Bioinformatic exploration reveals features of tenpIN family of type III toxin-antitoxin systems in bacteria and viruses.

Toxin-antitoxin (TA) systems in bacteria consist of two genes: one encoding a toxin that inhibits essential cellular processes and the other encoding an antitoxin that neutralizes the toxin under homeostatic conditions. TA systems are classified into eight types (I to VIII) based on the mechanism of toxin inhibition by the antitoxin. Type III TA systems comprise a protein toxin that is usually an endoribonuclease and an RNA antitoxin and are further classified into toxIN, cptIN, and tenpIN families based on toxin sequence homology. These systems primarily function in phage defence and plasmid maintenance. While toxIN and cptIN systems are well-studied for their structures and functions, tenpIN systems remain poorly characterized. Here, we report identification of over 700 putative TenpN toxin sequences across different bacteria and viruses - a significant expansion beyond the previously documented 25 bacterial sequences. Using sequence alignments and structure prediction tools, we identified unique signatures in the TenpN toxins and tenpI RNA antitoxins that may play crucial roles for their structure and function. These findings are illustrated through case studies on tenpIN systems in ESKAPE pathogens, E. coli, and viruses. Despite sequence diversity, most TenpN proteins are predicted to have similar tertiary structures with a conserved core. Some TenpN toxins show N- and C-terminal extensions, which could affect their oligomeric states and substrate binding. Additionally, the tenpI antitoxins exhibit longer, non-identical repeats than toxI and cptI antitoxins but retain the ability to form pseudoknot structures.