CBASS /lab/aaron-whiteley/ en A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins /lab/aaron-whiteley/2025/03/28/minimal-crispr-polymerase-produces-decoy-cyclic-nucleotides-detect-phage-anti-defense <span>A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins</span> <span><span>Aaron Whiteley</span></span> <span><time datetime="2025-03-28T23:00:00-06:00" title="Friday, March 28, 2025 - 23:00">Fri, 03/28/2025 - 23:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/focal_image_wide/public/2025-04/mCpol%20Thumbnail_v1.png?h=28a486fc&amp;itok=I5-WhXIM" width="1200" height="800" alt="Panoptes System Thumbnail"> </div> </div> <div role="contentinfo" class="container ucb-article-categories" itemprop="about"> <span class="visually-hidden">Categories:</span> <div class="ucb-article-category-icon" aria-hidden="true"> <i class="fa-solid fa-folder-open"></i> </div> <a href="/lab/aaron-whiteley/taxonomy/term/349"> Research Articles </a> <a href="/lab/aaron-whiteley/taxonomy/term/153"> Spotlight Publications </a> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/lab/aaron-whiteley/taxonomy/term/360" hreflang="en">Acb2</a> <a href="/lab/aaron-whiteley/taxonomy/term/285" hreflang="en">CBASS</a> <a href="/lab/aaron-whiteley/taxonomy/term/362" hreflang="en">S-2TMβ</a> <a href="/lab/aaron-whiteley/taxonomy/term/361" hreflang="en">cyclic oligonucleotide based antiphage signaling system</a> </div> <a href="/lab/aaron-whiteley/ashley-sullivan">Ashley Sullivan</a> <span>,&nbsp;</span> <span>Nabhani A</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/kate-schinkel">Kate Schinkel</a> <span>,&nbsp;</span> <span>Dinh DM</span> <span>,&nbsp;</span> <span>Duncan ML</span> <span>,&nbsp;</span> <span>Ednacot EMQ</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/charlotte-hoffman">Charlotte Hoffman</a> <span>,&nbsp;</span> <span>Izrailevsky DS</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/emily-kibby">Emily Kibby</a> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/toni-nagy">Toni Nagy</a> <span>,&nbsp;</span> <span>Nguyen CM</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/uday-tak">Uday Tak</a> <span>,&nbsp;</span> <span>Burroughs AM</span> <span>,&nbsp;</span> <span>Aravind L</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/aaron-whiteley">Aaron Whiteley</a> <span>,&nbsp;</span> <span>Morehouse BR</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default 3"> <div class="ucb-article-row-subrow row"> <div class="ucb-article-text col-lg d-flex align-items-center" itemprop="articleBody"> <div><div><div><p><em>BioRxiv</em> (2025). <span>2025.03.28.646047; doi: https://doi.org/10.1101/2025.03.28.646047</span></p><h2>Abstract</h2><p><span>Bacteria use antiphage systems to combat phages, their ubiquitous competitors, and evolve new defenses through repeated reshuffling of basic functional units into novel reformulations. A common theme is generating a nucleotide-derived second messenger in response to phage that activates an effector protein to halt virion production. Phages respond with counter-defenses that deplete these second messengers, leading to an escalating arms race with the host. Here we discover a novel antiphage system we call Panoptes that detects phage infection by surveying the cytosol for phage proteins that antagonize the nucleotide-derived second messenger pool. Panoptes is a two-gene operon, </span><em>optSE</em><span>. OptS is predicted to synthesize a second messenger using a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in Type III CRISPR systems (Cas10) that is distantly related to GGDEF and Thg1 tRNA repair polymerase domains. OptE is predicted to be a transmembrane effector protein that binds cyclic nucleotides. </span><em>optSE</em><span> potently restricted phage replication but mutant phages that had loss-of-function mutations in anti-CBASS protein 2 (Acb2) escaped defense. These findings were unexpected because Acb2 is a nucleotide “sponge” that antagonizes second messenger signaling. Using genetic and biochemical assays, we found that Acb2 bound the OptS-synthesized nucleotide, 2′,3′-cyclic adenosine monophosphate (2′,3′-c-di-AMP); however, 2′,3′-c-di-AMP was synthesized constitutively by OptS and inhibited OptE. Nucleotide depletion by Acb2 released OptE toxicity thereby initiating abortive infection to halt phage replication. These data demonstrate a sophisticated immune strategy that hosts use to guard their second messenger pool and turn immune evasion against the virus.