02/28/2018

First Snapshot of a Bacterial Microcompartment’s Protein Shell

Reveals construction principles for nanobioreactor. 

The Science

Bacteria, unicellular organisms, are often defined by what they lack: membrane-bound organelles. However, many bacteria express highly organized primitive organelles, known as bacterial microcompartments (BMCs), composed of an outer protein shell and an internal core of enzymes. BMCs can be thought of as individual bioreactors; they segregate, within a bacterial cell, enzyme-catalyzed chemical reactions important for metabolism. A team of scientists has now provided for the first time a clear picture at atomic level resolution of the structure and assembly of a BMC’s protein shell.

The Impact

The most commonly known type of BMC is the carboxysome, which converts CO2 into carbon-containing compounds important for cellular metabolism. Carboxysomes and BMCs involved with other metabolic processes, also relevant to DOE’s mission areas of bioenergy and the environment, exist in a wide variety of bacteria. The clear picture of how a BMC protein shell is assembled furthers the potential for scientists to design and engineer microcompartments, thereby harnessing bacteria’s biosynthetic processing power for advanced biofuels production.

Summary

Researchers at the Department of Energy (DOE) Lawrence Berkley National Laboratory (LBNL) and Michigan State University (MSU) demonstrated how a combination of five different proteins assemble in a variety of shapes (hexagons, pentagons, and a pair of stacked hexagons) to form a 20-sided protein shell. Under controlled laboratory conditions, scientists genetically altered a bacterium to produce a BMC shell using the five different protein types. The BMC was 40 nanometers across—to put this size in perspective, an average E. coli bacterium is about 2000 nm in length. In order to visualize the protein mega-complex the researchers isolated the BMCs from the bacteria and gathered X-ray diffraction data at the Stanford Synchrotron Radiation Lightsource (SSRL). Also, they collected X-ray diffraction data for two of the protein components that were previously uncharacterized at the Berkley Lab Advance Light Source (ALS). Using a low-resolution map, generated by cryo-electron microscopy, of the BMC to locate the positions of the five individual protein components and help interpret the higher resolution X-ray data, the complete BMC atomic level structure was determined. Although BMCs have been observed within their hosts in a wide variety of sizes, 55 to 600 nm, the structure of the constructed BMC in this study suggests the general assembly principles remain the same regardless of BMC size. Understanding how a BMC shell assembles can be used to inform the design of shells with novel functionalities such as bioproduct synthesis or otherwise-optimized metabolism for advanced biofuels production.

Principal Investigator(s)

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

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Funding

This work was supported by the National Institutes of Health-National Institute of Allergy and Infectious Diseases grant 1R01AI114975-01 and the U.S. DOE, Office of Science, Office of Basic Energy Sciences under contract no. DE-FG02-91ER20021. The Advanced Light Source is supported by the U.S. DOE, Director, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-05CH11231. B.G. was supported by an advanced postdoctoral mobility fellowship from the Swiss National Science Foundation (project P300PA_160983). The Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the U.S. DOE, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515.  The SSRL resources used are supported, in part, by the DOE, Office of Science, Office of Biological and Environmental Research.

References

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