Balancing at survival's edge: the structure and adaptive benefits of prokaryotic toxin–antitoxin partners
Introduction
Throughout their evolutionary histories, bacteria have experienced intense selective pressure from the physical and chemical environment and from astronomical numbers of niche competitors and predators. They must cope with fluctuations in nutrient availability and the challenges of diverse toxic compounds, including antimicrobials and damaging oxidising agents. Accordingly, bacteria have evolved highly refined response mechanisms to handle a wide spectrum of stress conditions. Toxin–antitoxin (TA) systems provide one such strategy for general and specific stress responses. Originally identified as post-segregational killing systems that ensure the selfish maintenance of plasmids [1], TA systems are now recognised as contributing more selectively beneficial attributes to their host organism. These include responses to antibiotics and nutrient depletion [2], the genesis of subpopulations that survive and persist after antibiotic exposure [3•], protection from phage infection [4] and the regulation of pathogenicity [5], amongst others [6, 7].
The fundamental genetic module for a TA system comprises a single promoter controlling expression of bicistronic antitoxin and toxin genes. These genetic loci can be grouped into distinct classes according to the nature of the interacting molecules (Figure 1). In Type I loci, the antitoxin is a transcript that is antisense to the toxin mRNA, and pairing of the two RNAs promotes mutual degradation. Type I systems will not be covered here, but are reviewed elsewhere [8]. In Type II loci, both toxin and antitoxin are proteins and together they form a complex that masks the activity of the toxin. The distinguishing feature of the recently discovered Type III systems is that a proteinaceous toxin is inhibited by an antitoxic RNA [9]. In response to stimuli, the antitoxins are degraded and toxins take effect, often inducing bacteriostasis. Once the stress abates, antitoxin levels are restored, the cognate toxin becomes safely sequestered, and cell growth continues.
TA systems are prevalent throughout the eubacteria and archaea [10, 11, 12, 13], though accruing structural data on representatives of the different TA classes have revealed that toxin proteins belong to only a restricted group of structural families.
Section snippets
Six structural classes of toxin
Toxins of the Type II and Type III TA systems can be sub-divided into six groups, according to toxin structural homology (Table 1). The toxins within a group often show only limited sequence similarity, despite having a common fold [14].
The Kid family members have compact globular folds with twisted anti-parallel beta-sheet cores, enshrouded by alpha-helices [15, 16••]. Many Kid-like toxins cleave mRNAs and have accordingly been dubbed mRNA ‘interferases’ [17]. One exception is CcdB, which
RNA binding and cleavage by Kid family toxins
The Type III system, ToxIN [16••], was identified originally as a phage abortive infection system [4, 31]. The crystal structure of the ToxIN complex reveals that ToxN belongs to the Kid structural family (Table 1). This relationship was not anticipated in advance of the ToxIN crystal structure, because the sequence identity between the ToxN and Kid proteins is very low (∼10% based on the a posteriori structure-based alignment) [16••]. ToxN, however, has more extensive RNA interaction surfaces
Ribosome-dependent endoribonucleases
Great insight into the RelE toxin mechanism has been provided by the structures of Escherichia coli RelE alone and in complex with the Thermus thermophilus ribosome and substrate mRNA [20••]. When bound to the ribosome, RelE mimics A site tRNA facing the P site tRNA. A surface patch of RelE forms extensive interactions with 16S rRNA, but RelE makes few contacts with the 50S subunit or ribosomal proteins [20••]. At the A site, RelE re-orients the 2′OH of the mRNA substrate at the second codon
Antitoxins inactivate toxins in complex
For continued survival, bacterial cells must hold toxins in check, prior to activation. Antitoxins negate cognate toxin activity through a toxin binding domain, which is often natively unstructured until complex formation. Within the Kid family, the C-terminal domain of MazE acts as a single-stranded RNA decoy, wrapping across the surface of MazF, blocking the active site and forcing out the S1–S2 loop that, in Kid, provides the stabilizing H17 of the catalytic triad [38]. The Kid family
Transcriptional autoregulation by toxin–antitoxin complexes
Known Type II antitoxins, though diverse, usually have a second, structured, DNA-binding domain. They can be loosely grouped according to this motif (Table 1). Via this domain, certain antitoxins maintain a balanced stoichiometry of toxin to antitoxin by negatively regulating transcription of their cognate locus. Often, a TA complex will have greater repressive action over the antitoxin alone. Within a specific toxin group, cognate antitoxins will have differing DNA-binding domains, such as for
Concluding remarks
TA systems are ubiquitous throughout prokaryotic lineages, and work from recent years has expanded our knowledge of their structures and illuminated their functions. There are currently few basic toxin folds, which appear to have diverged tremendously in sequence whilst adapting to stresses of varied nature. Much still remains to be learned for these systems regarding their functionality, substrate binding specificity and how particular stresses are sensed and lead to activation. As mechanistic
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
The authors are supported by grants from the Biotechnology and Biological Sciences Research Council (UK) and the Wellcome Trust (UK).
