| Living systems fluctuate, constantly. Individual cells and individual molecules that seem identical at one moment will undergo disparate changes in chemical or physical states. Cells will produce or degrade biomolecules stochastically; these biomolecules will bind or unbind substrates stochastically. The presence of such variability is an axiom of modern biology.;Whether such fluctuations have nontrivial biological roles, however, is still, for most cases, an open problem. Discovering the answer requires sensitive measurement techniques, relevant modeling tools, and a system-wide view of the underlying biology. This thesis presents work to address the role of fluctuations or variability with respect to several topics.;We first study the role of transcription factors fluctuations in controlling a cell's phenotype, using the model system of lactose metabolism by E. coli. We find that a single instance of a specific binding fluctuation is the key event driving phenotype switching between two bistable states.;We next develop a framework for the analysis of phenotype switching in the presence of transcription factor fluctuations. Our model encompasses and explains the different switching behaviors arising from fast and slow binding fluctuations.;We then examine the regulation of protein number variations in the E. coli proteome. By measuring the abundance and variation of a large fraction of the proteome, we are able to discern the structure of variation, and a cellular strategy for adapting to this variation.;Finally, we measure in vivo transcription kinetics of T7 RNA polymerase and find novel sources of fluctuations. In particular, we find that T7 RNA polymerase molecules initiate transcription with different rates, depending on the state of the chromosomal template.;In these examples, we learn how microscopic fluctuations of one component influence another biological property, whether that is metabolism, fitness, or promoter strength. We find that fluctuations indeed have a significant role in regulation and we emphasize the mechanistic insights of these results. |
