP function to sequester toxic propionaldehyde, and additional collection of data points between 6 and 24 hours or characterization of enzyme inhibition rates could further reduce uncertainty and provide better permeability estimates. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_23445 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Uncertainty Quantification of Bacterial Microcompartment Permeability Archer, Andre Palmero, Brett J. Abrahamson, Charlotte Mills, Carolyn E. Kennedy, Nolan W. Tullman-Ercek, Danielle Mangan, Niall M. Quantitative Methods Subcellular Processes Salmonella expresses bacterial microcompartments (MCPs) upon 1,2-propanediol exposure. MCPs are nanoscale protein-bound shells that encase enzymes for the cofactor-dependent 1,2-propanediol metabolism. They are hypothesized to limit exposure to the toxic intermediate, propionaldehyde, decrease cofactor involvement in competing reactions, and enhance flux. We construct a mass-action mathematical model of purified MCPs and calibrate parameters to measured metabolite concentrations. We constrain mass-action kinetic parameters to previously estimated Michaelis-Menten parameters. We identified two distinct fits with different dynamics in the pathway product, propionate, but similar goodness of fit. Across fits, we inferred that the MCP 1,2-propanediol and propionaldehyde permeability should be greater than 10^{-6} and 10^{-8} m/s, respectively. Our results identify parameter ranges consistent with prevailing theories that MCPs impose preferential diffusion to 1,2-propanediol over propionaldehyde, and sequester toxic propionaldehyde away from the cell cytosol. The bimodality of the posterior distribution arises from bimodality in the estimated coenzyme-A (CoA) permeability and inhibition rates. The MCP permeability to CoA was inferred to be either less than 10^{-8.8} m/s or greater than 10^{-7.3} m/s. In a high CoA permeability environment with low rates of CoA inhibition, enzymes produced metabolites by recycling (NAD+)/(NADH). In a low CoA permeability environment with high rates of CoA inhibition, enzymes required external NAD+/H to produce metabolites. Dynamics are consistent with prevailing hypotheses about MCP function to sequester toxic propionaldehyde, and additional collection of data points between 6 and 24 hours or characterization of enzyme inhibition rates could further reduce uncertainty and provide better permeability estimates. |
| title | Uncertainty Quantification of Bacterial Microcompartment Permeability |
| topic | Quantitative Methods Subcellular Processes |
| url | https://arxiv.org/abs/2509.23445 |