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Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A

Author

Listed:
  • Géraldine Farge

    (VU University)

  • Niels Laurens

    (VU University)

  • Onno D. Broekmans

    (VU University)

  • Siet M.J.L. van den Wildenberg

    (VU University)

  • Linda C.M. Dekker

    (VU University)

  • Martina Gaspari

    (Karolinska Institutet)

  • Claes M. Gustafsson

    (University of Gothenburg)

  • Erwin J.G. Peterman

    (VU University)

  • Maria Falkenberg

    (University of Gothenburg)

  • Gijs J.L. Wuite

    (VU University)

Abstract

Mitochondria organize their genome in protein–DNA complexes called nucleoids. The mitochondrial transcription factor A (TFAM), a protein that regulates mitochondrial transcription, is abundant in these nucleoids. TFAM is believed to be essential for mitochondrial DNA compaction, yet the exact mechanism has not been resolved. Here we use a combination of single-molecule manipulation and fluorescence microscopy to show the nonspecific DNA-binding dynamics and compaction by TFAM. We observe that single TFAM proteins diffuse extensively over DNA (sliding) and, by collisions, form patches on DNA in a cooperative manner. Moreover, we demonstrate that TFAM induces compaction by changing the flexibility of the DNA, which can be explained by local denaturation of the DNA (melting). Both sliding of TFAM and DNA melting are also necessary characteristics for effective, specific transcription regulation by TFAM. This apparent connection between transcription and DNA organization clarifies how TFAM can accomplish two complementary roles in the mitochondrial nucleoid at the same time.

Suggested Citation

  • Géraldine Farge & Niels Laurens & Onno D. Broekmans & Siet M.J.L. van den Wildenberg & Linda C.M. Dekker & Martina Gaspari & Claes M. Gustafsson & Erwin J.G. Peterman & Maria Falkenberg & Gijs J.L. Wu, 2012. "Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
    • Handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms2001
    DOI: 10.1038/ncomms2001
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    Cited by:

    1. Artur P. Kaczmarczyk & Anne-Cécile Déclais & Matthew D. Newton & Simon J. Boulton & David M. J. Lilley & David S. Rueda, 2022. "Search and processing of Holliday junctions within long DNA by junction-resolving enzymes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Hyun Huh & Jiayu Shen & Yogeeshwar Ajjugal & Aparna Ramachandran & Smita S. Patel & Sang-Hyuk Lee, 2024. "Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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