Structural Mechanism of Transcriptional Autorepression of the Escherichia coli RelB/RelE Antitoxin/Toxin Module

The Escherichia coli chromosomal relBE operon encodes a toxin–antitoxin system, which is autoregulated by its protein products, RelB and RelE. RelB acts as a transcriptional repressor and RelE functions as a cofactor to enhance the repressor activity of RelB. Here, we present the NMR-derived structure of a RelB dimer and show that a RelB dimer recognizes a hexad repeat in the palindromic operator region through a ribbon–helix–helix motif. Our biochemical data show that two weakly associated RelB dimers bind to the adjacent repeats in the 3′-site of the operator (OR) at a moderate affinity (Kd, ∼ 10− 5 M). However, in the presence of RelE, a RelB tetramer binds two distinct binding sites within the operator region, each with an enhanced affinity (Kd, ∼ 10− 6 M for the low-affinity site, OL, and 10− 8 M for the high-affinity site, OR). We propose that the enhanced affinity for the operator element is mediated by a cooperative DNA binding by a pair of RelB dimers and that the interaction between RelB dimers is strongly augmented by the presence of the cognate toxin RelE.