Natural history of sensor domains in bacterial signaling systems
L. Aravind, Lakshminarayan M. Iyer and Vivek Anantharaman
from: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition (Edited by: Stephen Spiro and Ray Dixon). Caister Academic Press, U.K. (2010)
Organisms sense stimuli at the molecular level using a relatively small set of protein domains. Computational analysis of protein sequences along with directed experimental studies have played a major role in the characterization of these protein domains. These sensor domains directly or indirectly detect a vast array of sensory inputs such as solutes, gases, redox potential and light. Here, we systematically survey the types of sensor domains found in bacterial signaling proteins. We summarize the key aspects of their structure that are central to their functions and their associations with other signaling domains. Despite the advances several of these domains remain poorly understood in terms of their structure, ligands and functional significance. We accordingly try to highlight the significance of some of the under-appreciated sensor domains. Genomic analysis reveals that the architectural complexity of sensory domains increases with the number of sensor proteins in a genome, with a gradual plateau towards a point where newer combinations of domains do not provide major selective advantage. Syntactical analysis of domain architectures shows several discernable patterns that have functional relevance, especially in terms of the constraints introduced by signal transmission domains such as HAMP and S-helix modules. Across bacteria, the number of signaling proteins shows a positive correlation with respect to proteome size. However, there is a clear distinction in the trends between bacteria that react directly and rapidly to a large number of small molecule signals vis-à-vis those that possess distinct signaling systems related to developmental complexity. Analysis of scaling trends for individual sensor domains shows that lifestyle strategies play a major role in the selection of the type and number of these domains in an organism. From an evolutionary viewpoint, the vast majority of sensory domains appear to have their origins in the bacteria and have been widely transferred to other superkingdoms of life. In particular most major eukaryotic sensor domains appear to have their antecedents in bacteria read more ...