3Historically, researchers have studied bacterial signaling as if it functioned as a set of isolated, linear pathways. More recent studies, however, have demonstrated that many signaling pathways interact and that these interacting pathways should be construed as an intricate network. This network integrates diverse signals, both extracellular and intracellular, to ensure that the the correct amount of the appropriate subset of genes is expressed at the proper time. Complete delineation of this complex signal transduction network and use of the network to predict the full range of cellular behaviors are major goals of systems biology.Despite considerable progress, we remain near the beginning of this process, which thus far has been dominated by the development of enabling technologies and the compilation of gene lists. Although development and compilation will continue to be essential, the next critical step must be to organize the copious data compiled over 5 decades of pregenomics research and the massive amount of postgenomics data generated over the last decade. This minireview, in which we describe a portion of the overall network of Escherichia coli, is an attempt to perform part of this next step.
THE NETWORKAs the model organism for this network, we chose the enterobacterium E. coli. We focused specifically on the common laboratory strain K-12 in order to mine the wealth of information available for it. When appropriate, we included observations made with other E. coli variants (e.g., enterohemorragic E. coli [EHEC] or uropathogenic E. coli) or with the close relative Salmonella enterica. With easy to moderate effort, the network can be adapted to other enterobacterial relatives. However, more distantly related species may lack some of the global regulators discussed here.As a unifying theme, we chose the early stages of biofilm development. Defined as a sessile community of bacteria encased in a matrix, a biofilm tends to develop on a surface or an interface in a series of ordered steps, designated reversible attachment, irreversible attachment, maturation-1, maturation-2, and dispersion (121). Each step requires reprogramming of gene expression that occurs in response to the changing environment (122). The reprogramming associated with the earliest steps of biofilm development can be identified easily by the distinct organelles that decorate the bacterial surface. For example, reversible attachment often involves flagella that permit individual planktonic cells to swim toward an appropriate biotic or abiotic surface. Irreversible attachment involves the loss of these flagella and the elaboration of adhesive organelles (e.g., curli or type 1 fimbriae); the type of organelle depends on the environment. Finally, production of the colanic acid capsule permits construction of the distinctive three-dimensional structure typical of mature biofilms (for a recent review of biofilm formation, see reference 149).For the surface organelles to appear in proper order, expression of these organelles must be coordin...