Self-assembling and self-organizing systems are the Holy Grails of nanotechnology,
but nature has been producing such systems for millions of years. A team of
scientists has taken a unique look at how thousands of bacterial membrane proteins
are able to assemble into clusters that direct cell movement to select chemicals
in their environment. Their results provide valuable insight into how complex
periodic patterns in biological systems can be generated and repaired.
“It is not widely appreciated that complex periodic patterns can spontaneously
emerge from simple mechanisms, but that is probably what is happening here,”
said Jan Liphardt, the biophysicist who led this research.
Liphardt holds a joint appointment with Berkeley
Lab’s Physical Biosciences Division and UC Berkeley’s Physics
Department. He is the principal author of a paper now available on-line in the
Public Library of Science entitled: “Self-Organization of the Escherichia
coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy.”
Co-authoring the paper with Liphardt were Derek Greenfield, Ann McEvoy, Hari
Shroff, Gavin Crooks, Ned Wingreen and Eric Betzig.
Key to a cell’s survival is the manner in which its critical components
- proteins, lipids, nucleic acids, etc. - are arranged. For cells to thrive,
the organization of these components must be optimized for their respective
activities and also reproducible for succeeding generations of cells. Eukaryotic
cells feature distinct subcellular structures, such as membrane-bound organelles
and protein transport systems, whose complex organization is readily apparent.
However, there is also complex spatial organization to be found within prokaryotic
cells, such as rod-shaped bacteria like E. coli.
“It has remained somewhat mysterious how bacteria are able to organize
and spatially segregate their interiors and membranes,” said Liphardt.
“Two cells which are biochemically identical can have very different behaviors,
depending upon their spatial organization. With new technologies such as PALM,
we are able to see exactly how cells are organized and relate spatial organization
with biological function.”
PALM and the Chemotaxis Network
In the PALM technique, target proteins are labeled with tags that fluoresce
when activated by weak ultraviolet light. By keeping the intensity of this light
sufficiently low, researchers can photoactivate individual proteins.
“Since individual proteins are imaged one at a time, we can localize
and count them, and then computationally assemble the locations of all proteins
into a composite, high-precision image,” said Liphardt. “With other
technologies, we have to choose between observing large clusters or observing
single proteins. With PALM, we can examine a cell and see single proteins, protein
dimers, and so forth, all the way up to large clusters containing thousands
of proteins. This enables us to see the relative organization of individual
proteins within clusters and at the same time see how clusters are arranged
with respect to one-another.”
Liphardt and his colleagues applied the PALM technique to the E.coli chemotaxis
network of signaling proteins, which direct the movement of the bacteria towards
or away from sugars, amino acids, and many other soluble molecules in response
to environmental cues. The E.coli chemotaxis network is one of the best-understood
of all biological signaling systems and is a model for studying bacterial spatial
organization because its components display a nonrandom, periodic distribution
in the cell membrane.
“Chemotaxis proteins cluster into large sensory complexes that localize
to the poles of the bacterial cell,” Liphardt said. “We wanted to
understand how these clusters form, what controls their size and density, and
how the cellular location of clusters is robustly maintained in growing and
Using PALM, Liphardt and his colleagues mapped the cellular locations of three
proteins central to the chemotaxis signaling network - Tar, CheY and CheW -
with a mean precision of 15 nanometers. They found that cluster sizes were distributed
with no one size being “characteristic.” For example, a third of
the Tar proteins were part of smaller lateral clusters and not of the large
polar clusters. Analysis of the relative cellular locations of more than one
million individual proteins from 326 cells determined that they are not actively
distributed or attached to specific locations in cells, as had been hypothesized.
“Instead,” said Liphardt, “random lateral protein diffusion
and protein-protein interactions are probably sufficient to generate the observed
complex, ordered patterns. This simple stochastic self-assembly mechanism, which
can create and maintain periodic structures in biological membranes without
direct cytoskeletal involvement or active transport, may prove to be widespread
in both prokaryotic and eukaryotic cells.”
Liphardt and his research group are now applying PALM to signaling complexes
in eukaryotic membranes to see how widespread is stochastic self-assembly in
nature. Given that biological systems are nature’s version of nanotechnology,
the demonstration that stochastic self-assembly is capable of organizing thousands
of proteins into complex and reproducible patterns holds promise for a wide
range of applications in nanotechnology, including the fabrication of nanodevices
and the development of nanoelectronic circuits.
This work was funded by the U.S. Department of Energy’s Office of Science,
Energy Biosciences Program, the Sloan and Searle Foundations, and National Institutes
of Health grants.
Berkeley Lab is a U.S. Department of Energy national laboratory located in
Berkeley, California. It conducts unclassified scientific research and is managed
by the University of California. Visit our Website at www.lbl.gov