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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 何孟樵(Meng-Chiao Ho) | |
| dc.contributor.author | Wai-Kuen Hung | en |
| dc.contributor.author | 洪偉權 | zh_TW |
| dc.date.accessioned | 2022-11-23T08:59:45Z | - |
| dc.date.available | 2021-11-03 | |
| dc.date.available | 2022-11-23T08:59:45Z | - |
| dc.date.copyright | 2021-11-03 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-10-22 | |
| dc.identifier.citation | 1. Giuntoli, B. and P. Perata, Group VII Ethylene Response Factors in Arabidopsis: Regulation and Physiological Roles. Plant Physiol, 2018. 176(2): p. 1143-1155. 2. White, M.D., et al., Structures of Arabidopsis thaliana oxygen-sensing plant cysteine oxidases 4 and 5 enable targeted manipulation of their activity. Proc Natl Acad Sci U S A, 2020. 117(37): p. 23140-23147. 3. White, M.D., et al., The plant cysteine oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors. J Biol Chem, 2018. 293(30): p. 11786-11795. 4. Gibbs, D.J., et al., Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature, 2011. 479(7373): p. 415-8. 5. Licausi, F., Evolution of Plant Cysteine Oxidases. 2020. 6. Houghton, J., Global warming. Reports on Progress in Physics, 2005. 68(6): p. 1343-1403. 7. Lesk, C., P. Rowhani, and N. Ramankutty, Influence of extreme weather disasters on global crop production. Nature, 2016. 529(7584): p. 84-7. 8. Golden, G.K.G.S.P.P.M.K.A.N.J.M.O.B.R., Impacts and management strategies for crop production in waterlogged or flooded soils: A review. Agronomy Journal, 2019: p. 1475-1501. 9. Krämer, U., The natural history of model organisms: Planting molecular functions in an ecological context with Arabidopsis thaliana. Elife, 2015. 4: p. e06100. 10. Meyerowitz, E.M., Arabidopsis thaliana. Annual review of genetics, 1987. 21(1): p. 93-111. 11. Bumett, L.E. and W.B. Stickle, Physiological responses to hypoxia. Coastal hypoxia: consequences for living resources and ecosystems, 2001. 58: p. 101-14. 12. Cho, H., et al., On-target efficacy of a HIF-2α antagonist in preclinical kidney cancer models. Nature, 2016. 539(7627): p. 107-111. 13. Maxwell, P.H. The HIF pathway in cancer. in Seminars in cell developmental biology. 2005. Elsevier. 14. Varshavsky, A., The N‐end rule pathway and regulation by proteolysis. Protein science, 2011. 20(8): p. 1298-1345. 15. Graciet, E. and F. Wellmer, The plant N-end rule pathway: structure and functions. Trends Plant Sci, 2010. 15(8): p. 447-53. 16. Müller, M. and S. Munné-Bosch, Ethylene Response Factors: A Key Regulatory Hub in Hormone and Stress Signaling. Plant physiology, 2015. 169(1): p. 32-41. 17. Weits, D.A., et al., Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nature communications, 2014. 5(1): p. 1-10. 18. White, M.D., et al., Plant cysteine oxidases are dioxygenases that directly enable arginyl transferase-catalysed arginylation of N-end rule targets. Nature communications, 2017. 8(1): p. 1-9. 19. Masson, N., et al., Conserved N-terminal cysteine dioxygenases transduce responses to hypoxia in animals and plants. Science, 2019. 365(6448): p. 65-69. 20. Hayes, B., Characterisation of Plant Cysteine Dioxygenase. 2018. 21. Weits, D.A., et al., Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes. bioRxiv, 2020: p. 2020.06.24.169417. 22. Licausi, F., et al., Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature, 2011. 479(7373): p. 419-22. 23. 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. 24. Lin, C.-C., et al., Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. Proceedings of the National Academy of Sciences, 2019. 116(8): p. 3300-3309. 25. 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. 26. Licausi, F., et al., HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J, 2010. 62(2): p. 302-15. 27. Hinz, M., et al., Arabidopsis <em>RAP2.2</em>: An Ethylene Response Transcription Factor That Is Important for Hypoxia Survival. Plant Physiology, 2010. 