id: MODULE:anti_crispr_suppression title: Anti-CRISPR suppression of host CRISPR-Cas immunity description: Proteins encoded by bacteriophages, archaeal viruses, prophages and other mobile genetic elements suppress host CRISPR-Cas immunity through alternative mechanisms. These include blocking effector assembly or target recognition, sequestering an effector subunit or disabling its nuclease, modifying Cas proteins, cleaving guide RNA, and degrading an immune second messenger. A mobile element may combine several inhibitors, but these are not compulsory sequential steps. Optional anti-CRISPR-associated regulators control inhibitor expression. The examples span bacterial and archaeal hosts; plasmid and conjugative-element inhibitors need not have a viral origin. status: DRAFT scope: CONCRETE evidence: - source_id: PMID:23242138 statement: Phage genes can inhibit bacterial CRISPR-Cas immunity. - source_id: PMID:26416740 statement: Different anti-CRISPR proteins independently inhibit target-DNA binding or downstream nuclease recruitment. - source_id: PMID:32503371 statement: Review distinguishes stoichiometric inhibitors from enzymatic modifications and signal degradation; the families have diverse structures and mechanisms. - source_id: PMID:32186918 statement: Review surveys anti-CRISPR proteins produced by viruses and other mobile elements. - source_id: PMID:32218510 statement: AcrIIA16–19 occur in plasmids, conjugative elements, prophages and other contexts; defined inhibitors protect targeted plasmids during Enterococcus faecalis conjugation. Mobile-element origin is not synonymous with viral origin. - source_id: PMID:38987591 statement: Aca2 represses transcription by binding DNA and represses translation by binding RNA stem-loops that limit ribosome access. - source_id: PMID:40240860 statement: The Comment tested native SIRV2 gp37 and SIRV1 gp29 transplanted into SIRV2, with early-expression rescue. It did not test native SIRV1 infection. Physiological generalization remains disputed. - source_id: PMID:40240850 statement: The Reply disputes physiological generalization of the infection experiments and raises possible experimental confounders; these remain objections attributed to its authors. notes: 'The participant taxon envelope includes viral proteins and proteins deposited under bacterial genomes, including prophages and nonviral mobile elements. Hosts are bacteria or archaea as specified for each experimental system; heterologous human-cell editing assays do not extend the native host range. Inhibitory occupancy depends on affinity, concentration, binding stoichiometry and timing: a stoichiometric blocker does not universally require molar excess. Catalytic turnover can permit substoichiometric inhibition in vitro without establishing effective native expression. Families are sampled by tested members; conserved membership alone does not establish all targets or native counterdefense. Host CRISPR functions are described separately in MODULE:crispr_cas_adaptive_immunity. Host self-regulatory ring nucleases and unrelated anti-defense mechanisms remain outside the functional boundary.' module: id: anti_crispr_suppression label: anti-CRISPR suppression of host CRISPR-Cas immunity module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system description: Inhibition or disruption of a host CRISPR-Cas system by a symbiont, here a phage or other mobile genetic element. context: taxa: - preferred_term: Viruses term: id: NCBITaxon:10239 label: Viruses description: Bacteriophages and archaeal viruses encode several directly tested representatives. - preferred_term: Bacteria term: id: NCBITaxon:2 label: Bacteria description: Bacterial genomic records contain prophage-associated and nonviral mobile-element Acrs. A bacterial source accession is not evidence that every member is host self-regulatory or that its mobile element is viral. cellular_components: - preferred_term: host cell cytoplasm term: id: GO:0030430 label: host cell cytoplasm description: This host-relative location applies to viral proteins acting within infected cells. Proteins encoded in bacterial genomic records are reviewed as cytoplasmic; the host-relative term is not