Barrett, Palsson, Herring, and Reed simulated the behavior of 1,010 of E. coli's 4,200 genes. This particular subset of the bacterium's genome is tightly organized into interacting networks involved in metabolism or regulation of gene activation, or transcription. These linked networks are devoted to sensing, ingesting, and degrading potential "food" in the form of sugars and other energy-rich organic molecules.
E. coli must also have an efficient way to eliminate waste products. It, like all living things, generates energy in a process that involves the removal of electrons from food molecules and attaching them to acceptor molecules. For aerobic organisms, the final electron acceptor is usually oxygen, which is converted into water in the process.
E. coli can grow with or without oxygen, using nitrate or other molecules as its final electron acceptor. "We found that the type of terminal electron acceptor in the growth environment and the presence or absence of glucose is very important to E. coli," said Barrett. "Our simulations show that these two factors are key determinants of how the bacterium organizes itself."
Barrett, Palsson, and their colleagues simulated the "functional states" of E. coli's metabolic and transcriptional regulatory networks in the 15,580 environments of food sources and electron acceptors. To their surprise, no matter what carbon source it ingests or electron acceptor used, E. coli exhibits only six distinct functional states.
"This study gives a systems biology view of how a phenotype, or a 'network state' advantageous to a microorganism is comprised of a tiny subset of a much larger universe of possibilities as provided for in the genome," said Palsson. "On a high level we can say that E. coli is obsessed with how it breathes and whether or not glucose is available to eat. All of its genetic complexity basically enables it to generate a
Source:University of California - San Diego