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For: Makarova KS, Anantharaman V, Grishin NV, Koonin EV, Aravind L. CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Front Genet 2014;5:102. [PMID: 24817877 PMCID: PMC4012209 DOI: 10.3389/fgene.2014.00102] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/08/2014] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Baca CF, Majumder P, Hickling JH, Ye L, Teplova M, Brady SF, Patel DJ, Marraffini LA. The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity. Cell 2024;187:7183-7195.e24. [PMID: 39471810 PMCID: PMC11645235 DOI: 10.1016/j.cell.2024.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 09/06/2024] [Accepted: 10/02/2024] [Indexed: 11/01/2024]
2
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y. Antiviral signaling of a type III CRISPR-associated deaminase. Science 2024:eadr0393. [PMID: 39666823 DOI: 10.1126/science.adr0393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 12/01/2024] [Indexed: 12/14/2024]
3
Blankenchip CL, Corbett KD. Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression. Nucleic Acids Res 2024;52:13723-13732. [PMID: 39588753 DOI: 10.1093/nar/gkae1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 10/04/2024] [Accepted: 10/26/2024] [Indexed: 11/27/2024]  Open
4
Johnson SR, Weigele PR, Fomenkov A, Ge A, Vincze A, Eaglesham JB, Roberts RJ, Sun Z. Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems. Nucleic Acids Res 2024:gkae1175. [PMID: 39657740 DOI: 10.1093/nar/gkae1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 11/07/2024] [Accepted: 11/15/2024] [Indexed: 12/12/2024]  Open
5
Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and activation mechanism of the bacterial PARIS defence system. Nature 2024;634:432-439. [PMID: 39112702 PMCID: PMC11479591 DOI: 10.1038/s41586-024-07772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/02/2024] [Indexed: 08/17/2024]
6
Binder S, Schneberger N, Schmitz M, Engeser M, Geyer M, Rouillon C, Hagelueken G. The SAVED domain of the type III CRISPR protease CalpL is a ring nuclease. Nucleic Acids Res 2024;52:10520-10532. [PMID: 39166476 PMCID: PMC11417357 DOI: 10.1093/nar/gkae676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/18/2024] [Accepted: 07/27/2024] [Indexed: 08/23/2024]  Open
7
Bilger R, Migur A, Wulf A, Steglich C, Urlaub H, Hess WR. A type III-Dv CRISPR-Cas system is controlled by the transcription factor RpaB and interacts with the DEAD-box RNA helicase CrhR. Cell Rep 2024;43:114485. [PMID: 38996066 DOI: 10.1016/j.celrep.2024.114485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/26/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]  Open
8
Hoikkala V, Graham S, White MF. Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families. Nucleic Acids Res 2024;52:7129-7141. [PMID: 38808661 PMCID: PMC11229360 DOI: 10.1093/nar/gkae462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]  Open
9
Bosi E, Taviani E, Avesani A, Doni L, Auguste M, Oliveri C, Leonessi M, Martinez-Urtaza J, Vetriani C, Vezzulli L. Pan-Genome Provides Insights into Vibrio Evolution and Adaptation to Deep-Sea Hydrothermal Vents. Genome Biol Evol 2024;16:evae131. [PMID: 39007295 PMCID: PMC11247349 DOI: 10.1093/gbe/evae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2024] [Indexed: 07/16/2024]  Open
10
Fuentenebro Navas D, Steens JA, de Lannoy C, Noordijk B, Pfeffer M, de Ridder D, H.J. Staals R, Schmid S. Nanopores Reveal the Stoichiometry of Single Oligoadenylates Produced by Type III CRISPR-Cas. ACS NANO 2024;18:16505-16515. [PMID: 38875527 PMCID: PMC11223493 DOI: 10.1021/acsnano.3c11769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
11
Yang H, Patel DJ. Structures, mechanisms and applications of RNA-centric CRISPR-Cas13. Nat Chem Biol 2024;20:673-688. [PMID: 38702571 PMCID: PMC11375968 DOI: 10.1038/s41589-024-01593-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
12
Bell RT, Sahakyan H, Makarova KS, Wolf YI, Koonin EV. CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA. eLife 2024;13:RP94800. [PMID: 38739430 PMCID: PMC11090510 DOI: 10.7554/elife.94800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]  Open
13
Kretz J, Börner J, Friedrich T, McIntosh M, Procida-Kowalski T, Gerken F, Wilhelm J, Klug G. Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus. Front Microbiol 2024;15:1384543. [PMID: 38741736 PMCID: PMC11089165 DOI: 10.3389/fmicb.2024.1384543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]  Open
14
Beavogui A, Lacroix A, Wiart N, Poulain J, Delmont TO, Paoli L, Wincker P, Oliveira PH. The defensome of complex bacterial communities. Nat Commun 2024;15:2146. [PMID: 38459056 PMCID: PMC10924106 DOI: 10.1038/s41467-024-46489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024]  Open
15
Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K. Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res 2024;52:1435-1449. [PMID: 38142455 PMCID: PMC10853764 DOI: 10.1093/nar/gkad1198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/26/2023]  Open
16
