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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 何孟樵 | |
| dc.contributor.author | Yu-Lin Tsai | en |
| dc.contributor.author | 蔡侑霖 | zh_TW |
| dc.date.accessioned | 2021-06-15T12:44:56Z | - |
| dc.date.available | 2018-08-23 | |
| dc.date.copyright | 2016-08-23 | |
| dc.date.issued | 2016 | |
| dc.date.submitted | 2016-07-26 | |
| dc.identifier.citation | 1. Huang, X., et al., A map of rice genome variation reveals the origin of cultivated rice. Nature, 2012. 490(7421): p. 497-501.
2. Vaughan, D.A., B.-R. Lu, and N. Tomooka, The evolving story of rice evolution. Plant Science, 2008. 174(4): p. 394-408. 3. Ujjal J. Phukana, S.M.R.K.S., Waterlogging and submergence stress: affects and acclimation. Critical Reviews in Biotechnology, 2015. 4. Jung, K.-H., et al., The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors. Plant Physiology, 2010. 152(3): p. 1674-1692. 5. Bailey-Serres, J., et al., Making sense of low oxygen sensing. Trends in Plant Science. 17(3): p. 129-138. 6. Fukao, T. and J. Bailey-Serres, Plant responses to hypoxia – is survival a balancing act? Trends in Plant Science, 2004. 9(9): p. 449-456. 7. van Dongen, J.T. and F. Licausi, Oxygen Sensing and Signaling. Annual Review of Plant Biology, 2015. 66(1): p. 345-367. 8. Voesenek, L. and J. Bailey-Serres, Flooding tolerance: O2 sensing and survival strategies. Current Opinion in Plant Biology, 2013. 16(5): p. 647-653. 9. Xu, K., et al., Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature, 2006. 442(7103): p. 705-708. 10. Mickelbart, M.V., P.M. Hasegawa, and J. Bailey-Serres, Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet, 2015. 16(4): p. 237-251. 11. Voesenek, L.A.C.J. and J. Bailey-Serres, Plant biology: Genetics of high-rise rice. Nature, 2009. 460(7258): p. 959-960. 12. Hattori, Y., et al., The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature, 2009. 460(7258): p. 1026-1030. 13. Abdelbagi M. Ismail, U.S.S., Sudhanshu Singh, Manzoor H. Dar, David J. Mackill, The contribution of submergence-tolerant (Sub1) rice varieties to food security in flood-prone rainfed lowland areas in Asia. Field Crops Research, 2013. 152: p. 83-93. 14. Fukao, T., T. Harris, and J. Bailey-Serres, Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice. Annals of Botany, 2009. 103(2): p. 143-150. 15. Zennia Jean C. Gonzaga, J.C., Darlene L. Sanchez, David J. Mackill, Endang M. Septiningsih, Mapping additional QTLs from FR13A to increase submergence tolerance in rice beyond SUB1. Euphytica, 2016. 209(3): p. 627-636. 16. Gibbs, D.J., et al., Group VII Ethylene Response Factors Coordinate Oxygen and Nitric Oxide Signal Transduction and Stress Responses in Plants. Plant Physiology, 2015. 169(1): p. 23-31. 17. Toshitsugu Nakano, K.S., Tatsuhito Fujimura and Hideaki Shinshi, Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice. Plant Physiology, 2006. 140: p. 411-432. 18. Licausi, F., M. Ohme-Takagi, and P. Perata, APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytologist, 2013. 199(3): p. 639-649. 19. Bornhorst, J.A. and J.J. Falke, [16] Purification of Proteins Using Polyhistidine Affinity Tags. Methods in enzymology, 2000. 326: p. 245-254. 20. Porath, J., Immobilized metal ion affinity chromatography. Protein Expression and Purification, 1992. 3(4): p. 263-281. 21. Porath, J. and B. Olin, Immobilized metal affinity adsorption and immobilized metal affinity chromatography of biomaterials. Serum protein affinities for gel-immobilized iron and nickel ions. Biochemistry, 1983. 22(7): p. 1621-1630. 22. Gaberc-Porekar, V. and V. Menart, Perspectives of immobilized-metal affinity chromatography. Journal of Biochemical and Biophysical Methods, 2001. 49(1–3): p. 335-360. 23. Mori, S. and H.G. Barth, Size exclusion chromatography. 2013: Springer Science & Business Media. 24. Striegel, A., et al., Modern size-exclusion liquid chromatography: practice of gel permeation and gel filtration chromatography. 2009: John Wiley & Sons. 25. Wen, J., T. Arakawa, and J.S. Philo, Size-Exclusion Chromatography with On-Line Light-Scattering, Absorbance, and Refractive Index Detectors for Studying Proteins and Their Interactions. Analytical Biochemistry, 1996. 240(2): p. 155-166. 