Bacteria live in diverse environments, in which conditions and resources are continually fluctuating. To face such a challenge, bacteria must be able to respond quickly to environmental stimuli; they must be able to utilise a variety of resources, quickly switching between alternative metabolic pathways by activating the required set of genes and repressing unwanted ones. Bacteria achieve this delicate balance with a wealth of transcription factors, which work alone or in concert to bring about the desired effect through transcriptional activation and repression.
Transcription activation is a complex process brought about by a combination of different proteins. In bacteria, RNA polymerase (RNAP) binds to the promoter of a gene in the presence of different gene activators, which do a variety of jobs from unwinding the DNA helix to promoting RNAP function. Transcription activation by the catabolite activator protein (CAP; also known as cAMP receptor protein, CRP) is one of the simplest gene activation models in bacteria, requiring only CAP and RNAP protein factors for transcription at CAP-dependent promoters; by comparison, transcriptional activation in eukaryotes can require dozens of proteins involving several DNA sites. Hence, CAP-promoted transcription has provided a useful model for understanding the mechanisms of transcriptional activation.
CAP is one of over 300 transcription factors used by Escherichia coli alone. CAP can promote transcription at several sites, affecting the metabolism of sugars and amino acids, transport processes, protein folding, toxin production and pilus synthesis. CAP is able to promote transcription at numerous catabolite-sensitive operons in the presence of the allosteric effector cAMP (cyclic adenosine monophosphate). cAMP is a central regulator of hundreds of genes that responds to different nutrient states; the intracellular concentration of cAMP changes in response to the presence of different nutrients in the environment, which results in the induction of the catabolic enzymes required to utilise those nutrients, and the concomitant repression of those that are not required. For instance, in the presence of glucose, the intracellular level of cAMP drops, repressing transcription at the lac operon; in the absence of glucose, intracellular cAMP levels rise, and the lac operon is activated in response to cAMP-induced CAP binding. cAMP is able to promote CAP binding to CAP-dependent promoters by inducing a conformational change in CAP.
CAP binds DNA as a dimer that consists of two identical subunits, each subunit being comprised of two domains: an N-terminal domain required for CAP dimerisation and the binding of cAMP, and a C-terminal domain that contains a helix-turn-helix motif required for the binding of DNA. Three sites on CAP are of particular importance for the ability of CAP to function as a gene activator: the AR1 (activating region 1) region within the C-terminal domain, which interacts with the C-terminal domain of the RNAP alpha subunit (aCTD); the AR2 (activating region 2) region within the N-terminal domain, which interacts with the N-terminal domain of RNAP alpha subunit (aNTD); and the AR3 (activating region 3) region within the N-terminal domain, which interacts with the RNAP sigma70 (s70) subunit.