153(2): p. 757-772. 28. Bui, L.T., et al., Constitutively expressed ERF-VII transcription factors redundantly activate the core anaerobic response in Arabidopsis thaliana. Plant Science, 2015. 236: p. 37-43. 29. Colmer, T. and L. Voesenek, Flooding tolerance: Suites of plant traits in variable environments. Functional Plant Biology, 2009. 36. 30. Bailey-Serres, J. and L.A. Voesenek, Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol, 2008. 59: p. 313-39. 31. Loreti, E., et al., Gene Regulation and Survival under Hypoxia Requires Starch Availability and Metabolism. Plant Physiology, 2018. 176(2): p. 1286-1298. 32. Manzur, M.E., et al., Escape from water or remain quiescent? Lotus tenuis changes its strategy depending on depth of submergence. Ann Bot, 2009. 104(6): p. 1163-9. 33. Dunker, A.K., et al., Intrinsically disordered protein. Journal of molecular graphics and modelling, 2001. 19(1): p. 26-59. 34. Striker, G., Flooding Stress On Plants: Anatomical, Morphological And Physiological Responses. 2012. 35. Healthcare, G., Size exclusion chromatography: Principles and Methods. GE Heal. Handbooks, 2012. 139. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79404 | - |
| dc.description.abstract | "第七群乙烯反應因子是植物在無氧環境誘導的轉錄因子。當植物在無氧的狀態下，他們只會透過無氧呼吸產生的小量三磷酸腺苷（ATP）去維持它的生命。這一個系統可以保護植物免受水災的危害。第七群乙烯反應因子是否存在是由植物的N-end rule pathway來決定。第七群乙烯反應因子都有一個共同的特徵，它們的氨基酸序列都是從MCGG開始。這個特徵賦與他們可以被修飾，氧化及降解。第七群乙烯反應因子的降解必需要經過一系列的酵素，但這些酵素不只是單純為第七群乙烯反應因子而存在。這群酵素裡只有Plant cysteine oxidase (PCO)是只處理無氧基因。PCO 是對於植物轉為生長或者保護模式的最關鍵酵素。這個開關可以讓植物逃離全球暖化造成的大量自然災害。PCO 1是這個研究的目標，他是植物PCO中表現量最大的。同時，PCO 1亦是能夠被無氧環境誘導表達的B型PCO. 為了完全明白PCO 1, 他的晶體結構是必不可少。經過了無數次的序列和結晶條件優化，最終蛋白結晶成功被找出來。" | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-23T08:59:45Z (GMT). No. of bitstreams: 1 U0001-2010202114161600.pdf: 22803456 bytes, checksum: 57c8a529e16347a8327c6a600e299f43 (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | "口試委員會審定書 i 致謝 ii 摘要 iii Abstract iv Table of contents v Index of figures x Index of tables xii Chapter 1: Introduction 1 1 Global warming 1 1.1 Extreme weather 1 1.2 Arabidopsis thaliana 2 1.2.1 Hypoxia response 2 1.2.2 Hypoxia response in animal 3 1.2.3 Hypoxia response in the plant 3 1.3 N-end rule pathway 4 1.3.1 N-degron 4 1.3.2 N-recognin 4 1.4 Plant cysteine oxidases (PCO) 5 1.5 Target protein 6 1.6 Submergence 7 1.6.1 Hypoxia response element 7 1.6.2 Related to Apetala2 8 1.7 Plant submergence survive strategy, escape, and quiescence strategies 9 1.8 Research aim 10 Chapter 2: Material and methods 11 2.1 Materials 11 2.1.1 Bacterial strains 11 2.1.2 Molecular cloning Materials 11 2.1.3 Molecular cloning Materials 12 2.1.4 Instruments and equipment 13 2.2 Methods 15 2.2.1 Plant Cysteine Oxidase 1 cloning 15 2.2.2 Plant Cysteine Oxidase 1 truncation 15 2.2.3 Bovine serum albumin (BSA) standard curve 16 2.2.4 Plant Cysteine Oxidase expression 16 2.2.5 Resuspend cell pellet 17 2.3 Cell lysis by sonicator 18 2.3.1 Cell lysis by nanolyzer 18 2.3.2 cell pellet centrifugation 19 2.3.3 Immobilized-metal affinity chromatography (IMAC) 20 2.3.4 Immobilized-metal affinity chromatography (IMAC) pH elution 21 2.3.5 Immobilized-metal affinity chromatography (IMAC) Imidazole elution 22 2.3.6 SDS-PAGE 24 2.3.7 Running SDS-PAGE 25 2.3.8 SDS-PAGE staining 26 2.3.9 Dialysis and TEV proteinase digestion 26 2.3.10 Dialysis and TEV proteinase digestion 26 2.3.11 Size-exclusion chromatography (SEC) 27 2.3.12 Protein Thermal Shift Assay 28 2.3.13 Pre-Crystallization Test (PCT) 29 2.3.14 Sitting Drop Vapor Diffusion Crystal screening 29 2.3.15 Trypsin digestion 30 2.3.16 Anaerobic incubator 30 2.3.17 Crystal freezing 31 2.3.18 Plant Cysteine Oxidase 1 activity assay 31 Chapter 3: Results and discussions 32 3.1 His-TEV-AtPCO 1 purification 32 3.2 Protein melting test 33 3.3 Trypsin digested AtPCO 1 sequence cloning 34 3.4 AtPCO 1 Deletion 1 and AtPCO1 Deletion 2 purification 34 3.5 AtPCO pellet comparing 