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Related Experiment Videos

The bacteriophage D108 Ner repressor binds a conformationally distinct operator.

G Kukolj1, M S DuBow

  • 1Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.

Molecular & General Genetics : MGG
|June 14, 2000
PubMed
Summary

The Ner repressor protein binds a specific DNA operator sequence. This binding is influenced by the operator's unique structure, including an AT-rich spacer that bends the DNA.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Structural Biology

Background:

  • The Ner protein is a lambda Cro-like repressor encoded by the transposable coliphage D108.
  • It regulates gene expression by binding to specific DNA operator sequences.

Purpose of the Study:

  • To investigate the DNA binding characteristics of the Ner repressor.
  • To elucidate the structural requirements of the Ner operator sequence for protein binding.

Main Methods:

  • Electrophoretic mobility shift assay (EMSA) to assess protein-DNA affinity.
  • DNase I protection analysis to map protein binding sites.
  • Circular-permutation binding assays to study DNA conformation.

Main Results:

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  • The Ner operator features two 11-bp inverted repeats separated by an 8-bp AT-rich spacer.
  • The AT-rich spacer exhibits a bent conformation, indicated by hyperreactivity to chemical probes.
  • Ner protein showed low affinity for a single repeat site.
  • Alterations to the spacer length/sequence significantly impacted Ner-operator interactions.
  • Ner binding induced conformational changes in the operator DNA.

    • Conclusions:

    • The Ner repressor's interaction with its operator is dependent on the operator's specific DNA structure, particularly the bent AT-rich spacer.
    • The Ner operator undergoes conformational changes upon protein binding, highlighting the dynamic nature of protein-DNA recognition.