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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
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Structural insights into promoter recognition by Aca7.

So Yeon Lee1,2, Hyun Ho Park1,2

  • 1College of Pharmacy, Chung-Ang University, Seoul, Korea.

The FEBS Journal
|January 16, 2026
PubMed
Summary

Anti-CRISPR associated (Aca) proteins regulate anti-CRISPR (Acr) gene expression. This study reveals the structure of Aca7 bound to DNA, detailing how it represses AcrIF11 transcription in Halomonas caseinilytica.

Keywords:
Aca7CRISPR‐Cas systemanti‐CRISPRanti‐CRISPR associatecrystal structure

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • CRISPR-Cas systems offer bacterial adaptive immunity against phages.
  • Anti-CRISPR (Acr) proteins are phage-encoded inhibitors of CRISPR-Cas.
  • Anti-CRISPR associated (Aca) proteins regulate Acr expression via DNA binding.

Purpose of the Study:

  • To identify and characterize the DNA binding motif for the Aca7 protein.
  • To determine the crystal structure of Aca7 bound to its target DNA.
  • To elucidate the molecular mechanism of AcrIF11 transcriptional repression by Aca7.

Main Methods:

  • Identification of inverted repeat (IR) DNA motif in the AcrIF11-Aca7 operon promoter.
  • X-ray crystallography to determine the Aca7-DNA complex structure.
  • Biochemical assays to confirm sequence-specific DNA binding.

Main Results:

  • First identification of an IR motif in the AcrIF11-Aca7 promoter from Halomonas caseinilytica.
  • Crystal structure reveals a symmetric Aca7 dimer bound to the IR DNA.
  • Aca7 utilizes helix-turn-helix motifs for major groove binding and minor groove contacts for DNA bending.
  • Specific residues (R38, Q42, K46, K49) are crucial for sequence recognition.

Conclusions:

  • Aca7 specifically recognizes and binds the IR element in the AcrIF11-Aca7 promoter.
  • The study provides a detailed molecular mechanism for Aca7-mediated transcriptional repression.
  • Findings expand the understanding of Aca protein diversity and transcriptional regulation strategies.