Distinct oligomeric structures of the YoeB–YefM complex provide insights into the conditional cooperativity of type II toxin–antitoxin system

Abstract

YoeB–YefM, the widespread type II toxin–antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB–YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB–YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB–YefM2–YoeB) and heterohexamer (YoeB–YefM2–YefM2–YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5′-TTGTACAN6AGTACAA-3′ palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.

Edwardsiella piscicida YefM-YoeB: A Type II Toxin-Antitoxin System That Is Related to Antibiotic Resistance, Biofilm Formation, Serum Survival, and Host Infection

“…Among type II TA systems, YefM-YoeB is one of most frequently encountered TA systems in many pathogenic bacteria. In S. aureus , there are two distinct oligomeric assemblies: heterotetramer (YoeB-YefM2-YoeB) and heterohexamer (YoeB-YefM2-YefM2-YoeB) ( Xue et al, 2020 ). In S. pneumoniae , it is reported that YefM-YoeB participates in oxidative stress and biofilm formation ( Chan et al, 2018 ).…”

Interactions of the Streptococcus pneumoniae Toxin-Antitoxin RelBE Proteins with Their Target DNA

“…The solution of the structure of the pneumococcal RelB and RelB:RelE proteins alone and in complex with their target DNA could provide better insights into the interaction of these proteins with their target DNA, as has been the case for the Staphylococcus aureus yefM-yoeB TAs [ 64 ].…”

Entropic pressure controls oligomerization ofVibrio choleraeParD2 antitoxin

“…In many TA systems, the antitoxin often binds to two or more binding sites on the operator. In most cases, the toxin increases antitoxin-DNA affinity by bridging adjacent antitoxin dimers (Garcia-Pino et al, 2010; Vandervelde et al, 2016; Xue et al, 2020), or by otherwise stabilizing the DNA-binding assembly the antitoxin (Bøggild et al, 2012; Qian et al, 2019; Jurėnas et al, 2019). Higher toxin to antitoxin ratios lead to de-repression via the formation of toxin-antitoxin complexes with altered stoichiometry.…”

“…Transcription regulation of TA modules is often complex and involves the ratio-dependent interplay between toxin and antitoxin (Garcia-Pino et al, 2010; Jurėnas et al, 2019; Page & Peti, 2016; Vandevelde et al, 2017; Xue et al, 2020). In these mechanisms, intrinsically disordered segments on antitoxin or toxin often play a major role (De Jonge et al, 2009; Garcia-Pino et al, 2016; Loris & Garcia-Pino, 2014; Talavera et al, 2019).…”