Cellular signaling is fundamental to many biological processes, from the development of embryos to the growth of cancerous cells. Signaling systems are composed of a cluster of genes and their expression products, proteins, which can interact with each other by controlling the expression of the corresponding gene. Transcription factors are proteins that regulate the expression of a group of genes within signaling systems and do so by binding to a specific DNA sequence motif upstream of targeting genes. By measuring the amount of transcription factors from a population of cells with traditional biochemistry assays, biologists have shown that environmental inputs (i.e., stresses or extracellular ligands) can alter the concentrations of transcription factors that regulate gene expression. The objective of this project is to understand how individual cells encode external inputs as time-based signals and how these signals are transmitted to downstream genes, and to examine how the single cell behavior differs from the behavior of the population of cells. The collaborative team of investigators from the California Institute of Technology (US) and the University of Edinburgh (UK) will use new single-cell measurements based on fluorescent protein and time-lapse optical microscopy techniques can provide new and distinct information about the signal processing capabilities of individual cells. Through its broader impacts, this project will promote understanding of the dynamic nature of cellular information processing. Furthermore, this project will provide new techniques and tools to perturb and control cell functions.
Cellular signaling is fundamental to many biological processes, from embryo development to disease progression. It is often considered to be a continuous and concentration-based process, where extracellular input is encoded in the concentrations of one or more transcription factors (TFs) or other regulators, which are in turn decoded to control gene expression in a continuous fashion. In contrast, recent single-cell studies have revealed that many central TFs are activated in stochastic pulses in response to inputs. Examples include nuclear factor-kappa-B and p53 in mammals, and the general stress regulator Msn2 in yeast. In these systems, inputs generate pulses of TF activity, which are then decoded by target promoters in a dynamic fashion. The extent of signal encoding and decoding in pulsing systems as well as the potential physiological functions of these systems remain largely unexplored. This project will address these questions in budding yeast through collaborative efforts between the Swain and the Elowitz laboratories. The team will integrate single-cell time-lapse microscopy, microfluidics, and techniques from information theory to measure the information transfer within dynamic signaling systems by investigating the encoding and decoding of TF dynamics in single cells. This project will contribute to the understanding of three aspects of dynamic signaling: First, the team will produce an extensive dataset of input- output relationship between stresses and TF dynamics, providing a comprehensive understanding of dynamic cellular responses. Second, information theoretical analysis of single-cell signaling will provide a more comprehensive view of dynamics-based information transduction and pulse-based signal encoding and decoding. Third, it will explore the physiological roles of dynamic pulsing, to open up the possibility of controlling cellular behaviors through the perturbation of TF dynamics. Through its broader impacts, this analysis of pulse-based signaling in cells should allow scientists to understand the design principles of natural signaling systems.
This collaborative US/UK project is supported by the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council.
