One-component systems dominate signal transduction in prokaryotes

Abstract

Two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. By analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. One-component systems are evolutionarily older, more widely distributed among bacteria and archaea, and display a greater diversity of domains than two-component systems.

Figure 1

Two-component and one-component signal transduction. (a) A prototypical two-component signal transduction system contains input (colored red) and output (colored yellow) domains in two different proteins that communicate via a His-Asp phosphotransfer. A one-component system is a protein that contains input and output domains but lacks His-Asp phosphotransfer domains (colored grey and white). (b) Examples of two-component and one-component systems that use the same type of input and output domains. Experimentally studied proteins are identified by name, whereas proteins predicted from genome sequences are identified by their GenBank ID number: FixJ (GenBank accession number 120202), FixL (GenBank accession number 120208), NtrB (GenBank accession number 128594), NtrC (GenBank accession number 417388), RocR (GenBank accession number 34395962), TraR (GenBank accession number 17743220). Organism abbreviations: A. tumefaciens, Agrobacterium tumefaciens; B. anthracis, Bacillus anthracis; B. japonicum, Bradyrhizobium japonicum; B. pertussis, Bordetella pertussis; B. subtilis, Bacillus subtilis; C. violaceum, Chromobacterium violaceum; E. coli, Escherichia coli; N. punctiforme, Nostoc punctiforme; P. putida, Pseudomonas putida; S. meliloti, Sinorhizobium meliloti; S. oneidensis, Shewanella oneidensis; T. maritima, Thermotoga maritima.

Figure 2

Distribution of input and output domains in bacterial and archaeal signal transduction systems. The counts of the 25 most abundant input and output domains in bacterial and archaeal one-component and two-component systems are shown. Domain names are from the curated Pfam-A database (http:www.sanger.ac.uk/Software/Pfam/). Detailed information on domain distribution is available at the following website (http://genomics.biology.gatech.edu/research/TIM).

Figure 3

Dependence of the number of one-component and two-component signal transduction systems on the genome size. The plot is in a double logarithmic scale. One hundred forty-five genomes were ranked by size and split into 16 size classes. Each point indicates the average number of genes for one-component or two-component signal-transduction systems in the respective class.