Beating a Toxin-Antitoxin System; Evading Suicide

Bacteria have evolved many different systems to evade viral predation. One strategy, abortive infection (Abi), involves altruistic suicide. Mediated by a toxin-antitoxin (TA) system, the suicide of the infected cell protects the clonal bacterial population by preventing the spread of replicated bacteriophage. A new paper in Plos Genetics has discovered a molecular mimicry-based strategy that allows phage to escape abortive infection.

Toxin-antitoxin systems are widespread prokaryotic genetic elements found on both plasmids and bacterial chromosomes. Encoding a relatively long-lived toxin and a more labile antitoxin expressed from a single bi-cistronic operon, they were originally characterised as ‘addiction modules’. In the event that a plasmid expressing a TA system fails to be inherited by a daughter cell, the absence of antitoxin allows the persisting toxin to kill the cell – post-segregational killing. These attributes as ‘selfish elements’ made it slightly surprising that so many TA systems have been found encoded on bacterial chromosomes themselves. I’ve previously written about an example of one such TA system’s activity in mediating a stress response in E. coli, and they’ve also been implicated in the formation of antibiotic resisting ‘persister’ cells.

TA systems have been classified into three different classes defined by the level of the molecular interaction between their two components. In type I systems, translation of the toxin is prevented by an antisense RNA antitoxin binding to its’ transcript, whilst in type II systems both partners are proteins. Most recently, type III TA systems have been characterised in which the toxin is neutralised by binding of an RNA antitoxin. Examples of all three varieties have been found to protect bacteria from phage infection via abortive infection; phage replication disrupts the normal cellular transcriptional program, interrupting antitoxin production and hence leading to cell death.

The first type III TA system to be characterised, ToxIN, was found on plasmids in the phytopathogen, Pectobacterium atrosepticum (Pba), and shown to inhibit the propagation of multiple different bacteriophage. ToxN is an endoribonuclease, whilst the antitoxin ToxI, is a 36nt RNA structured as a ‘pseudoknot’. The partners combine into a hetero-hexameric structure composed of 3 ToxN molecules and 3 ToxI pseudoknots.

Blower et al. have discovered that phage can evade the Abi system by producing molecular mimics of the ToxI RNA. The lytic bacteriophage ΦTE, normally fails to infect Pba carrying a toxIN-containing plasmid. At low frequency however, new phage strains emerge capable of evading the Abi system. Upon sequencing the genomes of these ‘escape strains’, the researchers discovered that they all contained sequence expansions at one specific locus. The toxI locus contains 5.5 repeats of the 36nt RNA pseudoknot-encoding sequence. The ‘escape locus’ from the phage normally encoded 1.5 repeats of a pseudo-ToxI sequence. In all the escape strains this repeat had been expanded so that it contained either 4.5 or 5.5 repeats. These expansions had probably arisen due to strand-slippage during phage replication. In one escape strain homologous recombination had occurred between the phage pseudo-ToxI and the endogenous toxI; the phage had effectively hijacked a normal antitoxin- encoding gene.

The 1.5 repeat pseudo-ToxI could not inhibit Abi (as the sequence was out of phase it did not actually encode a functional psudoknot). However, the repeat expansions had allowed the phage to make an antitoxin mimic that protected them from the TA system and hence Abi.

ΦTE is capable of generalised transduction – the ability to package and transfer chromosomal and plasmid DNA from its’ host and transfer it during infection. Blower et al. showed that one of the ΦTE escape strains is able to transduce the plasmid encoded ToxIN – a case of a bacteriophage horizontally transferring an anti-phage defence mechanism. This brings into focus the complex evolutionary dynamics operating between the three different genetic entities being studied; the bacterial cell, the plasmid encoding the TA system, and the bacteriophage evading it and potentially propagating it. From the selfish viewpoint of the TA module what’s best, preventing the spread of the phage or being disseminated by it? These speculations aren’t about to be easily answered, however, it is an interesting way to analyse further examples of similar systems.

Blower, T., Evans, T., Przybilski, R., Fineran, P., & Salmond, G. (2012). Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism PLoS Genetics, 8 (10) DOI: 10.1371/journal.pgen.1003023

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