Evidence map›Paper›PMID 39229129›Full record

ArticlebioRxiv : the preprint server for biology2024

Exploring the diversity of anti-defense systems across prokaryotes, phages, and mobile genetic elements.

Florian Tesson, Erin Huiting, Linlin Wei, Jie Ren, Matthew Johnson, Rémi Planel, Jean Cury, Yue Feng, Joseph Bondy-Denomy, Aude Bernheim

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Florian TessonInstitut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France.ORCID 0000-0003-4038-1154
Erin HuitingDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA.ORCID 0000-0002-5454-2679
Linlin WeiState Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
Jie RenState Key Laboratory for Biology of Plant Diseases and Insect Pests, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Matthew JohnsonDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA.ORCID 0000-0003-4534-5697
Rémi PlanelInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France.ORCID 0000-0002-7826-3316
Jean CuryInstitut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France.ORCID 0000-0002-6462-8783
Yue FengState Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.ORCID 0000-0002-1576-1385
Joseph Bondy-DenomyDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA.ORCID 0000-0002-4909-9481
Aude BernheimInstitut Pasteur, CNRS UMR3525, Molecular Diversity of Microbes Lab, Paris, France.ORCID 0000-0003-0212-777X

Funding

Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
Identifying the mechanism of bacteriophage detection by cyclic-oligonucleotide signaling systemsR21AI168811 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BONDY-DENOMY, JOSEPH · 2022 to 2023
$444k
NIAID NIH HHS R21 AI168811NIAID NIH HHS T32 AI060537
6 · The paper itself

Abstract

The co-evolution of prokaryotes, phages, and mobile genetic elements (MGEs) over the past billions of years has driven the emergence and diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences, and are typically small, creating a challenge to detect anti-defense homologs across the prokaryotic genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired genome or MGE. Here, we developed "AntiDefenseFinder" - a free open-source tool and web service that detects 156 anti-defense systems (of one or more proteins) in any genomic sequence. Using this dataset, we identified 47,981 anti-defense systems distributed across prokaryotes, phage, and MGEs. We found that some genes co-localize in "anti-defense islands", including

Identifiers

PMID39229129
PMCPMC11370490

What OpenQuestion holds

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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.