Bacteria's Hidden Traffic Control

Not unlike an urban restaurant, the success of a bacterial cell depends on three things: localization, localization and localization. But the complete set of controls by which bacteria control the movement of proteins and other essential biological materials globally within the confines of their membrane walls has been something of a mystery. Now, researchers at the University of Washington have parsed out the localization mechanisms that E. coli use to sort through and organize their subcellular components.

“Despite their small size and relative simplicity, bacterial cells appear to possess a robust and complex level of subcellular organization, both spatially and temporally, that was once thought to only exist in more complex organisms,” said Nathan Kuwada, a postdoctoral fellow in the lab of Paul Wiggins at the University of Washington.

“We wanted to know how many mechanisms bacteria possess to localize subcellular components, and to answer this question, we set out to image the localization pattern of nearly every protein in a bacterial cell for the entire cell cycle.”

Kuwada will describe the group's findings this week at the Biophysical Society's 59th annual meeting in Baltimore, Md.

E. coli localize nearly one-fifth of their proteins to specific subcellular sites, but until now, the cell-cycle localization behavior of only a small subset of proteins had been characterized in detail.

Kuwada and his colleagues sought to remedy this by imaging an existing library of green-fluorescent protein fusions in E. coli by use of a high-throughput live-cell imaging scheme. This allowed them to image close to a thousand individual protein fusions in growing cells for 6-8 hours, providing them with hundreds of complete cell cycles for each protein.

Using custom image processing software, the researchers processed and organized the thousands of images from each experiment, allowing them to quantitatively compare the localization patterns on a genomic scale. The researchers also developed a public online database with all of their raw and processed data in a browsable and searchable form at: http://mtshasta.phys.washington.edu/localizome

Rather than a small number of patterns combining in various permutations determined by function, the researchers found that bacteria possess a large number of distinct patterns with subtle spatial and temporal differences.

For example, Kuwada and his colleagues also observed that the DNA-binding proteins were asymmetrically distributed towards the daughter cell during cell divisions, despite the morphological symmetry between parent and daughter cells.

“Although the asymmetry is somewhat weak, it is still statistically significant and we think it must have an exciting biological significance,” Kuwada said. “This finding, which is only observable using our complete-cell-cycle approach, potentially has many biological consequences that we are currently trying to better understand.”

Future work for Kuwada and his colleagues includes further exploring the specific mechanisms that drive subcellular organization, through targeting the behavior of specific groups of proteins such as transcription factors with increased precision.

The presentation, “Global characterization of transcription factor localization and partitioning in Escherichia coli” by Nathan J. Kuwada and Paul A. Wiggins, is at 1:45 PM, on Sunday, February 8, 2015, at the Baltimore Convention Center, in Hall C, poster 383. ABSTRACT: http://bit.ly/1KkOgN0

ABOUT THE MEETING

Each year, the Biophysical Society Annual Meeting brings together more than 6,500 researchers working in the multidisciplinary fields representing biophysics. With more than 3,600 poster presentations, over 200 exhibits, and more than 20 symposia, the BPS Annual Meeting is the largest meeting of biophysicists in the world. Despite its size, the meeting retains its small-meeting flavor through its subgroup symposia, platform sessions, social activities and committee programs. The 59th Annual Meeting will be held at the Baltimore Convention Center.

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The Biophysical Society, founded in 1958, is a professional, scientific Society established to encourage development and dissemination of knowledge in biophysics. The Society promotes growth in this expanding field through its annual meeting, bi-monthly journal, and committee and outreach activities. Its 9,000 members are located throughout the U.S. and the world, where they teach and conduct research in colleges, universities, laboratories, government agencies, and industry.

For more information on the Society, or the 2015 Annual Meeting, visit http://www.biophysics.org

Contact Information
Jason Socrates Bardi, AIP
jbardi@aip.org
240-535-4954
@jasonbardi