Steens JA, Bravo JP, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen SH, Andres AS, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJ, van der Oost J, Taylor DW, Staals RH. Type III-B CRISPR-Cas cascade of proteolytic cleavages. Science 2024;383:512-519. [PMID: 38301007 PMCID: PMC11220425 DOI: 10.1126/science.adk0378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
17
Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and infection-sensing mechanism of the bacterial PARIS defense system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573835. [PMID: 38260510 PMCID: PMC10802264 DOI: 10.1101/2024.01.02.573835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
18
Keller LML, Flattich K, Weber-Ban E. Novel WYL domain-containing transcriptional activator acts in response to genotoxic stress in rapidly growing mycobacteria. Commun Biol 2023;6:1222. [PMID: 38042942 PMCID: PMC10693628 DOI: 10.1038/s42003-023-05592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]  Open
19
Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023;51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]  Open
20
McQuarrie S, Athukoralage JS, McMahon SA, Graham S, Ackermann K, Bode BE, White MF, Gloster TM. Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open. Nucleic Acids Res 2023;51:10590-10605. [PMID: 37747760 DOI: 10.1093/nar/gkad739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]  Open
21
McBride TM, Cameron SC, Fineran PC, Fagerlund RD. The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochem J 2023;480:471-488. [PMID: 37052300 PMCID: PMC10212523 DOI: 10.1042/bcj20220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
22
Keller LM, Weber-Ban E. An emerging class of nucleic acid-sensing regulators in bacteria: WYL domain-containing proteins. Curr Opin Microbiol 2023;74:102296. [PMID: 37027901 DOI: 10.1016/j.mib.2023.102296] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 04/09/2023]
23
Scrascia M, Roberto R, D'Addabbo P, Ahmed Y, Porcelli F, Oliva M, Calia C, Marzella A, Pazzani C. Bioinformatic survey of CRISPR loci across 15 Serratia species. Microbiologyopen 2023;12:e1339. [PMID: 37186230 PMCID: PMC9981886 DOI: 10.1002/mbo3.1339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/02/2022] [Indexed: 03/06/2023]  Open
24
Structural Studies of Pif1 Helicases from Thermophilic Bacteria. Microorganisms 2023;11:microorganisms11020479. [PMID: 36838444 PMCID: PMC9964779 DOI: 10.3390/microorganisms11020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023]  Open
25
Tesson F, Bernheim A. Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system? Curr Opin Microbiol 2023;71:102238. [PMID: 36423502 DOI: 10.1016/j.mib.2022.102238] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022]
26
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G. Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 2023;614:168-174. [PMID: 36423657 DOI: 10.1038/s41586-022-05571-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
27
Kurasz JE, Crawford MC, Porwollik S, Gregory O, Tadlock KR, Balding EC, Weinert EE, McClelland M, Karls AC. Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium. J Bacteriol 2023;205:e0026222. [PMID: 36622230 PMCID: PMC9879122 DOI: 10.1128/jb.00262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023]  Open
28
Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA. Nature 2023;613:588-594. [PMID: 36599979 PMCID: PMC9811890 DOI: 10.1038/s41586-022-05559-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 01/05/2023]
29
RNA-targeting CRISPR-Cas systems. Nat Rev Microbiol 2023;21:21-34. [PMID: 36171275 DOI: 10.1038/s41579-022-00793-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2022] [Indexed: 12/15/2022]
30
Wang J, Wei J, Li H, Li Y. High-efficiency genome editing of an extreme thermophile Thermus thermophilus using endogenous type I and type III CRISPR-Cas systems. MLIFE 2022;1:412-427. [PMID: 38818488 PMCID: PMC10989782 DOI: 10.1002/mlf2.12045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 06/01/2024]
31
Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Mol Cell 2022;82:4471-4486.e9. [PMID: 36395770 DOI: 10.1016/j.molcel.2022.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/13/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
32
Molina R, Garcia-Martin R, López-Méndez B, Jensen ALG, Ciges-Tomas JR, Marchena-Hurtado J, Stella S, Montoya G. Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases. Nucleic Acids Res 2022;50:11199-11213. [PMID: 36271789 PMCID: PMC9638899 DOI: 10.1093/nar/gkac923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022]  Open
33
Athukoralage JS, White MF. Cyclic Nucleotide Signaling in Phage Defense and Counter-Defense. Annu Rev Virol 2022;9:451-468. [PMID: 35567297 DOI: 10.1146/annurev-virology-100120-010228] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
34
Iyer LM, Burroughs AM, Anantharaman V, Aravind L. Apprehending the NAD+-ADPr-Dependent Systems in the Virus World. Viruses 2022;14:1977. [PMID: 36146784 PMCID: PMC9503650 DOI: 10.3390/v14091977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022]  Open
35
