Aca2 repressor from bacteriophage ZF40 that functions as a dual transcriptional and translational repressor of the acrIF8-aca2 operon. This 116 amino acid protein forms homodimers and uses its N-terminal helix-turn-helix domain to bind specific DNA inverted repeats in the operon promoter, blocking RNA polymerase access. Additionally, Aca2 binds conserved RNA stem-loops in the mRNA to inhibit ribosome access. This dual regulatory mechanism ensures tight control of anti-CRISPR (AcrIF8) expression during phage infection, preventing toxic overexpression while allowing sufficient production to evade host CRISPR-Cas immunity. The protein is essential for phage viability, as uncontrolled AcrIF8 expression is detrimental to both phage replication and host cell fitness.
| 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. Proposed replacements: DNA-binding transcription factor 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. 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 file:BPZF4/ACA2/ACA2-deep-research.md See deep research file for comprehensive analysis |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | REMOVE | Summary: This annotation has minimal support. While crystallographic structures show Mg2+ bound at position 92, this appears to be a crystallization artifact rather than a functionally relevant metal-binding site. There is no evidence that metal binding is required for Aca2's repressor function. |
| GO:0017148 negative regulation of translation | IEA | 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: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 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 | IEA | 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 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:0045892 negative regulation of DNA-templated transcription | IEA | 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 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 |
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Download this section (compressed HTML)Q: How does ACA2 coordinate its dual functions as both a transcriptional regulator and an anti-CRISPR protein?
Q: What determines the specificity of ACA2 for its DNA binding sites in the phage genome?
Q: How does the timing of ACA2 expression affect phage replication success in CRISPR-containing hosts?
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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