Bacteriophages articles within Nature

Featured

  • Article
    | Open Access

    A screen utilizing an environmental DNA library in Escherichia coli is used to identify Brig1, a previously unknown anti-phage defence system with homologues across distinct clades of bacteria.

    • Amer A. Hossain
    • , Ying Z. Pigli
    •  & Luciano A. Marraffini

  • Article |

    Cryo-electron microscopy and molecular dynamics studies of a Vitiosangium gasdermin pore reveal insights into the assembly of this large and diverse family of membrane pore-forming proteins.

    • Alex G. Johnson
    • , Megan L. Mayer
    •  & Philip J. Kranzusch

  • Article
    | Open Access

    X-ray crystallography, cryo-EM and biochemical analysis provide insight into the assembly of the bacterial Gabija complex, an anti-phage system, and reveal how viruses can evade this defence mechanism.

    • Sadie P. Antine
    • , Alex G. Johnson
    •  & Philip J. Kranzusch

  • Article
    | Open Access

    Staphylococcus CdnE03 cyclase recognizes structured RNA molecules produced by staphylococcal phages, triggering cyclic oligonucleotide production and, thereby, bacterial cell death—a mechanism of antiviral defence conserved across domains of life.

    • Dalton V. Banh
    • , Cameron G. Roberts
    •  & Luciano A. Marraffini

  • Article
    | Open Access

    In response to bacterial CRISPR–Cas immunity, phages and plasmids have evolved small non-coding RNA anti-CRISPRs, known as Racrs, that sequester Cas proteins in abberrant complexes and thereby inhibit immunity.

    • Sarah Camara-Wilpert
    • , David Mayo-Muñoz
    •  & Rafael Pinilla-Redondo

  • Article
    | Open Access

    The Bacteroides fragilis type III CRISPR protein Cmr conjugates ATP to S-adenosyl methionine, generating S-adenosyl methionine (SAM)-AMP, a novel second messenger with a role in antiviral signalling.

    • Haotian Chi
    • , Ville Hoikkala
    •  & Malcolm F. White

  • Article
    | Open Access

     Prophage lysogeny-to-lysis transitions are controlled by regulatory modules consisting of transcription factors and partner small proteins that are activated through DNA-damage-independent pathways, including by quorum sensing, and these modules determine inter-prophage competition outcomes.

    • Justin E. Silpe
    • , Olivia P. Duddy
    •  & Bonnie L. Bassler

  • Article
    | Open Access

    The tail fibre of an extracellular contractile injection system (eCIS) from Photorhabdus asymbiotica recognizes targets expressed on eukaryotic host cells, and can be reprogrammed to target specific organisms and cell types for delivery of novel protein payloads.

    • Joseph Kreitz
    • , Mirco J. Friedrich
    •  & Feng Zhang

  • Article |

    We identified Tad1, a large family of phage-encoded proteins that inhibit Thoeris immunity, and define the chemical structure of a central immune signalling molecule, showing a new mode of action by which pathogens can suppress host immunity.

    • Azita Leavitt
    • , Erez Yirmiya
    •  & Rotem Sorek

  • Article |

    Retron-Sen2 of Salmonella Typhimurium encodes a toxin and a reverse transcriptase, which, together with the Sen2 multi-copy single-stranded DNA synthesized by the reverse transcriptase make up a tripartite toxin–antitoxin system that functions in anti-phage defence.

    • Jacob Bobonis
    • , Karin Mitosch
    •  & Athanasios Typas

  • Article
    | Open Access

    A study using a biochemical screen of 57 phages in two bacterial species identifies and characterizes proteins enabling phages to evade CBASS and Pycsar immune systems, and describes the mechanisms involved.

    • Samuel J. Hobbs
    • , Tanita Wein
    •  & Philip J. Kranzusch

  • Article |

    The mechanism of Thoeris—a bacterial anti-phage defence system—is described in detail, revealing that bacterial TIR-domain proteins recognize infection and produce signalling molecules to execute cell death, akin to the roles of these proteins in plants.

