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Curr Opin Microbiol. 2003 Apr;6(2):125-34.

Motifs, modules and games in bacteria.

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Department of Bioengineering, University of California, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, 1 Cyclotron Road, MS 3-144, Berkeley, CA 94720, USA.


Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology. From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games. Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks. They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses. The dynamical functioning of modules defines the organism's strategy to survive in a game, pitting cell against cell, and cell against environment. Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function. This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering.

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