Researchers Decipher the Structure of a Bacterial Microcompartment

Understanding assembly principles may inspire new approaches for making valuable products.

The Science

Unlike higher forms of life, bacteria do not possess internal “organs,” or organelles. This means that certain vital enzymatic reactions can’t be sequestered from the rest of cell. However, some bacteria possess highly organized structures that compartmentalize reactions. These structures are known as bacterial microcompartments (BMCs). Instead of having an organelle’s outer membrane, however, BMCs are surrounded by an outside “shell.” The shell is made of different modular protein building blocks. A team of scientists has, for the first time, provided a clear picture of how these modular components fit together to form a BMC shell. They also showed the pores let selected molecules enter and exit.

The Impact

These results provide a structural basis to better understand how molecules cross the BMC shell via the pores, what biophysical processes guide the self-assembly of the shell, and how specific enzymes end up inside of the BMC while others do not. Understanding how BMCs assemble and function may eventually enable scientists to design and engineer BMCs with improved functions. For example, BMCs could be designed for carbon dioxide fixation or photosynthetic efficiency. The shells could also be created for novel purposes such as producing specialty chemicals.

Summary

The best known type of BMC is the carboxysome. It contains the enzymes that photosynthetic bacteria need to incorporate carbon dioxide into organic compounds. Sequestering this process in the BMC helps enhance the efficiency of carbon dioxide fixation by minimizing an undesirable side reaction that occurs with molecular oxygen. Not only does the protein shell of the carboxysome help keep molecular oxygen out, but the elevated concentration of carbon dioxide inside ensures that the reaction proceeds more efficiently than it would otherwise. Researchers at the Lawrence Berkeley National Laboratory (LBNL) and at the Michigan State University-Department of Energy Plant Research Laboratory showed that a combination of five BMC shell proteins of the carboxysome self-assemble into a 20-sided polyhedron—somewhat like a soccer ball—with pentagon-shaped proteins at the vertices and hexagon-shaped proteins forming the facets. Pores needed to let reactants in and out form at the centers of the hexagons; encased within the shell structure, there is room for about 300 average-sized proteins. Although BMCs come in larger sizes as well, the underlying structural principles for all BMCs are believed to be the same. To deduce the structure of the carboxysome, the researchers isolated them from bacteria and gathered x-ray diffraction data at both the Stanford Synchrotron Radiation Lightsource and the Advanced Light Source at LBNL. The team also employed cryo-electron microscopy to locate the positions of the individual protein components of the shell and help interpret the x-ray data. These fundamental studies offer new insights into the self-assembly and function of the carboxysomes and other BMCs and can provide a possible roadmap to designing new or enhanced functions.

Contact

Cheryl A. Kerfeld
Michigan State University
Lawrence Berkeley National Laboratory
Ckerfeld@lbl.gov

Funding

This research was supported by the National Institutes of Health, National Institute of Allergy and Infectious Diseases and the Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. The Advanced Light Source (ALS) is supported by the DOE, Director, Office of Science, Office of Basic Energy Sciences. B.G. was supported by an advanced postdoctoral mobility fellowship from the Swiss National Science Foundation. The Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the DOE, Office of Science, Office of Basic Energy Sciences. The SSRL resources used are supported, in part, by the DOE, Office of Science, Office of Biological and Environmental Research.  Both the ALS and SSRL are DOE Office of Science scientific user facilities.

Publications

M. Sutter, B. Greber, C. Aussignargues, and C.A. Kerfeld, “Assembly principles and structure of a 6.5-MDa bacterial microcomponent shell.” Science 356 (6344), 1293 (2017). [DOI: 10.1126/science.aan3289]

Related Links

Michigan State University-Department of Energy Plant Research Laboratory news article: Our first ever look at a bacterial organelle shells

Stanford Synchrotron Radiation Lightsource: Structural molecular biology

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Program: BES , CSGB , SUF , BER , BSSD

Performer: University , DOE Laboratory , SC User Facilities , BES User Facilities , ALS , SSRL

Additional: Collaborations , Non-DOE Interagency Collaboration