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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 何孟樵(Meng-Chiao Ho) | |
| dc.contributor.author | Yan-Cih Cao | en |
| dc.contributor.author | 曹晏慈 | zh_TW |
| dc.date.accessioned | 2022-11-24T03:13:27Z | - |
| dc.date.available | 2021-11-04 | |
| dc.date.available | 2022-11-24T03:13:27Z | - |
| dc.date.copyright | 2021-11-04 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-10-20 | |
| dc.identifier.citation | Mackill, D.J., Rainfed lowland rice improvement. 1996: International Rice Research Institute. Arunrat, N., et al., Assessment of climate change impact on rice yield and water footprint of large-scale and individual farming in Thailand. Science of the Total Environment, 2020. 726: p. 137864. Boonwichai, S., et al., Evaluation of climate change impacts and adaptation strategies on rainfed rice production in Songkhram River Basin, Thailand. Science of the Total Environment, 2019. 652: p. 189-201. Howell, T.A., Relationships between crop production and transpiration, evapotranspiration, and irrigation. 1990. Khush, G., Terminology for rice growing environments. 1984. Bailey-Serres, J., et al., Submergence tolerant rice: SUB1’s journey from landrace to modern cultivar. Rice, 2010. 3(2): p. 138-147. Ella, E.S., et al., Blocking ethylene perception enhances flooding tolerance in rice seedlings. Functional Plant Biology, 2003. 30(7): p. 813-819. Pan, T., et al., Silicon Enhances Plant Resistance of Rice against Submergence Stress. Plants, 2021. 10(4): p. 767. Jackson, M. and T. Colmer, Response and adaptation by plants to flooding stress. Annals of botany, 2005. 96(4): p. 501-505. Siddiqui, M.N., et al., Glutathione improves rice tolerance to submergence: insights into its physiological and biochemical mechanisms. Journal Biotechnology, 2021. 325: p. 109-118. Voesenek, L.A. and J. Bailey-Serres, Flooding tolerance: O2 sensing and survival strategies. Current Opinion in Plant Biology, 2013. 16(5): p. 647-53. Catling, D., Rice in deep water. 1993: Springer. Kende, H., E. van der Knaap, and H.T. Cho, Deepwater rice: A model plant to study stem elongation. Plant Physiology, 1998. 118(4): p. 1105-10. Métraux, J.-P. and H. Kende, The role of ethylene in the growth response of submerged deep water rice. Plant Physiology, 1983. 72(2): p. 441-446. Raskin, I. and H. Kende, Role of gibberellin in the growth response of submerged deep water rice. Plant Physiology, 1984. 76(4): p. 947-950. Hoffmann-Benning, S. and H. Kende, On the role of abscisic acid and gibberellin in the regulation of growth in rice. Plant Physiology, 1992. 99(3): p. 1156-1161. Hattori, Y., et al., The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature, 2009. 460(7258): p. 1026-30. Fukao, T., et al., A variable cluster of ethylene response factor–like genes regulates metabolic and developmental acclimation responses to submergence in rice. The Plant Cell, 2006. 18(8): p. 2021-2034. Fukao, T. and J. Bailey-Serres, Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proceedings of the National Academy of Science of the United States America, 2008. 105(43): p. 16814-9. Nakano, T., et al., Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice. Plant Physiology, 2006. 140(2): p. 411-432. Tournier, B., et al., New members of the tomato ERF family show specific expression pattern and diverse DNA‐binding capacity to the GCC box element. FEBS letters, 2003. 