identifier: traitmech:000222 label: SspABCD-SspE system definition: A phosphorothioate defense system in which an organism possesses an SspABCD-SspE locus that pairs an SspABCD single-stranded DNA phosphorothioation module with the SspE restriction enzyme to sense host phosphorothioate marks and nick invading DNA. definition_source: DOI:10.1038/s41564-020-0700-6 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000213 synonyms: - synonym_text: SspABCD-SspE PT system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41564-020-0700-6 evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: Here, we describe an unusual SspABCD-SspE PT system in Vibrio cyclitrophicus, Escherichia coli and Streptomyces yokosukanensis notes: Xiong et al. name SspABCD-SspE as a bacterial phosphorothioation system distinct from Dnd. - reference: DOI:10.1038/s41564-020-0700-6 snippet: SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase notes: Xiong et al. support the SspABCD modification module and its single-stranded high-frequency PT output. - reference: DOI:10.1038/s41564-020-0700-6 snippet: SspABCD coupled with SspE provides protection against phages notes: Xiong et al. support the modification-plus-restriction architecture and the antiphage output of SspABCD-SspE. - reference: DOI:10.1038/s41467-022-34505-0 snippet: In the PT-based defense system Ssp, SspABCD confers a single-stranded PT modification of host DNA notes: Gao et al. support Ssp as a PT-based defense system with host-DNA phosphorothioation by SspABCD. - reference: DOI:10.1038/s41467-022-34505-0 snippet: SspE relies on PT modification in host DNA to exert antiphage activity notes: Gao et al. connect host PT modification to SspE-mediated antiphage activity. - reference: DOI:10.1128/mbio.00933-23 snippet: a novel PT-related R-M system, composed of the modification module SspABCD paired with a single restriction enzyme, SspE notes: Jiang et al. support defining this child by the SspABCD modification module paired with single-enzyme SspE restriction, separate from DndFGH and SspFGH systems. canonical_examples: - taxon_id: NCBITaxon:47951 taxon_label: Vibrio cyclitrophicus note: Xiong et al. describe an SspABCD-SspE PT system in Vibrio cyclitrophicus and analyze its SspABCD-dependent single-stranded PTs plus SspE-dependent antiphage activity. reference: DOI:10.1038/s41564-020-0700-6 causal_graphs: - graph_id: sspabcd_sspe_pt_site_dependent_dna_nicking title: SspABCD-SspE systems couple Ssp PT marks to DNA nicking description: Evidence-backed process sketch linking an SspABCD-SspE locus to single-stranded host DNA phosphorothioation, SspE PT-site recognition, SspE GTPase-linked nuclease activation, and reduced phage DNA replication. scope_status: NONMECHANISTIC scope_notes: The graph captures SspABCD-SspE restriction at the system level without asserting one universal host taxon, PT frequency, DNA motif outside 5'-CPSCA-3'-characterized systems, full SspE conformational cycle, or relationship to SspFGH and archaeal PT antiviral systems. nodes: - node_id: sspabcd_sspe_locus label: SspABCD-SspE locus node_type: GENETIC_ELEMENT description: An Ssp phosphorothioation-dependent restriction locus pairing the SspABCD DNA modification module with SspE restriction activity. - node_id: ssp_single_stranded_dna_phosphorothioation label: Ssp single-stranded DNA phosphorothioation node_type: BIOLOGICAL_PROCESS description: SspABCD-mediated installation of single-stranded phosphorothioate marks on host DNA. - node_id: sspe_pt_site_recruitment label: SspE PT-site recruitment node_type: BIOLOGICAL_PROCESS description: Preferential recruitment of SspE to phosphorothioate-marked DNA sites. - node_id: sspe_gtpase_activation label: SspE GTPase activation node_type: BIOLOGICAL_PROCESS description: PT-dependent enlargement of the SspE GTP-binding pocket and stimulation of GTP hydrolysis. - node_id: sspe_dna_nicking label: SspE DNA nicking node_type: BIOLOGICAL_PROCESS description: SspE nuclease activation and DNA nicking during phosphorothioate-dependent self/nonself discrimination. - node_id: phage_dna_replication