propagated to every bacterial source accession. - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm description: Bacterial source accessions are reviewed in their cytoplasmic context, including AcrVA1, AcrIIC1 and AcrIIA4. This source-record convention does not establish that the protein is a host self-regulator or identify its native mobile element. parts: - role: One or more alternative counterdefense mechanisms node: id: counterdefense_routes label: alternative anti-CRISPR mechanisms module_type: BIOLOGICAL_PROCESS variant_sets: - id: anti_crispr_mechanism label: independent inhibition mechanisms axis: effector target and inhibitory mechanism selection: ONE_OR_MORE notes: A realization uses a compatible inhibitor and susceptible host target. These variants are alternatives that may coexist, not an obligate series; the AcrIII-1 branch additionally requires a permissive expression context. variants: - id: acrif8_recognition_blockade label: 'AcrIF8: Csy/crRNA blockade' module_type: BIOLOGICAL_PROCESS description: AcrIF8 uses protein and guide-RNA contacts to inhibit the tested type I-F complex. annotons: - id: acrif8_csy_blocker label: AcrIF8 Csy complex and crRNA-contacting blocker participant: selector_type: FAMILY family: preferred_term: AcrF8 (AcrIF8) anti-CRISPR family description: Official InterPro API verification places H9C181 in IPR057730 across residues 1–92; the family integrates Pfam PF25699. CDD cd22241 independently corroborates AcrIF8 identity. Raw responses and retrieval provenance are preserved in modules/anti_crispr_suppression-source-analysis/README.md. term: id: InterPro:IPR057730 label: Anti-CRISPR protein AcrF8 representative_members: - preferred_term: ZF40_0031 / acrIF8 (Pectobacterium phage ZF40) term: id: UniProtKB:H9C181 label: Anti-CRISPR protein AcrF8 description: ZF40 AcrIF8 engages the Pseudomonas type I-F surveillance complex used in structural assays; this does not imply that all host Csy orthologs are susceptible. function: preferred_term: ribonucleoprotein complex binding term: id: GO:0043021 label: ribonucleoprotein complex binding targets: - preferred_term: host type I-F Csy surveillance complex (Cas7f backbone and crRNA) evidence: - source_id: PMID:32170016 statement: Cryo-EM resolves contacts to both Cas7f and crRNA, explaining inhibition of target-DNA engagement. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Occupies the Csy ribonucleoprotein complex and prevents productive R-loop formation. Inhibitory occupancy is stoichiometric; no universal molar-excess threshold is asserted. - id: acrif2_recognition_blockade label: 'AcrIF2: DNA mimicry at Cascade' module_type: BIOLOGICAL_PROCESS description: DNA mimicry can inhibit distinct class 1 surveillance systems, with effector-specific susceptibility. annotons: - id: acrif2_csy_blocker label: AcrIF2-family Csy complex blocker participant: selector_type: FAMILY family: preferred_term: AcrF2 anti-CRISPR family term: id: InterPro:IPR057728 label: Anti-CRISPR protein AcrF2 representative_members: - preferred_term: orf30 / gp30 (Pseudomonas phage D3112) term: id: UniProtKB:Q6TM72 label: Anti-CRISPR protein 30 description: One of the first anti-CRISPR genes identified, in the type I-F system of Pseudomonas aeruginosa. function: preferred_term: nucleic acid mimicry-based competitive inhibitor activity description: An acidic DNA-mimicking surface occupies the DNA-capture region of the surveillance complex. targets: - preferred_term: host type I-F Cas8f/Cas7f DNA-capture pocket evidence: - source_id: PMID:28340349 statement: AcrIF2 occupies the type I-F Cas8f/Cas7f DNA-capture pocket and mimics duplex DNA. