Evidence map›Paper›PMID 40315827›Full record

ArticleMolecular cell2025

Activation of bacterial programmed cell death by phage inhibitors of host immunity.

Sukrit Silas, Héloïse Carion, Kira S Makarova, Eric S Laderman, Thomas Todeschini, Pradeep Kumar, Matthew Johnson, Michael Bocek, Franklin L Nobrega, Eugene V Koonin and 1 more

Abstract read
In one paragraph

Article in Molecular cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. How bacterial immune systems sense phage infection.Nature reviews. Microbiology · 2026
    Review
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  14. Viral effectors trigger innate immunity across the tree of life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025
    Review
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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

11 authors.

Sukrit SilasDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Virology, J. David Gladstone Institutes, San Francisco, CA 94158, USA. Electronic address: sukrit.silas@gladstone.ucsf.edu.
Héloïse CarionDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Kira S MakarovaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Eric S LadermanDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Thomas TodeschiniSchool of Biological Sciences, University of Southampton, Southampton, UK.
Pradeep KumarONI Linacre house, Banbury Road, Oxford OX2 8TA, UK.
Matthew JohnsonDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Michael BocekTwist Biosciences, South San Francisco, CA 94080, USA.
Franklin L NobregaSchool of Biological Sciences, University of Southampton, Southampton, UK.
Eugene V KooninNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Joseph Bondy-DenomyDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: joseph.bondy-denomy@ucsf.edu.

Funding

Genetic and Proteomic Approaches to Reveal Bacterial Vulnerabilities to Phage PredationR01AI167412 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joseph Bondy-Denomy · 2022 to 2026
$3.5M
NIAID NIH HHS R01 AI167412
6 · The paper itself

Abstract

Bacterial and archaeal viruses are replete with diverse uncharacterized accessory genes (AGs), which likely interface with host processes. However, large-scale discovery of virus AG functions remains challenging. Here, we developed an integrated computational and experimental discovery platform to identify viral AGs and assign functions. We show that multiple AGs activate unexpected programmed cell death (PCD) activity of distinct restriction-modification (R-M) systems. We describe an exapted type I R-M decoy that kills the host upon sensing several different anti-defense AGs and a self-guarded type III R-M system that restricts phages but also induces PCD when bound by anti-R-M proteins. Other phage counter-defense genes additionally activate non-R-M-based abortive infection systems encoded by prophages. This defense strategy creates a conundrum: lose AGs and be exposed to immunity or keep AGs and trigger PCD. Strategies employed by viruses to avoid this double bind could be an important factor in virus evolution that remains to be explored.

Indexed as

ApoptosisBacteriaBacteriophagesDNA Restriction-Modification EnzymesHost-Pathogen InteractionsProphagesViral ProteinsDNA Restriction-Modification EnzymesViral Proteinsabortive immunityaccessory genesbacteriacomparative genomicsimmune inhibitorsphagephage defenserestriction-modification

Identifiers

PMID40315827
PMCPMC12088041

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.