Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin

Abstract

ParD2 is the antitoxin component of the parDE2 toxin–antitoxin module from Vibrio cholerae and consists of an ordered DNA-binding domain followed by an intrinsically disordered ParE-neutralizing domain. In the absence of the C-terminal intrinsically disordered protein (IDP) domain, V. cholerae ParD2 (VcParD2) crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than by hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open decamer or dodecamer, which is likely to be a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows an extended operator to wrap around the VcParD2 oligomer.

Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module

“…For the Vc ParE2- Vc ParD2 interaction, the cell contained Vc ParE2 (6 μM), and the syringe was loaded with Vc ParD2 (80 μM monomer equivalent). On the basis of the information of the aggregation state of the interacting proteins ( 44 ), the ITC curve was described by the following single binding eventE+112D12⇌12E2D2…”

“…S2F). Nevertheless, this interface is not stable in solution, as VcParE2, like all other ParE proteins studied to date, remains monomeric even at high-protein concentration (44). The 6:2 VcParDE2 complex can be titrated with VcParE2 to form a complex with 2:2 stoichiometry In the VcParDE2 complex, only two of the six VcParD2 monomers interact each with a VcParE2 toxin molecule (Fig.…”

“…For the VcParE2-VcParD2 interaction, the cell contained VcParE2 (6 μM), and the syringe was loaded with VcParD2 (80 μM monomer equivalent). On the basis of the information of the aggregation state of the interacting proteins (44), the ITC curve was described by the following single binding event Fitting of the corresponding model function to the ITC curve at a given temperature results in values of the corresponding association (K A ) or dissociation (K d = 1/K A ) constants and standard enthalpies of association (∆H A ). K A and K d are dimensionless thermodynamic equilibrium constant defined in terms of species activities.…”

“…Transcription regulation has been studied for some parDE loci in vivo and indicates highly specific interactions ( 22 , 41 – 43 ). However, only limited in vitro data are now available for the isolated RK2 ParD and Vc ParD2 ( 26 , 44 ). The early work on plasmid RK2 parDE suggested that ParD alone can act as a repressor for the operon ( 26 ), but it is not known whether the ParE toxin modulates this action.…”

Structural insights into the PrpTA toxin–antitoxin system in Pseudoalteromonas rubra

“…RHH superfamily transcription factors (TFs) are of physiological importance toward the recognition between human pathogens and hosts ( Schreiter and Drennan, 2007 ). RHH superfamily TFs always dock into the major grooves of duplex nucleic acid as a multi-dimer and further transcriptionally autoregulate ( Knight and Sauer, 1989 ; Raumann et al, 1994 ; Schreiter and Drennan, 2007 ; Schumacher et al, 2015 ; Garcia-Rodriguez et al, 2021b ). Even though some of them are dimeric in solution, they will instantly build up contacts in the corresponding DNA-bound complex with the exception of TraY whose polypeptide has two repeats of the RHH motif ( Raumann et al, 1994 ; Costa et al, 2001 ; Solar et al, 2002 ; Schreiter and Drennan, 2007 ).…”