A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains
Year: 2022
Type: article
Abstract: Toxin-Antitoxin (TA) gene pairs are ubiquitous in microbial chromosomal genomes and plasmids, as well as bacteriophages. They act as regulatory switches, with the toxin limiting the growth of bacteria and archaea by compromising diverse essential cellular targets, and the antitoxin counteracting the toxic effect. To uncover previously uncharted TA diversity across microbes and bacteriophages, we analysed the conservation of genomic neighbourhoods using our computational tool FlaGs (for Fla nking G ene s ), which allows high-throughput detection of TA-like operons. Focussing on the widespread but poorly experimentally characterised antitoxin domain DUF4065, our in silico analyses indicated that DUF4065-containing proteins serve as broadly distributed antitoxin components in putative TA-like operons with dozens of different toxic domains with multiple different folds. Given the versatility of DUF4065, we have renamed the domain to Panacea (and proteins containing the domain, PanA) after the Greek goddess of universal remedy. We have experimentally validated nine PanA-neutralised TA pairs. While the majority of validated PanA-neutralised toxins act as translation inhibitors or membrane disruptors, a putative nucleotide cyclase toxin from a Burkholderia prophage compromises replication and translation, as well as inducing RelA-dependent accumulation of the nucleotide alarmone (p)ppGpp. We find that Panacea-containing antitoxins form a complex with their diverse cognate toxins, characteristic of the direct neutralisation mechanisms employed by Type II TA systems. Finally, through directed evolution we have selected PanA variants that can neutralise non-cognate TA toxins, thus experimentally demonstrating the evolutionary plasticity of this hyperpromiscuous antitoxin domain. Significance Toxin-antitoxin systems are enigmatic and diverse elements of bacterial and bacteriophage genomes. We have uncovered remarkable versatility of an antitoxin protein domain, that has evolved to neutralise dozens of different toxin domains. We find that antitoxins carrying this domain – Panacea – form complexes with their cognate toxins, indicating a direct neutralisation mechanism, and that Panacea can be evolved to neutralise a non-cognate and non-homologous toxin with just two amino acid substitutions. This raises the possibility that this domain could be an adaptable universal, or semi-universal protein neutraliser with significant biotechnological and medical potential.
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,682
Funders: Ragnar Söderbergs stiftelse, Joint Programming Initiative on Antimicrobial Resistance, UK Research and Innovation, Research Councils UK, European Commission, Eesti Teadusagentuur, Carl Tryggers Stiftelse för Vetenskaplig Forskning, Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, Umeå Universitet, Kempestiftelserna, Umeå Centre for Microbial Research, Directorate for Biological Sciences, Horizon 2020 Framework Programme, Medical Research Council, Biotechnology and Biological Sciences Research Council, European Regional Development Fund
Awards: Small Alarmone Synthetases: novel bacterial RNA-binding proteins, Elucidating protein synthesis-related processes underlying heterogeneity of bacterial populations during infection, Resolving the molecular evolution, epidemiology and mechanism of ABCF-mediated antibiotic resistance, Molecular Infection Biology Estonia - Research capacity building, G2474800141, G2628364946, G2970072724, G2975900969, G3996816461, G4615129728, DTP Bid Led by University of Sheffield, G4937468798, Cell wall synthetic lipid microdomains: composition and mechanism of formation, G5181495137, Development of novel ribosome-targeting antibiotics, G5600842165, G5800125675, G6687064808, G7048215259, G712881263, G8621116774
OpenAlex ID: W4210647992