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Nucleic acids research v.45 no.2, 2017년, pp.951 - 967   SCI SCIE
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DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p

Chakraborty, Arka (Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain ) ; Lyonnais, Sébastien (Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain ) ; Battistini, Federica (Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain ) ; Hospital, Adam (Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain ) ; Medici, Giorgio (Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain ) ; Prohens, Rafel (Unitat de Polimorfisme i Calorimetria, Centres Cientéàífics i Tecnoléàíògics, University of Barcelona, Barcelona 08028, Spain ) ; Orozco, Modesto (Institute for ) ; Vilardell, Josep ; Soléà, Maria ;
  • 초록  

    The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast ( Saccharomyces cerevisiae ), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct ‘phased-binding’ at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction.


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