{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T10:24:20Z","timestamp":1790159060467,"version":"4.1.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32430103"],"award-info":[{"award-number":["32430103"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["B2302024"],"award-info":[{"award-number":["B2302024"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFD1800503"],"award-info":[{"award-number":["2023YFD1800503"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC2604200"],"award-info":[{"award-number":["2022YFC2604200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jiangsu Key Laboratory of Zoonosis Major Independent Research","award":["RZZ202302"],"award-info":[{"award-number":["RZZ202302"]}]},{"name":"Jiangsu Funding Program for Excellent Postdoctoral Talent","award":["2024ZB284"],"award-info":[{"award-number":["2024ZB284"]}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2023B1515120016"],"award-info":[{"award-number":["2023B1515120016"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010877","name":"Shenzhen Science and Technology Innovation Commission","doi-asserted-by":"publisher","award":["JCYJ20220818100616034"],"award-info":[{"award-number":["JCYJ20220818100616034"]}],"id":[{"id":"10.13039\/501100010877","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007062","name":"Yangzhou University","doi-asserted-by":"publisher","award":["KYCX24_3850"],"award-info":[{"award-number":["KYCX24_3850"]}],"id":[{"id":"10.13039\/501100007062","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Priority Academic Program Development of Jiangsu Higher Education Institution","award":["32430103"],"award-info":[{"award-number":["32430103"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,6,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>In prokaryotes, the CRISPR\u2013Cas system provides immunity to invading mobile genetic elements, but its expression is commonly repressed in the absence of phage infection to prevent autoimmunity. How bacteria senses phage infection and activates CRISPR\u2013Cas system are poorly understood. Here, we demonstrate that an essential promoter Pcas, located within the cas1 gene, is the primary promoter driving expression of cas genes encoding the Cas10\u2013Csm interference complex in Staphylococcus aureus\u00a0type III-A CRISPR\u2013Cas system during phage infection. As a conserved promoter in Staphylococci type III-A CRISPR\u2013Cas system, the Pcas loses its ability to activate cas genes expression when mutated at the C186 site. Importantly, we find that the transcriptional regulator MgrA directly represses type III-A CRISPR\u2013Cas system by interacting with Pcas to prevent autoimmunity. Upon phage infection, MgrA senses oxidative stress and dissociates from the Pcas, alleviating the transcriptional repression and subsequently triggering a robust immunity against phages. Our work provides evidence for the requirement of Pcas within cas1 during type III-A CRISPR\u2013Cas interference stage, and reveals that MgrA-mediated regulation provides an effective mechanism for bacteria to balance avoiding autoimmunityand defending against phages.<\/jats:p>","DOI":"10.1093\/nar\/gkaf541","type":"journal-article","created":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T01:04:49Z","timestamp":1751159089000},"source":"Crossref","is-referenced-by-count":10,"title":["Oxidative stress elicited by phage infection induces <i>Staphylococcal<\/i> type III-A CRISPR\u2013Cas system"],"prefix":"10.1093","volume":"53","author":[{"given":"Yang","family":"Li","sequence":"first","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changbin","family":"Zhao","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingqian","family":"Cao","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinhai","family":"Chen","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyue","family":"Tang","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Public Health and Emergency Management, Southern University of Science and Technology ,\u00a0 Shenzhen 518055 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanne","family":"Ingmer","sequence":"additional","affiliation":[{"name":"University of Copenhagen Department of Veterinary and Animal Sciences, , Copenhagen 1870 ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinan","family":"Jiao","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0923-9758","authenticated-orcid":false,"given":"Qiuchun","family":"Li","sequence":"additional","affiliation":[{"name":"Jiangsu