The highly diverse antiphage defence systems of bacteria

[1]  M. Wiedmann,et al.  Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy , 2023, Nature Microbiology.

[2]  Yina Gao,et al.  Molecular basis of RADAR anti-phage supramolecular assemblies , 2023, Cell.

[3]  J. Ren,et al.  Bacteriophages inhibit and evade cGAS-like immune function in bacteria , 2023, Cell.

[4]  R. Kishony,et al.  Multistep diversification in spatiotemporal bacterial-phage coevolution , 2022, Nature Communications.

[5]  T. Zhang,et al.  Direct activation of a bacterial innate immune system by a viral capsid protein , 2022, Nature.

[6]  Huilin Zhou,et al.  The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. , 2022, Molecular cell.

[7]  M. Laub,et al.  A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome , 2022, Nature Microbiology.

[8]  Gil Amitai,et al.  Discovery of phage determinants that confer sensitivity to bacterial immune systems , 2022, Cell.

[9]  Gil Amitai,et al.  Cryo-EM structure of the RADAR supramolecular anti-phage defense complex , 2022, Cell.

[10]  E. Koonin,et al.  Prokaryotic innate immunity through pattern recognition of conserved viral proteins , 2022, Science.

[11]  G. Douce,et al.  Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors , 2022, Cell.

[12]  T. A. Nagy,et al.  Bacterial NLR-related proteins protect against phage , 2022, Cell.

[13]  G. Zeller,et al.  Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems , 2022, Nature.

[14]  Kristin N. Parent,et al.  Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria , 2022, Nature Microbiology.

[15]  Gil Amitai,et al.  Bacteria deplete deoxynucleotides to defend against bacteriophage infection , 2022, Nature Microbiology.

[16]  Kathryn M. Kauffman,et al.  Phage–host coevolution in natural populations , 2022, Nature Microbiology.

[17]  R. Sorek,et al.  The defense island repertoire of the Escherichia coli pan-genome , 2022, bioRxiv.

[18]  L. Aravind,et al.  Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. , 2022, Annual review of biomedical data science.

[19]  M. F. White,et al.  Cyclic Nucleotide Signaling in Phage Defense and Counter-Defense. , 2022, Annual review of virology.

[20]  Gil Amitai,et al.  An expanding arsenal of immune systems that protect bacteria from phages , 2022, bioRxiv.

[21]  Gil Amitai,et al.  Viruses inhibit TIR gcADPR signaling to overcome bacterial defense , 2022, bioRxiv.

[22]  Shiraz A. Shah,et al.  A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. , 2022, Cell host & microbe.

[23]  R. Sorek,et al.  Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity , 2022, Nature.

[24]  M. Laub,et al.  Toxin-Antitoxin Systems as Phage Defense Elements. , 2022, Annual review of microbiology.

[25]  M. Blokesch,et al.  Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae , 2022, Nature.

[26]  S. Bari,et al.  A unique mode of nucleic acid immunity performed by a multifunctional bacterial enzyme. , 2022, Cell host & microbe.

[27]  E. Rocha,et al.  Phages and their satellites encode hotspots of antiviral systems , 2022, Cell host & microbe.

[28]  Joshua W. Modell,et al.  Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. , 2022, Molecular cell.

[29]  E. Rocha,et al.  Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? , 2022, PLoS biology.

[30]  Gil Amitai,et al.  Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion , 2021, bioRxiv.

[31]  Č. Venclovas,et al.  Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion , 2021, bioRxiv.

[32]  Gil Amitai,et al.  Antiviral activity of bacterial TIR domains via immune signalling molecules , 2021, Nature.

[33]  Marjolein E. Crooijmans,et al.  Reversible bacteriophage resistance by shedding the bacterial cell wall , 2021, bioRxiv.

[34]  R. Sorek,et al.  Effector-mediated membrane disruption controls cell death in CBASS antiphage defense. , 2021, Molecular cell.

[35]  Kathryn M. Kauffman,et al.  Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages , 2021, Science.

[36]  S. L. Shipman,et al.  Precise genome editing across kingdoms of life using retron-derived DNA , 2021, Nature Chemical Biology.

[37]  Darren L. Smith,et al.  The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses , 2021, Nucleic acids research.

[38]  Peter C. Fineran,et al.  Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types , 2021, Nucleic acids research.

[39]  Gil Amitai,et al.  Cyclic CMP and cyclic UMP mediate bacterial immunity against phages , 2021, Cell.

