Mechanism of transcription regulation by conditional co - operativity

Much of the knowledge we have about regulation of transcription in prokaryotes comes from two particularly well-studied systems: the Lac repressor-lac operon [1] and the λ-repressor and λ-Cro for the control of the lysogenic/lytic cycles of λ-phage [2]. In both cases, the repressors are well-folded species lacking appreciable structural disorder. Eukaryotic transcription factors on the other hand are characterized by frequently possessing intrinsically disordered (ID) segments or domains [3]. Intrinsic disorder however, can be detected in the genomes of prokaryotes as well but its functional relevance is less well understood [4], [5]. Here we present a novel mechanism of prokaryotic transcription regulation that crucially depends on the intrinsically disordered nature of the transcription factor. In toxin-antitoxin modules autoregulation of the operon happens through the antitoxin protein, which is DNA binding protein and is entirely or in part intrinsically unstructured. The DNA repressor activity is modulated by the well-folded toxin protein. A C-terminal ID domain of the antitoxin binds to the toxin in two distinct conformations to two binding sites. These binding events trigger a disorder-to-order transition in the N-terminal domain of the antitoxin, thus increasing its affinity for the operator DNA and illustrating for the first time allostery between two distinct disordered protein domains [6]. In addition, excess of toxin will drive a switch to a different toxin-antitoxin complex which is no longer able to bind to the operator DNA. This functioning of the toxin as coor de-repressor depending on the ratio between toxin and antitoxin protein is known as conditional co-operativity and can now be explained by a switch between a high and a low affinity binding mode [6], [7]. Transcription regulation by conditional co-operativity is intimately linked to regulation of protein activity [7]. Indeed, the same allosteric interactions between toxin and antitoxin function to control gene repression and toxin activity such as gyrase poisono-ing in the case of the ccd TA module. Furthermore, the difference in affinity of the two antitoxin binding sites on the toxin serve to fine-tune these tow levels of regulation with respect to each other.