Key Lab of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University , Yangzhou 225100 ,","place":["China"]},{"name":"Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University , Yangzhou 225100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,23]]},"reference":[{"key":"2025062821044132500_B1","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1038\/s41586-019-1894-8","article-title":"The arms race between bacteria and their phage foes","volume":"577","author":"Hampton","year":"2020","journal-title":"Nature"},{"key":"2025062821044132500_B2","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1126\/science.1138140","article-title":"CRISPR provides acquired resistance against viruses in prokaryotes","volume":"315","author":"Barrangou","year":"2007","journal-title":"Science"},{"key":"2025062821044132500_B3","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1126\/science.1165771","article-title":"CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA","volume":"322","author":"Marraffini","year":"2008","journal-title":"Science"},{"key":"2025062821044132500_B4","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41579-019-0299-x","article-title":"Evolutionary classification of CRISPR\u2013Cas systems: a burst of class 2 and derived variants","volume":"18","author":"Makarova","year":"2020","journal-title":"Nat Rev Micro"},{"key":"2025062821044132500_B5","doi-asserted-by":"publisher","first-page":"eadi1910","DOI":"10.1126\/science.adi1910","article-title":"Uncovering the functional diversity of rare CRISPR\u2013Cas systems with deep terascale clustering","volume":"382","author":"Altae-Tran","year":"2023","journal-title":"Science"},{"key":"2025062821044132500_B6","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature15386","article-title":"CRISPR\u2013Cas immunity in prokaryotes","volume":"526","author":"Marraffini","year":"2015","journal-title":"Nature"},{"key":"2025062821044132500_B7","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/nature14237","article-title":"Integrase-mediated spacer acquisition during CRISPR\u2013Cas adaptive immunity","volume":"519","author":"Nu\u00f1ez","year":"2015","journal-title":"Nature"},{"key":"2025062821044132500_B8","doi-asserted-by":"publisher","first-page":"5569","DOI":"10.1093\/nar\/gks216","article-title":"Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli","volume":"40","author":"Yosef","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B9","doi-asserted-by":"publisher","first-page":"3489","DOI":"10.1101\/gad.1742908","article-title":"Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes","volume":"22","author":"Carte","year":"2008","journal-title":"Genes Dev"},{"key":"2025062821044132500_B10","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1126\/science.1159689","article-title":"Small CRISPR RNAs guide antiviral defense in prokaryotes","volume":"321","author":"Brouns","year":"2008","journal-title":"Science"},{"key":"2025062821044132500_B11","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nature09523","article-title":"The CRISPR\u2013Cas bacterial immune system cleaves bacteriophage and plasmid DNA","volume":"468","author":"Garneau","year":"2010","journal-title":"Nature"},{"key":"2025062821044132500_B12","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1038\/nature13637","article-title":"Conditional tolerance of temperate phages via transcription-dependent CRISPR\u2013Cas targeting","volume":"514","author":"Goldberg","year":"2014","journal-title":"Nature"},{"key":"2025062821044132500_B13","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1016\/j.cell.2015.04.027","article-title":"Co-transcriptional DNA and RNA cleavage during Type III CRISPR\u2013Cas immunity","volume":"161","author":"Samai","year":"2015","journal-title":"Cell"},{"key":"2025062821044132500_B14","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1111\/mmi.12152","article-title":"A novel interference mechanism by a type IIIB CRISPR\u2013Cmr module in Sulfolobus","volume":"87","author":"Deng","year":"2013","journal-title":"Mol Microbiol"},{"key":"2025062821044132500_B15","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1101\/gad.272153.115","article-title":"Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR\u2013Cas system","volume":"30","author":"Elmore","year":"2016","journal-title":"Genes