26. Cole, J.L., et al., Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium. Methods in cell biology, 2008. 84: p. 143-179. 27. Schuck, P., On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Analytical Biochemistry, 2003. 320(1): p. 104-124. 28. Brown, P.H. and P. Schuck, Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophysical journal, 2006. 90(12): p. 4651-4661. 29. Laue, T.M., Analytical ultracentrifugation. Current Protocols in Protein Science, 2001: p. 7-5. 30. Laue, T.M. and W.F. Stafford Iii, Modern applications of analytical ultracentrifugation. Annual review of biophysics and biomolecular structure, 1999. 28(1): p. 75-100. 31. Lebowitz, J., M.S. Lewis, and P. Schuck, Modern analytical ultracentrifugation in protein science: a tutorial review. Protein Science, 2002. 11(9): p. 2067-2079. 32. Folta-Stogniew, E., Oligomeric States of Proteins Determined by Size-Exclusion Chromatography Coupled With Light Scattering, Absorbance, and Refractive Index Detectors, in New and Emerging Proteomic Techniques, D. Nedelkov and R.W. Nelson, Editors. 2006, Humana Press: Totowa, NJ. p. 97-112. 33. Tarazona, M.P. and E. Saiz, Combination of SEC/MALS experimental procedures and theoretical analysis for studying the solution properties of macromolecules. Journal of Biochemical and Biophysical Methods, 2003. 56(1–3): p. 95-116. 34. Hellman, L.M. and M.G. Fried, Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic Acid Interactions. Nature protocols, 2007. 2(8): p. 1849-1861. 35. Moerke, N.J., Fluorescence Polarization (FP) Assays for Monitoring Peptide-Protein or Nucleic Acid-Protein Binding, in Current Protocols in Chemical Biology. 2009, John Wiley & Sons, Inc. 36. Rossi, A.M. and C.W. Taylor, Analysis of protein-ligand interactions by fluorescence polarization. Nat. Protocols, 2011. 6(3): p. 365-387. 37. Belford, G.G., R.L. Belford, and G. Weber, Dynamics of fluorescence polarization in macromolecules. Proceedings of the National Academy of Sciences, 1972. 69(6): p. 1392-1393. 38. Checovich, W.J., R.E. Bolger, and T. Burke, Fluorescence polarization-a new tool for cell and molecular biology. Nature, 1995. 375: p. 254-256. 39. Allen, M.D., et al., A novel mode of DNA recognition by a β‐sheet revealed by the solution structure of the GCC‐box binding domain in complex with DNA. The EMBO Journal, 1998. 17(18): p. 5484-5496. 40. Weber, K. and M. Osborn, The Reliability of Molecular Weight Determinations by Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis. Journal of Biological Chemistry, 1969. 244(16): p. 4406-4412. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/50533 | - |
| dc.description.abstract | 由於全球暖化，近年來氣候變遷導致的洪水與旱災比過往更加頻繁並且對全球糧食安全產量造成了嚴重的威脅。稻米餵養世界將近一半的人口，因此保護水稻免於受到天災成為一項重要的課題。多數種植的水稻品種遇到完全滅頂的情況下皆活不過一個禮拜但某些稻米種卻擁有絕佳對抗洪水的能力。藉由基因體的分析，目前已經了解SUBMERGENCE(Sub1)這個位點水稻具有抗淹水能力而其產物為一關鍵的轉錄因子Sub1A-1。然而目前對於Sub1A-1如何活化其他下游基因等分子機制仍未了解。Sub1A-1屬於第七群Ethylene Responsive factor (ERFVII) 的一員，這群蛋白具有一AP2 domain 結合GCC box (AGCCGCC) 。但水稻的基因中具有超過3000個以上的基因其啟動子區域具有GCC box。以傳統基因的方式一一篩選幾乎是不可能的而且也缺乏細胞能及的Submergence assay來檢測。因此我們想出了利用Fluorescence Polarization (FP) assay去減少可能的DNA序列。藉由FP assay及protein truncation 我們發現了AP2 domain本身可能並不能提供完整的DNA結合能力，必須要有N-terminal domain一起結合DNA。這項發現可增加我們對於ERFVII家族蛋白的了解。同時了解這些資訊也可為將Sub1A-1與DNA共結晶鋪路。目前我們已經發現某些條件下能形成小微晶。微調這些條件也許能解出結構，為我們的發現提供切實的證據。 | zh_TW |
| dc.description.abstract | Due to the global warming, recent climate changes result more frequent flood and drought than the pass and becomes a serious threat to the global food security. Rice feeding over half of the population in the world and it is an emerging issue to protect rice production from weather damage. Most domesticated rice cultivars die within a week of complete submergence (flooding). However, some wild rice has a remarkable ability to withstand flood. By Genome-wide studies, it is shown that SUBMERGENCE 1 (SUB1) locus is response for the submergence resistant and the transcription factor, Sub1A-1 coded in SUB1 locus is the key factor. However, the molecular mechanism of Sub1A-1 remains unknown. Sub1A-1 is a member of group VII ethylene responsive factors (ERFVIIs) which contain an AP2 domain for GCC box (AGCCGCC) binding. More than 3,000 genes in rice genome have GCC box in their promoter region. It is virtually impossible