Cost and Capacity of Signaling in the Escherichia coli Protein Reaction Network

TL;DR

This paper analyzes the signaling capacity and efficiency of the E. coli protein regulation network, introducing measures for cost and spread of signals to understand modularity and signaling specificity.

Contribution

It develops simplified topological measures to quantify signal propagation, cost, and spread in the E. coli protein regulation network, linking network structure to signaling efficiency.

Findings

Modules identified via strong components facilitate signal transmission.

Signaling cost and spread decrease over longer reaction chains.

Network modularity correlates with signaling efficiency.

Abstract

In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained descriptions of the topology of the molecular networks at the scale of the whole organism. In order to bridge these two disparate approaches one needs to develop simplified descriptions of dynamics and topological measures which address the propagation of signals in molecular networks. Here, we consider the directed network of protein regulation in E. coli, characterizing its modularity in terms of its potential to transmit signals. We demonstrate that the simplest measure based on identifying sub-networks of strong components, within which each node could send a signal to every other node, indeed partitions the network into functional modules. We then suggest measures to quantify the cost and spread associated with sending a signal between any particular pair of proteins. Thereby, we address the signalling specificity within and between modules, and show that in the regulation of E.coli there is a systematic reduction of the cost and spread for signals traveling over more than two intermediate reactions.