How Mitochondria Read Their DNA

Aging, neurological diseases and our bodies’ stress response are all linked to the tiny power plants inside each cell known as mitochondria. To function properly, mitochondria must first read instructions from their DNA and then copy it over into mRNA in a process called transcription. Now, researchers at Thomas Jefferson University have reconstructed transcription in human mitochondria in unprecedented detail. The findings, published in Molecular Cell, show how the molecular machinery works and reveal potential drug targets for mitochondrial diseases.

“When we understand this key process, we can validate targets for a new class of drugs that restore mitochondrial potential,” says structural biologist and senior author Dmitry Temiakov, PhD.

Dr. Temiakov, a member of Sidney Kimmel Medical College, and his lab were the first to determine the structure of a key enzyme, known as human mitochondrial RNA polymerase, in 2011. Since then, he and his team have worked to understand the enzyme’s “molecular gymnastics.” It changes shape and interacts with other proteins in the cell as it begins its job of transcription. In this latest study, the researchers used high-powered microscopes and advanced computational methods to visually capture the enzyme and its helper proteins.

The team reconstituted the process of transcription in a test tube, flash froze samples on microscopic grids and painstakingly imaged them from multiple angles with an electron microscope. This method, known as cryo-EM, can reveal a protein’s 3D structures in near-atomic detail.

Karl Herbine, a graduate student who led the project (presently a postdoctoral fellow at University of Pennsylvania), assessed more than 1 million images over the course of three years. The fruits of his perseverance is a molecular movie that shows just how the enzyme recognizes the correct starting point on DNA, brings in helper proteins, begins to copy the genetic code into mRNA, and finally transitions into a fully active and stable mode.

With one in 5,000 people affected by mitochondrial disease, the findings open the door to discovering drugs designed to restore mitochondrial health.

“When we see how this fundamental process works,” says Dr. Temiakov, “we can begin to fix what’s broken.”

Reference: Herbine K, Nayak AR, Zamudio-Ochoa A, Temiakov D. Structural basis for promoter recognition and transcription factor binding and release in human mitochondria. Molecular Cell. 2025;85(16):3123-3136.e7. doi: 10.1016/j.molcel.2025.06.016

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