Ancient chemoreceptors retain their flexibility.

B acterial and archaeal microbes possess a wide array of surfacedeployed receptors for monitoring their chemical and physical surroundings. Particularly prominent among microbial chemoreceptors are the so-called methyl-accepting chemotaxis proteins (MCPs), which sense changes in the cell’s chemical environment and generate intracellular signals that control the organism’s pattern of locomotion or gene expression. MCPs have long been known to mediate attractant-seeking and repellent-avoiding behaviors in Escherichia coli and other motile microbes, but more recently, MCPs have also been shown to regulate complex developmental programs, such as fruiting body formation (1). The sequenced microbial genomes contain thousands of MCP genes, so it seems likely that evolution has put these versatile chemical sensors to other uses as well. In this issue of PNAS, Alexander and Zhulin (2) describe an insightful structure-guided analysis of MCP sequences that reveals common architectural features conserved over the long evolutionary history of these chemoreceptors. Their work provides important new clues to the molecular signaling mechanism(s) of these remarkable molecules. Much of our knowledge about MCPs has come from studies of chemotaxis receptors in E. coli and Salmonella (see refs. 3 and 4 for reviews). Most MCPs are transmembrane proteins with a periplasmic ligand-binding domain for chemical sensing and a cytoplasmic domain for generating and modulating output signals (Fig. 1A). Native MCP molecules are homodimers with predominantly -helical subunits. In the cytoplasmic domain, the subunits form coiled-coil hairpins that intertwine in a four-helix bundle (Fig. 1B). The signaling subdomain centered on the hairpin tip of the cytoplasmic domain (Fig. 1, blue) contains highly conserved determinants for interactions with other receptor molecules and with two partner proteins: CheA, a histidine autokinase, and CheW, which couples CheA activity to receptor control. CheA donates its phosphoryl groups to CheY, a response regulator that shuttles between the receptor-signaling complexes and the flagellar motors to control cell movement. Ternary receptor complexes have a kinase-on mode with high autophosphorylation activity and a kinase-off mode with low activity. Ligand occupancy changes drive the signaling equilibrium toward one state or the other to modulate the cell’s behavior. MCPs sense temporal concentration changes by comparing current ligand occupancy with that averaged over the past few seconds. Chemical history is recorded in the form of reversible methyl ester modifications to specific glutamic acid residues in the cytoplasmic domain. MCP molecules constantly update their methylation record through feedback and substrate-level control of the modification enzymes. Increasing methylation shifts MCP signaling complexes toward the kinase-on state, thereby countering the kinase-off signals elicited by attractant increases. This sensory adaptation mechanism operates over a 5to 6-log concentration range, enabling MCPs to adjust their window of maximum detection sensitivity to match ambient chemoeffector levels. The source of the prodigious signal amplification or gain exhibited by MCP molecules remains the outstanding mystery in the field. Measurements of FRET between tagged signaling proteins in living cells have shown that each receptor controls the activity of 35 CheA kinase molecules, many more than it could interact with directly (5). The mechanism responsible for this high signal gain appears to involve physical interactions between receptor molecules, which are known to form macroscopic clusters at the cell poles (6). Clustering may allow receptor signaling complexes to form networked arrays that operate in a highly cooperative manner (7). Alexander and Zhulin (2) looked for common sequence features in MCPs that could provide clues to their highgain signaling mechanism. They began with all available MCP sequences and devised algorithms for aligning the mol-