Allostery and Intrinsic Disorder Mediate Transcription Regulation by Conditional Cooperativity

Abstract

Regulation of the phd/doc toxin-antitoxin operon involves the toxin Doc as co- or derepressor depending on the ratio between Phd and Doc, a phenomenon known as conditional cooperativity. The mechanism underlying this observed behavior is not understood. Here we show that monomeric Doc engages two Phd dimers on two unrelated binding sites. The binding of Doc to the intrinsically disordered C-terminal domain of Phd structures its N-terminal DNA-binding domain, illustrating allosteric coupling between highly disordered and highly unstable domains. This allosteric effect also couples Doc neutralization to the conditional regulation of transcription. In this way, higher levels of Doc tighten repression up to a point where the accumulation of toxin triggers the production of Phd to counteract its action. Our experiments provide the basis for understanding the mechanism of conditional cooperative regulation of transcription typical of toxin-antitoxin modules. This model may be applicable for the regulation of other biological systems.

Transition from a plasmid to a chromosomal mode of replication entails additional regulators

“…The 39-mer most likely acts as a DNA chaperone that remodels RctB to a form that enhances protein-protein interactions involved in handcuffing. Protein remodeling upon interaction with DNA is well known (22)(23)(24). It has been shown also for the two initiators of the iteron-bearing plasmids (23,25) and for the E. coli initiator (26).…”

The ParE2–PaaA2 toxin–antitoxin complex fromEscherichia coliO157 forms a heterodocecamer in solution and in the crystal

“…CcdAB, Kis-Kid and Phd-Doc) have also been shown to form larger aggregates under certain conditions, but in these cases nonglobular chains of variable length consisting of alternating toxin and antitoxin molecules were identified (Dao-Thi et al, 2002;Kamphuis et al, 2007;Garcia-Pino et al, 2010). These extended structures have recently been interpreted in terms of a specific mechanism of transcription regulation called 'conditional cooperativity' (De Jonge et al, 2009;Garcia-Pino et al, 2010). This type of gene regulation has recently also been demonstrated for vapBC TA modules, in which the toxin-antitoxin complex displays a distinct molecular architecture (Winther & Gerdes, 2012).…”

Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen Enterococcus faecalis

“…Generally, TA-II toxin and antitoxin repress their own transcription via 'conditional cooperativity', a process relying on the DNA-binding properties of the antitoxin, the affinity between the toxin and the antitoxin, and their limited abundance. [28][29][30] Different activities have been characterized among TA-II toxins, and most of them inhibit translation acting as endoribonucleases (endoRNases), including MazF. 7,12,31,32 Although TAs are key players in adjusting physiology during adaptation processes, how bacteria coordinate their expression individually and as a whole set remain poorly understood.…”