Characterization Of A Glycyl-Radical Enzyme Bacterial Microcompartment Pathway In Rhodobacter capsulatus .

Bacterial microcompartments (BMCs) are large (∼100 nm) protein shells that encapsulate enzymes, their substrates, and cofactors for the purposes of increasing metabolic reaction efficiency and protecting cells from toxic intermediates. The best-studied microcompartment is the carbon fixing carboxysome that encapsulates RuBisCO and carbonic anhydrase. Other well-known BMCs include the Pdu and Eut BMCs, which metabolize 1,2-propanediol and ethanolamine, respectively, with B12 -dependent diol dehydratase enzymes. Recent bioinformatics analyses identified a new prevalent type of BMC, hypothesized to utilize B12 -independent glycyl radical enzymes to metabolize substrates. Here we use genetic and metabolic analysis to undertake in vivo characterization of the newly identified GRM3 class of microcompartment clusters. RNA-seq analyses show that the microcompartment gene cluster in the genome of the purple photosynthetic bacterium Rhodobacter capsulatus is expressed under dark anaerobic respiratory conditions in the presence of 1,2-propanediol. HPLC and GC-MS analyses also show that enzymes coded by this cluster metabolize 1,2-propanediol into propionaldehyde, propanol, and propionate. Surprisingly, the microcompartment pathway does not protect these cells from toxic propionaldehyde under the conditions used in this study, with build-up of this intermediate contributing to arrest of cell growth. We further show that expression of microcompartment genes is regulated by a two-component system located downstream of the microcompartment cluster. IMPORTANCE BMCs are protein shells that are designed to compartmentalize enzymatic reactions that require either sequestration of a substrate or the sequestration of toxic intermediates. Due to their ability to compartmentalize reactions, BMCs have also become attractive targets for bioengineering novel enzymatic reactions. Despite these useful features, little is known about the biochemistry of newly identified classes of BMCs. In this study we have undertaken genetic and in vivo metabolic analysis of the newly identified GRM3 BMC gene cluster.