Structural characterizations of phage antitoxin Dmd and its interactions with bacterial toxin RnlA

Wei, Yong; Gao, Zengqiang; Zhang, H.; Dong, Yuhui

doi:10.1016/j.bbrc.2016.03.025

Cited by 17 publications

(17 citation statements)

References 23 publications

(15 reference statements)

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“…B). This unique conformation represents a novel fold and also has low structural homology compared with known structures according to a DALI search (Wei et al ., ). There are no significant conformational changes in Dmd upon binding to LsoA compared with the apo form (PDB: 4I8R; with an r.m.s.d.…”

Section: Resultsmentioning

confidence: 97%

See 1 more Smart Citation

Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd

Wei

Otsuka

Gao

et al. 2016

Molecular Microbiology

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Bacteria have obtained a variety of resistance mechanisms including toxin-antitoxin (TA) systems against bacteriophages (phages), whereas phages have also evolved to overcome bacterial anti-phage mechanisms. Dmd from T4 phage can suppress the toxicities of homologous toxins LsoA and RnlA from Escherichia coli, representing the first example of a phage antitoxin against multiple bacterial toxins in known TA systems. Here, the crystal structure of LsoA-Dmd complex showed Dmd is inserted into the deep groove between the N-terminal repeated domain (NRD) and the Dmd-binding domain (DBD) of LsoA. The NRD shifts significantly from a 'closed' to an 'open' conformation upon Dmd binding. Site-directed mutagenesis of Dmd revealed the conserved residues (W31 and N40) are necessary for LsoA binding and the toxicity suppression as determined by pull-down and cell toxicity assays. Further mutagenesis identified the conserved Dmd-binding residues (R243, E246 and R305) of LsoA are vital for its toxicity, and suggested Dmd and LsoB may possess different inhibitory mechanisms against LsoA toxicity. Our structure-function studies demonstrate Dmd can recognize LsoA and inhibit its toxicity by occupying the active site possibly via substrate mimicry. These findings have provided unique insights into the defense and counter-defense mechanisms between bacteria and phages in their co-evolution.

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Section: Resultsmentioning

confidence: 97%

“…S3). Especially, the highly conserved residues W31 and N40 are responsible for LsoA‐binding and toxicity inhibition, consistent with their important roles in RnlA‐binding (Wei et al ., ). These observations indicate they may have evolved to suppress the toxicity of their respective toxin homologs by a universal recognition mechanism.…”

Section: Discussionmentioning

confidence: 97%

Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd

Wei

Otsuka

Gao

et al. 2016

Molecular Microbiology

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“…The activity of the TA toxin RnlA is induced after T4 phage infection. RnlA cleaves most of the cellular and phage-derived mRNA in the absence of the antitoxin RnlB, hence blocking the reproduction and spreading of T4 phage [85,102,103,104,105]. mazEF antagonizes the induction of phage T4, as well as P1 [106,107].…”

Section: Physiological Rolesmentioning

confidence: 99%

Toxins of Prokaryotic Toxin-Antitoxin Systems with Sequence-Specific Endoribonuclease Activity

Masuda

Inouye

2017

Toxins

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Protein translation is the most common target of toxin-antitoxin system (TA) toxins. Sequence-specific endoribonucleases digest RNA in a sequence-specific manner, thereby blocking translation. While past studies mainly focused on the digestion of mRNA, recent analysis revealed that toxins can also digest tRNA, rRNA and tmRNA. Purified toxins can digest single-stranded portions of RNA containing recognition sequences in the absence of ribosome in vitro. However, increasing evidence suggests that in vivo digestion may occur in association with ribosomes. Despite the prevalence of recognition sequences in many mRNA, preferential digestion seems to occur at specific positions within mRNA and also in certain reading frames. In this review, a variety of tools utilized to study the nuclease activities of toxins over the past 15 years will be reviewed. A recent adaptation of an RNA-seq-based technique to analyze entire sets of cellular RNA will be introduced with an emphasis on its strength in identifying novel targets and redefining recognition sequences. The differences in biochemical properties and postulated physiological roles will also be discussed.

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“…In the Type III systems, the ToxIN-sensitive phage TE was shown to produce low frequency spontaneous mutants that escaped the ToxIN Pa system [36]. Analysis of the escape mutants revealed that the majority of the mutants had extended a short viral sequence similar to the repeats of the ToxI sRNA into a ‘pseudo-ToxI’ which functionally suppressed the toxin.…”

Section: Functions Of Type III Ta Systemmentioning

confidence: 99%

“…In one case, recombination had allowed the phage escape mutant to obtain natural ToxI repeats from the original plasmid antitoxin sequences. Both scenarios allowed phage replication unaffected by the Abi/TA system [36]. …”

Section: Functions Of Type III Ta Systemmentioning

confidence: 99%

Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems

Goeders

Chai

Chen

et al. 2016

Toxins

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Toxin-antitoxin (TA) systems are small genetic modules that encode a toxin (that targets an essential cellular process) and an antitoxin that neutralises or suppresses the deleterious effect of the toxin. Based on the molecular nature of the toxin and antitoxin components, TA systems are categorised into different types. Type III TA systems, the focus of this review, are composed of a toxic endoribonuclease neutralised by a non-coding RNA antitoxin in a pseudoknotted configuration. Bioinformatic analysis shows that the Type III systems can be classified into subtypes. These TA systems were originally discovered through a phage resistance phenotype arising due to a process akin to an altruistic suicide; the phenomenon of abortive infection. Some Type III TA systems are bifunctional and can stabilise plasmids during vegetative growth and sporulation. Features particular to Type III systems are explored here, emphasising some of the characteristics of the RNA antitoxin and how these may affect the co-evolutionary relationship between toxins and cognate antitoxins in their quaternary structures. Finally, an updated analysis of the distribution and diversity of these systems are presented and discussed.

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Structural characterizations of phage antitoxin Dmd and its interactions with bacterial toxin RnlA

Cited by 17 publications

References 23 publications

Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd

Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd

Toxins of Prokaryotic Toxin-Antitoxin Systems with Sequence-Specific Endoribonuclease Activity

Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems

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