550(1-3): p. 149-154. Gibbs, D.J., et al., Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature, 2011. 479(7373): p. 415-418. Bailey-Serres, J., et al., Making sense of low oxygen sensing. Trends Plant Science, 2012. 17(3): p. 129-38. Bachmair, A., D. Finley, and A. Varshavsky, In vivo half-life of a protein is a function of its amino-terminal residue. Science, 1986. 234(4773): p. 179-86. Bachmair, A. and A. Varshavsky, The degradation signal in a short-lived protein. Cell, 1989. 56(6): p. 1019-32. Graciet, E. and F. Wellmer, The plant N-end rule pathway: structure and functions. Trends Plant Science, 2010. 15(8): p. 447-53. Hanna, J. and D. Finley, A proteasome for all occasions. FEBS Letters, 2007. 581(15): p. 2854-61. Choi, W.S., et al., Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nature structural molecular biology, 2010. 17(10): p. 1175. Sriram, S.M., B.Y. Kim, and Y.T. Kwon, The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nature Reviews Molecular Cell Biology, 2011. 12(11): p. 735-47. Hu, R.G., et al., The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators. Nature, 2005. 437(7061): p. 981-6. Lee, M.J., et al., RGS4 and RGS5 are in vivo substrates of the N-end rule pathway. Proceedings of the National Academy of Science of the United States America, 2005. 102(42): p. 15030-5. Stary, S., et al., PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. Plant Physiology, 2003. 133(3): p. 1360-6. Garzón, M., et al., PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Letters, 2007. 581(17): p. 3189-96. Dissmeyer, N., Conditional Protein Function via N-Degron Pathway-Mediated Proteostasis in Stress Physiology. Annual Review of Plant Biology, 2019. 70: p. 83-117. Lupas, A.N. and K.K. Koretke, Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation. Journal of Structural Biology, 2003. 141(1): p. 77-83. Varshavsky, A., The N-end rule: functions, mysteries, uses. Proceedings of the National Academy of Science of the United States America, 1996. 93(22): p. 12142-9. Ponting, C.P., et al., ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins. Trends in Biochemical Science, 1996. 21(1): p. 11-13. Worley, C.K., R. Ling, and J. Callis, Engineering in vivo instability of firefly luciferase and Escherichia coli beta-glucuronidase in higher plants using recognition elements from the ubiquitin pathway. Plant Mol Biol, 1998. 37(2): p. 337-47. Schlögelhofer, P. and A. Bachmair, A test of fusion protein stability in the plant Arabidopsis thaliana reveals degradation signals from ACC synthase and from the plant N-end rule pathway. Plant Cell Reports, 2002. 21(2): p. 174-179. Kim, L., et al., Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway. Journal of Biological Chemistry, 2020. 295(9): p. 2590-2600. Graciet, E., F. Mesiti, and F. Wellmer, Structure and evolutionary conservation of the plant N-end rule pathway. Plant Journal, 2010. 61(5): p. 741-51. Schägger, H., Tricine-SDS-PAGE. Nature Protocols, 2006. 1(1): p. 16-22. Muñoz-Escobar, J., et al., Bound waters mediate binding of diverse substrates to a ubiquitin ligase. Structure, 2017. 25(5): p. 719-729. e3. Levinson, N.M. and S.G. Boxer, A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity. Nature chemical biology, 2014. 10(2): p. 127-132. Breiten, B., et al., Water networks contribute to enthalpy/entropy compensation in protein–ligand binding. Journal of the American Chemical Society, 2013. 135(41): p. 15579-15584. Urakubo, Y., T. Ikura, and N. Ito, Crystal structural analysis of protein–protein interactions drastically destabilized by a single mutation. Protein Science, 2008. 17(6): p. 1055-1065. Ladbury, J.E., Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chemistry biology, 1996. 3(12): p. 973-980. Hofer, F., et al., Catalytic Site pK(a) Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. Journal of Chemical Information and Modeling, 2020. 60(6): p. 3030-3042. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/80703 | - |
