title: DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3.
abstract: Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and directing it to cellular compartments critical for gene expression, the biochemical mechanism of how TDRD3 can affect the functions of Top3β is not known. We report here sensitive biochemical assays for the activities of Top3β on DNA and RNA substrates in resolving topological entanglements and for the analysis of TDRD3 functions. TDRD3 stimulates the relaxation activity of Top3β on hypernegatively supercoiled DNA and changes the reaction from a distributive to a processive mode. Both supercoil retention assays and binding measurement by fluorescence anisotropy reveal a heretofore unknown preference for binding single-stranded nucleic acids over duplex. Whereas TDRD3 has a structure-specific binding preference, it does not discriminate between DNA and RNA. This unique property for binding with nucleic acids can have an important function in serving as a hub to form nucleoprotein complexes on DNA and RNA. To gain insight into the roles of Top3β on RNA metabolism, we designed an assay by annealing two single-stranded RNA circles with complementary sequences. Top3β is capable of converting two such single-stranded RNA circles into a double-stranded RNA circle, and this strand-annealing activity is enhanced by TDRD3. These results demonstrate that TDRD3 can enhance the biochemical activities of Top3β on both DNA and RNA substrates, in addition to its function of targeting Top3β to critical sites in subcellular compartments.
authors: Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; mike.been@duke.edu graceelsiaw@gmail.com.
authors: Grace Ee-Lu
authors: GE
authors: Siaw
authors: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan;
authors: I-Fen
authors: IF
authors: Liu
authors: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan;
authors: Po-Yen
authors: PY
authors: Lin
authors: Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 mike.been@duke.edu graceelsiaw@gmail.com.
authors: Michael D
authors: MD
authors: Been
authors: Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710.
authors: Tao-Shih
authors: TS
authors: Hsieh
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D026942:DNA Topoisomerases / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics; D046911:Macromolecular Substances / Q000737:chemistry; D009698:Nucleoproteins / Q000737:chemistry / Q000235:genetics*; D011485:Protein Binding; D014176:Protein Biosynthesis; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic; D000071856:Tudor Domain / Q000235:genetics
chemical_list: D004277:DNA, Single-Stranded; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D046911:Macromolecular Substances; D009698:Nucleoproteins; D012330:RNA, Double-Stranded; D026942:DNA Topoisomerases
keywords: DNA topoisomerases; RNA circles; RNA duplex; RNA topoisomerases; Tudor domain-containing domain 3