博碩士論文 104826013 詳細資訊




以作者查詢圖書館館藏 以作者查詢臺灣博碩士 以作者查詢全國書目 勘誤回報 、線上人數:17 、訪客IP:18.118.93.61
姓名 廖君宇(Chun-Yu Liao)  查詢紙本館藏   畢業系所 系統生物與生物資訊研究所
論文名稱 利用酵母菌蛋白質體晶片找出與前信使核糖核酸加 工因子19泛素連接?經泛素化作用之受質
(Ubiquitination subtract screening of ubiquitin ligase pre-mRNA-processing factor 19 using yeast proteome microarrays)
相關論文
★ 以生物資訊分析與實驗驗證探討大腸桿菌蛋白質體晶片找出的乳鐵胜肽B胞內目標蛋白★ 結合奈米脂粒與抗體微陣列晶片的高通量快速檢測系統之發展並應用於婦女子宮頸炎病因之診斷與研究
★ 蛋白質 G 與具硫基反應性的釕複合物之生物接合作為螢光免疫試驗的通用試劑★ 利用微陣列蛋白質晶片帥選GNRA tetraloop結合蛋白
★ 利用大腸桿菌蛋白質體晶片分析新生兒血液中的免疫球蛋白★ 利用大腸桿菌蛋白質體晶片找出參與第一型線毛表現之細菌蛋白質
★ 利用人類蛋白質體微陣列晶片探究C型肝炎病毒非轉譯區與宿主之交互作用★ 利用大腸桿菌蛋白體微陣列晶片系統性探討抗菌肽的胞內作用目標
★ 利用大腸桿菌蛋白質體晶片找出與2-氧基組胺酸交互作用之蛋白質★ 發展微珠式96孔過濾盤競爭型免疫分析法偵測硫酸紫菌素
★ 異質性核醣核酸蛋白K (hnRNP K) 抑制成熟miRNA-122轉錄後調控機制之研究★ 腸道共生黴菌與酒精性肝病的相關性
★ 在大腸桿菌與酵母菌蛋白質體晶片中量化其蛋白質的濃度★ 應用大腸桿菌與酵母菌蛋白質體晶片系統性分析抗菌肽及抗生素作用之目標蛋白質
檔案 [Endnote RIS 格式]    [Bibtex 格式]    [相關文章]   [文章引用]   [完整記錄]   [館藏目錄]   [檢視]  [下載]
  1. 本電子論文使用權限為同意立即開放。
  2. 已達開放權限電子全文僅授權使用者為學術研究之目的,進行個人非營利性質之檢索、閱讀、列印。
  3. 請遵守中華民國著作權法之相關規定,切勿任意重製、散佈、改作、轉貼、播送,以免觸法。