Kushwaha SK, Narasimhan LP, Chithananthan C, Marathe SA. Clustered regularly interspaced short palindromic repeats-Cas system: diversity and regulation in Enterobacteriaceae. Future Microbiol 2022;17:1249-1267. [PMID: 36006039 DOI: 10.2217/fmb-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
36
Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res 2022;50:6084-6101. [PMID: 35648479 PMCID: PMC9226505 DOI: 10.1093/nar/gkac467] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022]  Open
37
Aravind L, Iyer LM, Burroughs AM. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Annu Rev Biomed Data Sci 2022;5:367-391. [PMID: 35609893 DOI: 10.1146/annurev-biodatasci-122220-101119] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
38
Blankenchip CL, Nguyen JV, Lau RK, Ye Q, Gu Y, Corbett KD. Control of bacterial immune signaling by a WYL domain transcription factor. Nucleic Acids Res 2022;50:5239-5250. [PMID: 35536256 PMCID: PMC9122588 DOI: 10.1093/nar/gkac343] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]  Open
39
Luyten Y, Hausman DE, Young JC, Doyle L, Higashi K, Ubilla-Rodriguez N, Lambert AR, Arroyo CS, Forsberg K, Morgan R, Stoddard B, Kaiser B. Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Nucleic Acids Res 2022;50:5171-5190. [PMID: 35511079 PMCID: PMC9122589 DOI: 10.1093/nar/gkac311] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]  Open
40
Picton DM, Harling-Lee JD, Duffner SJ, Went SC, Morgan RD, Hinton JCD, Blower TR. A widespread family of WYL-domain transcriptional regulators co-localizes with diverse phage defence systems and islands. Nucleic Acids Res 2022;50:5191-5207. [PMID: 35544231 PMCID: PMC9122601 DOI: 10.1093/nar/gkac334] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 01/21/2023]  Open
41
Rousset F, Depardieu F, Miele S, Dowding J, Laval AL, Lieberman E, Garry D, Rocha EPC, Bernheim A, Bikard D. Phages and their satellites encode hotspots of antiviral systems. Cell Host Microbe 2022;30:740-753.e5. [PMID: 35316646 PMCID: PMC9122126 DOI: 10.1016/j.chom.2022.02.018] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 11/18/2022]
42
van Riet J, Saha C, Strepis N, Brouwer RWW, Martens-Uzunova ES, van de Geer WS, Swagemakers SMA, Stubbs A, Halimi Y, Voogd S, Tanmoy AM, Komor MA, Hoogstrate Y, Janssen B, Fijneman RJA, Niknafs YS, Chinnaiyan AM, van IJcken WFJ, van der Spek PJ, Jenster G, Louwen R. CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. Commun Biol 2022;5:338. [PMID: 35396392 PMCID: PMC8993844 DOI: 10.1038/s42003-022-03249-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/09/2022] [Indexed: 11/09/2022]  Open
43
Xia P, Dutta A, Gupta K, Batish M, Parashar V. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. J Biol Chem 2022;298:101591. [PMID: 35038453 PMCID: PMC8844856 DOI: 10.1016/j.jbc.2022.101591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023]  Open
44
Pan S, Zhang H. Discovery in CRISPR-Cas9 system. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021;46:1392-1402. [PMID: 35232910 PMCID: PMC10930580 DOI: 10.11817/j.issn.1672-7347.2021.210169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 06/14/2023]
45
Charbonneau AA, Eckert DM, Gauvin CC, Lintner NG, Lawrence CM. Cyclic Tetra-Adenylate (cA4) Recognition by Csa3; Implications for an Integrated Class 1 CRISPR-Cas Immune Response in Saccharolobus solfataricus. Biomolecules 2021;11:biom11121852. [PMID: 34944496 PMCID: PMC8699464 DOI: 10.3390/biom11121852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023]  Open
46
Dadashi M, Chen L, Nasimian A, Ghavami S, Duan K. Putative RNA Ligase RtcB Affects the Switch between T6SS and T3SS in Pseudomonas aeruginosa. Int J Mol Sci 2021;22:12561. [PMID: 34830443 PMCID: PMC8619066 DOI: 10.3390/ijms222212561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/22/2023]  Open
47
Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson C, Fineran P, Nobrega F, Jackson S. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res 2021;49:10868-10878. [PMID: 34606606 PMCID: PMC8565338 DOI: 10.1093/nar/gkab883] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022]  Open
48
Picton DM, Luyten YA, Morgan RD, Nelson A, Smith DL, Dryden DTF, Hinton JCD, Blower TR. The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses. Nucleic Acids Res 2021;49:11257-11273. [PMID: 34657954 PMCID: PMC8565348 DOI: 10.1093/nar/gkab906] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 01/21/2023]  Open
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Kolesnik MV, Fedorova I, Karneyeva KA, Artamonova DN, Severinov KV. Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System. BIOCHEMISTRY. BIOKHIMIIA 2021;86:1301-1314. [PMID: 34903162 PMCID: PMC8527444 DOI: 10.1134/s0006297921100114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
50
van Beljouw SPB, Haagsma AC, Rodríguez-Molina A, van den Berg DF, Vink JNA, Brouns SJJ. The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase. Science 2021;373:1349-1353. [PMID: 34446442 DOI: 10.1126/science.abk2718] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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