References (53)
Hypothetical functions of toxin–antitoxin systems
J Bacteriol
(2007)- et al.
Structural and functional analysis of the Kid toxin protein from E. coli plasmid R1
Structure
(2002) - et al.
A processed non-coding RNA regulates an altruistic bacterial antiviral system
Nat Struct Mol Biol
(2011) - et al.
Molecular basis of gyrase poisoning by the addiction toxin CcdB
J Mol Biol
(2005) - et al.
Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin
Mol Cell
(2005) - et al.
The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin
J Biol Chem
(2009) - et al.
Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation
J Biol Chem
(2008) - et al.
Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit
Proc Natl Acad Sci U S A
(2008) - et al.
Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin–antitoxin operon
Proteins
(2008) - et al.
Molecular and structural characterization of the PezAT chromosomal toxin–antitoxin system of the human pathogen Streptococcus pneumoniae
J Biol Chem
(2007)
PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function
J Biol Chem
Characterization of dual substrate binding sites in the homodimeric structure of Escherichia coli mRNA interferase MazF
J Mol Biol
Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition
Mol Cell
Crystal structure of archaeal toxin–antitoxin RelE–RelB complex with implications for toxin activity and antitoxin effects
Nat Struct Mol Biol
Inhibitory mechanism of Escherichia coli RelE-RelB toxin–antitoxin module involves a helix displacement near an mRNA interferase active site
J Biol Chem
Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties
PLoS Pathog
Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA
J Mol Biol
Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity
Cell
Structural and thermodynamic characterization of Vibrio fischeri CcdB
J Biol Chem
Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain
Mol Cell
Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein
J Mol Biol
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding
Protein Sci
Programmed cell death in bacterial populations
Science
Prokaryotic toxin–antitoxin stress response loci
Nat Rev Microbiol
Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence
Proc Natl Acad Sci U S A
The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair
Proc Natl Acad Sci U S A
Cited by (77)
Toxin–antitoxin systems as mediators of phage defence and the implications for abortive infection
2023, Current Opinion in MicrobiologyUnveiling the duality of Pantoea dispersa: A mini review
2023, Science of the Total EnvironmentStructure and allosteric coupling of type Ⅱ antitoxin CopA<inf>SO</inf>
2019, Biochemical and Biophysical Research CommunicationsStructural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB
2019, International Journal of Biological MacromoleculesCitation Excerpt :Meanwhile, the antitoxin molecule, which under normal conditions acts as a potent inhibitor of its cognate toxin, is usually degraded under stress conditions, thus allowing the toxin to function [2,6]. Based on the toxin-neutralizing mechanisms of the antitoxin, TA systems are classified into six different types (type I to VI) [6,7]. Type II system constitutes the most-well characterized group of TAs, and these employ proteins as both the toxin and antitoxin molecules [8].
Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology
2018, Molecular Cell