The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics

Abstract

It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins (“hubs”). As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many “shortest paths” going through them, analogous to major bridges and tunnels on a highway map). Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., “bottleneck-ness”) is a much more significant indicator of essentiality than degree (i.e., “hub-ness”). Furthermore, bottlenecks correspond to the dynamic components of the interaction network—they are significantly less well coexpressed with their neighbors than nonbottlenecks, implying that expression dynamics is wired into the network topology.

Author Summary

A network is a graph consisting of a number of nodes with edges connecting them. Recently, network models have been widely applied to biological systems. Here, we are mainly interested in two types of biological networks: the interaction network, where nodes are proteins and edges connect interacting partners; and the regulatory network, where nodes are proteins and edges connect transcription factors and their targets. Betweenness is one of the most important topological properties of a network. It measures the number of shortest paths going through a certain node. Therefore, nodes with the highest betweenness control most of the information flow in the network, representing the critical points of the network. We thus call these nodes the “bottlenecks” of the network. Here, we focus on bottlenecks in protein networks. We find that, in the regulatory network, where there is a clear concept of information flow, protein bottlenecks indeed have a much higher tendency to be essential genes. In this type of network, betweenness is a good predictor of essentiality. Biological researchers can therefore use the betweenness as one more feature to choose potential targets for detailed analysis.