Spotlight Publications

The Panoptes system uses decoy cyclic nucleotides to defend against phage

Aaron Whiteley — Wed, 01 Oct 2025 15:00:00 +0000

The Panoptes system uses decoy cyclic nucleotides to defend against phage Aaron Whiteley Wed, 10/01/2025 - 09:00

Ashley Sullivan , Ali Nabhani , Daniel S Izrailevsky , Kate Schinkel , Charlotte Hoffman , Laurel Robbins , Toni Nagy , Melissa Duncan , Hannah Ledvina , Annette Erbse , Emily Kibby , Uday Tak , David Dinh , Eirene Ednacot , Christy Nguyen , A Maxwell Burroughs , L Aravind , Aaron Whiteley , Benjamin Morehouse

Nature (2025). PubMed PMID: 41034579

Abstract

Bacteria combat phage infection using antiphage systems and many systems generate nucleotide-derived second messengers upon infection that activate effector proteins to mediate immunity. Phages respond with counter-defences that deplete these second messengers, leading to an escalating arms race with the host. Here we outline an antiphage system we call Panoptes that indirectly detects phage infection when phage proteins antagonize the nucleotide-derived second-messenger pool. Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. Crystal structures show that OptS is a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in type III CRISPR systems (Cas10). OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2',3'-cyclic diadenosine monophosphate (2',3'-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. These findings were unexpected because Acb2 is a nucleotide 'sponge' that antagonizes second-messenger signalling. Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. These data demonstrate a sophisticated immune strategy that bacteria use to guard their second-messenger pool and turn immune evasion against the virus.

News and Commentaries

Bacteria use a decoy defence molecule to set a trap for viruses [Nature]
Read Ashley's Thread [BlueSky]

Citation

Sullivan AE, Nabhani A, Izrailevsky DS, Schinkel K, Hoffman CRK, Robbins LK, Nagy TA, Duncan ML, Ledvina HE, Erbse AH, Kibby EM, Tak U, Dinh DM, Ednacot EMQ, Nguyen CM, Burroughs AM, Aravind L, Whiteley AT, Morehouse BR. The Panoptes system uses decoy cyclic nucleotides to defend against phage. Nature. 2025 Oct 1. doi: 10.1038/s41586-025-09557-z. Epub ahead of print. PMID: 41034579.

Illustration depicting a bacterium under assault by phage. The bacterium “sees” phage immune evasion proteins and protects itself using a newly described antiphage system called Panoptes, named for the many-eyed mythical giant Argus Panoptes. Credit: Clair Huffine Insight Illustrations LLC

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Identifying phage proteins that activate the bacterial innate immune system

Aaron Whiteley — Wed, 02 Jul 2025 15:00:00 +0000

Identifying phage proteins that activate the bacterial innate immune system Aaron Whiteley Wed, 07/02/2025 - 09:00

Toni Nagy , Gina Gersabeck , Amy Conte , Aaron Whiteley

BioRxiv (2025). PubMed PMID: 40631175; PubMed Central PMCID: PMC12236752

Abstract

Bacteria have evolved sophisticated antiphage systems that halt phage replication upon detecting specific phage triggers. Identifying phage triggers is crucial to our understanding of immune signaling, however, they are challenging to predict. Here we used an expansive plasmid library that expressed 400 phage protein-coding genes from 6 different phages to identify novel triggers of known and undiscovered antiphage systems. We transformed our library into 72 diverse strains of E. coli . Each strain natively harbors a different suite of antiphage systems whose activation typically inhibits growth. By tracking plasmids that were selectively depleted, we identified over 100 candidate phage trigger- E. coli pairs. Two phage trigger proteins were investigated in detail, revealing a novel antiphage system that detects multiple phage tail fiber proteins and identifying major capsid protein as the activating ligand of the antiphage system Avs8. These experiments provide a unique dataset for continued definition of the molecular details of the bacterial immune system.

News and Commentaries

Read Toni's Thread [BlueSky]

Citation

Nagy TA, Gersabeck GW, Conte AN, Whiteley AT. Identifying phage proteins that activate the bacterial innate immune system. bioRxiv [Preprint]. 2025 Jul 2:2025.07.02.662641. doi: 10.1101/2025.07.02.662641. PMID: 40631175; PMCID: PMC12236752.

Nagy TA, Gersabeck GW, Conte AN, ➤Whiteley AT | BioRxiv 2025

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Functional amyloid proteins confer defence against predatory bacteria

Aaron Whiteley — Wed, 02 Jul 2025 15:00:00 +0000

Functional amyloid proteins confer defence against predatory bacteria Aaron Whiteley Wed, 07/02/2025 - 09:00

Hannah Ledvina , Ryan Sayegh , Ricardo Carale , Burroughs AM , Alexa Macklin , Azadeh AL , Layla Borja , Aravind L , Aaron Whiteley

Nature (2025). PubMed PMID: 40604283; PubMed Central PMCID: PMC12419547

Abstract

Bdellovibrio bacteriovorus is a predatory bacterium that non-selectively preys on Gram-negative bacteria by invading the prey-cell periplasm, leaching host nutrients and ultimately lysing the infected cell to exit and find a new host. The predatory life cycle of B. bacteriovorus is, in many ways, comparable to a bacteriophage. However, unlike phage defence, defence against B. bacteriovorus has not been widely investigated. Here we screened a collection of diverse Escherichia coli strains for resistance to B. bacteriovorus and identified that roughly one-third of strains robustly defended against predation by producing curli fibres. Curli fibres are oligomers of the functional amyloid protein CsgA, which is exceptionally durable3. Using genetics and microscopy, we demonstrate that curli fibres provide a barrier that protects susceptible cells independent of genes required for biofilm formation. This barrier further protected E. coli against attack by the predatory bacterium Myxococcus xanthus and select phages. Bioinformatic analysis of bacterial amyloids showed these systems are diverse and widespread in diderm bacteria (those with both inner and outer membranes). One of these, an evolutionarily distinct amyloid encoded by Pseudomonas aeruginosa, also protected against B. bacteriovorus. This work establishes that functional amyloids defend bacteria against a wide range of threats.

News and Commentaries

When predators meet the matrix: Natural resistance via amyloid fibers [Cell Host & Microbe]
In microbial wars, bacteria suit up with a protein linked to Alzheimer’s [CU Boulder Today]
Read Hannah's Thread [BlueSky]

Citation

Ledvina HE, Sayegh R, Carale RO, Burroughs AM, Macklin AR, Azadeh AL, Borja Najera LD, Aravind L, Whiteley AT. Functional amyloid proteins confer defence against predatory bacteria. Nature. 2025 Aug;644(8075):197-204. doi: 10.1038/s41586-025-09204-7. Epub 2025 Jul 2. PubMed PMID: 40604283; PubMed Central PMCID: PMC12419547.

Ledvina HE, Sayegh R, Carale RO, Burroughs AM, Macklin AR, Azadeh AL, Borja Najera LD, Aravind L, ➤Whiteley AT | Nature 2025

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The Panoptes system uses decoy cyclic nucleotides to defend against phage

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Identifying phage proteins that activate the bacterial innate immune system

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Functional amyloid proteins confer defence against predatory bacteria

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