to screen them by genetic approaches. Not to mention that there is no cell-based submergence assay. In order to narrow down its downstream targets, we have developed a binding assay by Fluorescence Polarization (FP). In addition, we have discovered that AP2 domain itself may not provide sufficient binding ability. Only with the N-terminal domain could AP2 domain of Sub1A-1 bind to DNA. This new finding could enlarge our knowledge about ERFVII family. Currently, our knowledge about ERFVII family is limited to containing one AP2 domain for DNA binding. Moreover, knowing more about Sub1A-1 protein can facilitate our Sub1A-1 and DNA co-crystallization work. Currently, we have found out several conditions which could form small crystallite. Refining these conditions may solve the 3D-structure of Sub1A-1/DNA complex which could provide solid evidence for our new finding. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T12:44:56Z (GMT). No. of bitstreams: 1 ntu-105-R03B46015-1.pdf: 7958769 bytes, checksum: ccfce9d93051c78c5b544ebd2eb35dff (MD5) Previous issue date: 2016 | en |
| dc.description.tableofcontents | 口試委員會審定書 - 1 -
致謝 i 中文摘要 ii English abstract iii Contents iv Index of tables vii Index of figures viii Chapter 1: Introduction 1 1.1 Flood is a serious threat against rice production 1 1.2 The strategies of rice to survive submergence 2 1.3 The unknown pathway of the quiescence strategy 4 1.4 Studies of biophysical and biochemical characters of Sub1A-1 4 Chapter 2: Materials and Methods 6 2.1: Cloning of recombinant Sub1A-1 proteins 6 2.2: Expression and purification of recombinant FL-Sub1A-1 and truncated Sub1A-1 proteins 8 2.3: DNA probes 11 2.4: Immobilized metal ion affinity chromatography (IMAC) 12 2.5: Heparin affinity chromatography 13 2.6: Size exclusion chromatography (SEC) 14 2.7: Analytical Ultracentrifuge (AUC) 15 2.8: Size exclusion-multiangle light scattering (SEC-MALS) 16 2.9: Electrophoretic Mobility Shift Assay (EMSA) 17 2.10: Fluorescence Polarization Assay 18 2.11: Crystallization 21 Chapter 3: Result 22 3.1 Result of size exclusion chromatography (SEC) 22 3.2 Result of analytical ultracentrifuge (AUC) 23 3.3 The oligomerization state of Sub1A-1 24 3.4 The Sub1A-1 oligomerization state upon DNA binding 26 3.5 The function of N-terminal domains in DNA binding 27 3.6. DNA sequence specificity for Sub1A-1 29 3.7. Protein Crystallization 33 Chapter 4: Discussion 34 4.1 New domain function on Sub1A-1 protein 34 4.2 Probe length determination 34 4.3 Functional oligomer 35 Chapter 5: Tables and Figures 37 Reference 83 | |
| dc.language.iso | en | |
| dc.subject | 水稻轉錄因子 Sub1A-1 | zh_TW |
| dc.subject | 水稻轉錄因子 Sub1A-1 | zh_TW |
| dc.subject | 淹水 | zh_TW |
| dc.subject | 螢光極化 | zh_TW |
| dc.subject | 乙烯反應因子VII | zh_TW |
| dc.subject | AP2 domain | zh_TW |
| dc.subject | AP2 domain | zh_TW |
| dc.subject | 蛋白質結晶 | zh_TW |
| dc.subject | 乙烯反應因子VII | zh_TW |
| dc.subject | 蛋白質結晶 | zh_TW |
| dc.subject | 螢光極化 | zh_TW |
| dc.subject | 淹水 | zh_TW |
| dc.subject | Submergence | en |
| dc.subject | Transcription factor Sub1A-1 | en |
| dc.subject | Fluorescence polarization | en |
| dc.subject | ERFVII | en |
| dc.subject | AP2 domain | en |
| dc.subject | Protein crystal | en |
| dc.subject | Transcription factor Sub1A-1 | en |
| dc.subject | Submergence | en |
| dc.subject | Fluorescence polarization | en |
| dc.subject | ERFVII | en |
| dc.subject | AP2 domain | en |
| dc.subject | Protein crystal | en |
| dc.title | 對稻米抗淹水機制蛋白Sub1A-1之生物物理特性研究 | zh_TW |
| dc.title | The biophysical characterization of Sub1A-1, the transcription factor for rice submergence survival | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 104-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 吳世雄,梁博煌,葉國禎 | |
| dc.subject.keyword | 水稻轉錄因子 Sub1A-1,淹水,螢光極化,乙烯反應因子VII,AP2 domain,蛋白質結晶, | zh_TW |
| dc.subject.keyword | Transcription factor Sub1A-1,Submergence,Fluorescence polarization,ERFVII,AP2 domain,Protein crystal, | en |
| dc.relation.page | 85 | |
| dc.identifier.doi | 10.6342/NTU201601222 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2016-07-26 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科學研究所 | zh_TW |
| 顯示於系所單位： | 生化科學研究所 | |
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