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研究生:詹蕙鎂
研究生(外文):Hui-mei Chan
論文名稱:澳洲球形海綿粒線體介入子之自我剪切能力研究
論文名稱(外文):Self-splicing of Group I Intron of the Mitochondrial Genome of the Sponge, Cinachyrella australiensis
指導教授:徐基新徐基新引用關係
指導教授(外文):Chi-Hsin Hsu
學位類別:碩士
校院名稱:國立中山大學
系所名稱:海洋生物科技暨資源學系研究所
學門:自然科學學門
學類:海洋科學學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:146
中文關鍵詞:自我剪切內切酶第一型介入子澳洲球形海綿環化反應
外文關鍵詞:group I introncyclizationself-splicingC. australiensishoming endonuclease
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真核生物基因轉錄的過程,必須經過RNA剪切將介入子去除,形成成熟型的RNA;根據剪切機制可將這些進行RNA剪切的介入子分為第一型介入子、第二型介入子、剪接體介入子和轉運RNA介入子,其中,多數的第一型介入子和第二型介入子具自我剪切能力。第一型介入子分布廣泛,其剪切與否會影響宿主基因的蛋白質功能,對含有多重嵌入的原生生物和真菌而言,更可以反過來利用進而抑制病原微生物生長,卻鮮見於後生動物。本篇研究在澳洲球形海綿粒線體的細胞色素氧化酶次單位I基因,發現具有第一型介入子特徵的序列,經分析得知其開放式轉譯框架可轉譯出與移動性相關的兩LAGLI-DADG主題內切酶,結構比對的初步推測屬於IB2子群。實驗結果經由生物體和非生物體證實此段基因可進行完整的剪切。介入子主要利用自身的結構摺疊,催化游離態鳥糞嘌呤的攻擊,進行兩次轉酯化反應完成自我剪切,並使兩端外顯子連接形成成熟型的RNA。特別的是,細胞色素氧化酶次單位I基因介入子除5’端與3’端結合形成環狀外,還發現5’端與介入子內部至少二處形成環狀結構。另外,對照其他已發表會影響剪切的保守性鹼基相對位置,再以點突變破壞RNA二級結構中最保守的P7配對區會降低第一型介入子的剪切活性。
Intragenic regions (introns) are found in all classes of organism. Transcription of such genes must undergo a splicing reaction to produce the mature, functional form of RNAs. Introns can be divided into four categories by their splicing mechanisms, namely Group I, Group II, spliceosomal, and nuclear tRNA introns. The former two are self-splicing introns. Group I introns are ubiquitous, however, most metazoan mitochondrial genomes lack introns. A novel group I intron in the mitochondrial cytochrome oxidase I gene (cox1) of Cinachyrella auctraliensis, which belongs to the IB2 subgroup, encodes a putative homing endonuclease with two amino acid motifs of the LAGLIDADG family. The homing endonuclease may perform intron translocation. Splicing in the cox1 of the sponge was demonstrated by comparing the length of DNA and RNA sequences. The intron was spliced in vivo or in vitro as revealed by RT-PCR and sequencing. Group I introns are classified as ribozymes. The pre-mRNAs fold into specific configurations that facilitate attacks of free guanosine followed by two consecutive trans-esterification steps to remove the introns. The excised cox1 intron was found to form a circle with the 5’-end linked to the 3’-end. Two other forms of lariats were also found with the 5’-end linked to the inside sequence of the intron. Mutagenesis of a key nucleotide, which participates base pairing of RNA secondary structure, in P7 region decreased the splicing activity of the intron.