| dc.description.abstract | OsPRT6是一種E3泛素蛋白連接酶，可以識別ERFVII (第七群乙烯反應因子)的N端特定胺基酸序列，我們稱這種受質為N端降解決定子。在植物中，第七群乙烯反應因子可以調節缺氧反應，這個類群的蛋白在有氧環境時，其N端的序列會經過一連串的修飾，最後被E3泛素蛋白連接酶的泛素識別區域辨識到，進而被降解；相反地，在缺氧環境中，此類群蛋白能夠穩定存在。舉例來說，當洪水來臨時，植物會被淹沒在水中，此時第七群乙烯反應因子可以促進植物生長使植物能夠更快速地到達水面進行氧氣交換；或者是使植物停止發育以保存所有能量，直到洪水退去。根據先前的研究，我們已經知道N端降解決定子是有特定修飾過的序列才會泛素蛋白連接酶給辨識到，因此，我們想要利用蛋白結構的方式去了解受質與E3蛋白連接酶之間的交互作用為何。我們發現在pH 5.5的環境中無論是精胺酸-天門冬胺酸-甘胺酸所形成的多肽序列或是精胺酸-絲胺酸-甘胺酸多肽鍊，它們的精胺酸都會與泛素蛋白連接酶的泛素識別區域中的水分子產生交互作用，再加上泛素識別區域中有一胺基酸—精胺酸17，會更靠近受質多肽序列的結合區域，造成受質與結合區域連結更緊密。最後，我們也有拿精胺酸-色胺酸-甘胺酸多肽進行實驗，雖然我們沒有得到多肽序列與泛素蛋白連接酶所形成的蛋白結構，但是有發現，受質結合區域有因為我們把此種多肽鍊與其結合，使得泛素蛋白連接酶的結構有產生明顯的變化，結合區域的環有往內縮且精胺酸17更遠離受質結合區域。 | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-24T03:13:27Z (GMT). No. of bitstreams: 1 U0001-1810202111011500.pdf: 3386949 bytes, checksum: b111c8e4e1f07a17ca51698e93e1c97f (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | "摘要 1 Abstract 2 Index of figures 6 Index of tables 7 Chapter 1 Introduction 8 1.1 Effect of flooding on rice 8 1.2 The strategy aimed at submergence tolerance 8 1.3 EFFVIIs 10 1.4 N-end rule pathway 10 1.4.1 N-end rule pathway in yeast 11 1.4.2 N-end rule pathway in mammals 12 1.4.3 N-end rule pathway in plants 12 1.5 Structure of the UBR domain 14 1.6 Specific Aim 16 Chapter 2 Materials and Methods 18 2.1 Materials 18 2.1.1 Bacterial strains 18 2.1.2 Materials of molecular cloning 18 2.1.3 Chemicals and Reagents 18 2.1.4 Resins and Columns 20 2.1.5 Instrument 20 2.2 Methods 21 2.2.1 Construct design 21 2.2.2 Protein expression 22 2.2.3 Protein purification 23 2.2.4 Protein crystallization 25 2.2.5 Apo crystals of OsPRT6_UBR were soaked with different peptides under different pH conditions 25 Chapter 3 Results and discussions 26 3.1 Results 26 3.1.1 Purification of OsPRT6_UBR 26 3.1.2 Structure of OsPRT6_UBR in complex with RDG peptide 26 3.1.3 Structure of OsPRT6_UBR in complex with RSG peptide 28 3.1.4 Improving the crystallization of OsPRT6_UBR (R17+TG) with peptide RRG by using the LC3B fusion tag to construct the LC3B-substrate (RRG) -OsPRT6_UBR (R17+TG) 29 3.2 Discussion 31 3.2.1 High similarity structures for recognition of different peptides 31 3.2.2 The side chain of Arg 17 alternation depends on pH values 32 3.2.3 Variation of the side chain of Arg 15 in peptide-bound complex 34 Chapter 4 Conclusion 36 Chapter 5 Figures and Tables 38 5.1 Figures 38 Figure 1. Various constructs of recombinant OsPRT6 38 Figure 2. Primer design and PCR strategy of constructing His-LC3B-RRGGEV-OsPRT6 _UBR (R17+TG) expression plasmid and pET21 His vector………………………………………………………………………...39 Figure 3. Primer design and PCR product 42 Figure 4. Purification of His-GST-OsPRT6_UBR 44 Figure 5. Purification of His-GST-OsPRT6_UBR (R17+TG) 48 Figure 6. Purification of His-LC3B-RRGGEV-OsPRT6_UBR (R17+TG) 52 Figure 7. SDS-PAGE results of the expression and nickel-nitrilotriacetic affinity purification of His-hATG4B. 63 Figure 8. The crystal of OsPRT6_UBR. 64 Figure 9. Structures of OsPRT6_UBR in complex with RDG peptide for the recognition of Arg of N-degron 65 Figure 10. The interaction between the RDG backbone and rice UBR domain ……………………………………………………………………………………………………69 Figure 11. The interaction between Asp, the second position of N-degron, and the UBR domain. 