Evidence map›Paper›PMID 40112800›Full record

ArticleCell2025

Jumbo phage killer immune system targets early infection of nucleus-forming phages.

Li Yuping, Linlin Guan, Isabelle Becher, Kira S Makarova, Xueli Cao, Surabhi Hareendranath, Jingwen Guan, Frank Stein, Siqi Yang, Arne Boergel and 8 more

Abstract read
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed.

  1. Article
  2. How bacterial immune systems sense phage infection.Nature reviews. Microbiology · 2026
    Review
  3. Article
  4. Article
  5. Review
  6. Article
  7. The biology of jumbo phages.Nature communications · 2026
    Review
  8. Article
  9. Article
  10. Article
  11. Phage cocktails containing a dual-receptorApplied and environmental microbiology · 2026
    Article
  12. A methylome-derived mbioRxiv : the preprint server for biology · 2026
    Article
  13. Bacteriophage genome-wide transposon mutagenesis.bioRxiv : the preprint server for biology · 2025
    Article
  14. Article
  15. Review
  16. Licence to knockdown - the phage gene silencer.Nature reviews. Microbiology · 2025
    Article
  17. Article
  18. Jumbo phage-mediated transduction of genomic islands.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Li YupingDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA. Electronic address: yuping.li@unibas.ch.
Linlin GuanState Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
Isabelle BecherEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Kira S MakarovaComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Xueli CaoState Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
Surabhi HareendranathDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA.
Jingwen GuanDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA.
Frank SteinEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Siqi YangState Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
Arne BoergelEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Karine LapougeEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Kim RemansEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
David AgardThe Chan-Zuckerberg Institute for Advanced Biological Imaging and the Department of Biochemistry, University of California, San Francisco, San Francisco, CA 94143, USA.
Mikhail SavitskiEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Athanasios TypasEuropean Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
Eugene V KooninComputational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Yue FengState Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. Electronic address: fengyue@mail.buct.edu.cn.
Joseph Bondy-DenomyDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94403, USA. Electronic address: joseph.bondy-denomy@ucsf.edu.

Funding

Structure & Mechanism: microtubule nucleation, centrosomes, phage cytoskeletonR35GM118099 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AGARD, DAVID A. · 2016 to 2022
$3.6M
Investigating the mechanisms that make jumbophages impervious to bacterial immune systemsR01AI171041 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joseph Bondy-Denomy · 2022 to 2026
$2.1M
NIAID NIH HHS R01 AI171041NIGMS NIH HHS R35 GM118099
6 · The paper itself

Abstract

Jumbo bacteriophages of the ϕKZ-like family assemble a lipid-based early phage infection (EPI) vesicle and a proteinaceous nucleus-like structure during infection. These structures protect the phage from nucleases and may create selective pressure for immunity mechanisms targeting this specific phage family. Here, we identify "jumbo phage killer" (Juk), a two-component immune system that terminates infection of ϕKZ-like phages, suppressing the expression of early phage genes and preventing phage DNA replication and phage nucleus assembly while saving the cell. JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241, and then directly recruits JukB. The JukB effector structurally resembles a pore-forming toxin and destabilizes the EPI vesicle. Functional anti-ϕKZ JukA homologs are found across bacterial phyla, associated with diverse effectors. These findings reveal a widespread defense system that specifically targets early events executed by ϕKZ-like jumbo phages prior to phage nucleus assembly.

Indexed as

BacteriophagesCell NucleusViral ProteinsViral Proteinsanti-phage defensejumbo phagephage nucleusphage vesicleϕKZ

Identifiers

PMID40112800
PMCPMC12147104

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.