目錄
誌謝......................................................................................................... i
Abstract................................................................................................ iii
目錄....................................................................................................... iv
表目錄.................................................................................................. vii
圖目錄................................................................................................. viii
附錄.........................................................................................................x
第一章 前言 ..........................................................................................1
一、RNA 剪接 (RNA splicing)..............................................................................1
1.1 核醣酶 (Ribozyme)...........................................................................................2
1.2 自我剪接 (self-splicing) ...................................................................................3
二、第一型介入子 (Group I intron).....................................................................4
2.1 分佈 (distribution).............................................................................................4
2.2 結構 (structure) .................................................................................................5
2.3 剪切反應 (autoexcision)...................................................................................7
2.4 環化反應 (cyclization or circularization) .........................................................8
2.5 移動性 (mobile genetic element)......................................................................9
三、研究目的.........................................................................................................11
第二章材料與方法 ............................................................................13
1、DNA 萃取與純化: .........................................................................................13
1.1 DNA 萃取.........................................................................................................13
1.2 引子設計..........................................................................................................14
1.3 PCR 增幅 (Amplification) ...............................................................................14
1.4 PCR 產物純化..................................................................................................15
1.5 膠體純化..........................................................................................................15
2、Cox1 intron 在E.coli 系統表現製備:..........................................................16
2.1 接合反應 (ligation)..........................................................................................16
2.2 勝任細胞 (competent cell) 製備與轉型作用 (transformation)....................16
2.3 質體DNA 的萃取與篩選...............................................................................17
3、Cox1 intron 在in vitro 表現系統製備:........................................................18
3.1 直線質體的製備..............................................................................................18
3.2 胞外轉錄反應 (in vitro transcription) ............................................................19
4、RNA 萃取: .....................................................................................................19
4.1 海綿的RNA 萃取...........................................................................................19
4.2 大腸桿菌的RNA 萃取....................................................................................20
4.3 In vitro RNA 萃取.............................................................................................21
5、胞外剪切反應 (In vitro splicing):................................................................22
6、RT-PCR (reverse transcriptase-polymerase chain reaction):..................22
6.1 One-step RT-PCR .............................................................................................22
6.2 Two-Step RT-PCR ............................................................................................23
7、點突變 (PCR site-directed mutagenesis):..................................................23
8、β-galactosidase 酵素活性分析:....................................................................24
9、序列分析與軟體...............................................................................................25
第三章結果 ........................................................................................26
一、澳洲球形海綿 cox1 intron 特性...................................................................26
1.1 介入子的位置..................................................................................................26
1.2 介入子的初級結構..........................................................................................27
1.3 內切酶..............................................................................................................28
1.4 介入子的二級結構..........................................................................................29
1.5 澳洲球形海綿cox1 intron 的歸類..................................................................30
1.6 親緣關係..........................................................................................................31
二、剪接與環化反應.............................................................................................31
2.1 Cox1 intron 在真核澳洲球形海綿的表現.......................................................31
2.2 Cox1 intron 在原核大腸桿菌的表現...............................................................32
2.3 Cox1 intron 在in vitro 的表現.........................................................................33
三、細胞色素氧化酶I 基因介入子的結構對剪切之影響.................................35
3.1 結構與剪切的相關性......................................................................................35
3.2 P7 配對的重要性..............................................................................................35
第四章討論 ........................................................................................37
一、澳洲球形海綿粒線體具有第一型介入子.....................................................37
1.1 海綿的粒線體介入子......................................................................................37
1.2 LAGLIDADG 主題的內切酶..........................................................................37
1.3 第一型介入子的子群差異..............................................................................38
