title: DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.
abstract: 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.
authors.affiliation: Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain.
authors.forename: Arka
authors.initials: A
authors.lastname: Chakraborty
authors.affiliation: Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lyonnais
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain.
authors.forename: Federica
authors.initials: F
authors.lastname: Battistini
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.affiliation: Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Medici
authors.affiliation: Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, Barcelona 08028, Spain.
authors.forename: Rafel
authors.initials: R
authors.lastname: Prohens
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, Barcelona 08028, Spain.|Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.affiliation: Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain.|Molecular Genomics Department, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, 08028, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Vilardell
authors.affiliation: Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain maria.sola@ibmb.csic.es.
authors.forename: Maria
authors.initials: M
authors.lastname: Solà
mesh_terms: D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D054629:Genome, Mitochondrial; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011061:Poly A; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D018741:Replication Origin; D013816:Thermodynamics
chemical_list: D004272:DNA, Mitochondrial; D004268:DNA-Binding Proteins; D011061:Poly A