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研究生:鍾岳霖
研究生(外文):Yue-Lin Chung
論文名稱:探討OsCCR4a 與 OsCCR4b兩個水稻CCR4同源蛋白之去腺苷酸酵素活性
論文名稱(外文):Studying on deadenylation capabilities of two homologous rice carbon catabolite repression 4 proteins, OsCCR4a and OsCCR4b
指導教授:陸重安
指導教授(外文):Chung-An Lu
學位類別:碩士
校院名稱:國立中央大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2016
畢業學年度:104
語文別:中文
論文頁數:128
中文關鍵詞:mRNA的降解CCR4-NOT複合體去腺苷酸酵素
外文關鍵詞:mRNADeadenylaseCCR4-NOT complex
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從單細胞酵母菌一直到多細胞動物,如:老鼠、人類等真核生物中都具有CCR4-NOT複合體,這個複合體對於基因表達是整體的調節者。複合體中的各個蛋白質對於不同層面的mRNA代謝都有關聯,包括transcription initiation、elongation 和mRNA degradation。控制mRNA的半衰期是調控基因表現的重要一環,大部分的情況下,調控真核細胞mRNA半衰期的主要途徑是先將mRNA的poly (A) tail縮短。在酵母菌的研究得知,CCR4蛋白質是CCR4-NOT複合體的其中一個成員,並已經證實在細胞質中具有deadenylation的功能。然而,水稻CCR4的功能目前尚未清楚,因此本篇論文將進一步探討CCR4在水稻中的功能。
透過胺基酸序列比對分析發現兩個水稻CCR4 homolog,並命名為OsCCR4a和OsCCR4b。水稻CCR4的C端nuclease domain重組蛋白質:His-OsCCR4a EEP 和His-OsCCR4b EEP,在in vitro的實驗中證實具有deadeanylase的酵素活性,在水稻CCR4的activity site點突變會使其deadeanylase的酵素活性消失。processing bodies是存在真核細胞的細胞質中顆粒狀結構,裡面包含了很多跟mRNA turnover有關的酵素,我們發現水稻CCR4會在細胞質的processing bodies中。基因表現的部分,發現OsCCR4a和OsCCR4b基因在葉子和劍葉的部分表現量比較高,並且會受到熱逆境所誘導,但是在賀爾蒙2,4D以及NAA的處理下,OsCCCR4b會被誘導而OsCCR4a的基因表現不會受到影響。兩個OsCCR4蛋白質都具有deadenylase的酵素活性,並且會在細胞質的processing bodies中,推測OsCCR4蛋白質可能參與水稻中 mRNA的deadeylation;從基因表現的部分,發現在水稻發育過程或受到環境壓力下OsCCR4a和OsCCR4b並不是完全的functional redundancy。

The CCR4-NOT (carbon catabolite repression, negative on TATA-less) complex is a global regulator of gene expression that is conserved from yeast to human. The complex is involved in several aspects of mRNA metabolism, including transcription initiation, elongation and mRNA degradation. Control of mRNA turnover is a critical mechanism for regulating of gene expression in eukaryotice cells. One of major pathway of mRNA turnover in eukaryotic cells is initiated by mRNA deadenylation (also called as poly(A) tail shortening). In yeast, the CCR4 protein, as part of the CCR4-NOT complex, has been shown that take a responsibility for cytoplasmic deadenylation. However, the function of CCR4 in rice is not clear yet. In this study, we identified and cloned two CCR4 homologs, OsCCR4a and OsCCR4b, from Oryza sativa. The OsCCR4s C-terminal nuclease domain recombinant proteins, His-OsCCR4a EEP and His-OsCCR4b EEP, exhibited deadenylase activity in vitro, and mutation in their activity site abolished their deadenylase activities, respectively. Subcellular localization analysis showed that OsCCR4a-GFP and OsCCR4b-GFP are localized in cytoplasmic mRNA processing bodies (P-bodies), which are specific granules consisting of enzymes involved in mRNA turnover. Both OsCCR4s were suggested are heat stress related genes while their expression were induced by heat stress in rice. However, only OsCCR4b was induced by 2,4D and NAA treatments. Our findings provide biochemical evidence that two OsCCR4 proteins may be involved in the deadenylation in rice. The various expression patterns between two OsCCR4s implied that OsCCR4a and OsCCR4b aren’t completely functional redundancy in the developmental process and stress response of the rice.
