Response regulator

Response regulator receiver domain
The response regulator CheY from E. coli, with the aspartate phosphorylation site highlighted in green. From PDB: 3CHY​.
Identifiers
Symbol	Response_reg
Pfam	PF00072
Pfam clan	CL0304
InterPro	IPR001789
SMART	REC
PROSITE	PDOC50110
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

A response regulator is a protein that mediates a cell's response to changes in its environment as part of a two-component regulatory system. Response regulators are coupled to specific histidine kinases which serve as sensors of environmental changes. Response regulators and histidine kinases are two of the most common gene families in bacteria, where two-component signaling systems are very common; they also appear much more rarely in the genomes of some archaea, yeasts, filamentous fungi, and plants. Two-component systems are not found in metazoans.^[1][2][3][4]

Function

The crystal structure of the yeast histidine phosphotransfer protein Ypd1 in complex with the response regulator Sln1. Ypd1 appears on the right with the conserved four-helical bundle in yellow and variable helices in red. Sln1 appears on the left with beta sheets in tan and helices in brown. The key residues - Asp from Sln1 and His from Ypd1 - are highlighted with green sticks. A bound magnesium ion is shown as an orange sphere and beryllium trifluoride, a phosphoryl analog, is shown in pink. From PDB: 2R25​.^[5]

Response regulator proteins typically consist of a receiver domain and one or more effector domains, although in some cases they possess only a receiver domain and exert their effects through protein-protein interactions. In two-component signaling, a histidine kinase responds to environmental changes by autophosphorylation on a histidine residue, following which the response regulator receiver domain catalyzes transfer of the phosphate group to its own recipient aspartate residue. This induces a conformational change that alters the function of the effector domains, usually resulting in increased transcription of target genes. The mechanisms by which this occurs are diverse and include allosteric activation of the effector domain or oligomerization of phosphorylated response regulators.^[2] In a common variation on this theme, called a phosphorelay, a hybrid histidine kinase possesses its own receiver domain, and a histidine phosphotransfer protein performs the final transfer to a response regulator.^[4]

In many cases, histidine kinases are bifunctional and also serve as phosphatases, catalyzing the removal of phosphate from response regulator aspartate residues, such that the signal transduced by the response regulator reflects the balance between kinase and phosphatase activity.^[4] Many response regulators are also capable of autodephosphorylation, which occurs on a wide range of time scales.^[2] In addition, phosphoaspartate is relatively chemically unstable and may be hydrolyzed non-enzymatically.^[1]

Histidine kinases are highly specific for their cognate response regulators; there is very little cross-talk between different two-component signaling systems in the same cell.^[6]

Classification

Response regulators can be divided into at least three broad classes:^[3]

• Single-domain response regulators, which contain only a receiver domain and which use protein-protein interactions to exert their downstream biological effects; for example, the chemotaxis regulator CheY.
• Response regulators with a DNA-binding effector domain, usually of helix-turn-helix architecture.
• Response regulators with effector domains that have enzymatic functions, giving rise to secondary messenger molecules such as cAMP.

More comprehensive classifications based on more detailed analysis of domain architecture are possible, and find that response regulators with DNA-binding domains are by far the most common.^[7]

Evolution

The number of two-component systems present in a bacterial genome is highly correlated with genome size as well as ecological niche; bacteria that occupy niches with frequent environmental fluctuations possess more histidine kinases and response regulators.^[4][7] New two-component systems may arise by gene duplication or by lateral gene transfer, and the relative rates of each process vary dramatically across bacterial species.^[8] In most cases, response regulator genes are located in the same operon as their cognate histidine kinase;^[4] lateral gene transfers are more likely to preserve operon structure than gene duplications.^[8] The small number of two-component systems present in eukaryotes most likely arose by lateral gene transfer from endosymbiotic organelles; in particular, those present in plants likely derive from chloroplasts.^[4]

References