title: A molecular mechanism realizing sequence-specific recognition of nucleic acids by TDP-43.
abstract: TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA-binding protein containing two consecutive RNA recognition motifs (RRM1 and RRM2) in tandem. Functional abnormality of TDP-43 has been proposed to cause neurodegeneration, but it remains obscure how the physiological functions of this protein are regulated. Here, we show distinct roles of RRM1 and RRM2 in the sequence-specific substrate recognition of TDP-43. RRM1 was found to bind a wide spectrum of ssDNA sequences, while no binding was observed between RRM2 and ssDNA. When two RRMs are fused in tandem as in native TDP-43, the fused construct almost exclusively binds ssDNA with a TG-repeat sequence. In contrast, such sequence-specificity was not observed in a simple mixture of RRM1 and RRM2. We thus propose that the spatial arrangement of multiple RRMs in DNA/RNA binding proteins provides steric effects on the substrate-binding site and thereby controls the specificity of its substrate nucleotide sequences.
authors.affiliation: Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522, JAPAN.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Furukawa
authors.affiliation: Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522, JAPAN.
authors.forename: Yoh
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522, JAPAN.
authors.forename: Mami
authors.initials: M
authors.lastname: Fukuoka
authors.affiliation: Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522, JAPAN.
authors.forename: Kenichi
authors.initials: K
authors.lastname: Nagasawa
authors.affiliation: Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522, JAPAN.
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakagome
authors.affiliation: RIKEN Center for Life Science Technologies, Yokohama 230-0045, JAPAN.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Shimizu
authors.affiliation: Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, Okazaki 444-8585, JAPAN.|Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, JAPAN.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Mukaiyama
authors.affiliation: Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, Okazaki 444-8585, JAPAN.|Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, JAPAN.
authors.forename: Shuji
authors.initials: S
authors.lastname: Akiyama
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012313:RNA / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D012313:RNA
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