目錄
摘要 I
Abstract II
目錄 III
壹、 序論 1
1. mRNA數量的調控機制 1
2. mRNA的降解 2
3. Deadenylase 4
4. CCR4-NOT complex 6
5. CCR4 7
6. Processing bodies 12
7. OsCCR4 14
貳、 材料與方法 15
1. CCR4同源性基因的鑑定與親緣關係樹的分析 15
1.1 CCR4同源性基因的鑑定 15
1.2 CCR4同源性基因的序列比對與親緣關係樹的建立 15
2. cDNA的製備 15
2.1 製備DEPC-treated ddH2O (RNase-free)溶液 15
2.2 萃取Total RNA 15
2.3 去除染色體DNA之汙染 16
2.4 cDNA之合成 16
3. 質體的建構 16
3.1 設計引子 16
3.2 利用PCR合成水稻CCR4基因片段 17
3.3 水稻CCR4基因點突變片段的合成 17
3.4 瓊脂膠體回收DNA 18
3.5 DNA片段接合至T&A載體中 18
3.6 蛋白質表達質體的建構 19
3.7 螢光蛋白融合OsCCR4s表達質體的建構 19
4. 細菌的轉型作用 19
4.1 製備E. coli competent cell (DH5α strain,BL21 strain) 19
4.2 細菌的轉型(transformation) 20
4.3 小量純化細菌質體DNA 20
5. 水稻原生質體的轉型方法 21
5.1 水稻植株的培養 21
5.2 原生質體製備 (protoplast isolation) 21
5.3 PEG transformation 22
6. 洋蔥表皮細胞利用微粒子投射法(particle bombardment)的轉型 22
6.1 洋蔥表皮細胞的準備 22
6.2 基因槍設定 22
6.3 金粒子的製備 23
6.4 DNA附著 23
6.5 轉型樣品處理 23
7. 蛋白質的表達與純化 23
7.1 利用E. coli表達目標蛋白質 23
7.2 蛋白質表達 23
7.3 蛋白質萃取 24
7.4 蛋白質純化 24
7.5 蛋白質電泳(SDS-PAGE) 25
7.6 西方墨點法 25
7.7 蛋白質濃縮以及濃度測定 26
8. In vitro deadenylase活性測試 26
8.1 受質RNA設計 26
8.2 活性測試 26
8.3 RNA電泳 27
9. 在逆境下OsCCR4s基因表現之分析 27
9.1 水稻植株的培養 27
9.2 逆境的處理 27
9.3 基因表現的分析 27
參、 實驗結果 29
1. 水稻CCR4同源性基因的鑑定與親緣關係樹的分析 29
2. 水稻CCR4同源性蛋白質胺基酸序列比對分析 29
3. OsCCR4s蛋白質結構預測 30
4. OsCCR4s蛋白質的表達與純化 31
5. OsCCR4s的deadenylase活性測試 33
6. OsCCR4s在細胞中的位置 34
7. OsCCR4s與OsCAF1s基因在水稻不同組織中以及受到環境壓力時的表現 35
肆、 討論 37
1. CCR4同源性基因的鑑定與親緣關係樹的分析 37
2. 水稻CCR4同源性蛋白質胺基酸序列比對分析與蛋白質結構預測 38
3. 水稻CCR4蛋白質的表達與純化 39
4. 水稻CCR4的deadenylase活性測試 39
5. 水稻CCR4在細胞中的位置 40
6. 水稻CCR4基因在水稻不同組織中以及受到環境壓力時的表現 41
伍、 參考資料 43
陸、 圖表 55
柒、 附錄 94


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