Structure of Carboxysomes and Other Bacterial Microcompartments

Electron micrograph of carboxysomes (courtesy of Vim Vermaas, adapted from Kerfeld, et al., 2005)
Electron micrograph of carboxysomes (courtesy of Vim Vermaas, adapted from Kerfeld, et al., 2005)

Bacterial microcompartments are giant, polyhedrally shaped structures found within many bacteria. They consist of a thin outer protein shell assembled from a few thousand protein subunits — in a fashion reminiscent of a viral capsid — encapsulating a series of sequentially-acting enzymes. They function as simple protein-based metabolic organelles by sequestering key pathways within the cell. The carboxysome is the founding member; it encapsulates the enzymes carbonic anhydrase and RuBisCO in cyanabacteria and some chemoautotrophs in order to enhance CO2 fixation. Other types of microcompartments have been studied that metabolize two and three carbon compunds such as ethanolamine and 1,2-propanediol in various enteric bacteria. Those microcompartments serve to retain chemically reactive and/or volatile pathway intermediates like acetaldehyde and propionaldehyde so they can be converted to less reactive compounds before being released into the cytosol.

Metabolic functions of two kinds of microcompartments. (Adapted from Yeates, Crowley, & Tanaka, 2010)
Metabolic functions of two kinds of microcompartments. (Adapted from Yeates, Crowley, & Tanaka, 2010)

We have determined crystal structures of many of the shell proteins that compose various microcompartments, including from the carboxysome, the Pdu (propanediol utilization), and the Eut (ethanolamine) shells. These have been extremely helpful in illuminating form and function. From these studies we understand that the main shell proteins (known as BMC proteins) assemble as hexamers, which then further assemble side-by-side in a molecular sheet that forms the flat facets of the intact shell. In our models, special pentameric shell proteins are postulated to form the vertices of the icosahedral-like shell. These valuable structural findings are the result of efforts by numerous graduate students, postodocs and researchers in the laboratory over the years, beginning with Kerfeld et al. in 2005.

A simplified model of microcompartment assembly. (Adapted from Yeates, Thompson & Bobik, 2011)
A simplified model of microcompartment assembly. (Adapted from Yeates, Thompson & Bobik, 2011)

Each of the hexamers bears a narrow central pore. These pores are presumed to be the routes by which substrates and products — and likely cofactors for some of the enclosed enzymatic reactions — cross into and out of the microcompartment. Some of the shell proteins undergo conformational changes between open and closed forms, providing a clue about how transport might be controlled. We have also determined that certain special shell proteins bind an iron-sulfur metal cluster at the center of their pore, we presume in order to facilitate transport of electrons or possibly intact metal clusters; most microcompartment types involve internal redox reactions as well as internal iron-sulfur enzymes. Our collaborator, Tom Bobik at Iowa State, has established that some of the enzymes inside microcompartments are targeted to the interior surface of the shell by special N-terminal sequence extensions. An understanding of this mechanism has opened up prospects for engineering microcompartments with novel interior enzymes.

Open and closed pore forms of a BMC shell protein (EutL). (Adapted from Tanaka, et al., 2010)
Open and closed pore forms of a BMC shell protein (EutL). (Adapted from Tanaka, et al., 2010)

Our ongoing aims are: to provide futher structural data in order to establish more complete three-dimensional models of microcompartments; to engineer microcompartments with different properties; and to use bioinformatics methods to discover new types of compartments in bacteria.

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structural, computational, and synthetic biology