摘要(中) 泛素為一常見於細胞中的小蛋白質,主要用以標記蛋白質受質,並進行後續如去氧
核醣核酸修復、蛋白質水解等路徑。標記泛素的過程稱謂泛素化,其透過泛素活化?、 泛素結合?與泛素連接?將特定受質接上泛素。其中,泛素連接?負責辨識特定的受質, 扮演泛素化中的關鍵角色。前信使核糖核酸加工因子 19 為其中一種泛素連接?,與去 氧核醣核酸修復與信使核糖核酸剪接有所關聯,並被發現在肺癌中有過度表現的現象。 我對大於五千八百種蛋白質的酵母菌蛋白質體晶片進行前信使核糖核酸加工因子 19 的 胞外泛素化實驗,篩選出其對應的四十五個受質,並透過生物資訊的方式找到這四十五 個受質共有結合序列與前信使核糖核酸加工因子 19 透過泛素化受質而進一步產生關聯 的十類生物機制、七類細胞組件、六類分子功能與十二類路徑。另外,在四十五個受質 中,四十個牽涉到七類生物機制、四類細胞組件以及兩類路徑與前信使核糖核酸加工因 子 19 有關聯。此外,有三類生物機制、六類細胞組件和三類分子功能呈現顯著富集。 還有,我找出兩組受質分別有不同的序列模組,提供與前信使核糖核酸加工因子 19 可 能的結合點。根據結果,我找到這些基因本體論與路徑可能透過受質泛素化而被前信使 核糖核酸加工因子 19 所調控,對前信使核糖核酸加工因子 19 進一步的研究方向。
摘要(英) Ubiquitin is a common small protein in cells, it usually served as tag conjugated to the substrate, for DNA repair, proteolysis, and others. This process is called ubiquitination, which ubiquitinates specific substrates by ubiquitin activation enzyme, ubiquitin conjugating enzyme and ubiquitin ligase. Ubiquitin ligase serves as a critical point for substrates specificity. Pre- mRNA-processing factor 19 (PRP19) is one of the ubiquitin ligases, involves in DNA repair, mRNA splicing, and has been found overexpressed in lung cancer. I found forty-five substrates of PRP19 from in vitro ubiquitination assay on yeast proteome chip which contains more than 5800 kinds of the yeast protein. I used bioinformatics analysis to find PRP19 further involving ten classes of biological processes, seven classes of cellular components, six classes of molecule functions, and twelve classes of pathways by ubiquitinates its substrates. Forty of forty-five substrates involved in seven classes of biological processes, four classes of cellular components and two pathways which relate to PRP19.In addition, there were three classes of biological processes, six classes of cellular components, three classes of molecule functions were significantly enriched. Also, I found two groups of substrates had different consensus motifs as putative binding sites with PRP19. According to the result, I found those GO and pathways might be regulated by PRP19-substrates ubiquitination, it gave the direction for
further study on PRP19.
關鍵字(中) ★ 前信使核糖核酸加 工因子19
★ 泛素
★ 泛素化
★ 酵母菌蛋白質體晶片
★ 受質
關鍵字(英) ★ pre-mRNA-processing factor 19
★ ubiquitin
★ Ubiquitination
★ yeast proteome microarrays
★ subtract
論文目次 中文摘要.i
Abstract.ii
Acknowledgments iii
Table of contentsiv
List of figuresvi
List of tables. viii
I. Introduction 1
II. Method10
II.1 Yeast proteome chips production 10
II.2 Ubiquitination enzyme expression and purification12
II.3 Ubiquitination yeast proteome chip assay 12
II.4 Chip image align and data analysis 13
II.5 Bioinformatics analyses 14
II.5.1 Protein annotation information collection14
II.5.2 Gene ontology classification 15
II.5.3 Pathway classification 15
II.5.4 GLAM2 Motif search 16
III. Result 23
III.1 Purification of ubiquitin enzymes23
III.2 Ubiquitination yeast proteome chip assay 24
III.3 Gene ontology classification 24
III.4 Pathway analysis 26
III.5 Motif study 27
IV. Discussion 51
V. Reference 54
參考文獻 1. Hershko, A. and A. Ciechanover, The ubiquitin system. Annu Rev Biochem, 1998. 67: p. 425-79.
2. Pickart, C.M., Mechanisms underlying ubiquitination. Annu Rev Biochem, 2001. 70: p. 503-33.
3. Pickart, C.M. and D. Fushman, Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol, 2004. 8(6): p. 610-6.
4. Berndsen, C.E. and C. Wolberger, New insights into ubiquitin E3 ligase mechanism. Nat Struct Mol Biol, 2014. 21(4): p. 301-7.
5. Finley, D., et al., The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics, 2012. 192(2): p. 319-60.
6. Dawson, T.M. and V.L. Dawson, Molecular pathways of neurodegeneration in Parkinson′s disease. Science, 2003. 302(5646): p. 819-22.
7. Liu, Y.C., Ubiquitin ligases and the immune response. Annu Rev Immunol, 2004. 22: p. 81-127.
8. Confalonieri, S., et al., Alterations of ubiquitin ligases in human cancer and their association with the natural history of the tumor. Oncogene, 2009. 28(33): p. 2959- 68.
9. Gupta, R., et al., Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol, 2007. 3: p. 116.
10. Loch, C.M., M.J. Eddins, and J.E. Strickler, Protein microarrays for the identification of praja1 e3 ubiquitin ligase substrates. Cell Biochem Biophys, 2011. 60(1-2): p. 127-35.
11. Andrews, P.S., et al., Identification of substrates of SMURF1 ubiquitin ligase activity utilizing protein microarrays. Assay Drug Dev Technol, 2010. 8(4): p. 471-87.
12. Marechal, A., et al., PRP19 transforms into a sensor of RPA-ssDNA after DNA
damage and drives ATR activation via a ubiquitin-mediated circuitry. Mol Cell, 2014.
53(2): p. 235-46.
13. Song, E.J., et al., The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme
control reversible ubiquitination at the spliceosome. Genes Dev, 2010. 24(13): p.
1434-47.
14. Das, T., et al., USP15 regulates dynamic protein-protein interactions of the
spliceosome through deubiquitination of PRP31. Nucleic Acids Res, 2017. 45(8): p. 4866-4880.
54
15. Bellare, P., et al., A role for ubiquitin in the spliceosome assembly pathway. Nat Struct Mol Biol, 2008. 15(5): p. 444-51.
16. Zhu, H., et al., Global analysis of protein activities using proteome chips. Science, 2001. 293(5537): p. 2101-5.
17. Chen, Y.W., et al., Identification of bacterial factors involved in type 1 fimbria expression using an Escherichia coli K12 proteome chip. Mol Cell Proteomics, 2014. 13(6): p. 1485-94.
18. Lu, J.Y., et al., Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics, 2008. 7(1): p. 35-45.
19. Apweiler, R., et al., UniProt: the Universal Protein knowledgebase. Nucleic Acids Res, 2004. 32(Database issue): p. D115-9.
20. Ashburner, M., et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25-9.
21. Huang da, W., B.T. Sherman, and R.A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc, 2009. 4(1): p. 44-57.
22. Croft, D., et al., Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 2011. 39(Database issue): p. D691-7.
23. Frith, M.C., et al., Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol, 2008. 4(4): p. e1000071.
24. Carlson, M., GO.db: A set of annotation maps describing the entire Gene Ontology. R package version 3.4.1. 2017.
25. Binns, D., et al., QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics, 2009. 25(22): p. 3045-6.
26. Norbeck, J., et al., Purification and Characterization of Two Isoenzymes of DL- Glycerol-3-phosphatase from Saccharomyces cerevisiae. Journal of Biological Chemistry, 1996. 271(23): p. 13875-13881.
指導教授 陳健生(Chien-Sheng Chen) 審核日期 2017-8-25
推文 facebook   plurk   twitter   funp   google   live   udn   HD   myshare   reddit   netvibes   friend   youpush   delicious   baidu   
網路書籤 Google bookmarks   del.icio.us   hemidemi   myshare   

若有論文相關問題,請聯絡國立中央大學圖書館推廣服務組 TEL:(03)422-7151轉57407,或E-mail聯絡  - 隱私權政策聲明