Solution Structure of the DNA Binding Domain of Rice Telomere Binding Protein RTBP1†,‡
- Sunggeon Ko ,
- Eun Young Yu ,
- Joon Shin ,
- Hyun Hee Yoo ,
- Toshiyuki Tanaka ,
- Woo Taek Kim ,
- Hyun-Soo Cho ,
- Weontae Lee , and
- In Kwon Chung
Abstract
RTBP1 is a rice telomeric protein that binds to the duplex array of TTTAGGG repeats at chromosome ends. The DNA binding domain of RTBP1 contains a Myb-type DNA binding motif and a highly conserved C-terminal Myb extension that is unique to plant telomeric proteins. Using an electrophoretic mobility shift assay, we identified the C-terminal 110-amino acid region (RTBP1506−615) as the minimal telomeric DNA binding domain, suggesting that the Myb extension is required for binding plant telomeric DNA. Like other telomeric proteins such as human TRF1 and yeast Rap1, RTBP1 induced a DNA bending in the telomeric repeat sequence, suggesting that RTBP1 may play a role in establishing and/or maintaining an active telomere configuration in vivo. To elucidate the DNA binding mode of RTBP1, we determined the three-dimensional structure of RTBP1506−615 in solution by NMR spectroscopy. The overall structure of RTBP1506−615 is composed of four α-helices and stabilized by three hydrophobic patches. The second and third helices in RTBP1 form a helix−turn−helix motif that interacts directly with DNA. The fourth helix located in the Myb extension is essential for binding to telomeric DNA via stabilization of the overall structure of the RTBP1 DNA binding domain. When DNA bound to RTBP1506−615, large chemical shift perturbations were induced in the N-terminal arm, helix 3, and the loop between helices 3 and 4. These results suggest that helix 3 functions as a sequence-specific recognition helix while the N-terminal arm stabilizes the DNA binding.
Cited By
This article is cited by 13 publications.
- Mi Young Byun, Li Hua Cui, Hyoungseok Lee, Woo Taek Kim. Telomere association of Oryza sativa telomere repeat-binding factor like 1 and its roles in telomere maintenance and development in rice, Oryza sativa L.. BMB Reports 2018, 51 (11) , 578-583. https://doi.org/10.5483/BMBRep.2018.51.11.122
- Hiroshi Mizuno, Takashi Matsumoto, Jianzhong Wu. Composition and Structure of Rice Centromeres and Telomeres. 2018,,, 37-52. https://doi.org/10.1007/978-981-10-7461-5_3
- , . Rice Genomics, Genetics and Breeding. 2018,,https://doi.org/10.1007/978-981-10-7461-5
- Nick Fulcher, Karel Riha. Using Centromere Mediated Genome Elimination to Elucidate the Functional Redundancy of Candidate Telomere Binding Proteins in Arabidopsis thaliana. Frontiers in Genetics 2016, 6 https://doi.org/10.3389/fgene.2015.00349
- Koel Mukherjee, Dev Mani Pandey, Ambarish Saran Vidyarthi. In Silico Characterization and Analysis of RTBP1 and NgTRF1 Protein Through MD Simulation and Molecular Docking: A Comparative Study. Interdisciplinary Sciences: Computational Life Sciences 2015, 7 (3) , 275-286. https://doi.org/10.1007/s12539-015-0268-7
- Ji-Hye Yun, Sunggeon Ko, Chung-Kyung Lee, Hae-Kap Cheong, Chaejoon Cheong, Jong-Bok Yoon, Weontae Lee, . Solution Structure and Rpn1 Interaction of the UBL Domain of Human RNA Polymerase II C-Terminal Domain Phosphatase. PLoS ONE 2013, 8 (5) , e62981. https://doi.org/10.1371/journal.pone.0062981
- Won Kyung Lee, Ji-Hye Yun, Weontae Lee, Myeon Haeng Cho. DNA-Binding Domain of AtTRB2 Reveals Unique Features of a Single Myb Histone Protein Family that Binds to Both Arabidopsis- and Human-Type Telomeric DNA Sequences. Molecular Plant 2012, 5 (6) , 1406-1408. https://doi.org/10.1093/mp/sss063
- Michael B. Prouse, Malcolm M. Campbell. The interaction between MYB proteins and their target DNA binding sites. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2012, 1819 (1) , 67-77. https://doi.org/10.1016/j.bbagrm.2011.10.010
- Shu-Yi Wei, Yuan-Chao Lou, Jia-Yin Tsai, Meng-Ru Ho, Chun-Chi Chou, M. Rajasekaran, Hong-Ming Hsu, Jung-Hsiang Tai, Chwan-Deng Hsiao, Chinpan Chen. Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal β-hairpin conformation. Nucleic Acids Research 2012, 40 (1) , 449-460. https://doi.org/10.1093/nar/gkr707
- S. Campagne, V. Gervais, A. Milon. Nuclear magnetic resonance analysis of protein–DNA interactions. Journal of The Royal Society Interface 2011, 8 (61) , 1065-1078. https://doi.org/10.1098/rsif.2010.0543
- Sunggeon Ko, Heeyoun Kim, Jihye Yun, Adelinda Yee, Cheryl H. Arrowsmith, Chaejoon Cheong, Weontae Lee. Solution structure of MTH1821, a putative structure homologue to RNA polymerase α subunit from Methanobacterium thermoautotrophicum. Proteins: Structure, Function, and Bioinformatics 2011, 79 (4) , 1347-1351. https://doi.org/10.1002/prot.22956
- J. Matthew Watson, Karel Riha. Comparative biology of telomeres: Where plants stand. FEBS Letters 2010, 584 (17) , 3752-3759. https://doi.org/10.1016/j.febslet.2010.06.017
- Marie-Josèphe Giraud-Panis, Sabrina Pisano, Anaïs Poulet, Marie-Hélène Le Du, Eric Gilson. Structural identity of telomeric complexes. FEBS Letters 2010, 584 (17) , 3785-3799. https://doi.org/10.1016/j.febslet.2010.08.004