Mathematical modeling of 1,2-propanediol utilization bacterial microcompartments in vivo activity

TL;DR

This study uses kinetic modeling and experiments to understand how bacterial microcompartments in Salmonella contribute to 1,2-propanediol metabolism in vivo, revealing differences from purified enzyme assays and proposing a revised metabolic model.

Contribution

The paper introduces a kinetic model that explains in vivo MCP activity differences and suggests most downstream reactions occur in the cytosol, refining understanding of bacterial microcompartment function.

Findings

In vivo activity differs from purified MCP assays due to cytosolic enzymes.

Knocking out PduQ reduces activity, linking cytosolic enzymes to metabolism.

Most downstream Pdu activity occurs in the cytosol, not within MCPs.

Abstract

On exposure to 1,2-propanediol (1,2-PD), Salmonella enterica serovar Typhimurium LT2 produces 1,2-PD utilization (Pdu) microcompartments (MCPs), nanoscale protein-bound shells that encapsulate metabolic enzymes. MCPs serve as a bioengineering platform to study reaction organization and enhance flux through specific pathways. However, a recently published assay of purified wild-type (WT) MCPs reported metabolic activity that differed markedly from that observed in vivo. Using kinetic modeling, we attribute these discrepancies to in vivo cell growth and to the cytosolic presence of MCP-associated enzymes and promiscuous alcohol dehydrogenases, which are not present in the purified MCPs. Assays of purified MCPs in E. coli lysate, together with an LT2 growth assay in which the native Pdu MCP-associated alcohol dehydrogenase, PduQ, was knocked out, support the conclusion that exogenous Pdu cytosolic enzyme activity can narrow the gap between in vitro and in vivo experiments. Our modeling further suggests that MCP-localized enzymes contribute little to in vivo metabolic flux downstream of PduCDE. We therefore propose a revised in vivo model of WT growth on 1,2-PD in which PduCDE is fully encapsulated, while much of the downstream Pdu activity occurs in the cytosol.