Principles of signal processing and fidelity in biological networks

Biological signaling networks define the ways in which cells are able to sense and respond to their environment. These networks transmit environmental information from the exterior of the cell to the interior, triggering an appropriate cellular response. We explored how signal processing and fidelity in these networks dictate cellular behavior and decision making. We began by investigating the mechanisms used by signaling networks to avoid unwanted cross-talk and respond faithfully to their specific input despite shared protein components. We developed a general model and experimental methodology which allow specificity provided by mutual inhibition to be distinguished from specificity provided by component sequestration. We applied this methodology to the mating and high osmolarity glycerol (HOG) pathways in Saccharomyces cerevisiae which share multiple components. We found that mutual inhibition is an important mechanism for maintaining specificity between these two pathways. We then asked how signaling networks process time-varying input and how this processing is set by the in vivo kinetics of the network. We developed a novel microfluidic device which allowed us to measure the response of the HOG pathway to input oscillating over a range of frequencies using a localization reporter of pathway activity. This experimental technique coupled with a basic model allowed us to characterize the pathway bandwidth, which puts a lower bound on the in vivo kinetics of the HOG pathway. We studied the dependence of the bandwidth on HOG pathway architecture, and discovered that one input branch to the pathway dominates the signaling. We then extended this model and technique to allow measurement of in vivo kinetics from fluorescent transcriptional reporters. We demonstrate the use of this technique in the HOG pathway. This technique will allow us to compare transcriptional targets in the HOG pathway to understand the importance of chromatin remodeling and transcription factor combinatorics on transcriptional response. Furthermore, the ability to measure in vivo kinetics from transcriptional reporters is important for studying signaling networks without a localization reporter of activity.