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system evidence: - source_id: PMID:23242138 statement: The D3112 inhibitor was identified in phage counterdefense. - source_id: PMID:36805026 statement: AcrIF2 also inhibits the tested Desulfovibrio vulgaris type I-C system; activity against one subtype or ortholog does not imply universal susceptibility. role_description: Prevents target-DNA engagement by susceptible surveillance complexes; type I-F and selected type I-C activity are compatible with one inhibitor. - id: acriia4_recognition_blockade label: 'AcrIIA4: Cas9 PAM-site occlusion' module_type: BIOLOGICAL_PROCESS description: A DNA mimic blocks target recognition and access to a nuclease pocket in RNA-loaded SpyCas9. annotons: - id: acriia4_dna_mimic label: AcrIIA4 PAM-duplex mimic participant: selector_type: FAMILY family: preferred_term: AcrIIA4-like anti-CRISPR family term: id: InterPro:IPR056215 label: Anti-CRISPR Suppressor AcrIIA4-like representative_members: - preferred_term: acrIIA4 (Listeria monocytogenes prophage) term: id: UniProtKB:A0A247D711 label: Anti-CRISPR protein AcrIIA4 description: The 87-residue prophage-encoded SpyCas9 inhibitor used widely as an off-switch reagent. function: preferred_term: DNA mimicry-based competitive occlusion of the Cas9 PAM-recognition site description: An acidic surface mimics target DNA at sgRNA-loaded SpyCas9, occupying PAM-recognition and RuvC-access surfaces. targets: - preferred_term: host Cas9 PAM-interacting domain - preferred_term: host Cas9 RuvC non-target-strand cleavage pocket evidence: - source_id: PMID:28602637 statement: The AcrIIA4–sgRNA–SpyCas9 structure explains PAM-site occlusion and blockade of target-strand access. - source_id: PMID:28706995 statement: AcrIIA4 inhibits Cas9 before stable target-DNA binding; preformed DNA-bound complexes are resistant under the tested conditions. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Inhibits productive target binding by susceptible RNA-loaded Cas9; this is a time- and effector-dependent mechanism, not universal reversal of already bound Cas9. - id: acriia2_recognition_blockade label: 'AcrIIA2: convergent Cas9 DNA mimicry' module_type: BIOLOGICAL_PROCESS description: The LP-101 representative is an ortholog-based example of a separately characterized DNA-mimic family. annotons: - id: acriia2_dna_mimic label: AcrIIA2 DNA-mimicking Cas9 inhibitor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: LP101_024 / acrIIA2 (Listeria phage LP-101) term: id: UniProtKB:A0A059T5F6 label: Anti-CRISPR protein AcrIIA2 description: LP-101 AcrIIA2 ortholog. Existing notes identify nine residue differences from the directly assayed prophage protein; structural mechanism is ortholog-supported rather than an exact LP-101 construct assay. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system evidence: - source_id: PMID:30606466 statement: Characterized AcrIIA2 proteins inhibit Cas9 through DNA mimicry at the PAM-recognition surface; exact LP-101 construct identity is not asserted. role_description: A distinct AcrIIA2 family converges on Cas9 target-site occlusion. Sequence identity and target specificity must be checked for individual orthologs. - id: acriic2_assembly_blockade label: 'AcrIIC2: guide-loading blockade' module_type: BIOLOGICAL_PROCESS description: Binding apo-Cas9 prevents effector ribonucleoprotein assembly, an alternative to attacking an assembled effector. annotons: - id: acriic2_assembly_inhibitor label: AcrIIC2 Cas9 assembly inhibitor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: acrIIC2 (Neisseria meningitidis) term: id: UniProtKB:A0A425B3G2 label: Phage associated protein function: preferred_term: Cas9 ribonucleoprotein assembly inhibitor activity targets: - preferred_term: Nme1Cas9 bridge helix evidence: - source_id: PMID:31243272 statement: AcrIIC2 binds the positively charged Cas9 bridge helix and prevents guide-RNA loading. - source_id: PMID:30850331 statement: Structural and biochemical experiments establish dimeric AcrIIC2 inhibition of Cas9 assembly. term: id: GO:0140721 label: nuclease inhibitor activity processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Acts before a functional Cas9–guide complex forms; it need not first block target-DNA recognition. - id: acrif3_nuclease_sequestration label: 'AcrIF3: Cas2/3 sequestration' module_type: BIOLOGICAL_PROCESS description: In the tested type I-F system a separate nuclease-helicase is sequestered. This does not describe all class 1 effector architectures. annotons: - id: acrif3_cas3_sequestration label: AcrF3 Cas3 sequestering inhibitor participant: selector_type: FAMILY required_function: preferred_term: protein sequestering activity term: id: GO:0140311 label: protein sequestering activity