35 3.6 AtPCO 1 deletion adds GST tag in N-terminal purification 36 3.7 AtPCO1 disorder region prediction 37 3.8 AtPCO 1 Deletion 3 purification 38 3.9 AtPCO 1 deletion 4 purification 39 3.10 AtPCO 1 deletion 5 purification 39 3.11 AtPCO 1 deletion 6 purification 40 3.12 AtPCO1 deletion 6 crystal discover 41 3.13 Crystal forming conditions refine 41 3.14 AtPCO 1 deletion form activity test 42 Chapter 4: Conclusion and perspective 43 4.1 The specialty of Arabidopsis thaliana plant cysteine oxidase 1 43 4.2 Disorder region of Arabidopsis thaliana plant cysteine oxidase 1 43 4.3 Trypsin digestion 44 4.4 Intrinsic disorder region of AtPCO 45 4.5 Role of Arabidopsis thaliana plant cysteine oxidase 1 in physiology 46 4.6 Sequence editing produces Arabidopsis thaliana plant cysteine oxidase 1 protein crystal 47 4.7 Sequence editing refine and disorder region physiological research 47 Chapter 5: Tables and figures 49 Chapter 6: References 84 Figure 1. Arabidopsis thaliana worldwide distribution 54 Figure 2. Plant N-end rule pathway 55 Figure 3. Different types of Cystine Oxidases amino acid sequence alignment comparing [2] 56 Figure 4. Dioxygenation of Plant cysteine oxidases 57 Figure 5. Escape and Quiescence strategy 58 Figure 6. Ligand binding sites difference between Nickel NTA and IDA (A handbook for high-level expression and purification of 6xHis-tagged proteins, The QI expressionist) 59 Figure 7. The bead of size exclusion column [35] 60 Figure 8. Bovine serum albumin standard curve 61 Figure 9. Purification of AtPCO 1 62 Figure 10. AtPCO1 trypsin digestion 63 Figure 11. AtPCO1 Protein melting test 64 Figure 12. Purification of AtPCO 1 Deletion 1 65 Figure 13. Purification of AtPCO1 Deletion 2 66 Figure 14. GST tag-AtPCO1 Deletion 2 purification and TEV protease digestion 67 Figure 15. AtPCO pellet comparing 68 Figure 16. AtPCO 1 simulation structure 69 Figure 17. AtPCO 1 disorder region prediction 70 Figure 18. AtPCO1 deletion 3 purification 71 Figure 19. AtPCO1 deletion 3 Protein melting test 72 Figure 20. AtPCO 1 deletion 4 purification 73 Figure 21. AtPCO 1 deletion 5 purification 74 Figure 22. AtPCO 1 deletion 6 purification 75 Figure 23. AtPCO 1 deletion 6 protein melting test 76 Figure 24. AtPCO1 deletion 6 protein crystal 77 Figure 25. AtPCO1 deletion 6 condition refined protein crystal 78 Figure 26. AtPCO1 deletion 6 bigger protein crystal by temperature and protein concentration refine 79 Figure 27. AtPCO1 deletion 6 protein crystal from phenol additive 80 Figure 28. AtPCO1 deletion 6 protein crystal from anaerobic 81 Figure 29. AtPCO1 deletion 3 activity test by Mass ID examination 82 Figure 30. AtPCO1 deletion 6 activity test by Mass ID examination 83 Table 1. PCR program setting 49 Table 2. Arabidopsis thaliana Plant cysteine oxidase 1 deletion primer 50 Table 3.Buffer screen of protein melting test 51 Table 4. Nickel chromatography buffer composition of AtPCO 1 and deletion 1, 2 52 Table 5. Nickel chromatography buffer composition of AtPCO 1 deletion 3, 4, 5 52 Table 6. Nickel chromatography buffer composition of AtPCO 1 deletion 6 52 Table 7. Size exclusion chromatography buffer composition of AtPCO 1 and deletion 1, 2, 3 53 Table 8. Size exclusion chromatography buffer composition of AtPCO 1 deletion 6 53 " | |
| dc.language.iso | en | |
| dc.title | 阿拉伯芥的植物半胱胺酸氧化酶 AtPCO 1之生物物理 與結構特性研究 | zh_TW |
| dc.title | "Structural and biophysical studies of Arabidopsis thaliana plant cysteine oxidase 1, AtPCO 1 " | 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 | 蛋白結晶,全球暖化,AtPCO1,ERF VII,N-end rule pathway, | zh_TW |
| dc.subject.keyword | AtPCO1,ERF VII,N-end rule pathway,crystallization,global warming, | en |
| dc.relation.page | 86 | |
| dc.identifier.doi | 10.6342/NTU202103924 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-10-25 | |
| 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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