[40]  T. Zhang,et al.  The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA , 2021, Nature Microbiology.

[41]  M. Touchon,et al.  Systematic and quantitative view of the antiviral arsenal of prokaryotes , 2021, Nature Communications.

[42]  Charles L. Dulberger,et al.  Prophages encode phage-defense systems with cognate self-immunity , 2021, Cell host & microbe.

[43]  T. Ahmed,et al.  Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts , 2021, Science.

[44]  P. Graumann,et al.  A Bacterial Dynamin-Like Protein Confers a Novel Phage Resistance Strategy on the Population Level in Bacillus subtilis , 2021, bioRxiv.

[45]  Gil Amitai,et al.  Bacterial gasdermins reveal an ancient mechanism of cell death , 2021, bioRxiv.

[46]  C. Gätgens,et al.  Aminoglycoside Antibiotics Inhibit Phage Infection by Blocking an Early Step of the Infection Cycle , 2021, bioRxiv.

[47]  M. Laub,et al.  Shutoff of host transcription triggers a toxin-antitoxin system to cleave phage RNA and abort infection. , 2021, Molecular cell.

[48]  S. Ben-Yehuda,et al.  Bacteria elicit a phage tolerance response subsequent to infection of their neighbors , 2021, bioRxiv.

[49]  Feng-Ting Huang,et al.  A nucleotide-sensing endonuclease from the Gabija bacterial defense system , 2020, bioRxiv.

[50]  Gil Amitai,et al.  Prokaryotic viperins produce diverse antiviral molecules , 2020, Nature.

[51]  R. Sorek,et al.  STING cyclic dinucleotide sensing originated in bacteria. , 2020, Nature.

[52]  L. Marraffini,et al.  Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria. , 2020, Annual review of genetics.

[53]  Jonathan L. Schmid-Burgk,et al.  Diverse enzymatic activities mediate antiviral immunity in prokaryotes , 2020, Science.

[54]  Gil Amitai,et al.  Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems , 2020, Nature Microbiology.

[55]  R. Sorek,et al.  Bacterial Retrons Function In Anti-Phage Defense , 2020, Cell.

[56]  R. Sorek,et al.  Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy. , 2020, Annual review of virology.

[57]  P. J. Kranzusch,et al.  CBASS Immunity Uses CARF-Related Effectors to Sense 3′–5′- and 2′–5′-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection , 2020, Cell.

[58]  Z. Deng,et al.  SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities , 2020, Nature Microbiology.

[59]  Lucas P. P. Braga,et al.  Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios , 2020, Microbiome.

[60]  Daniel B. Goodman,et al.  High-throughput functional variant screens via in vivo production of single-stranded DNA , 2020, Proceedings of the National Academy of Sciences.

[61]  Ming Sun,et al.  The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments , 2020, The ISME Journal.

[62]  P. C. Fineran,et al.  The arms race between bacteria and their phage foes , 2020, Nature.

[63]  R. Sorek,et al.  The pan-immune system of bacteria: antiviral defence as a community resource , 2019, Nature Reviews Microbiology.

[64]  E. Koonin,et al.  Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire , 2019, Nature Reviews Genetics.

[65]  M. F. White,et al.  A viral ring nuclease anti-CRISPR subverts type III CRISPR immunity , 2019, Nature.

[66]  Max J. Kellner,et al.  SHERLOCK: nucleic acid detection with CRISPR nucleases , 2019, Nature Protocols.

[67]  Gil Amitai,et al.  Cyclic GMP–AMP signalling protects bacteria against viral infection , 2019, Nature.

[68]  P. J. Kranzusch,et al.  Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity , 2019, bioRxiv.

[69]  P. Silver,et al.  Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model , 2019, Cell host & microbe.

[70]  Z. Deng,et al.  A new type of DNA phosphorothioation-based antiviral system in archaea , 2019, Nature Communications.

[71]  E. Westra,et al.  Bacterial biodiversity drives the evolution of CRISPR-based phage resistance , 2019, Nature.

[72]  R. Barrangou,et al.  Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci , 2019, Nature Microbiology.

[73]  P. J. Kranzusch,et al.  Bacterial cGAS-like enzymes synthesize diverse nucleotide signals , 2019, Nature.

[74]  K. Maxwell,et al.  A chemical defence against phage infection , 2018, Nature.

[75]  R. Morgan,et al.  BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site , 2018, Nucleic acids research.

