Nucleotide signals coordinate activation and inhibition of bacterial immunity
Summary
Article Date: 18 February 2026
Article URL: https://www.nature.com/articles/s41586-026-10135-0
Article Image: not provided in the input
This Nature paper describes the Clover anti-phage defence system and shows how small nucleotide signals toggle a bacterial dGTPase between active and inhibited states. The team combine cryo-EM, X-ray crystallography, LC–MS, biochemical assays and phage plaque tests to demonstrate that a nucleotidyltransferase (CloB) makes thymidine-containing oligomers (p1/p2/p3diT) that bind and inhibit the dGTPase CloA, while cellular dTTP levels activate CloA’s dGTPase activity to deplete dGTP and protect cells from phage infection. Structural models and multiple deposited PDB/EMDB entries back the mechanism.
Key Points
- The Clover system comprises CloA (a dGTPase effector) and CloB (an NTase that synthesises thymidine-containing nucleotide signals).
- CloB produces a mixture of p1/p2/p3diT species; p3diT binds CloA and locks it in a suppressed conformation.
- dTTP binding to CloA induces a conformational change that completes the dGTPase active site and activates dGTP hydrolysis.
- Structures (cryo-EM and crystallography) and deposited coordinates/EM maps (PDB: 9P8S–9P8W; EMDB: EMD-71386–EMD-71390) reveal the binding pockets and conformational changes underlying activation/inhibition.
- Mutations in the p3diT and dTTP pockets alter defence in plaque assays, confirming the functional relevance of the structural observations.
Content summary
The authors identify and characterise the bacterial Clover anti-phage defence operon. CloB is shown to synthesise thymidine-dependent oligomeric nucleotide signals (p1/p2/p3diT), detected and chemically validated by LC–MS. These nucleotide products bind CloA and inhibit its dGTPase activity. Conversely, elevated cellular dTTP promotes CloA activation: dTTP binding stabilises a loop and positions the substrate dGTP for hydrolysis, triggering depletion of dGTP and limiting phage replication.
Structural biology (cryo-EM reconstructions and X-ray data) defines the octameric/hexameric assemblies and maps the distinct binding pockets for inhibitory p3diT and activating dTTP. Biochemical assays (phosphate release, ITC) quantify ligand binding and enzymatic responses, while bacterial growth and plaque assays link molecular changes to anti-phage defence. Mutational experiments in both pockets demonstrate predictable loss or gain of defence, tying mechanism to phenotype.
Context and relevance
This study adds a clear example of nucleotide-based regulation in prokaryotic innate immunity: rather than a single activating second messenger, bacteria can use opposing nucleotide signals to fine-tune an immune effector. That interplay — a small molecule produced by a partner enzyme to inhibit an effector, overridden by metabolite levels that activate it — is a neat regulatory motif likely widespread among nucleotide-targeting systems (CBASS, Pycsar, Thoeris and related pathways).
Relevance extends beyond basic microbiology: understanding how phage–host arms races leverage nucleotide chemistry informs phage therapy, synthetic biology and the development of molecular tools that harness or evade bacterial defences. The structural snapshots and deposited datasets also provide a strong platform for rational engineering or inhibitor design.
Author style
Punchy: this is a crisp mechanistic paper with complementary structural, biochemical and genetic evidence. If your work touches on phage defence, nucleotide signalling or enzyme regulation, the data are immediately useful; the structures and mutants give you handles to test or repurpose the system.
Why should I read this?
Short version: clever molecular toggle. These bacteria use tiny thymidine-containing nucleotides to flip an anti-phage weapon off — and normal dTTP levels flip it back on. It’s a tidy on/off switch with structural proof, real functional outcomes in phage assays, and deposited structures you can dive into. If you want to know how nucleotide signals can both activate and inhibit immunity (and how phages might counter that), read it.