label: phage DNA replication node_type: BIOLOGICAL_PROCESS description: Replication of invading bacteriophage DNA after host cell entry. - node_id: sspabcd_sspe_system_trait label: SspABCD-SspE system node_type: TRAIT grounding: traitmech:000222 description: Possession of a genome-encoded SspABCD-SspE restriction-modification defense system. - node_id: phosphorothioate_defense_system_trait label: phosphorothioate defense system node_type: TRAIT grounding: traitmech:000213 description: Possession of a genome-encoded phosphorothioate-based phage defense system. edges: - subject: sspabcd_sspe_locus predicate: contributes to predicate_id: RO:0002326 object: ssp_single_stranded_dna_phosphorothioation description: The SspABCD modification module installs single-stranded, high-frequency PT marks on host DNA. evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase notes: Xiong et al. support SspABCD-dependent host DNA phosphorothioation. - subject: sspabcd_sspe_locus predicate: contributes to predicate_id: RO:0002326 object: sspe_pt_site_recruitment description: SspABCD-SspE loci pair SspABCD host-DNA phosphorothioation with single-enzyme SspE restriction activity. evidence: - reference: DOI:10.1128/mbio.00933-23 snippet: the modification module SspABCD paired with a single restriction enzyme, SspE notes: Jiang et al. support the paired SspABCD modification and SspE restriction architecture. - subject: ssp_single_stranded_dna_phosphorothioation predicate: contributes to predicate_id: RO:0002326 object: sspe_pt_site_recruitment description: SspE relies on host DNA PT marks and is preferentially recruited to PT sites. evidence: - reference: DOI:10.1038/s41467-022-34505-0 snippet: SspE relies on PT modification in host DNA to exert antiphage activity notes: Gao et al. support PT-dependent SspE activity. - subject: sspe_pt_site_recruitment predicate: activates predicate_id: RO:0002213 object: sspe_gtpase_activation description: PT-site recognition stimulates the SspE GTPase cycle. evidence: - reference: DOI:10.1038/s41467-022-34505-0 snippet: PT recognition enlarges the GTP-binding pocket, thereby increasing GTP hydrolysis activity notes: Gao et al. support PT-induced SspE GTPase activation. - subject: sspe_gtpase_activation predicate: activates predicate_id: RO:0002213 object: sspe_dna_nicking description: GTPase-linked conformational switching activates SspE nuclease nicking activity. evidence: - reference: DOI:10.1038/s41467-022-34505-0 snippet: turns on the DNA nicking nuclease activity of CTD notes: Gao et al. support activation of SspE DNA-nicking nuclease activity. - subject: sspe_dna_nicking predicate: mitigates predicate_id: METPO:2007407 object: phage_dna_replication description: SspE-linked DNA nicking inhibits phage propagation by impairing phage DNA replication. evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication notes: Xiong et al. directly connect SspE DNA-nicking damage to impaired phage DNA replication. - subject: sspe_dna_nicking predicate: confers predicate_id: METPO:2007700 object: sspabcd_sspe_system_trait description: SspE DNA nicking realizes the SspABCD-SspE antiphage defense trait. evidence: - reference: DOI:10.1038/s41467-022-34505-0 snippet: enabling SspE to accomplish self-nonself discrimination and limit phage predation notes: Gao et al. support SspE self/nonself discrimination as the Ssp antiphage output. - subject: sspabcd_sspe_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phosphorothioate_defense_system_trait description: SspABCD-SspE possession is a phosphorothioate-defense-system trait. evidence: - reference: DOI:10.1038/s41564-020-0700-6 snippet: SspABCD coupled with SspE provides protection against phages notes: Xiong et al. place SspABCD-SspE within phosphorothioation-dependent antiphage defense systems. curation_history: - timestamp: '2026-09-15T16:38:06Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted SspABCD-SspE system as a DOI-backed GENOMICS TraitRecord under the phosphorothioate defense system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v99. llm_assisted: true