Using topology to tame the complex biochemistry of genetic networks

Abstract

Living cells are controlled by networks of interacting genes, proteins and biochemicals. Cells use the emergent collective dynamics of these networks to probe their surroundings, perform computations and generate appropriate responses. Here, we consider genetic networks, interacting sets of genes that regulate one another's expression. It is possible to infer the interaction topology of genetic networks from high-throughput experimental measurements. However, such experiments rarely provide information on the detailed nature of each interaction. We show that topological approaches provide powerful means of dealing with the missing biochemical data. We first discuss the biochemical basis of gene regulation, and describe how genes can be connected into networks. We then show that, given weak constraints on the underlying biochemistry, topology alone determines the emergent properties of certain simple networks. Finally, we apply these approaches to the realistic example of quorum-sensing networks: chemical communication systems that coordinate the responses of bacterial populations. © 2012 The Author(s) Published by the Royal Society. All rights reserved.