CBASS

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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Bacterial cGAS-like enzymes produce 2′,3′-cGAMP to activate an ion channel that restricts phage replication

Anonymous — Wed, 26 Jul 2023 16:44:22 +0000

Bacterial cGAS-like enzymes produce 2′,3′-cGAMP to activate an ion channel that restricts phage replication Anonymous (not verified) Wed, 07/26/2023 - 10:44

Uday Tak , Peace Holguin-Walth , Aaron Whiteley

BioRxiv (2023) PubMed PMID: 37546940; PubMed Central PMCID: PMC10402079.

Abstract

The mammalian innate immune system uses cyclic GMP–AMP synthase (cGAS) to synthesize the cyclic dinucleotide 2′,3′-cGAMP during antiviral and antitumor immune responses. 2′,3′-cGAMP is a nucleotide second messenger that initiates inflammatory signaling by binding to and activating the stimulator of interferon genes (STING) receptor. Bacteria also encode cGAS/DncV-like nucleotidyltransferases (CD-NTases) that produce nucleotide second messengers to initiate antiviral (antiphage) signaling. Bacterial CD-NTases produce a wide range of cyclic oligonucleotides but have not been documented to produce 2′,3′-cGAMP. Here we discovered bacterial CD-NTases that produce 2′,3′-cGAMP to restrict phage replication. Bacterial 2′,3′-cGAMP binds to CD-NTase associated protein 14 (Cap14), a transmembrane protein of unknown function. Using electrophysiology, we show that Cap14 is a chloride-selective ion channel that is activated by 2′,3′-cGAMP binding. Cap14 adopts a modular architecture, with an N-terminal transmembrane domain and a C-terminal nucleotide-binding SAVED domain. Domain-swapping experiments demonstrated the Cap14 transmembrane region could be substituted with a nuclease, thereby generating a biosensor that is selective for 2′,3′-cGAMP. This study reveals that 2′,3′-cGAMP signaling extends beyond metazoa to bacteria. Further, our findings suggest that transmembrane proteins of unknown function in bacterial immune pathways may broadly function as nucleotide-gated ion channels.

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Read Uday's Tweetorial [Twitter]

Citation

Tak U, Walth P, Whiteley AT. Bacterial cGAS-like enzymes produce 2',3'-cGAMP to activate an ion channel that restricts phage replication.bioRxiv. 2023 Jul 24;. doi: 10.1101/2023.07.24.550367. PubMed PMID: 37546940; PubMed Central PMCID: PMC10402079.

Tak U, Walth P, ➤Whiteley AT | BioRxiv 2023

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Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense

Anonymous — Tue, 01 Jun 2021 06:00:00 +0000

Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense Anonymous (not verified) Tue, 06/01/2021 - 00:00

Govande AA , Duncan-Lowey B , Eaglesham JB , Aaron Whiteley , Kranzusch PJ

Cell Reports (2021) PubMed PMID: 34077735

Abstract

cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are signaling proteins that initiate antiviral immunity in animal cells and cyclic-oligonucleotide-based anti-phage signaling system (CBASS) phage defense in bacteria. Upon phage recognition, bacterial CD-NTases catalyze synthesis of cyclic-oligonucleotide signals, which activate downstream effectors and execute cell death. How CD-NTases control nucleotide selection to specifically induce defense remains poorly defined. Here, we combine structural and nucleotide-analog interference-mapping approaches to identify molecular rules controlling CD-NTase specificity. Structures of the cyclic trinucleotide synthase Enterobacter cloacae CdnD reveal coordinating nucleotide interactions and a possible role for inverted nucleobase positioning during product synthesis. We demonstrate that correct nucleotide selection in the CD-NTase donor pocket results in the formation of a thermostable-protein-nucleotide complex, and we extend our analysis to establish specific patterns governing selectivity for each of the major bacterial CD-NTase clades A-H. Our results explain CD-NTase specificity and enable predictions of nucleotide second-messenger signals within diverse antiviral systems.

Citation

Govande AA, Duncan-Lowey B, Eaglesham JB, Whiteley AT, Kranzusch PJ. Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense. Cell Rep. 2021 Jun 1;35(9):109206. doi: 10.1016/j.celrep.2021.109206. PubMed PMID: 34077735.

Govande AA, Duncan-Lowey B, Eaglesham JB, ➤Whiteley AT, Kranzusch PJ. | Cell Reports 2021

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CBASS

The Panoptes system uses decoy cyclic nucleotides to defend against phage

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Bacterial cGAS-like enzymes produce 2′,3′-cGAMP to activate an ion channel that restricts phage replication

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Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense

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