Dev"},{"key":"2025062821044132500_B16","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1101\/gad.273722.115","article-title":"RNA-activated DNA cleavage by the Type III-B CRISPR\u2013Cas effector complex","volume":"30","author":"Estrella","year":"2016","journal-title":"Genes Dev"},{"key":"2025062821044132500_B17","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.molcel.2016.03.024","article-title":"Spatiotemporal control of Type III-A CRISPR\u2013Cas immunity: coupling DNA degradation with the target RNA recognition","volume":"62","author":"Kazlauskiene","year":"2016","journal-title":"Mol Cell"},{"key":"2025062821044132500_B18","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1126\/science.aao0100","article-title":"A cyclic oligonucleotide signaling pathway in type III CRISPR\u2013Cas systems","volume":"357","author":"Kazlauskiene","year":"2017","journal-title":"Science"},{"key":"2025062821044132500_B19","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature23467","article-title":"Type III CRISPR\u2013Cas systems produce cyclic oligoadenylate second messengers","volume":"548","author":"Niewoehner","year":"2017","journal-title":"Nature"},{"key":"2025062821044132500_B20","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1038\/s41564-018-0353-x","article-title":"Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR\u2013Cas immunity","volume":"4","author":"Rost\u00f8l","year":"2019","journal-title":"Nat Microbiol"},{"key":"2025062821044132500_B21","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nrmicro.2015.14","article-title":"CRISPR\u2013Cas adaptation: insights into the mechanism of action","volume":"14","author":"Amitai","year":"2016","journal-title":"Nat Rev Micro"},{"key":"2025062821044132500_B22","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1128\/JB.01130-13","article-title":"Genetic characterization of antiplasmid immunity through a Type III-A CRISPR\u2013Cas system","volume":"196","author":"Hatoum-Aslan","year":"2014","journal-title":"J Bacteriol"},{"key":"2025062821044132500_B23","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1016\/j.ijmm.2016.08.005","article-title":"Identification and functional study of type III-A CRISPR\u2013Cas systems in clinical isolates of Staphylococcus aureus","volume":"306","author":"Cao","year":"2016","journal-title":"Int J Med Microbiol"},{"key":"2025062821044132500_B24","doi-asserted-by":"publisher","first-page":"8913","DOI":"10.1093\/nar\/gkv882","article-title":"Interference activity of a minimal Type I CRISPR\u2013Cas system from Shewanella putrefaciens","volume":"43","author":"Dwarakanath","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B25","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.1038\/s41589-024-01659-5","article-title":"Cas1 mediates the interference stage in a phage-encoded CRISPR\u2013Cas system","volume":"20","author":"Zhang","year":"2024","journal-title":"Nat Chem Biol"},{"key":"2025062821044132500_B26","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1016\/j.cell.2020.12.017","article-title":"A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR\u2013Cas expression","volume":"184","author":"Workman","year":"2021","journal-title":"Cell"},{"key":"2025062821044132500_B27","doi-asserted-by":"publisher","first-page":"113849","DOI":"10.1016\/j.celrep.2024.113849","article-title":"Anti-CRISPR proteins trigger a burst of CRISPR\u2013Cas9 expression that enhances phage defense","volume":"43","author":"Workman","year":"2024","journal-title":"Cell Rep"},{"key":"2025062821044132500_B28","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1016\/j.molcel.2016.11.012","article-title":"Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR\u2013Cas systems","volume":"64","author":"Patterson","year":"2016","journal-title":"Mol Cell"},{"key":"2025062821044132500_B29","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1073\/pnas.1617415113","article-title":"Quorum sensing controls the Pseudomonas aeruginosa CRISPR\u2013Cas adaptive immune system","volume":"114","author":"H\u00f8yland-Kroghsbo","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025062821044132500_B30","doi-asserted-by":"publisher","DOI":"10.1101\/2023.01.17.524377","article-title":"Quorum sensing inhibits Type III-A CRISPR\u2013Cas system activity through repressing positive regulators SarA and ArcR in Staphylococcus