The 90-residue gene product 30 of Pseudomonas phage D3112 is AcrIF2 (AcrF2), an acidic DNA-mimicking anti-CRISPR protein. It occupies the target-DNA capture pocket of the type I-F Csy surveillance complex, preventing PAM recognition and R-loop formation. The same protein also binds and inhibits the tested Desulfovibrio vulgaris type I-C Cascade through a related PAM-blocking mechanism. Its specificity therefore spans these tested systems rather than being restricted to all and only type I-F systems.
Definition: A molecular function inhibitor activity in which a protein presents a surface whose shape and charge distribution imitate a nucleic acid and occupies its binding site on a target protein or protein-containing complex, thereby preventing engagement of the genuine nucleic acid ligand.
Justification: The proposed term distinguishes inhibition through nucleic acid mimicry from other forms of inhibition. Existing nuclease inhibitor or molecular function inhibitor terms can describe the broader activity, and ribonucleoprotein complex binding describes the interaction. The proposal adds the mechanism shared by structurally unrelated AcrIF2, AcrIIA2 and AcrIIA4 proteins. It does not imply rapid reversibility, displacement of pre-bound substrate, or a universal requirement for inhibitor molar excess; occupancy depends on affinity, assembly state and order of addition.
Parent term: molecular function inhibitor activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0039504 symbiont-mediated suppression of host adaptive immune response | IEA GO_REF:0000043 | MODIFY | Summary: Mapped electronically from Swiss-Prot keyword KW-1080 (Inhibition of host adaptive immune response by virus). The essence is right, in that gp30 suppresses a host immune system, but GO:0039504 is defined for antigen-receptor-based adaptive immunity with somatic diversification and immunological memory, which Pseudomonas aeruginosa does not have. GO:0098672 is the term that means what the keyword was trying to say. Reason: This is a definitional mismatch in a keyword-to-term mapping, not a disagreement about the biology. CRISPR-Cas is routinely called an adaptive immune system in the primary literature, including in the discovery paper cited here, and KW-1080 encodes that loose usage. The GO term, however, is explicitly about directed amplification of specific antigen receptors produced by somatic diversification, which is a vertebrate-style mechanism absent from bacteria. A QuickGO ancestor query confirms GO:0039504 is not an ancestor of GO:0098672, so this is a parallel wrong-branch assertion rather than a harmless generalisation. MODIFY rather than REMOVE because the intended claim is correct and the right term exists. This review prompted a correction to modules/anti_crispr_suppression.yaml, which had carried GO:0039504 for this annoton on the strength of this GOA row; the term is now deliberately absent there, for the reason given above. Proposed replacements: symbiont-mediated suppression of host CRISPR-cas system Supporting Evidence: PMID:23242138 Here we describe the first examples of genes that mediate the inhibition of a CRISPR/Cas system. Five distinct 'anti-CRISPR' genes were found in the genomes of bacteriophages infecting Pseudomonas aeruginosa. |
| GO:0052031 symbiont-mediated perturbation of host defense response | IEA GO_REF:0000043 | MODIFY | Summary: Mapped electronically from keyword KW-0899 (Viral immunoevasion). The term is true but is a direct ancestor of the specific term that GOA already carries for this protein, so it adds no information. Reason: A QuickGO ancestor query for GO:0098672 returns GO:0052031 among its ancestors, so this row is subsumed by the GO:0098672 row in the same GOA set. The mechanism is established at the level of the specific term, so the general one should give way to it. This is the same call the completed review of the type I-F inhibitor AcrF8 in genes/BPZF4/AcrF8 made for the over-general GO:0052170. Proposed replacements: symbiont-mediated suppression of host CRISPR-cas system Supporting Evidence: PMID:23242138 We conclude from these experiments that the anti-CRISPR genes exert their effects at a step occurring after formation of the crRNA-Cas complex, and that there is no effect on biogenesis of either the crRNA or Cas proteins. |
