Genetic characterization of a glycyl radical microcompartment used for 1,2-propanediol fermentation by uropathogenic Escherichia coli CFT073

Bacterial microcompartments (MCPs) are widespread protein-based organelles composed of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by confining toxic and/or volatile pathway intermediates. A major class of MCPs, known as glycyl radical MCPs has only been partially characterized. Here, we show that uropathogenic Escherichia coli CFT073 uses a glycyl radical MCP for 1,2-propanediol (1,2-PD) fermentation. Bioinformatic analyses identified a large gene cluster (named grp for [underln]g[/underln]lycyl [underln]r[/underln]adical [underln]p[/underln]ropanediol) that encodes homologs of a glycyl radical diol dehydratase, other 1,2-PD catabolic enzymes and MCP shell proteins. Growth studies showed that E. coli CFT073 grows on 1,2-PD under anaerobic conditions but not under aerobic conditions. All nineteen grp genes were individually deleted and 8/19 were required for 1,2-PD fermentation. Electron microscopy and genetic studies showed that a bacterial MCP is involved. Bioinformatics combined with genetic analyses support a proposed pathway of 1,2-PD degradation and suggest that enzymatic cofactors are recycled internally within the Grp MCP. A two-component system (grpP and grpQ) is shown to mediate induction of the grp locus by 1,2-PD. Tests of the ECOR collection indicate that >10% of E. coli strains ferment 1,2-PD using a glycyl radical MCP. In contrast to other MCP systems, individual deletions of MCP shell genes (grpE, grpH and grpI) eliminated 1,2-PD catabolism suggesting significant functional differences with known MCPs. Overall, the studies presented here are the first comprehensive genetic analysis of a Grp-type MCP. Importance Bacterial MCPs have a number of potential biotechnology applications and have been linked to bacterial pathogenesis, cancer and heart disease. Glycyl radical MCPs are a large but understudied class of bacterial MCPs. Here we show that uropathogenic E. coli CFT073 uses a glycyl radical MCP for 1,2-PD fermentation and conduct a comprehensive genetic analysis of the genes involved. Studies suggest significant functional differences between the glycyl radical MCP of E. coli CFT073 and better-studied MCPs. They also provide a foundation for building a deeper general understanding of glycyl radical MCPs in an organism where sophisticated genetic methods are available.