Condition-specific control of global gene expression in Escherichia coli

Since Jacob and Monod's operon model first elucidated that the genes needed to metabolize lactose are specifically induced by that substrate, decades of work have characterized metabolic pathways for many individual carbon substrates and have elucidated many more larers of the regulatory network. In this thesis, we have carried out a systematic study of the steady state gene expression levels of all E. coli genes during log phase growth on a range of carbon sources.; The results obtained reveal a remarkable phenomenon: E. coli paradoxically expresses more of its genome when growing on poor carbon sources, in a seeming waste of precious resources. Moreover, the specific genes turned on as carbon substrate quality declines, form a nested hierarchical set. E. coli progressively turns on genes for uptake and metabolism of carbon sources that would offer better nutritional quality than the one on which the cells are growing. The cell also increases cell motility under these conditions, another metabolically expensive activity. In hard times, the cell appears to invest substantially in the possibility of improving conditions.; This "optimistic" adaptation, is not what would be predicted on the spirit of the original operon model, where gene regulation provides a mechanism for avoidance of expenditure of energy on RNA and protein synthesis to metabolize substrates that are not present.; We also observe an inverse correlation between gene activation and ribosomal RNA (rRNA) synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Further examination on how gene expression changes after long-term adaptation in two parallel E. coli cultures that have grown for 1,000 generations on glycerol, as well as gene dynamic changes in response to entering stationary phase through glucose starvation, is in line with the above observation.; The expansion of the search for alternative energy sources when growing on less energy-rich substrates, appears to be a bacterial approximation to metazoan risk-prone foraging behavior. Despite the risk of more rapid exhaustion of the sole carbon supply, the increased costs, on an evolutionary time scale, is more likely to pay off than playing it safe through minimizing energy expenditures.