| GO:0098672 symbiont-mediated suppression of host CRISPR-cas system | IEA GO_REF:0000043 | ACCEPT | Summary: Mapped electronically from keyword KW-1257 (CRISPR-cas system evasion by virus). This is the correct and maximally specific process term for gp30, and although the GOA evidence code is IEA, the underlying Swiss-Prot FUNCTION line is curator-asserted with an experimental code from the discovery paper (ECO:0000269 PubMed:23242138). Deleting a protospacer-matched phage's anti-CRISPR gene abolishes its ability to plaque on a CRISPR-competent host, and expressing the gene restores plaquing, so necessity and sufficiency are both established. Reason: Correct term, maximally specific, and experimentally grounded upstream of the electronic mapping. This row is retained as the core process for gp30, and is the replacement proposed by the two MODIFY rows above. Supporting Evidence: PMID:23242138 Remarkably, expression of seven of these genes (Supplementary Fig. 7) led to dramatic increases in the plaquing efficiency of the CRISPR-sensitive phages PMID:23242138 Finally, we found that the anti-CRISPR genes did not inhibit a Type I-E CRISPR/Cas system functioning in E. coli |
| GO:0043021 ribonucleoprotein complex binding | IDA PMID:28340349 Structure Reveals Mechanisms of Viral Suppressors that Inter... | NEW | Summary: The cryo-EM structure places a copy of gp30 inside the assembled crRNA-loaded Csy surveillance complex, wedged between the N-terminal hook of Cas8f and the thumb of Cas7f. The entity bound is therefore a ribonucleoprotein, and mutation of residues in either Cas7f or Cas8f at that interface abolishes AcrF2 binding. Reason: GOA holds no molecular function term for Q6TM72. GO:0043021 is asserted because it is literally true, checkable against the deposited coordinates (PDB 5UZ9 and 6B47 both contain this accession), and is the same term used for the analogous type I-F inhibitor AcrF8 in genes/BPZF4/AcrF8. It is deliberately not offered as the core activity, because it records the entity bound and not the DNA mimicry that makes the binding inhibitory; the core activity is carried by the proposed term instead. GO:0005515 protein binding is avoided as uninformative. Supporting Evidence: PMID:28340349 AcrF2 is a small acidic protein wedged between positively charged residues in the N-terminal hook of Cas8 and the thumb of Cas7.6f PMID:28985564 AcrF2 binding wrenches the hook outwards away from the closed state PMID:36805026 previously characterized type I-F inhibitory protein, AcrIF2, also demonstrated the in vivo inhibition of the type I-C Cascade |
| GO:0030430 host cell cytoplasm | IC PMID:23242138 Bacteriophage genes that inactivate the CRISPR/Cas bacterial... | NEW | Summary: gp30 is translated from the injected or integrated D3112 genome inside the infected Pseudomonas aeruginosa cell and acts on the host Csy surveillance complex, which is a cytoplasmic ribonucleoprotein. Inhibition is demonstrated in living cells by plaquing and plasmid transformation assays, so the protein must reach the host cytoplasm; the structures themselves were determined in vitro, so the location is inferred rather than measured. Reason: This is the GO term for a symbiont gene product located in its host's cytoplasm, and the UniProt taxon for this entry is the phage, not the bacterium, so the host-qualified term is the right one. GO:0005737 cytoplasm would be wrong for a viral protein acting in another organism. The same assignment with the same IC code was made for the type I-F inhibitor AcrF8 in genes/BPZF4/AcrF8. Supporting Evidence: PMID:23242138 Remarkably, expression of seven of these genes (Supplementary Fig. 7) led to dramatic increases in the plaquing efficiency of the CRISPR-sensitive phages PMID:28340349 AcrF2 is a small acidic protein wedged between positively charged residues in the N-terminal hook of Cas8 and the thumb of Cas7.6f |
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Download this section (compressed HTML)Q: Which target-interface features determine why this AcrIF2 inhibits the tested type I-F and type I-C systems but not the tested type I-E system?
Q: How does AcrIF2 inhibition of target recognition affect primed spacer acquisition during native D3112 infection?
Experiment: Measure inhibitor occupancy and target-DNA binding with varied order of addition in matched type I-F and type I-C systems, allowing for slow dissociation and nonequilibrium trapping.
Experiment: Compare primed spacer acquisition during infection with wild-type D3112, an acrIF2 deletion and a complemented virus.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The intracellular occupancy and timing needed for AcrIF2 protection during native D3112 infection remain incompletely quantified.
OPEN BIOLOGY
What is known: Structural studies establish the target-binding sites and inhibition mechanism; they do not measure native inhibitor and effector copy numbers throughout infection.
Significance: Affinity, target availability and expression timing determine protection; stoichiometric binding alone does not establish a universal requirement for molar excess.
What would resolve it: Measure inhibitor and effector abundance through infection and relate occupancy to target-DNA recognition kinetics.
Provenance (the field's own admissions):
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