</span></p><h2>News and Commentaries</h2><ul><li><a href="https://bsky.app/profile/aesully98.bsky.social/post/3llpea75gzk2y" rel="nofollow">Read Ashley's Thread</a> [BlueSky]</li></ul><h2>Links</h2><ul><li>DOI: <a href="https://doi.org/10.1101/2025.03.28.646047" rel="nofollow"><span>https://doi.org/10.1101/2025.03.28.646047</span></a></li><li>Journal Link:</li><li><em>BioRxiv</em> Preprint, March 28 2025,&nbsp;<a href="https://doi.org/10.1101/2025.03.28.646047" rel="nofollow"><span>https://doi.org/10.1101/2025.03.28.646047</span></a><span>&nbsp;</span></li></ul><h2>Citation</h2><div>Sullivan AE, Nabhani A, Schinkel K, Dinh DM, Duncan ML, Ednacot EMQ, Hoffman CRK, Izrailevsky DS, Kibby EM, Nagy TA, Nguyen CM, Tak U, Burroughs AM, Aravind L, Whiteley AT, Morehouse BR. A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins. 2025 Mar 28; <a href="https://doi.org/10.1101/2025.03.28.646047" rel="nofollow"><span>https://doi.org/10.1101/2025.03.28.646047</span></a></div></div></div></div> </div> <div class="ucb-article-content-media ucb-article-content-media-right col-lg"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/large_image_style/public/2025-04/mCpol%20Thumbnail_v1.png?itok=jmUq-GLA" width="1500" height="1500" alt="Panoptes System Thumbnail"> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div>Sullivan AE, Nabhani A, Schinkel K, Dinh DM, Duncan ML, Ednacot EMQ, Hoffman CRK, Izrailevsky DS, Kibby EM, Nagy TA, Nguyen CM, Tak U, Burroughs AM, Aravind L, ➤Whiteley AT†, Morehouse BR† (†co-cor. author) | BioRxiv 2025</div> <h2> <div class="paragraph paragraph--type--ucb-related-articles-block paragraph--view-mode--default"> <div>Off</div> </div> </h2> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Sat, 29 Mar 2025 05:00:00 +0000 Aaron Whiteley 202 at /lab/aaron-whiteley Bacterial cGAS-like enzymes produce 2′,3′-cGAMP to activate an ion channel that restricts phage replication /lab/aaron-whiteley/2023/07/26/bacterial-cgas-enzymes-produce-23-cgamp-activate-ion-channel-restricts-phage-replication <span>Bacterial cGAS-like enzymes produce 2′,3′-cGAMP to activate an ion channel that restricts phage replication</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2023-07-26T10:44:22-06:00" title="Wednesday, July 26, 2023 - 10:44">Wed, 07/26/2023 - 10:44</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/focal_image_wide/public/article-thumbnail/bacteria_synthesize_23-cgamp.png?h=817377e6&amp;itok=q9HcIB94" width="1200" height="800" alt="Bacteria Synthesize 2',3'-cGAMP"> </div> </div> <div role="contentinfo" class="container ucb-article-categories" itemprop="about"> <span class="visually-hidden">Categories:</span> <div class="ucb-article-category-icon" aria-hidden="true"> <i class="fa-solid fa-folder-open"></i> </div> <a href="/lab/aaron-whiteley/taxonomy/term/349"> Research Articles </a> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/lab/aaron-whiteley/taxonomy/term/326" hreflang="en">2′3′-cGAMP</a> <a href="/lab/aaron-whiteley/taxonomy/term/285" hreflang="en">CBASS</a> <a href="/lab/aaron-whiteley/taxonomy/term/320" hreflang="en">Cap14</a> <a href="/lab/aaron-whiteley/taxonomy/term/217" hreflang="en">SAVED</a> <a href="/lab/aaron-whiteley/taxonomy/term/323" hreflang="en">Saf-2TM</a> <a href="/lab/aaron-whiteley/taxonomy/term/318" hreflang="en">antiphage signaling</a> <a href="/lab/aaron-whiteley/taxonomy/term/322" hreflang="en">biosensor</a> <a href="/lab/aaron-whiteley/taxonomy/term/163" hreflang="en">cGAS</a> <a href="/lab/aaron-whiteley/taxonomy/term/321" hreflang="en">ion channel</a> <a href="/lab/aaron-whiteley/taxonomy/term/324" hreflang="en">ligand-gated</a> <a href="/lab/aaron-whiteley/taxonomy/term/319" hreflang="en">phage</a> </div> <a href="/lab/aaron-whiteley/uday-tak">Uday Tak</a> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/peace-holguin-walth">Peace Holguin-Walth</a> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/aaron-whiteley">Aaron Whiteley</a> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default 3"> <div class="ucb-article-row-subrow row"> <div class="ucb-article-text col-lg d-flex align-items-center" itemprop="articleBody"> <div><p><em>BioRxiv</em> (2023) <span>PubMed PMID: 37546940; PubMed Central PMCID: PMC10402079.</span></p><h2>Abstract</h2><p>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.</p><h2>News and Commentaries</h2><ul><li><a href="https://twitter.com/snowkaryote/status/1683882461128953856?s=20" rel="nofollow">Read Uday's Tweetorial </a>[Twitter]</li></ul><h2>Links&nbsp;</h2><ul><li>DOI:&nbsp;<a href="https://doi.org/10.1101/2023.07.24.550367" rel="nofollow">https://doi.org/10.1101/2023.07.24.550367</a></li><li>Journal Link:&nbsp;</li><li><em>BioRxiv</em> Preprint, July 24 2023, <a href="https://doi.org/10.1101/2023.07.24.550367" rel="nofollow">https://doi.org/10.1101/2023.07.24.550367</a></li></ul><h2>Citation</h2><p><span>Tak U, Walth P, Whiteley AT. </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/37546940/" rel="nofollow">Bacterial cGAS-like enzymes produce 2',3'-cGAMP to activate an ion channel that restricts phage replication.