family: preferred_term: AcrF3-like Cas3 inhibitor family term: id: InterPro:IPR049085 label: Cas3 inhibitor AcrF3-like representative_members: - preferred_term: JBD5_035 / acrIF3 (Pseudomonas phage JBD5) term: id: UniProtKB:L7P7R7 label: Phage protein description: InterPro assigns this JBD5 protein to the AcrF3-like Cas3 inhibitor family; UniProt has not yet given it a mechanism-bearing name. function: preferred_term: protein sequestering activity term: id: GO:0140311 label: protein sequestering activity targets: - preferred_term: host type I-F Cas3 helicase-nuclease evidence: - source_id: PMID:27455460 statement: The AcrF3-Cas3 structure establishes that inhibition works by binding Cas3 directly and preventing its recruitment to the Cascade-bound target. - source_id: PMID:26416740 statement: One of the three mechanistically distinct inhibitors characterised in this work, and the one that acts on the nuclease rather than the surveillance complex. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: AcrIF3 binds the type I-F Cas2/3 nuclease-helicase and prevents productive recruitment to the target-bound Csy complex. DNA recognition can remain intact. - id: acriic1_catalytic_blockade label: 'AcrIIC1: Cas9 HNH-domain inhibition' module_type: BIOLOGICAL_PROCESS description: A catalytic-domain inhibitor can preserve target occupancy while inhibiting cleavage. annotons: - id: acriic1_hnh_blocker label: AcrIIC1 broad-spectrum Cas9 HNH inhibitor participant: selector_type: FAMILY family: preferred_term: AcrIIC1 anti-CRISPR family term: id: InterPro:IPR064626 label: Anti-CRISPR type II subtype C1 representative_members: - preferred_term: acrIIC1 (Neisseria meningitidis prophage) term: id: UniProtKB:A0A2D0TCG3 label: Anti-CRISPR protein description: The AcrIIC1 inhibitor of type II-C Cas9 orthologues. function: preferred_term: nuclease inhibitor activity term: id: GO:0140721 label: nuclease inhibitor activity description: Binding the conserved HNH domain inhibits nuclease function while permitting target-DNA association in the tested Cas9 systems. targets: - preferred_term: host Cas9 HNH nuclease domain evidence: - source_id: PMID:28844692 statement: AcrIIC1 binds the HNH domain and inhibits several tested Cas9 orthologs without requiring loss of DNA binding. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Suppresses cleavage by susceptible Cas9 proteins; broad activity across tested orthologs is not universal inhibition of all Cas9 enzymes. - id: acrid1_subunit_sequestration label: 'AcrID1: archaeal Cas10d sequestration' module_type: BIOLOGICAL_PROCESS description: A viral inhibitor disrupts subtype I-D effector assembly by trapping Cas10d in a nonfunctional oligomer. annotons: - id: acrid1_cas10d_sequesterer label: AcrID1 Cas10d sequestering inhibitor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: acrID1 / gp02 (Sulfolobus islandicus rod-shaped virus 3) term: id: UniProtKB:A0A1B3SN05 label: Uncharacterized protein function: preferred_term: protein sequestering activity targets: - preferred_term: type I-D Cas10d large subunit evidence: - source_id: PMID:29507349 statement: Insertion of SIRV3 gp02 restores infectivity of a deletion virus in a CRISPR-positive Sulfolobus host; AcrID1 directly interacts with Cas10d. - source_id: PMID:33239638 statement: Two AcrID1 dimers sequester two Cas10d subunits in a 4:2 assembly that cannot form a cleavage-competent effector complex. term: id: GO:0140311 label: protein sequestering activity processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Sequesters a large subunit whose HD nuclease and polymerase-like architecture differ from the separate type I-F Cas2/3 recruitment target. The completed target-bound effector complex resists inhibition under the tested conditions. - id: acrvia1_rna_target_blockade label: 'AcrVIA1: RNA-target recognition and activation blockade' module_type: BIOLOGICAL_PROCESS description: Type VI-A counterdefense inhibits an RNA-targeting immune effector rather than a DNA nuclease. annotons: - id: acrvia1_cas13a_blocker label: AcrVIA1 Lse Cas13a blocker participant: selector_type: GENE_PRODUCT gene_product: preferred_term: acrVIA1 (Listeria seeligeri phage phiLS46 gp2) term: id: UniProtKB:A0A6P3CWF5 label: AcrVIA1 description: The 229-residue UniProt sequence maps directly to PDB 6VRB. The discovery paper describes native gp2 as 232 residues; that sequence-length discrepancy is retained as a construct/provenance limitation, not silently resolved. function: preferred_term: Cas13a target-RNA recognition inhibitor activity targets: - preferred_term: guide-exposed face of Listeria seeligeri Cas13a evidence: - source_id: PMID:32467331 statement: Genetics, biochemistry and cryo-EM show that phiLS46 AcrVIA1 blocks target-RNA access and nuclease-activating conformational changes; an individual virion can evade the tested type VI-A defense. term: id: GO:0140721 label: nuclease inhibitor activity processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Prevents both target-RNA recognition and activation of collateral RNA cleavage in the susceptible Cas13a system. Native specificity and the phiLS46 sequence distinguish it from unrelated proteins sharing an AcrVIA name. - id: acrva1_guide_cleavage label: 'AcrVA1: Cas12a-dependent guide cleavage' module_type: BIOLOGICAL_PROCESS description: Guide cleavage and PAM-pocket interference inhibit susceptible Cas12a complexes through overlapping mechanisms. annotons: - id: acrva1_crrna_nuclease label: AcrVA1 crRNA-cleaving inhibitor of Cas12a participant: selector_type: FAMILY family: preferred_term: AcrVA1-like anti-CRISPR family term: id: InterPro:IPR064663 label: Anti-CRISPR type V subtype A1-like representative_members: - preferred_term: acrVA1 (Moraxella bovoculi) term: id: UniProtKB:A0A5H1ZR47 label: AcrVA1 description: The Moraxella AcrVA1 inhibitor of Cas12a orthologues. function: preferred_term: RNA endonuclease activity term: id: GO:0004521 label: RNA endonuclease activity description: Cas12a-dependent guide cleavage is experimentally established. The original biochemical paper did not identify the catalytic component; later structural work assigns an RNase site to AcrVA1 helix alpha2. This is not autonomous cleavage of free guide RNA. substrates: - preferred_term: Cas12a-bound crRNA guide products: - preferred_term: Cas12a-bound 5-prime crRNA fragment and released targeting 3-prime fragment evidence: - source_id: PMID:30936531 statement: AcrVA1 triggers multiple-turnover cleavage of Cas12a-bound crRNA and release of the targeting 3-prime fragment; the original study left catalytic-center attribution unresolved. - source_id: PMID:31155345 statement: Subsequent structural study reports an RNase active site in AcrVA1 helix alpha2 and Cas12a-dependent guide cleavage. processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Truncates the targeting region of Cas12a-bound crRNA and can act under substoichiometric assay conditions. The retained 5-prime fragment means the product is not simply apo-Cas12a; irreversibility in every assay context is not asserted. - id: acriii1_signal_degradation label: 'AcrIII-1: cA4 destruction with disputed native deployment' module_type: BIOLOGICAL_PROCESS description: 'cA4 degradation can dampen the cA4-dependent accessory-defense branch of type III systems. It does not abolish every type III activity: direct RNA cleavage, Cas10 nuclease activity and other cyclic-oligonucleotide specificities are distinct.' annotons: - id: acriii1_ring_nuclease label: AcrIII-1 viral cyclic oligoadenylate ring nuclease participant: selector_type: GENE_PRODUCT gene_product: preferred_term: orf114 / gp29 / AcrIII-1 (Sulfolobus islandicus rod-shaped virus 1) term: id: UniProtKB:Q8QL27 label: Uncharacterized protein 114 description: Exact assayed protein established by RefSeq NP_666617 and PDB 6SCF/2X4I. DUF1874/STIV B116-like membership is not sufficient to classify every homolog as a native anti-CRISPR. function: preferred_term: cyclic oligoadenylate ring nuclease activity description: A homodimeric ring nuclease cleaves cA4 to linear diadenylate with a 2-prime,3-prime cyclic phosphate. substrates: - preferred_term: cyclic tetra-adenylate (cA4) products: - preferred_term: linear diadenylate with a 2-prime,3-prime cyclic phosphate (ApA>p) evidence: - source_id: PMID:31942067 statement: Purified SIRV1 gp29 and the tested homolog cleave internal phosphodiester