Type II Toxin-Antitoxin Systems: Evolution and Revolutions

Abstract

Type II toxin-antitoxin (TA) systems are small genetic elements composed of a toxic protein and its cognate antitoxin protein, the latter counteracting the toxicity of the former. While TA systems were initially discovered on plasmids, functioning as addiction modules through a phenomenon called postsegregational killing, they were later shown to be massively present in bacterial chromosomes, often in association with mobile genetic elements. Extensive research has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules and to characterize the conditions leading to their activation. The diversity of their proposed roles, ranging from genomic stabilization and abortive phage infection to stress modulation and antibiotic persistence, in conjunction with the poor understanding of TA system regulation, resulted in the generation of simplistic models, often refuted by contradictory results. This review provides an epistemological and critical retrospective on TA modules and highlights fundamental questions concerning their roles and regulations that still remain unanswered. FIG 1 Type II TA systems, postsegregational killing and distribution. (A) Nonviable segregant or postsegregational killing model. TA genes, as well as proteins, are represented in red (toxins) and green (antitoxins).Rectangles denote TA genes encoded on a plasmid, and round shapes denote TA proteins produced from these genes. A TA-encoding plasmid can be lost during division in a way that one of the daughter cells does not inherit a plasmid copy. In these cells, TA proteins cannot be replenished due to the absence of TA genes. Since the antitoxin is degraded while its cognate toxin is stable, the free toxin concentration will increase, exert its activity, and, in time, induce cell death, therefore killing plasmid-free segregants. (B) Distribution of type II TA systems in various E. coli reference strains generated by TAfinder (23). Asterisks indicate systems that were not validated experimentally. Parentheses include name of the prophage a TA is encoded on when applicable. The strains are MG1655 (NCBI U00096.3), a common lab strain from phylogroup A; W (CP002967.1), a soil isolate from phylogroup B1; EDL933 (AE005174.2), an enterohemorrhagic pathogen from phylogroup E; and UTI89 (CP000243.1), a uropathogen from phylogroup B2. No TA systems are conserved within these four distantly related E. coli strains.

The Variety in the Common Theme of Translation Inhibition by Type II Toxin–Antitoxin Systems

“…The role(s) of TA systems in bacterial physiology and evolution is a long-standing debate (Magnuson, 2007;Tsilibaris et al, 2007;Van Melderen and Saavedra De Bast, 2009;Van Melderen, 2010;Ramisetty et al, 2016;Harms et al, 2017;Culviner and Laub, 2018;Goormaghtigh et al, 2018a,b;Holden and Errington, 2018;Mets et al, 2019;Pontes and Groisman, 2019;Wade and Laub, 2019;Fraikin et al, 2020). Since their discovery on plasmids in the 1980's and on chromosomes almost 20 years later, the TA field has been going through waves of hypothesis ranging from replicon maintenance, programmed cell death, stress response, generation of specialized ribosomes, persistence to antibiotics, to phage abortive infection mechanisms.…”

“…Therefore, our data strongly argue against the idea that TA systems are pivotal elements of antibiotic persistence. This basically leaves the principal questions in the field open (for a recent review see Fraikin et al, 2020). Conditions in which TA systems are activated and what the outcomes of such activations are, still remain undetermined.…”

A toxin-antitoxin system associated transcription factor ofCaulobacter crescentuscan influence cell cycle-regulated gene expression during the SOS response

“…However, it is also important not to infer too much from studies of mutant strains about the physiological roles of these proteins in wild type cells. A criticism which is often levelled at studies of TA systems is that phenotypes of antitoxin mutant strains are not equivalent to phenotypes of wild type cells experiencing high levels of toxin production and therefore not physiologically relevant (2,19,21), and therefore a phenotype associated with a given TA system should only be postulated if a phenotype can be observed for a toxin or whole TA system mutant. We do indeed observe such a phenotype for HigBA, since the loss of the toxin in the ΔlexA background substantially improved its resistance to ciprofloxacin.…”

“…Bacterial toxin-antitoxin (TA) systems have been the subject of intensive study since their widespread prevalence in prokaryotic chromosomes, as well as mobile genetic elements, was discovered (1). TA systems consist of two components, a toxin protein which can inhibit some aspect of central cellular metabolism and an antitoxin, either protein or RNA, which can inhibit the toxin activity or production at the post-transcriptional or post-translational level, depending on the type (2)(3)(4)(5)(6). The best characterised systems are those of type II where both toxin and antitoxin are small proteins which form a non-toxic complex with each other, of variable stoichiometry depending on the TA system and the organism in which it is found.…”

“…However, other mechanisms which lead to decreased metabolic rate and slow growth can also induce persistence, independently of TA system induction or activity (21). The current key factor in induction of persistence seems to be slow growth, regardless of the cause, and no TA system has yet been reproducibly found to be necessary or sufficient for this (2).…”