1.4 介入子的個體差異影響...................................................................................39
二、澳洲球形海綿粒線體介入子來源.................................................................39
三、表現系統對cox1 intron 進行剪接的影響...................................................42
3.1 澳洲球形海綿粒線體的剪切表現..................................................................42
3.2 原核E.coli 的β-galactosidase 表現活性........................................................43
3.3 大腸桿菌無法進行剪切的可能原因..............................................................43
3.4 原核與真核的表現差異..................................................................................44
3.5 In vitro 與in vivo 的差異.................................................................................45
四、RNA 結構對剪切的重要性...........................................................................46
4.1 非保守的前端引導序列..................................................................................46
4.2 保守的二級結構..............................................................................................47
4.3 剪切中心之P5-P4-P6 domain .........................................................................47
4.4 剪切中心之P9.0-P7-P3 domain .....................................................................48
4.5 聯結區域..........................................................................................................49
4.6 周邊區域..........................................................................................................50
4.7 剪切位置 (splice site) .....................................................................................50
五、RNA 剪切對生物體的影響...........................................................................51
六、展望.................................................................................................................53
參考文獻...............................................................................................54

表目錄
表一: RNA splicing 的主要分類............................................................................69
表二: 核醣酶的種類..............................................................................................70
表三: group I intron 的分類及基因分布................................................................71
表四: Cox1 intron 嵌入各物種的胺基酸序列比較表...........................................72
表五: 澳洲球形海綿的個體差異..........................................................................73
表六: 兩LAGLIDADG motif 的內切酶比較表..................................................74
表七: 兩LAGLIDADG motif 的內切酶鹼基與胺基酸百分比對照表..............75
表八: 第一型介入子前端引導序列 (IGS) 比較表.............................................76
表九: 第一型介入子保守區PQRS 比較表..........................................................77
表十: 子群分類結構對照表..................................................................................78
表十一: 篩選進行自我剪切的條件表..................................................................82
表十二: 第一型介入子進行自我剪接(in vitro splicing) 的影響因子..............84
表十三: 子群結構與自我剪接的相關性..............................................................86

圖目錄
圖一: Homing cycle ................................................................................................87
圖二: 轉酯化反應示意圖......................................................................................88
圖三: 實驗流程圖..................................................................................................89
圖四: 澳洲球形海綿型態圖..................................................................................90
圖五: 澳洲球形海綿粒線體COI 轉譯蛋白質序列及其intron ..........................91
圖六: 澳洲球形海綿粒線體基因圖譜與實驗所用的引子相對位置..................93
圖七: Cox1 intron 嵌入位置的排序比對圖...........................................................94
圖八: 嵌入cox1 的group I intron 相對位置圖....................................................99
圖九: 澳洲球形海綿cox1 序列的個體差異......................................................100
圖十: 澳洲球形海綿cox1 intron 所轉譯的內切酶二級結構預測....................104
圖十一: 澳洲球形海綿cox1 intron 所轉譯的內切酶三級結構預測................105
圖十二: 澳洲球形海綿cox1 intron 的二級結構................................................106
圖十三: 第一型介入子保守區PQRS 的相對位置............................................107
圖十四: 澳洲球形海綿cox1 intron 的剪切構型................................................108
圖十五: 第一型介入子的子群特性歸類示意圖................................................109
圖十六: IB2 子群的序列差異..............................................................................110
圖十七: Cox1 intron 的親緣關係圖.....................................................................112
圖十八: 澳洲球形海綿cox1 intron 的剪切電泳圖............................................113
圖十九: 澳洲球形海綿cox1 之DNA 與RNA 序列比對.................................114
圖二十: 澳洲球形海綿介入子環化電泳圖........................................................116
圖二十一: 澳洲球形海綿環化接點序列示意圖................................................117
圖二十二: 轉殖菌株對x-gal 的呈色反應.........................................................118
圖二十三: 轉殖菌株的cox1 intron 電泳圖........................................................119
圖二十四: In vitro cox1 intron splicing 電泳圖...................................................120
圖二十五: 單價陽離子對in vitro splicing 的影響............................................121
圖二十六: MgCl2 濃度對自我剪切的影響.........................................................122
圖二十七: GTP 濃度對自我剪切的影響............................................................123
圖二十八: 澳洲球形海綿cox1 intron 的剪切示意圖........................................124
圖二十九: β-galactosidase 活性分析圖...............................................................125
圖三十: In vitro 的鹼基突變電泳圖....................................................................126

附錄
附錄一: 介入子的剪切機制分類........................................................................127
附錄二: group I 與group II intron 基本結構圖...................................................128
附錄三: 第一型介入子的分布............................................................................129
附錄四: 第一型介入子的摺疊............................................................................130
附錄五: 第一型介入子的環化反應....................................................................131
附錄六: 第一型介入子的移動性........................................................................132
附錄七: pGEM®-T Easy vector 及其相關資訊...................................................133
附錄八: Cox1 intron 比對的所有物種分類.........................................................134
附錄九: Cox1 功能性蛋白的結構.......................................................................135
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