linkages in cA4 to yield cyclic-phosphate products; heterologous/plasmid expression can suppress cA4-dependent type III defense. role_description: Established cA4 chemistry provides a conditional suppression capability. Its contribution during native viral infection remains disputed, so no unconditional GO:0098672 process assertion is attached to this representative. evidence: - source_id: PMID:40240860 statement: Native SIRV2 gp37 and SIRV1 gp29 transplanted into SIRV2 did not provide protection under the tested expression conditions; earlier expression rescued protection. Native SIRV1 infection was not directly tested. - source_id: PMID:40240850 statement: The Reply challenges extrapolation to native physiology and identifies possible experimental confounders. The exchange does not negate the established cA4 cleavage. - id: acrva5_covalent_modification label: 'AcrVA5: covalent Cas12a acetylation' module_type: BIOLOGICAL_PROCESS description: Catalytic transfer of an acetyl group blocks target recognition without requiring permanent occupancy of the effector. annotons: - id: acrva5_cas12a_acetyltransferase label: AcrVA5 Cas12a acetyltransferase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: acrVA5 / AAX07_09540 (Moraxella bovoculi) term: id: UniProtKB:A0A0U2B867 label: N-acetyltransferase domain-containing protein description: Official UniSave version 17 of deleted UniProtKB A0A0U2B867; the 92-residue sequence matches PDB 6IUF apart from its N-terminal PLGS construct tag. Archived identity is preserved explicitly, not presented as a current UniProtKB record. function: preferred_term: Cas12a lysine acetyltransferase activity targets: - preferred_term: PAM-recognition lysine of susceptible Cas12a evidence: - source_id: PMID:30936526 statement: AcrVA5 transfers an acetyl group from acetyl-CoA to MbCas12a Lys635, disrupting PAM recognition; Lys635Arg is resistant. - source_id: PMID:35581175 statement: CobB-mediated deacetylation can reverse the inhibited state in the tested system. substrates: - preferred_term: acetyl-CoA - preferred_term: unmodified Cas12a lysine products: - preferred_term: CoA - preferred_term: N6-acetyllysine-containing Cas12a term: id: GO:0061733 label: protein-lysine-acetyltransferase activity processes: - preferred_term: symbiont-mediated suppression of host CRISPR-cas system term: id: GO:0098672 label: symbiont-mediated suppression of host CRISPR-cas system role_description: Covalently modifies a Cas protein instead of destroying it. Inhibition depends on the susceptible lysine and can be reversed enzymatically; GNAT-like fold membership does not establish anti-CRISPR function. - role: Optional local control of inhibitor expression optional: true node: id: aca_autoregulation label: Aca2 DNA/RNA autoregulation module_type: REGULATORY_STEP description: The ZF40 acrIF8–aca2 locus couples inhibitor expression to a regulator that represses its own operon at transcriptional and translational levels. The loop regulates expression rather than sensing whether Cas inhibition has succeeded. Other loci may lack Aca2 or use distinct regulators. annotons: - id: aca2_repressor label: Aca2 anti-CRISPR-associated repressor participant: selector_type: FAMILY required_function: preferred_term: DNA-binding transcription repressor activity term: id: GO:0001217 label: DNA-binding transcription repressor activity family: preferred_term: Aca2/YdiL-like anti-CRISPR-associated repressor family term: id: InterPro:IPR015060 label: Aca2/YdiL-like representative_members: - preferred_term: ZF40_0030 / aca2 (Pectobacterium phage ZF40) term: id: UniProtKB:H9C180 label: Aca2 repressor description: The repressor co-transcribed with acrIF8 in the same phage, which is why the regulatory part and the recognition-blockade part share an exemplar locus. description: This selector refers to anti-CRISPR-associated repressors with a demonstrated regulated locus; Aca2/YdiL-like homology alone does not establish the target operon or every regulatory mode. function: preferred_term: DNA-binding transcription repressor activity term: id: GO:0001217 label: DNA-binding transcription repressor activity targets: - preferred_term: shared aca2-acr promoter operator