aureus","author":"Li","year":"2023"},{"key":"2025062821044132500_B31","doi-asserted-by":"publisher","first-page":"6038","DOI":"10.1093\/nar\/gkv517","article-title":"Regulation of the Type I-F CRISPR\u2013Cas system by CRP-cAMP and GalM controls spacer acquisition and interference","volume":"43","author":"Patterson","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B32","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41564-020-0691-3","article-title":"Bacterial alginate regulators and phage homologs repress CRISPR\u2013Cas immunity","volume":"5","author":"Borges","year":"2020","journal-title":"Nat Microbiol"},{"key":"2025062821044132500_B33","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/s41564-020-00822-7","article-title":"The Rcs stress response inversely controls surface and CRISPR\u2013Cas adaptive immunity to discriminate plasmids and phages","volume":"6","author":"Smith","year":"2021","journal-title":"Nat Microbiol"},{"key":"2025062821044132500_B34","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1111\/j.1365-2958.2010.07482.x","article-title":"Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli","volume":"79","author":"Perez-Rodriguez","year":"2011","journal-title":"Mol Microbiol"},{"key":"2025062821044132500_B35","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.jmb.2009.10.057","article-title":"Transcription profile of Thermus thermophilus CRISPR systems after phage infection","volume":"395","author":"Agari","year":"2010","journal-title":"J Mol Biol"},{"key":"2025062821044132500_B36","doi-asserted-by":"crossref","first-page":"e38077","DOI":"10.1371\/journal.pone.0038077","article-title":"Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus","volume":"7","author":"Bruggemann","year":"2012","journal-title":"PLoS One"},{"key":"2025062821044132500_B37","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.biochi.2015.04.006","article-title":"Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR\u2013Cas system","volume":"118","author":"Fusco","year":"2015","journal-title":"Biochimie"},{"key":"2025062821044132500_B38","doi-asserted-by":"publisher","first-page":"e00277","DOI":"10.1128\/mBio.00277-11","article-title":"Transforming the untransformable: application of direct transformation to manipulate genetically Staphylococcus aureus and Staphylococcus epidermidis","volume":"3","author":"Monk","year":"2012","journal-title":"mBio"},{"key":"2025062821044132500_B39","doi-asserted-by":"publisher","first-page":"5763","DOI":"10.1128\/AEM.01385-16","article-title":"The presence of two receptor-binding proteins contributes to the wide host range of staphylococcal twort-like phages","volume":"82","author":"Takeuchi","year":"2016","journal-title":"Appl Environ Microb"},{"key":"2025062821044132500_B40","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.molcel.2013.08.020","article-title":"Structure of the CRISPR interference complex CSM reveals key similarities with cascade","volume":"52","author":"Rouillon","year":"2013","journal-title":"Mol Cell"},{"key":"2025062821044132500_B41","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.molcel.2014.09.027","article-title":"Programmable RNA shredding by the type III-A CRISPR\u2013Cas system of Streptococcus thermophilus","volume":"56","author":"Tamulaitis","year":"2014","journal-title":"Mol Cell"},{"key":"2025062821044132500_B42","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1016\/j.tim.2004.06.004","article-title":"Staphylococcus aureus: superbug, super genome?","volume":"12","author":"Lindsay","year":"2004","journal-title":"Trends Microbiol"},{"key":"2025062821044132500_B43","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/nchembio820","article-title":"An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus","volume":"2","author":"Chen","year":"2006","journal-title":"Nat Chem Biol"},{"key":"2025062821044132500_B44","doi-asserted-by":"publisher","first-page":"2181","DOI":"10.1073\/pnas.1425007112","article-title":"Generation of reactive oxygen species by lethal attacks from competing microbes","volume":"112","author":"Dong","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025062821044132500_B45","doi-asserted-by":"publisher","DOI":"10.1101\/2023.05.26.542521","article-title":"TPR domain assigns versatility of BcTir\/Tpr system against viral infection","author":"Liu","year":"2023"},{"key":"2025062821044132500_B46","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1128\/JB.183.2.468-475.2001","article-title":"In Staphylococcus