The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity

Abstract

The bacterial relBE locus encodes a toxin-antitoxin complex in which the toxin, RelE, is capable of cleaving mRNA in the ribosomal A site cotranslationally. The antitoxin, RelB, both binds and inhibits RelE, and regulates transcription through operator binding and conditional cooperativity controlled by RelE. Here, we present the crystal structure of the intact Escherichia coli RelB2E2 complex at 2.8 Å resolution, comprising both the RelB-inhibited RelE and the RelB dimerization domain that binds DNA. RelE and RelB associate into a V-shaped heterotetrameric complex with the ribbon-helix-helix (RHH) dimerization domain at the apex. Our structure supports a model in which relO is optimally bound by two adjacent RelB2E heterotrimeric units, and is not compatible with concomitant binding of two RelB2E2 heterotetramers. The results thus provide a firm basis for understanding the model of conditional cooperativity at the molecular level.

Figure 1

Structural Overview of the E. coli RelBE Complex (A) Sequences of E. coli RelE and RelB with conservation shown by colored letters as indicated. For RelE, residues that interact with RelB, as well as those involved in catalysis (active site), are shown, and the conserved interaction motif is indicated in bold letters below the corresponding motif. For RelB, individual domains are shown along with residues proposed to interact with the DNA major groove and those that make hydrophobic interactions with RelE. (B) Overview of the RelB₂E₂ heterotetramer in two perpendicular views, with RelE in blue and RelB in red. Secondary structure elements in RelB are indicated. (C) The dodecamer assembly observed in the RelBE crystals with an inset showing a simplified overview and colors as in (B). One RelB dimerization domain missing in the structure has been generated by symmetry to show the full assembly. All structure figures were prepared in PyMOL (version 1.3; Schrödinger, L.L.C., http://www.pymol.org). Also see Figure S1.

Figure 2

RelE Dimerization and RelB Binding (A) Overview of the RelE structures found in the P2₁ crystal form (monomer and symmetrical dimer), P2₁2₁2₁ crystal form (asymmetrical dimer), and the RelBE complex. RelE is shown in light blue, with the C-terminal helix α3 in a darker shade. RelB is shown in red. (B) Details of the interactions between the core of RelE and the C-terminal helix (P2₁ and P2₁2₁2₁ forms) or RelB (in the RelBE structure). Residues from RelE and RelB are shown in blue and red, respectively, with labels marked by an asterisk. Also see Figure S2.

Figure 3

RelB Binds DNA via an Arc-Like Motif (A) Top: The relO operator sequence, showing the −10 box (red) and the two sites required for cooperative RelBE binding (green and blue) that overlap with the transcriptional start site (bent arrow). Bottom: The corresponding region of the arc operator that provides the binding site for the bacteriophage P22 Arc repressor. (B) Crystal structure of the Arc DNA binding domain (gray) bound to its cognate DNA sequence (orange with bases in purple), with two copies of the RelB dimerization domain overlaid (red). (C) Structural model for binding of two adjacent heterotrimeric RelB₂E complexes to DNA. Also see Figure S3.

Figure 4

Model for RelBE DNA Binding and Conditional Cooperativity Top: In rapidly growing cells, RelB is in excess and the RelB₂E trimer initially binds the relO operator. Binding of the trimer strongly promotes binding of a second trimer, leading to a RelE-RelB₂-RelB₂-RelE heterohexamer binding to the two adjacent sites on DNA and blocking transcription. Bottom: During nutritional starvation, transcription is initially repressed, but the relative amounts of RelE increase as the labile RelB is degraded during translational pausing. Free RelE then binds the unoccupied C-terminal tails of RelB inside the heterohexamer on DNA, leading to a clash and release of the heterotetramer from the DNA. The remaining trimer on DNA also binds a second RelE molecule and is either released through allosteric changes or displaced by the polymerase.