identifier: traitmech:000403 label: Rst_RT-nitrilase-Tm system definition: A phage defense system in which an organism possesses a two-protein Rst_RT-nitrilase-Tm locus represented by DefenseFinder as a two-profile Rst_RT-Tm model requiring Rst_RT-Tm__RT and Rst_RT-Tm__RT-Tm and experimentally linked to AL505_P2 protection when expressed in Escherichia coli. definition_source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Rst_RT-nitrilase-Tm synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: RT-nitrilase-Tm synonym_type: RELATED_SYNONYM source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md - synonym_text: UG5-large synonym_type: RELATED_SYNONYM source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md - synonym_text: Rst_RT-Tm synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv - synonym_text: Rst_RT-Tm__RT synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Rst_RT-Tm__RT2 synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: Rst_RT-Tm__RT-Tm synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md - synonym_text: RT-Tm synonym_type: RELATED_SYNONYM source: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector notes: Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector. - reference: DOI:10.1016/j.chom.2022.02.018 snippet: Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages notes: The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae). notes: The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}. notes: The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: 'The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.' notes: The pinned DefenseFinder wiki page maps the Rst-prefixed name to a two-component RT/RT-Tm structure. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: The Rst_RT-Tm system in *Morganella morganii* (GCF_900478755.1, NZ_LS483498) is composed of 2 proteins RT (WP_061057569.1) RT-Tm (WP_004234654.1) notes: The DefenseFinder wiki illustrates a predicted two-protein Rst_RT-Tm locus in RefSeq assembly GCF_900478755.1 on NZ_LS483498. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: Expressed_0[Escherichia coli] ----> Al505_P2 notes: The DefenseFinder experimental-validation diagram links Escherichia coli expression of the Rst_RT-nitrilase-Tm system to protection against AL505_P2. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Rst_RT-nitrilase-Tm | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems notes: The DefenseFinder article registry maps the named Rst_RT-nitrilase-Tm system to the Rousset et al. preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\ \t\t" notes: The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_RT-Tm__RT | Rst_RT-Tm__RT | Rst_RT-Tm | Custom | 500 | | Rst_RT-Tm__RT2 | | Rst_RT-Tm | Custom | 100 | | Rst_RT-Tm__RT-Tm | Rst_RT-Tm__RT-Tm | Rst_RT-Tm | Custom | 100 |' notes: The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace. causal_graphs: - graph_id: rst_rt_nitrilase_tm_locus_restricts_al505_p2 title: Rst_RT-nitrilase-Tm loci restrict AL505_P2 description: Conservative system-level sketch linking a named Rst_RT-nitrilase-Tm two-gene locus model to AL505_P2 phage resistance. scope_status: NONMECHANISTIC scope_notes: The graph captures Rst_RT-nitrilase-Tm as a named DefenseFinder two-profile phage-defense system while leaving native host breadth, the exact Rst_RT-nitrilase-Tm-to-Rst_RT-Tm naming relationship, RT and RT-Tm molecular roles, the relationship to UG5-large systems, and the mechanism of AL505_P2 restriction unresolved. nodes: - node_id: rst_rt_nitrilase_tm_locus label: Rst_RT-nitrilase-Tm locus node_type: GENETIC_ELEMENT description: A two-gene reverse-transcriptase/nitrilase plus transmembrane-protein phage-defense locus represented by the DefenseFinder Rst_RT-Tm profiles. - node_id: al505_p2_phage_resistance label: AL505_P2 phage resistance node_type: BIOLOGICAL_PROCESS description: Resistance against phage AL505_P2 in a host expressing an Rst_RT-nitrilase-Tm locus. - node_id: rst_rt_nitrilase_tm_system_trait label: Rst_RT-nitrilase-Tm system node_type: TRAIT grounding: traitmech:000403 description: Possession of a genome-encoded Rst_RT-nitrilase-Tm phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: rst_rt_nitrilase_tm_locus predicate: contributes to predicate_id: RO:0002326 object: al505_p2_phage_resistance description: Rousset et al. linked a group-5 reverse transcriptase/nitrilase plus transmembrane effector locus to phage resistance, and DefenseFinder models Rst_RT-nitrilase-Tm as a two-profile Rst_RT-Tm system. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector notes: Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}. notes: The pinned DefenseFinder wiki page describes the reverse-transcriptase/nitrilase plus transmembrane-protein architecture. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: 'The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.' notes: The pinned DefenseFinder wiki page maps the Rst-prefixed name to a two-component RT/RT-Tm structure. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\ \t\t" notes: The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_RT-Tm__RT | Rst_RT-Tm__RT | Rst_RT-Tm | Custom | 500 | | Rst_RT-Tm__RT2 | | Rst_RT-Tm | Custom | 100 | | Rst_RT-Tm__RT-Tm | Rst_RT-Tm__RT-Tm | Rst_RT-Tm | Custom | 100 |' notes: The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace. - subject: al505_p2_phage_resistance predicate: confers predicate_id: METPO:2007700 object: rst_rt_nitrilase_tm_system_trait description: Rst_RT-nitrilase-Tm-linked AL505_P2 resistance realizes the Rst_RT-nitrilase-Tm system trait. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages notes: The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae). notes: The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: Expressed_0[Escherichia coli] ----> Al505_P2 notes: The DefenseFinder experimental-validation diagram links Escherichia coli expression of the Rst_RT-nitrilase-Tm system to protection against AL505_P2. - subject: rst_rt_nitrilase_tm_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Rst_RT-nitrilase-Tm system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: Phage resistance heatmap of the validated defense systems shows the mean fold resistance of three independent replicates against a panel of eight phages notes: The Figure 2 legend frames the cloned P4-hotspot hits, including the RT-nitrilase plus one-TM system, as validated defense systems in a replicated phage-resistance heatmap. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Rst_RT-nitrilase-Tm | 10\.1101/2021\.01\.21\.427644 | Prophage-encoded hotspots of bacterial immune systems notes: The DefenseFinder article registry maps the named Rst_RT-nitrilase-Tm system to the Rousset et al. preprint. discussions: - discussion_id: rst-rt-nitrilase-tm-host-mechanism-gap prompt: Resolve Rst_RT-nitrilase-Tm native host breadth, the Rst_RT-nitrilase-Tm and Rst_RT-Tm namespace relationship, accession-level RT/RT-Tm roles, the relationship to UG5-large source naming, and the mechanism of AL505_P2 restriction before minting narrower Rst_RT-nitrilase-Tm mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Rousset et al. support a two-gene P4-hotspot system that combines a group-5 reverse transcriptase with a C-terminal nitrilase domain and a transmembrane effector, and DefenseFinder maps Rst_RT-nitrilase-Tm to a required two-profile Rst_RT-Tm model. This first system-level record leaves native host breadth, exact profile-to-gene mapping, the model-namespace mismatch, the relationship to UG5-large source naming, the molecular activities of the RT and RT-Tm components, and the AL505_P2 restriction mechanism unresolved. evidence: - reference: DOI:10.1016/j.chom.2022.02.018 snippet: with a C-terminal nitrilase domain (Table S3) that is associated with a transmembrane effector notes: Rousset et al. described a validated P4-hotspot system containing a group-5 reverse transcriptase with a C-terminal nitrilase domain associated with a transmembrane effector. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/rst_rt-nitrilase-tm.md snippet: RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae). notes: The pinned DefenseFinder wiki page names RT-nitrilase-Tm, also called UG5-large, as a two-gene system and records AL505_P2 antiphage activity in Escherichia coli. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Rst_RT-nitrilase-Tm\tRst_RT-Tm\t2\t2\tRst_RT-Tm__RT, Rst_RT-Tm__RT-Tm\t\ \t\t" notes: The DefenseFinder rules table maps Rst_RT-nitrilase-Tm to a two-profile Rst_RT-Tm model requiring RT and RT-Tm profiles. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Rst_RT-Tm__RT | Rst_RT-Tm__RT | Rst_RT-Tm | Custom | 500 | | Rst_RT-Tm__RT2 | | Rst_RT-Tm | Custom | 100 | | Rst_RT-Tm__RT-Tm | Rst_RT-Tm__RT-Tm | Rst_RT-Tm | Custom | 100 |' notes: The DefenseFinder HMM inventory records the RT, alternate RT2, and RT-Tm profiles under the normalized Rst_RT-Tm system namespace. attaches_to: - causal_graphs#rst_rt_nitrilase_tm_locus_restricts_al505_p2 posed_by: codex posed_date: '2026-09-27' curation_history: - timestamp: '2026-09-27T06:35:23Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Rst_RT-nitrilase-Tm system as a DOI/stable-URL-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v280. llm_assisted: true - timestamp: '2026-09-27T06:35:24Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed Rst_RT-nitrilase-Tm during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support a cloned P4-hotspot RT/RT-Tm locus assayed in Escherichia coli and a DefenseFinder RefSeq model example, but not a direct native microbial host exemplar with experimentally verified Rst_RT-nitrilase-Tm activity. No paid research was used. llm_assisted: true