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The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA

Nature Structural & Molecular Biology volume 18, pages 1290–1296 (2011)Cite this article

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Abstract

Tfam (transcription factor A, mitochondrial), a DNA-binding protein with tandem high-mobility group (HMG)-box domains, has a central role in the expression, maintenance and organization of the mitochondrial genome. It activates transcription from mitochondrial promoters and organizes the mitochondrial genome into nucleoids. Using X-ray crystallography, we show that human Tfam forces promoter DNA to undergo a U-turn, reversing the direction of the DNA helix. Each HMG-box domain wedges into the DNA minor groove to generate two kinks on one face of the DNA. On the opposite face, a positively charged α-helix serves as a platform to facilitate DNA bending. The structural principles underlying DNA bending converge with those of the unrelated HU family proteins, which have analogous architectural roles in organizing bacterial nucleoids. The functional importance of this extreme DNA bending is promoter specific and seems to be related to the orientation of Tfam on the promoters.

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Figure 1: Overview of the Tfam–mtDNA complex.
Figure 2: Molecular mass of the Tfam–mtDNA complex determined by SEC-MALS.
Figure 3: Interactions of Tfam with DNA.
Figure 4: Comparison of Tfam and Hbb structures.
Figure 5: Tfam mutants with a selective defect at LSP.
Figure 6: Models for DNA bending and transcriptional activation.

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Acknowledgements

We thank N. Chan (California Institute of Technology) for making some mutant constructs, Y. Zhang and Z. Liu (California Institute of Technology) for suggestions on phase determination and structure refinement, T. Walton (California Institute of Technology) for advice on SEC-MALS, S. Shan (California Institute of Technology) for use of equipment and insightful discussions, the staff at the Stanford Synchrotron Radiation Lightsource (SSRL) for technical support with crystal screening and data collection, and members of the Chan laboratory for critical reading of the manuscript. We acknowledge the Gordon and Betty Moore Foundation for support of the Molecular Observatory at Caltech. SSRL is supported by the US Department of Energy and National Institutes of Health (NIH). This work was supported by NIH grants GM083121 (D.C.C.) and GM062967 (D.C.C.).

Author information

Authors and Affiliations

  1. Division of Biology, California Institute of Technology, Pasadena, California, USA

    Huu B Ngo & David C Chan

  2. Division of Chemistry, California Institute of Technology, Pasadena, California, USA

    Jens T Kaiser

  3. Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA

    David C Chan

Authors
  1. Huu B Ngo
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  2. Jens T Kaiser
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Contributions

H.B.N. and D.C.C. designed the experiments, analyzed the data and wrote the paper. H.B.N. carried out the crystallography and performed the experimental work. J.T.K. helped with the crystallographic analysis.

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Correspondence to David C Chan.

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Ngo, H., Kaiser, J. & Chan, D. The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA. Nat Struct Mol Biol 18, 1290–1296 (2011). https://doi.org/10.1038/nsmb.2159

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