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Allostery through protein-induced DNA bubbles.

Joseph J Traverso1, Valipuram S Manoranjan2, A R Bishop3

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Protein-induced DNA bubbles can coalesce, mediating allosteric interactions that drive protein aggregation. This mechanism, observed with mitochondrial transcription factor A (TFAM), regulates DNA flexibility and transcription machinery assembly.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Allostery mediated by DNA is crucial for modulating DNA functions.
  • Mitochondrial transcription factor A (TFAM) plays a key role in mitochondrial DNA (mtDNA) packaging and transcription initiation.
  • TFAM's ability to unwind DNA makes it a model for studying DNA-mediated allostery.

Purpose of the Study:

  • To investigate how protein-induced DNA bubbles mediate allosteric interactions.
  • To explore the role of DNA bubble coalescence in protein aggregation.
  • To elucidate the mechanism by which TFAM influences mtDNA packaging and transcription.

Main Methods:

  • Numerical simulations were employed to model TFAM-induced DNA bubble coalescence.
  • The study analyzed the structural consequences of bubble coalescence on DNA flexibility.
  • Experimental observations of TFAM oligomerization were used to validate simulation results.

Main Results:

  • Coalescence of TFAM-induced DNA bubbles drives TFAM oligomerization.
  • A ~10 base pair melted DNA segment at oligomer joints acts as a flexible hinge, facilitating DNA compaction.
  • This allosteric mechanism explains TFAM's efficiency in packaging mtDNA.

Conclusions:

  • Protein-induced DNA bubble coalescence is a novel mechanism for allosteric regulation.
  • TFAM utilizes this allosteric interaction for both mtDNA compaction and recruitment of mitochondrial polymerase (mitoRNAP) for transcription initiation.
  • This finding provides insights into the regulation of mitochondrial gene expression.