Prokaryotes regulate cellular functions in response to environmental cues via signal transduction pathways. In principal, there are two thematic organisations of signal transduction proteins: ? One-component proteins, in which the input and output domains are physically linked. These are commonly called activators (see article by Schubert & Shearwin) and repressors (reviewed in this article). ? Two-component systems consisting of histidine kinases and response regulators (see article by Cheung & Rood). A recent survey of 145 prokaryotic genomes has revealed the predominance of one-component systems in this domain of life and has provided the first indication of the diversity inherent in these signal transduction pathways.