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TitleMolecular characterisation of the Bacillus subtilis SpbK antiphage defence system.
Journal, issue, pagesNat Commun, Year 2025
Publish dateDec 29, 2025
AuthorsBiswa P Mishra / Christian L Loyo / Yanyao Cai / Thomas Litfin / Gause Miraj / Lou Brillault / Veronika Masic / Tamim Mosaiab / Premraj Rajaratnam / Santosh Rudrawar / Weixi Gu / Bostjan Kobe / Joseph P Gerdt / Alan D Grossman / Yun Shi / Thomas Ve /
PubMed AbstractBacteria 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 ...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.
External linksNat Commun / PubMed:41462020
MethodsEM (single particle) / EM (helical sym.)
Resolution3.3 Å
Structure data

71643

9pha

EMDB-71643, PDB-9pha:
CryoEM structure of the YonE portal protein from Bacillus phage SPbeta
Method: EM (single particle) / Resolution: 3.3 Å

71644

9phb

EMDB-71644, PDB-9phb:
CryoEM structure of filament of Bacillus subtilis TIR domain protein SpbK
Method: EM (helical sym.) / Resolution: 3.3 Å

Source
  • spbetavirus spbeta
  • bacillus subtilis (bacteria)
KeywordsVIRAL PROTEIN / Portal protein / antiphage defence / ANTIVIRAL PROTEIN / TIR domain protein

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