Evidence map›Paper›PMID 41462020›Full record

ArticleNature communications2025

Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system.

Biswa P Mishra, Christian L Loyo, Yanyao Cai, Thomas Litfin, Gause Miraj, Lou Brillault, Veronika Masic, Tamim Mosaiab, Premraj Rajaratnam, Santosh Rudrawar and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

16 authors.

Biswa P MishraInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Christian L LoyoDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Yanyao CaiDepartment of Chemistry, Indiana University, Bloomington, IN, USA.
Thomas LitfinStructural Biology Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia.
Gause MirajInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Lou BrillaultCentre for Microscopy and Microanalysis, University of Queensland, St Lucia, QLD, Australia.
Veronika MasicInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Tamim MosaiabInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Premraj RajaratnamInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Santosh RudrawarInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia.
Weixi GuSchool of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, QLD, Australia.
Bostjan KobeSchool of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, St Lucia, QLD, Australia.ORCID http://orcid.org/0000-0001-9413-9166
Joseph P GerdtDepartment of Chemistry, Indiana University, Bloomington, IN, USA.ORCID http://orcid.org/0000-0002-0375-4110
Alan D GrossmanDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8235-7227
Yun ShiInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia. yun.shi1@monash.edu.ORCID http://orcid.org/0000-0003-3365-4679
Thomas VeInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast, QLD, Australia. t.ve@griffith.edu.au.ORCID http://orcid.org/0000-0002-0113-1905

Funding

Elucidation of the first interspecies chemical signaling mechanisms in Capsaspora owczarzaki--the predator of a human pathogen and a model for the evolution of animal multicellularityR35GM138376 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI Joseph P. Gerdt · 2020 to 2026
$3.0M
Department of Health | National Health and Medical Research Council (NHMRC) 1196590Department of Health | National Health and Medical Research Council (NHMRC) 2025931NIGMS NIH HHS R35 GM138376
6 · The paper itself

Abstract

Bacteria have a variety of mechanisms for limiting predation by phages. SpbK is a Toll/interleukin-1 receptor (TIR) domain-containing antiphage defence protein from Bacillus subtilis that provides protection against the temperate phage SPβ via abortive infection. Here we structurally characterise SpbK and its interaction with the SPβ protein YonE. We demonstrate that SpbK is an NADase that produces both ADP-ribose (ADPR) and canonical cyclic ADPR with a N1-glycosidic bond (cADPR, also referred to as N1-cADPR). Combining cryo-EM, in silico predictions, site-directed mutagenesis, and phage infection assays, we show that formation of two-stranded head-to-tail assemblies of SpbK TIR domains is required for both NADase activity and antiphage defence. We also demonstrate that YonE is a dodecameric portal protein that activates the NADase function of SpbK by facilitating TIR domain clustering. Collectively, our results provide insight into how bacterial TIR NADases recognise phage infection.

Indexed as

Bacillus PhagesBacillus subtilisBacterial ProteinsBacteriophagesCryoelectron MicroscopyMutagenesis, Site-DirectedProtein DomainsBacterial Proteins

Identifiers

PMID41462020
PMCPMC12847820

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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.