71 Figure 12. Structure of OsPRT6_UBR in complex with tripeptide RSG 73 Figure 13. The superimpose of OsPRT6_UBR in complex with RDG at pH 8.5, RWG at pH 8.5, RDG at pH 5.5, RSG at pH 5.5, and OsPRT6_UBR apo form. ……………………………………………………………………………………………………75 Figure 14. Superimpose of OsPRT6_UBR and yeast UBR domain (PDB: 3NIH) ……………………………………………………………………………………………………77 Figure 15. Measuring binding affinity between OsPRT6_UBR and RDAAK peptide by Fluorescence polarization (FP) assay (data is from Ting-Jhen Lin), unit of Kd is μM 79 5.2 Tables 80 Table 1. The primers of cloning construct 80 Table 2. The amino acid sequence of recombinant His-GST-TEV protease recognition site-OsPRT6 UBR domain 81 Table 3. The amino acid sequence of recombinant His-GST-TEV protease recognition site-OsPRT6 UBR domain two swappings (R17+TG) 82 Table 4. The amino acid sequence of recombinant His-TEV protease recognition site-LC3B-RRGGEV-OsPRT6 UBR domain two swappings (R17+TG) 83 Table 5. The amino acid sequence of recombinant His-TEV protease recognition site-hATG4B 84 Table 6. The theoretical molecular weight and pI value of proteins 85 Table 7. Buffer components of nickel chromatography purification of His-GST-OsPRT6_UBR and His-GST- OsPRT6_UBR (R17+TG). 86 Table 8. Buffer components of nickel chromatography purification of His-LC3B-RRGGEV-OsPRT6_UBR (R17+TG). 86 Table 9. Buffer components of nickel chromatography purification of His-hATG4B. ……………………………………………………………………………………………………86 Table 10. Buffer components of dialysis buffer of His-GST-OsPRT6_UBR and His-GST- OsPRT6_UBR (R17+TG). 87 Table 11. Buffer components of dialysis buffer of RRGGEV-OsPRT6_UBR (R17+TG) 87 Table 12. Buffer components of size exclusion of His-GST-OsPRT6_UBR and His-GST- OsPRT6_UBR (R17+TG). 87 Table 13. Buffer components of crystallization of OsPRT6_UBR. 87 Table 14. Buffer components of soaking buffer in different environment. 88 Table 15. The Tricine-SDS-PAGE buffer and the casting gel prepare 89 Table 16. Data collection and refinement of OsPRT6 UBR box in complex with peptides ……………………………………………………………………………………………………90 Table. 17 The binding affinity (mM) of OsPRT6-UBR toward various RXG peptide (data is from Ting-Jhen Lin) 91 Chapter 6 References 92 " | |
| dc.language.iso | en | |
| dc.subject | 第七群乙烯反應因子 | zh_TW |
| dc.subject | N端規則路徑 | zh_TW |
| dc.subject | N端降解決定子 | zh_TW |
| dc.subject | 缺氧 | zh_TW |
| dc.subject | 泛素蛋白接酶 | zh_TW |
| dc.subject | hypoxia | en |
| dc.subject | N-end rule pathway | en |
| dc.subject | ERFVII | en |
| dc.subject | N-degron | en |
| dc.subject | OsPRT6_UBR | en |
| dc.title | 水稻蛋白水解酶6的泛素識別區域與其辨別受質之N端特異性結構之研究 | zh_TW |
| dc.title | Structural studies for the N-degron specificity of the UBR domain of Proteolysis 6 from Oryza sativa | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 梁博煌(Hsin-Tsai Liu),鄭貽生(Chih-Yang Tseng) | |
| dc.subject.keyword | 泛素蛋白接酶,第七群乙烯反應因子,缺氧,N端降解決定子,N端規則路徑, | zh_TW |
| dc.subject.keyword | OsPRT6_UBR,ERFVII,hypoxia,N-degron,N-end rule pathway, | en |
| dc.relation.page | 95 | |
| dc.identifier.doi | 10.6342/NTU202103813 | |
| dc.rights.note | 同意授權(限校園內公開) | |
| dc.date.accepted | 2021-10-20 | |
| 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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