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How E. coli bacterium generates simplicity from complexity

The ubiquitous and usually harmless E. coli bacterium, which has one-seventh the number of genes as a human, has more than 1,000 of them involved in metabolism and metabolic regulation. Activation of random combinations of these genes would theoretically be capable of generating a huge variety of internal states; however, researchers at UCSD will report in the Dec. 27 issue of Proceedings of the National Academy of Sciences (PNAS) that Escherichia coli doesn't gamble with its metabolism. In a surprise about E. coli that may offer clues about how human cells operate, the PNAS paper reports that only a handful of dominant metabolic states are found in E. coli when it is "grown" in 15,580 different environments in computer simulations.

"When it comes to genomes, a great deal of complexity boils down to just a few simple themes," said Bernhard Palsson, a professor of bioengineering at UCSD's Jacobs School of Engineering and co-author of the study, which was made available online Dec. 15. "Researchers have confirmed the complexity of individual parts of biochemical networks in E. coli and other model organisms, but our large-scale reconstruction of regulatory and metabolic networks involving hundreds of these parts has shown that all this genetic complexity yields surprisingly few physiological functions. This is possibly a general principal in many, if not all, species."

Palsson and his colleagues at UCSD, postdoctoral fellows Christian L. Barrett and Christopher D. Herring, and Ph.D. candidate Jennifer L. Reed, created a computer model of an E. coli cell based on the experimental results of thousands of previous experiments, some of which were completed decades ago. "The goal of this study was to comprehensively simulate all the possible molecular interactions in a well studied strain of E. coli to gain a global view of the range of functional network states," said Barrett. "Complex cellular networks can potentially generate lots of different beha
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Contact: Rex Graham
ragraham@ucsd.edu
858-822-3075
University of California - San Diego
15-Dec-2005


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