aureus, Fur is an interactive regulator with PerR, contributes to virulence, and is necessary for oxidative stress resistance through positive regulation of catalase and iron homeostasis","volume":"183","author":"Horsburgh","year":"2001","journal-title":"J Bacteriol"},{"key":"2025062821044132500_B47","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1038\/nsmb.2820","article-title":"Cas1\u2013Cas2 complex formation mediates spacer acquisition during CRISPR\u2013Cas adaptive immunity","volume":"21","author":"Nunez","year":"2014","journal-title":"Nat Struct Mol Biol"},{"key":"2025062821044132500_B48","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1016\/j.cell.2017.11.032","article-title":"The biology of CRISPR\u2013Cas: backward and forward","volume":"172","author":"Hille","year":"2018","journal-title":"Cell"},{"key":"2025062821044132500_B49","doi-asserted-by":"publisher","first-page":"517","DOI":"10.4161\/rna.8.3.15190","article-title":"Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum","volume":"8","author":"Przybilski","year":"2011","journal-title":"RNA Biol"},{"key":"2025062821044132500_B50","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1111\/j.1365-2958.2010.07315.x","article-title":"H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO","volume":"77","author":"Westra","year":"2010","journal-title":"Mol Microbiol"},{"key":"2025062821044132500_B51","doi-asserted-by":"publisher","first-page":"657404","DOI":"10.3389\/fmicb.2021.657404","article-title":"The CRISPR\u2013Cas system is involved in OmpR genetic regulation for outer membrane protein synthesis in SalmonellaTyphi","volume":"12","author":"Medina-Aparicio","year":"2021","journal-title":"Front Microbiol"},{"key":"2025062821044132500_B52","doi-asserted-by":"publisher","first-page":"e00074","DOI":"10.1128\/mBio.00074-13","article-title":"The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae","volume":"4","author":"Gunderson","year":"2013","journal-title":"mBio"},{"key":"2025062821044132500_B53","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.meegid.2015.10.019","article-title":"The effect of Mycobacterium tuberculosis CRISPR-associated Cas2 (Rv2816c) on stress response genes expression, morphology and macrophage survival of Mycobacterium smegmatis","volume":"40","author":"Huang","year":"2016","journal-title":"Infect Genet Evol"},{"key":"2025062821044132500_B54","doi-asserted-by":"publisher","first-page":"e1002615","DOI":"10.1371\/journal.pgen.1002615","article-title":"A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2","volume":"8","author":"Cameron","year":"2012","journal-title":"PLoS Genet"},{"key":"2025062821044132500_B55","doi-asserted-by":"publisher","first-page":"20361","DOI":"10.1074\/jbc.M803225200","article-title":"A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats","volume":"283","author":"Beloglazova","year":"2008","journal-title":"J Biol Chem"},{"key":"2025062821044132500_B56","doi-asserted-by":"publisher","first-page":"35943","DOI":"10.1074\/jbc.M112.382598","article-title":"Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein","volume":"287","author":"Nam","year":"2012","journal-title":"J Biol Chem"},{"key":"2025062821044132500_B57","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.1128\/IAI.03102-14","article-title":"Nuclease activity of Legionella pneumophila Cas2 promotes intracellular infection of amoebal host cells","volume":"83","author":"Gunderson","year":"2015","journal-title":"Infect Immun"},{"key":"2025062821044132500_B58","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nrmicro787","article-title":"The regulation of bacterial transcription initiation","volume":"2","author":"Browning","year":"2004","journal-title":"Nat Rev Micro"},{"key":"2025062821044132500_B59","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1146\/annurev-micro-091014-104047","article-title":"Regulation of transcript elongation","volume":"69","author":"Belogurov","year":"2015","journal-title":"Annu Rev Microbiol"},{"key":"2025062821044132500_B60","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1016\/j.molcel.2016.08.038","article-title":"CRISPR\u2013Cas systems optimize their immune response by specifying the site of spacer integration","volume":"64","author":"McGinn","year":"2016","journal-title":"Mol Cell"},{"key":"2025062821044132500_B61","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1089\/crispr.2021.0046","article-title":"Functional