[76]  Zixin Deng,et al.  DNA phosphorothioate modification—a new multi-functional epigenetic system in bacteria , 2018, FEMS microbiology reviews.

[77]  R. Sorek,et al.  Contemporary Phage Biology: From Classic Models to New Insights , 2018, Cell.

[78]  Emmanuelle Charpentier,et al.  The Biology of CRISPR-Cas: Backward and Forward , 2018, Cell.

[79]  A. Buckling,et al.  Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity , 2018, Cell.

[80]  Adair L. Borges,et al.  Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity , 2018, Cell.

[81]  Rotem Sorek,et al.  Systematic discovery of antiphage defense systems in the microbial pangenome , 2018, Science.

[82]  Alan R. Davidson,et al.  Anti-CRISPR: discovery, mechanism and function , 2017, Nature Reviews Microbiology.

[83]  R. Sorek,et al.  DISARM is a widespread bacterial defence system with broad anti-phage activities , 2017, Nature Microbiology.

[84]  E. Koonin,et al.  Reconstruction of the evolution of microbial defense systems , 2017, BMC Evolutionary Biology.

[85]  Courtney J. Robinson,et al.  Prophage-mediated defence against viral attack and viral counter-defence , 2017, Nature Microbiology.

[86]  H. Molina,et al.  A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages. , 2016, Cell host & microbe.

[87]  A. Buckling,et al.  Prophages mediate defense against phage infection through diverse mechanisms , 2016, The ISME Journal.

[88]  V. de Crécy-Lagard,et al.  Novel genomic island modifies DNA with 7-deazaguanine derivatives , 2016, Proceedings of the National Academy of Sciences.

[89]  R. Sorek,et al.  BREX is a novel phage resistance system widespread in microbial genomes , 2015, The EMBO journal.

[90]  H. Neve,et al.  Temperate Streptococcus thermophilus phages expressing superinfection exclusion proteins of the Ltp type , 2014, Front. Microbiol..

[91]  D. Dryden,et al.  Highlights of the DNA cutters: a short history of the restriction enzymes , 2013, Nucleic acids research.

[92]  Sylvain Moineau,et al.  Revenge of the phages: defeating bacterial defences , 2013, Nature Reviews Microbiology.

[93]  Elizabeth Pennisi,et al.  The CRISPR craze. , 2013, Science.

[94]  S. Moineau,et al.  CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance , 2013, Nature Communications.

[95]  E. Koonin,et al.  Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing , 2013, Biology Direct.

[96]  G. Salmond,et al.  Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism , 2012, PLoS genetics.

[97]  A. Buckling,et al.  Co-evolution with lytic phage selects for the mucoid phenotype of Pseudomonas fluorescens SBW25 , 2011, The ISME Journal.

[98]  S. Lemire,et al.  Escherichia coli rnlA and rnlB Compose a Novel Toxin–Antitoxin System , 2011, Genetics.

[99]  Adi Stern,et al.  The phage‐host arms race: Shaping the evolution of microbes , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.

[100]  Sylvain Moineau,et al.  Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.

[101]  G. Kaufmann,et al.  RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase , 2008, Molecular microbiology.

[102]  C. Suttle.  Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

[103]  E. Bidnenko,et al.  Phage abortive infection in lactococci: variations on a theme. , 2005, Current opinion in microbiology.

[104]  D. Dryden,et al.  The biology of restriction and anti-restriction. , 2005, Current opinion in microbiology.

[105]  Wenfang Wang,et al.  F exclusion of bacteriophage T7 occurs at the cell membrane. , 2004, Virology.

[106]  G. Kaufmann,et al.  Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems. , 1995, Journal of molecular biology.

[107]  L. Snyder,et al.  Translation elongation factor Tu cleaved by a phage-exclusion system. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[108]  L. Gold,et al.  The Rex system of bacteriophage lambda: tolerance and altruistic cell death. , 1992, Genes & development.

[109]  I. Molineux,et al.  Genes 1.2 and 10 of bacteriophages T3 and T7 determine the permeability lesions observed in infected cells of Escherichia coli expressing the F plasmid gene pifA , 1991, Journal of bacteriology.

[110]  F. Jacob,et al.  Evolution and tinkering. , 1977, Science.

[111]  OUP accepted manuscript , 2022, Nucleic Acids Research.

[112]  A. Davidson,et al.  Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation , 2017, Nature Microbiology.

[113]  R. Warren.  Modified bases in bacteriophage DNAs. , 1980, Annual review of microbiology.