    • Gal Ofir
    • , Ehud Herbst
    •  & Rotem Sorek

  • Article |

    In Staphylococcus epidermidis and Staphylococcus aureus, non-specific DNase activity of the type III-A CRISPR–Cas system increases the rate of mutations in the host and accelerates the evolution of resistance to antibiotics and to phage.

    • Charlie Y. Mo
    • , Jacob Mathai
    •  & Luciano A. Marraffini

  • Article |

    The RNA polymerase from the crAss-like bacteriophage phi14:2, which is translocated into the host cell with phage DNA and transcribes early phage genes, is structurally most similar to eukaryotic RNA interference polymerases, suggesting that the latter have a phage origin.

    • Arina V. Drobysheva
    • , Sofia A. Panafidina
    •  & Maria L. Sokolova

  • Article
    | Open Access

    Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.

    • Basem Al-Shayeb
    • , Rohan Sachdeva
    •  & Jillian F. Banfield

  • Article |

    CRISPR–Cas systems cannot eliminate temperate bacteriophages from bacterial populations and—in this context—the systems impose immunopathological costs on the host, creating selective pressures that may explain their patchy distribution in bacteria.

    • Clare Rollie
    • , Anne Chevallereau
    •  & Edze R. Westra

  • Article |

    The jumbo phage ΦKZ constructs a proteinaceous nucleus-like compartment around its genome that protects phage DNA from degradation by DNA-targeting immune effectors of the host, including CRISPR–Cas and restriction enzymes.

    • Senén D. Mendoza
    • , Eliza S. Nieweglowska
    •  & Joseph Bondy-Denomy

  • Article |

    Some phages—viruses that infect bacteria—encode peptides that are secreted from infected cells and that, beyond a certain threshold, stimulate other viruses to switch from the lytic (killing the host cell) to lysogenic (dormant) phase.

    • Zohar Erez
    • , Ida Steinberger-Levy
    •  & Rotem Sorek

  • Article |

    An integrated computational approach that explores the viral content of more than 3,000 metagenomic samples collected globally highlights the existing global viral diversity, increases the known number of viral genes by an order of magnitude, and provides detailed insights into viral distribution across diverse ecosystems and into virus–host interactions.

    • David Paez-Espino
    • , Emiley A. Eloe-Fadrosh
    •  & Nikos C. Kyrpides

  • Review Article |

    The CRISPR-Cas systems of bacteria and archaea provide adaptive immunity against invading mobile genetic elements such as phages and plasmids; this Review describes the discovery of these systems and the mechanisms of immunity, including recent progress in establishing the molecular basis of host immunization.

    • Luciano A. Marraffini

  • Letter |

    CRISPR/Cas systems are bacterial adaptive immune systems that provide sequence-specific protection from invading nucleic acids, including from bacteriophages; in a notable reverse a vibriophage-encoded CRISPR/Cas system, used to disable a bacteriophage inhibitory chromosomal island in Vibrio cholerae, is identified.

    • Kimberley D. Seed
    • , David W. Lazinski
    •  & Andrew Camilli

  • Letter |

    Viruses are isolated from the SAR11 bacterial clade, the most abundant group of bacteria in the ocean, that were thought to be resistant to viral infection; because of the essential role of SAR11 in carbon cycling these viruses are also an important factor in biogeochemical cycling.

    • Yanlin Zhao
    • , Ben Temperton
    •  & Stephen J. Giovannoni

  • Article |

    The structure of the bacteriophage transposase MuA bound to DNA sequences that mimic both the transposon ends and the target DNA ends is solved; the picture of this synaptic complex illustrates the intricacy of Mu transposition, and exposes the architectural diversity among DDE recombinases in complex with substrate DNAs.

    • Sherwin P. Montaño
    • , Ying Z. Pigli
    •  & Phoebe A. Rice

  • News |

    Antibiotic use may have driven the development of Europe's deadly E. coli.

    • Marian Turner

  • Article |

    CRISPR/Cas is a microbial immune system that is known to protect bacteria from virus infection. These authors show that the Streptococcus thermophilus CRISPR/Cas system can prevent both plasmid carriage and phage infection through cleavage of invading double-stranded DNA.

    • Josiane E. Garneau
    • , Marie-Ève Dupuis
    •  & Sylvain Moineau

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