SNIPE Gene Notes

Key Paper: Saxton et al. (2026) Nature

Title: A membrane-bound nuclease directly cleaves phage DNA during genome injection
Authors: Saxton DS, DeWeirdt PC, Doering CR, Roney IJ & Laub MT
DOI: 10.1038/s41586-026-10207-1
PMID: 41741653

Identification

• Originally identified as PD-lambda-1 in a functional genetic screen for anti-phage defence systems in the E. coli pangenome PMID:36123438
• Renamed SNIPE: Surface-associated Nuclease Inhibiting Phage Entry PMID:41741653
• Found in wild E. coli strains (ECOR collection, strain MOD1-ECOR26); NOT present in K-12 MG1655
• UniProt: A0A8T9CRB7 (TrEMBL, ECOLX; from strain T0181B.E-10, same RefSeq WP_001606968.1)

Protein Architecture (500 aa)

Three domains confirmed by AlphaFold, HHpred, and DeepTMHMM:

1. N-terminal transmembrane domain (aa 5-24): single-pass TM helix anchoring to inner membrane. N-terminus is periplasmic, rest of protein is cytoplasmic PMID:41741653
2. DUF4041 domain (aa 144-262, now IPR025280/PF13250 "SNIPE associated domain"): positively charged surface facilitates DNA binding; also interacts with phage tape measure proteins (TMPs) PMID:41741653
3. GIY-YIG nuclease domain (aa 357-450): catalytic DNA endonuclease; E414 is catalytic residue PMID:41741653

Mechanism of Action

SNIPE provides direct defence (infected cell survives), distinct from abortive infection:

• SNIPE pre-associates with ManYZ (mannose permease) in the inner membrane BEFORE infection PMID:41741653
• During phage genome injection through ManYZ, DUF4041 domain binds the phage tape measure protein (TMP), positioning the nuclease to cleave incoming DNA PMID:41741653
• 32P-labelled phage DNA is cleaved from ~42,000 bp down to <100 bp fragments during injection PMID:41741653
• SNIPE does NOT affect phage adsorption PMID:41741653
• SNIPE does NOT target pre-existing phage genomes (lysogens) PMID:41741653
• SNIPE does NOT block plasmid DNA transformation PMID:41741653

Auto-inhibition

• Membrane-localized SNIPE does NOT cleave host DNA PMID:41741653
• SNIPE(deltaTM) localizes to nucleoid and IS toxic — cleaves host DNA PMID:41741653
• The TM domain prevents autoimmunity by anchoring SNIPE away from chromosomal DNA

ManYZ Interaction

• ManYZ = mannose permease inner membrane complex, required for lambda genome injection
• SNIPE pre-associates with ManYZ (TurboID proximity labelling) PMID:41741653
• Robust defence requires ManYZ against lambda and related phages
• ManYZ-independent defence: SNIPE provides moderate defence against siphoviruses independently of ManYZ PMID:41741653

TMP Interaction

• DUF4041 interacts with phage tape measure proteins physically PMID:41741653
• UV crosslinking + mass spec confirms SNIPE-TMP direct contact via pBPA at residue N250 (adjacent to W257R mutation site) PMID:41741653
• SNIPE gain-of-function mutations (L253H, E264K, K305N; E223K, T319A; W257R, I308V) enhance binding to Bas14 TMP PMID:41741653
• Phage escape mutations map exclusively to TMP gene PMID:41741653

Evolutionary Diversity

• ~500 curated SNIPE homologues across many bacterial phyla PMID:41741653
• 33% of well-sequenced bacterial clades harbour at least one SNIPE homologue [PMID:36123438, PMID:41741653]
• GIY-YIG nuclease domain: most conserved region
• DUF4041: moderate conservation, positively charged DNA-binding interface conserved
• N-terminal region: highest variability — functions as adapter for phage specificity
• 59% have 1 TM domain
• 7% have 2 TM domains
• 34% lack TM domains — use alternative membrane-targeting strategies:
  • DivIVA domains (negative membrane curvature binding)
  • Type III secretion system domains
  • Pleckstrin homology domains (phospholipid binding)
  • Phage tail protein fusions PMID:41741653

Self/Non-Self Discrimination

SNIPE represents a novel strategy distinct from:
- CRISPR-Cas: sequence-specific recognition via guide RNAs
- Restriction-modification: recognition of DNA methylation marks
- SNIPE: exploits spatial organization — phage DNA must pass through the membrane during injection, and SNIPE is positioned there to intercept it PMID:41741653

Comparison to Other Systems

• Zorya: also localizes to membrane at genome injection sites, but senses perturbations rather than directly cleaving DNA [PMID:41741653 ref 34,35]
• Kiwa: membrane-embedded defence supercomplex at phage attachment sites [PMID:41741653 ref 37]
• IFITM proteins (eukaryotic): block viral membrane fusion — conceptual parallel [PMID:41741653 ref 38,39]

Key References

1. PMID:41741653 - Saxton et al. 2026, Nature. SNIPE characterization.
2. PMID:36123438 - Vassallo et al. 2022, Nat Microbiol. Original identification as PD-lambda-1.
3. PMID:37460672 - Georjon & Bernheim 2023, Cell Host Microbe. Systematic exploration of E. coli phage-host interactions (BASEL collection).
4. PMID:31857715 - Makarova et al. 2020. Classification of CRISPR-Cas systems.
5. PMID:36880887 - Branon et al. 2018, Nat Biotechnol. TurboID proximity labelling.