characterization of Type III-A CRISPR\u2013Cas in a clinical human Methicillin-R Staphylococcus aureus strain","volume":"4","author":"Li","year":"2021","journal-title":"CRISPR J"},{"key":"2025062821044132500_B62","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nature08756","article-title":"The primary transcriptome of the major human pathogen Helicobacter pylori","volume":"464","author":"Sharma","year":"2010","journal-title":"Nature"},{"key":"2025062821044132500_B63","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1099\/mic.0.28714-0","article-title":"Multiple promoters control expression of the Yersinia enterocolitica phage-shock-protein A (pspA) operon","volume":"152","author":"Maxson","year":"2006","journal-title":"Microbiology"},{"key":"2025062821044132500_B64","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1186\/1471-2180-9-247","article-title":"Transcriptional analysis of the jamaicamide gene cluster from the marine cyanobacterium Lyngbya majuscula and identification of possible regulatory proteins","volume":"9","author":"Jones","year":"2009","journal-title":"BMC Microbiol"},{"key":"2025062821044132500_B65","doi-asserted-by":"publisher","first-page":"7181","DOI":"10.1128\/JB.00915-07","article-title":"Essential internal promoter in the spoIIIA locus of Bacillus subtilis","volume":"189","author":"Guillot","year":"2007","journal-title":"J Bacteriol"},{"key":"2025062821044132500_B66","first-page":"20151270","article-title":"Costs of CRISPR\u2013Cas-mediated resistance in Streptococcus thermophilus","volume":"282","author":"Vale","year":"2015","journal-title":"Proc Biol Sci"},{"key":"2025062821044132500_B67","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1111\/j.1365-2958.2010.07073.x","article-title":"Identification and characterization of E. coli CRISPR\u2013Cas promoters and their silencing by H-NS","volume":"75","author":"Pul","year":"2010","journal-title":"Mol Microbiol"},{"key":"2025062821044132500_B68","doi-asserted-by":"publisher","first-page":"9508","DOI":"10.1093\/nar\/gkab704","article-title":"The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR\u2013Cas immune systems","volume":"49","author":"Campa","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B69","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1098\/rspb.2015.1270","article-title":"CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU","volume":"52","author":"Smith","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B70","first-page":"1902","article-title":"CRISPR\u2013Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b","volume":"45","author":"He","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025062821044132500_B71","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1038\/ismej.2016.3","article-title":"High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection","volume":"10","author":"De","year":"2016","journal-title":"ISME J"},{"key":"2025062821044132500_B72","doi-asserted-by":"publisher","first-page":"249","DOI":"10.3109\/08830185.2012.755176","article-title":"Reactive oxygen species in the immune system","volume":"32","author":"Yang","year":"2013","journal-title":"Int Rev Immunol"},{"key":"2025062821044132500_B73","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.chom.2016.07.009","article-title":"Bacterial stress responses during host infection","volume":"20","author":"Fang","year":"2016","journal-title":"Cell Host Microbe"},{"key":"2025062821044132500_B74","doi-asserted-by":"publisher","first-page":"114485","DOI":"10.1016\/j.celrep.2024.114485","article-title":"A type III-Dv CRISPR\u2013Cas system is controlled by the transcription factor RpaB and interacts with the DEAD-box RNA helicase CrhR","volume":"43","author":"Bilger","year":"2024","journal-title":"Cell Rep"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/12\/gkaf541\/63551192\/gkaf541.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/12\/gkaf541\/63551192\/gkaf541.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T01:04:52Z","timestamp":1751159092000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf541\/8171866"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,20]]},"references-count":74,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,6,20]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf541","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7,8]]},"published":{"date-parts":[[2025,6,20]]},"article-number":"gkaf541"}}