Specificity and mechanism of tRNA cleavage by the AriB Toprim nuclease of the PARIS bacterial immune system
Transfer RNA (tRNA) molecules have been recently recognized as widespread targets of bacterial immune systems. Translation inhibition through tRNA cleavage or modification inhibits phage propagation, thereby protecting the bacterial population. To counteract this, some viruses encode their own tRNA molecules, allowing infection to take place. The AriB effector of the PARIS defence system is a Toprim nuclease previously shown to target the <i>Escherichia coli</i> tRNA<sup>Lys(UUU)</sup>, but not a tRNA<sup>Lys(UUU)</sup> variant encoded by bacteriophage T5. We demonstrate here that the T5 tRNA<sup>Lys(UUU)</sup> is required but not sufficient to bypass PARIS immunity. Combining tRNA sequencing, genetics, phage infection and <i>in vitro</i> biochemical data, we reveal that the <i>E. coli</i> tRNA<sup>Thr(UGU)</sup> is another prime target of AriB, and tRNA<sup>Asn(GUU)</sup> represents a secondary, yet biologically relevant, target of the PARIS effector. Activated AriB protein cleaves these targets <i>in vitro</i>, and the cleavage reaction is not dependent on the presence of specific tRNA modifications. We show that the overexpression of phage T5 tRNA<sup>Lys(UUU)</sup>, tRNA<sup>Thr(UGU)</sup> and tRNA<sup>Asn(GUU)</sup> variants is sufficient to inhibit PARIS anti-viral defence. Finally, we propose a model for tRNA recognition by the AriB dimer and provide molecular details of its nuclease activity and specificity.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.
Authors
- Петр В. Сергиев (ORCID: https://orcid.org/0000-0001-8866-1863)
- Alexei Livenskyi (ORCID: https://orcid.org/0009-0001-2850-9904)
- Nadezhda Burmistrova
- Svetlana Belukhina
- Florence Depardieu (ORCID: https://orcid.org/0000-0002-2680-0589)
- Frédéric Barras (ORCID: https://orcid.org/0000-0003-3458-2574)
- Virginie Marchand (ORCID: https://orcid.org/0000-0002-8537-1139)
- Sarah Dubrac (ORCID: https://orcid.org/0000-0002-9810-5390)
- Tinashe P. Maviza (ORCID: https://orcid.org/0000-0001-8676-7445)
- Christophe Rouillon (ORCID: https://orcid.org/0000-0003-4038-315X)
- Marina V. Serebryakova (ORCID: https://orcid.org/0000-0002-5402-8215)
- David Bikard (ORCID: https://orcid.org/0000-0002-5729-1211)
- Artem Isaev (ORCID: https://orcid.org/0000-0002-9593-2745)
- Gregor Hagelueken (ORCID: https://orcid.org/0000-0001-8781-5664)
- Baptiste Saudemont (ORCID: https://orcid.org/0000-0002-8360-3565)
- Yuri Motorin (ORCID: https://orcid.org/0000-0002-8018-334X)
- Marouane Libiad (ORCID: https://orcid.org/0000-0003-1717-9206)
- Tom Lorthios
- Maria Aleksandrova
- Elizaveta Ukholkina
Institutions
- Skolkovo Institute of Science and Technology (RU)
- Centre National de la Recherche Scientifique (FR)
- University of Bonn (DE)
- Institut Pasteur (FR)
- Lomonosov Moscow State University (RU)
- Université Paris Cité (FR)
- Institute of Gene Biology (RU)
- Université de Lorraine (FR)
Publication Details
- Journal
- Philosophical Transactions of the Royal Society B Biological Sciences
- Published
- 2025-09-04
- DOI
- https://doi.org/10.1098/rstb.2024.0074
- Citations
- 3
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- Agence Nationale de la Recherche
- Russian Science Foundation
- Ministry of Science and Higher Education of the Russian Federation
- H2020 European Research Council