evidence: - source_id: PMID:31428783 statement: Aca2 dimers bind inverted repeats in the acrIF8–aca2 promoter and repress the shared operon. processes: - preferred_term: negative regulation of DNA-templated transcription term: id: GO:0045892 label: negative regulation of DNA-templated transcription role_description: Controls the abundance of the ZF40 AcrIF8 inhibitor through negative feedback on its shared operon. Aca2 is not itself a Cas inhibitor and need not sense successful immune suppression. - id: aca2_translation_repressor label: Aca2 RNA-dependent translational repression participant: selector_type: FAMILY required_function: preferred_term: DNA-binding transcription repressor activity term: id: GO:0001217 label: DNA-binding transcription repressor activity family: preferred_term: Aca2/YdiL-like anti-CRISPR-associated repressor family term: id: InterPro:IPR015060 label: Aca2/YdiL-like representative_members: - preferred_term: ZF40_0030 / aca2 (Pectobacterium phage ZF40) term: id: UniProtKB:H9C180 label: Aca2 repressor description: The repressor co-transcribed with acrIF8 in the same phage, which is why the regulatory part and the recognition-blockade part share an exemplar locus. description: This selector refers to anti-CRISPR-associated repressors with a demonstrated regulated locus; Aca2/YdiL-like homology alone does not establish the target operon or every regulatory mode. function: preferred_term: RNA binding term: id: GO:0003723 label: RNA binding targets: - preferred_term: conserved stem-loops in acrIF8–aca2 mRNA evidence: - source_id: PMID:38987591 statement: Aca2 binds conserved RNA stem-loops and blocks ribosome access, providing translational repression in addition to DNA-dependent transcriptional repression. processes: - preferred_term: negative regulation of translation term: id: GO:0017148 label: negative regulation of translation role_description: RNA recognition limits translation from the regulated transcript; this mode complements promoter repression in the characterized Aca2 system. knowledge_gaps: - gap_statement: When does native SIRV1 gp29 ring-nuclease expression provide a selective counterdefense benefit? gap_kind: - BIOLOGY status: OPEN boundary: Purified cA4 cleavage and suppression after plasmid/heterologous expression are established. The 2025 Comment tests native SIRV2 gp37 and SIRV1 gp29 transplanted into SIRV2, not native SIRV1 infection. The Reply disputes physiological generalization and raises possible confounders. Both main texts were inspected; the unresolved issue is native deployment, not source inaccessibility. significance: Expression timing and abundance can separate biochemical anti-defense capacity from protection during native infection. resolution: Compare native-promoter expression, early-expression replacements and catalytic mutants in the same host/virus backgrounds, with matched cA4 and infection measurements; assess the full comment/reply together before extending the conclusion across DUF1874. - gap_statement: How broadly do characterized Acrs inhibit natural effector orthologs in their mobile-element host ranges? gap_kind: - BIOLOGY status: OPEN boundary: The exemplars establish specific tested combinations, including type I-F/I-C, I-D, II, V and VI. Family or subtype names do not guarantee inhibition of every ortholog. significance: Effector variation, expression timing and regulatory control determine whether an inhibitor protects a mobile element in a new host. resolution: Test sequence-matched proteins against defined natural effector panels and distinguish infection/conjugation assays from heterologous editing inhibition. - gap_statement: How do local transcriptional and translational controls tune inhibitor production across different mobile elements? gap_kind: - BIOLOGY status: OPEN boundary: ZF40 Aca2 has dual DNA/RNA regulation; this does not establish identical regulation in every Aca family or plasmid Acr locus. significance: Regulatory timing can limit cost while preserving sufficient early inhibitor activity. resolution: Measure native transcript, translation and infection/conjugation phenotypes after separate disruption of DNA operators and RNA-binding stem-loops.