Structural and Functional Diversity of RNA-Containing Toxin-Antitoxin Systems

Toxin-antitoxin (TA) systems are ubiquitous prokaryotic genetic modules located on plasmids and chromosomes, contributing to plasmid stabilization, maintenance of genome integrity, phage defense, and bacterial pathogenesis. Canonically, these systems encode a metabolically stable toxin and a labile antitoxin that neutralizes the toxin activity under homeostatic conditions. Stress-induced antitoxin degradation unleashes the toxin, leading to growth arrest through inhibition of various cellular processes, including translation, DNA replication, and cell wall synthesis. TA systems are classified into eight types (type I-VIII) based on antitoxin identity and mode of action. Among these, types I, III, and VIII represent RNA-containing TA systems in which either only antitoxin (types I and III) or both toxin and antitoxin (type VIII) are RNA molecules. Type I systems utilize small cis- or trans-encoded antisense RNA antitoxins that base-pair with toxin mRNAs to block translation or promote degradation; their toxins are typically small hydrophobic peptides targeting membranes or inducing nucleoid condensation. Type III systems encode endoribonuclease toxins and structured RNA antitoxins that assemble into stoichiometric ribonucleoprotein complexes. Structural studies of ToxIN, CptIN, and AbiF type III TA complexes have highlighted the pseudoknot and stem-loop containing antitoxins that engage toxin active sites with high specificity. Type VIII systems, such as CreTA, are fully RNA-based systems, where the toxin sequesters rare tRNAs and the antitoxin mimics CRISPR RNAs to mediate Cas-dependent transcriptional repression of the toxin. In this review, we summarize current understanding of these systems, emphasizing their molecular mechanisms of assembly and action and their emerging applications in biotechnology and therapeutics. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.