Evidence map›Paper›PMID 42492495›Full record

ArticleCell2026

Bacteriophage genome-wide transposon mutagenesis.

Alex Chan, Wearn-Xin Yee, Deepto Mozumdar, Claire Kokontis, Matias Rojas-Montero, Miaoxi Liu, Ying Yang, Li Yuping, Joseph Bondy-Denomy

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. The Lysis cassette of jumbophage PhiKZ.Scientific reports · 2026
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Alex ChanDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Wearn-Xin YeeDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA. Electronic address: wearnxin.yee@ucsf.edu.
Deepto MozumdarDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Claire KokontisDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Matias Rojas-MonteroDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Miaoxi LiuDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Ying YangDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Li YupingDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
Joseph Bondy-DenomyDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA. Electronic address: joseph.bondy-denomy@ucsf.edu.

Funding

Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
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
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
Elucidation of the mechanisms of jumbophage genome protection during infectionF32GM149125 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MOZUMDAR, DEEPTO · 2023 to 2024
$143k
NIAID NIH HHS R01 AI167412NIAID NIH HHS R01 AI171041NIAID NIH HHS T32 AI060537NIGMS NIH HHS F32 GM149125
6 · The paper itself

Abstract

Bacteriophage genomes are densely packed with coding sequences and frequently encode genes of unknown function. Unbiased phage functional genomics approaches are therefore needed, particularly for large lytic phages. Here, we harness the mariner transposase to develop phage transposon mutagenesis and sequencing (phage TnSeq), which enables pooled sequencing to identify both fitness-conferring and dispensable genes. Using the Pseudomonas aeruginosa-infecting nucleus-forming jumbo phage ΦKZ (280,334 bp; 371 predicted genes), we show that ∼110 genes are fitness-conferring via phage TnSeq, identifying many known and previously unknown essential genes. Moreover, this phage harbors ∼261 non-essential genes, including some capsid and tail proteins, many of which are important for fitness across different clinical isolates or conditions. Phage TnSeq was also extended to a base-modified phage. Together, phage TnSeq is a scalable technology that can identify essential phage genes, generate knockouts in all non-essential genes, and sensitively assign the quantitative fitness contributions of every gene in parallel.

Indexed as

BacteriophagesDNA Transposable ElementsGenome, ViralMutagenesisPseudomonas aeruginosaDNA Transposable Elementsanti-CRISPRbase-modified phagecapsidsCRISPR-Cas13jumbophagetransposon mutagenesis

Identifiers

PMID42492495
PMCPMC13428642

What OpenQuestion holds

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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.