ScienceDaily (July 9, 2009) — 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.
Researchers with Berkeley Lab, the University of California (UC) Berkeley, the Howard Hughes Medical Institute, and Princeton University, used an ultrahigh-precision visible light microscopy technique called PALM - for Photo-Activated Localization Microscopy - to show that the chemotaxis network of signaling proteins in E.coli bacteria is able to spontaneously form from clusters of proteins without being actively distributed or attached to specific locations in cells. This simple organizational mechanism - dubbed “stochastic self-assembly” - is related to the self-organizing patterns first described in 1952 by the British computer scientist Alan Turing.
PALM is an an ultrahigh-precision visible light microscopy technique that enables scientists to photo-actively fluoresce and image individual proteins. This PALM composite of an E.coli bacterial cell shows the organization of proteins in the chemotaxis signaling network. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)
“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 PLoS Biology. Co-authoring the paper with Liphardt were Derek Greenfield, Ann McEvoy, Hari Shroff, Gavin Crooks, Ned Wingreen and Eric Betzig.
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Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy
Derek Greenfield1,2#, Ann L. McEvoy1#, Hari Shroff3, Gavin E. Crooks2, Ned S. Wingreen4, Eric Betzig3, Jan Liphardt1,2,5*
1 Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America, 2 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 3 Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of America, 4 Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America, 5 Department of Physics, University of California Berkeley, Berkeley, California, United States of America
Abstract Top
The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport.
Author Summary Top
Cells arrange their components—proteins, lipids, and nucleic acids—in organized and reproducible ways to optimize the activities of these components and, therefore, to improve cell efficiency and survival. Eukaryotic cells have a complex arrangement of subcellular structures such as membrane-bound organelles and cytoskeletal transport systems. However, subcellular organization is also important in prokaryotic cells, including rod-shaped bacteria such as E. coli, most of which lack such well-developed systems of organelles and motor proteins for transporting cellular cargoes. In fact, it has remained somewhat mysterious how bacteria are able to organize and spatially segregate their interiors. The E. coli chemotaxis network, a system important for the bacterial response to environmental cues, is one of the best-understood biological signal transduction pathways and serves as a useful model for studying bacterial spatial organization because its components display a nonrandom, periodic distribution in mature cells. Chemotaxis receptors aggregate and cluster into large sensory complexes that localize to the poles of bacteria. To understand how these clusters form and what controls their size and density, we use ultrahigh-resolution light microscopy, called photoactivated localization microscopy (PALM), to visualize individual chemoreceptors in single E. coli cells. From these high-resolution images, we determined that receptors are not actively distributed or attached to specific locations in cells. Instead, we show that random receptor diffusion and receptor–receptor interactions are sufficient to generate the observed complex, ordered pattern. This simple mechanism, termed stochastic self-assembly, may prove to be widespread in both prokaryotic and eukaryotic cells.
Citation: Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, et al. (2009) Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. PLoS Biol 7(6): e1000137. doi:10.1371/journal.pbio.1000137
Academic Editor: Howard C. Berg, Harvard University, United States of America
Received: October 27, 2008; Accepted: May 14, 2009; Published: June 23, 2009
This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
Funding: ALM thanks the NSF for graduate research support. This work was supported by the Sloan and Searle Foundations (JL), the DOE Office of Science, Energy Biosciences Program (JL), and National Institutes of Health grants R01 GM77856 (JL), R01 GM084716 (JL), and R01 GMO73186 (NSW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors declare competing financial interests. EB and Harald Hess (Janelia Farm) have licensed the PALM technology to Carl Zeiss Microimaging, GmbH.
Abbreviations: DIC, differential interference contrast; epi, epifluorescence; PALM, photoactivated localization microscopy; TIR, total internal reflection
* E-mail: Liphardt@berkeley.edu
# These authors contributed equally to this work.
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