Aca2 is the 116-residue helix-turn-helix regulator encoded beside acrIF8 in Pectobacterium phage ZF40. It forms a homodimer and represses transcription by binding inverted repeats in the operon promoter. The same HTH domain also recognizes conserved RNA stem-loops and blocks ribosome access, repressing translation. These complementary activities control anti-CRISPR production during phage infection; Aca2 is a regulator of the inhibitor rather than a direct Cas inhibitor.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: This annotation is correct but too general. Aca2 is specifically a sequence-specific DNA-binding transcription factor that recognizes inverted repeat operator sequences in the acrIF8-aca2 promoter through its N-terminal HTH domain. The protein binds as a homodimer to regulate transcription. Reason: Direct promoter binding represses acrIF8-aca2 transcription, supporting refinement to DNA-binding transcription repressor activity (GO:0001217), rather than only the broader transcription factor term. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:31428783 Aca2 is a dimer that represses the expression of the acrIF8–aca2 operon, and that this autoregulation is mediated through binding to inverted repeats in the promoter region |
| GO:0003723 RNA binding | IEA GO_REF:0000043 | ACCEPT | Summary: Correct annotation supported by experimental evidence. Aca2 binds conserved RNA stem-loops on the acrIF8-aca2 mRNA to block ribosome access and inhibit translation. This RNA-binding function, mediated by the same HTH domain that binds DNA, provides a second layer of regulatory control beyond transcriptional repression. Reason: Direct RNA binding by the HTH domain blocks ribosome access and provides a distinct translational regulatory function. Supporting Evidence: PMID:38987591 the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: A crystallographic metal association does not establish a physiological metal-binding function. Reason: UniProt records an Mg(2+) contact at residue 92 from apo structure 7VJO. PMID:34756887 reports crystallization in 0.2 M magnesium chloride. This is valid structural evidence of a contact, but does not establish a physiological metal-binding activity. Retain MARK_AS_OVER_ANNOTATED for the keyword-derived functional assertion; the concern is the high-magnesium crystallization context, not a requirement that metal binding be necessary for DNA/RNA repression. Supporting Evidence: file:BPZF4/ACA2/ACA2-uniprot.txt BINDING 92 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0007744|PDB:7VJO" PMID:34756887 The crystals of apo-Aca2 were crystallized in 0.2 M magnesium chloride hexahydrate; 0.1 M TRIS hydrochloride pH 8.5; 20% (w/v) PEG 8000. |
| GO:0017148 negative regulation of translation | IDA PMID:38987591 Phage anti-CRISPR control by an RNA- and DNA-binding helix-t... | NEW | Summary: Aca2 inhibits translation by binding conserved RNA stem-loops in the acrIF8-aca2 mRNA to block ribosome access. Reason: This biological process term captures Aca2's dual regulatory mechanism that includes translational repression through RNA binding. Supporting Evidence: PMID:38987591 the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access |
| GO:0042803 protein homodimerization activity | IDA PMID:31428783 The autoregulator Aca2 mediates anti-CRISPR repression | NEW | Summary: Aca2 forms homodimers that are essential for DNA binding and transcriptional repression of the acrIF8-aca2 operon. Reason: This molecular function term reflects Aca2's requirement for homodimerization to achieve functional DNA binding and gene regulation. Supporting Evidence: PMID:31428783 Aca2 is a dimer that represses the expression of the acrIF8–aca2 operon, and that this autoregulation is mediated through binding to inverted repeats in the promoter region |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:31428783 The autoregulator Aca2 mediates anti-CRISPR repression | NEW | Summary: Aca2 represses transcription of the acrIF8-aca2 operon by binding to inverted repeat operators in the promoter region. Reason: This biological process term captures Aca2's primary function as a transcriptional repressor that controls anti-CRISPR gene expression. Supporting Evidence: PMID:31428783 Aca2 is a dimer that represses the expression of the acrIF8–aca2 operon, and that this autoregulation is mediated through binding to inverted repeats in the promoter region |
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Download this section (compressed HTML)Q: How are DNA occupancy and RNA occupancy partitioned as phage genome copies and acrIF8-aca2 transcript abundance increase during infection?
Q: How does the benefit of dual transcriptional and translational repression vary among native hosts and phage expression regimes?
Experiment: ChIP-seq to map all ACA2 binding sites across the phage genome during infection
Experiment: Time-resolved transcriptomics to track ACA2-regulated gene expression during phage lifecycle
Experiment: Competition assays between ACA2 and host transcription factors for overlapping binding sites
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