</a><span>bioRxiv. 2023 Jul 24;. doi: 10.1101/2023.07.24.550367. PubMed PMID: 37546940; PubMed Central PMCID: PMC10402079.</span></p></div> </div> <div class="ucb-article-content-media ucb-article-content-media-right col-lg"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/large_image_style/public/article-image/website_biorxivcap14_resize.jpg?itok=dBydSPPI" width="1500" height="1003" alt="Bacteria Synthesize 2',3'-cGAMP"> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div>Tak U, Walth P, ➤Whiteley AT | BioRxiv 2023</div> <h2> <div class="paragraph paragraph--type--ucb-related-articles-block paragraph--view-mode--default"> <div>Off</div> </div> </h2> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Wed, 26 Jul 2023 16:44:22 +0000 Anonymous 175 at /lab/aaron-whiteley Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense /lab/aaron-whiteley/2021/06/01/molecular-basis-cd-ntase-nucleotide-selection-cbass-anti-phage-defense <span>Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense</span> <span><span>Anonymous (not verified)</span></span> <span><time datetime="2021-06-01T00:00:00-06:00" title="Tuesday, June 1, 2021 - 00:00">Tue, 06/01/2021 - 00:00</time> </span> <div> <div class="imageMediaStyle focal_image_wide"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/focal_image_wide/public/article-thumbnail/fx1_lrg_1.jpg?h=b1b266f7&amp;itok=P8q6QrWj" width="1200" height="800" alt="Graphical Abstract"> </div> </div> <div role="contentinfo" class="container ucb-article-tags" itemprop="keywords"> <span class="visually-hidden">Tags:</span> <div class="ucb-article-tag-icon" aria-hidden="true"> <i class="fa-solid fa-tags"></i> </div> <a href="/lab/aaron-whiteley/taxonomy/term/285" hreflang="en">CBASS</a> <a href="/lab/aaron-whiteley/taxonomy/term/286" hreflang="en">anti-phage</a> <a href="/lab/aaron-whiteley/taxonomy/term/219" hreflang="en">nucleotide second messenger</a> </div> <span>Govande AA</span> <span>,&nbsp;</span> <span>Duncan-Lowey B</span> <span>,&nbsp;</span> <span>Eaglesham JB</span> <span>,&nbsp;</span> <a href="/lab/aaron-whiteley/aaron-whiteley">Aaron Whiteley</a> <span>,&nbsp;</span> <span>Kranzusch PJ</span> <div class="ucb-article-content ucb-striped-content"> <div class="container"> <div class="paragraph paragraph--type--article-content paragraph--view-mode--default 3"> <div class="ucb-article-row-subrow row"> <div class="ucb-article-text col-lg d-flex align-items-center" itemprop="articleBody"> <div><p><em>Cell Reports</em> (2021) <span>PubMed PMID: </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/34077735/" rel="nofollow"><span>34077735</span></a></p><h2>Abstract</h2><p>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.</p><h2>Links&nbsp;</h2><ul><li>DOI:&nbsp;<a href="https://doi.org/10.1016/j.celrep.2021.109206" rel="nofollow">10.1016/j.celrep.2021.109206</a></li><li>Journal Link: <a href="https://www.sciencedirect.com/science/article/pii/S2211124721005556" rel="nofollow">https://www.sciencedirect.com/science/article/pii/S2211124721005556</a></li></ul><h2>Citation</h2><p><span>Govande AA, Duncan-Lowey B, Eaglesham JB, Whiteley AT, Kranzusch PJ. </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/34077735/" rel="nofollow">Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense. </a><span>Cell Rep. 2021 Jun 1;35(9):109206. doi: 10.1016/j.celrep.2021.109206. PubMed PMID: 34077735.</span></p></div> </div> <div class="ucb-article-content-media ucb-article-content-media-right col-lg"> <div> <div class="paragraph paragraph--type--media paragraph--view-mode--default"> <div> <div class="imageMediaStyle large_image_style"> <img loading="lazy" src="/lab/aaron-whiteley/sites/default/files/styles/large_image_style/public/article-image/fx1_lrg_0.jpg?itok=2NQHCrbN" width="1500" height="1500" alt="Graphical Abstract"> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div>Govande AA, Duncan-Lowey B, Eaglesham JB, ➤Whiteley AT, Kranzusch PJ. | Cell Reports 2021</div> <h2> <div class="paragraph paragraph--type--ucb-related-articles-block paragraph--view-mode--default"> <div>Off</div> </div> </h2> <div>Traditional</div> <div>0</div> <div>On</div> <div>White</div> Tue, 01 Jun 2021 06:00:00 +0000 Anonymous 151 at /lab/aaron-whiteley