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

Abelson, J., C. R. Trotta, and H. Li. 1998. tRNA splicing. J. Biol. Chem. 273: 12685-12688.
Adams, K., M. Clements, and J. Vaughn. 1998. The Peperomia Mitochondrial cox1 Group I intron: Timing of Horizontal Transfer and Subsequent Evolution of the Intron. J. Mol. Evol. 46: 689-96.
Ahn, S. J., and I. K. Park. 2003. The coenzyme thiamine pyrophosphate inhibits the self-splicing of the group 1 intron RNA. Int. J. Biochem. Cell Biol. 35: 57-167.
Barciszewska, M. Z., E. Wyszko, R. Bald, V. A. Erdmann, and J. Barciszewski. 2003. 5S rRNA is a leadzyme. A molecular basis for lead toxicity. J. Biochem. 133: 309-315.
Barfod, E. T., and T. R. Cech. 1988. Deletion of nonconserved helices near 3’ end of the rRNA intron of Tetrahymena thermophila alters self-splicing but not core catalytic activity. Genes Dev. 2: 652-663.
Bass, B. L., and T. R. Cech. 1984. Specific interaction between the self-splicing RNA of Tetrahymena and its guanosine substrate: implications for biological catalysis by RNA. Nature (London) 308: 820-826.
Beagley, C. T., N. A. Okada, and D. R. Wolstenholme. 1996. Two mitochondrial group I intron in a metazoan, the sea anemone Metridium senile: One intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proc. Natl. Acad. Sci. U. S. A. 93: 5619-5623.
Belfort, M. and P. S. Perlman. 1995. Mechanisms of intron mobility. J. Biol. Chem. 270: 30237-30240.
Belfort, M., and R. J. Roberts. 1997. Homing endonuclease: keeping the house in order. Nucleic Acids Res. 25: 3379-3388.
Belfort, M., J. L. G. Salvo, K. Ehrenman, and T. Coetzee. 1988. Towards defining the minimal structural requirements for self-splicing of the phage T4 td intron. UCLA Symp. in press.
Belfort, M., P. S. Chandry, and J. Pedersen-Lane. 1987. Genetic delineation of functional components of the group I intron in the phage T4 td gene. Cold Spring Harbor Symp. Quant. Biol. 52: 181-192.
Bentis, C. J., L. Kaufman, and S. Golubic. 2000. Endolithic fungi in reef-building corals (order: Scleractinia) are common, cosmopolitan, and potentially pathogenic. Biol. Bull. 198: 254-260.
Breathnach, R., and P. Chambon. 1981. Organization and expression of eukaryotic split genes coding for proteins. Annu. Rev. Biochem. 50: 349-383.
Brehm, S. L., and T. R. Cech. 1983. Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo. Biochemistry 22: 2390-2397.
Bryk, M., and J. E. Muller. 1996. Mobile of group I introns. In: Green R, Schroeder R, eds. Ribosomal RNA and group I introns. Austin, Texas: RG Landes Co. pp. 221-241.
Burke, J. M. 1987. Structural conventions for group I introns. Nucleic Acids Res. 15: 7217-7221.
Burke, J. M. 1988. Molecular genetics of group I introns: RNA structures and protein factors required for splicing. Gene 73: 273-294.
Burke, J. M., and U. L. RajBhandary. 1982. Intron within the large rRNA gene of N. crassa mitochondria: a long open reading frame and a consensus sequence possibly important in splicing. Cell 31: 509-20.
Burke, J. M., M. Belfort, T. R. Cech, R. W. Davis, R. J. Schweyen, D. A. Shub, J. W. Szostak, and H. F. Tabak. 1987. Structural conventions for group I intron. Nucleic Acids Res. 15: 7217-7221.
Butcher, S. E., and J. M. Burke. 1994. Structure mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. J. Mol. Biol. 244: 52-63.
Campbell, T. B., and T. R. Cech. 1996. Mutations in the Tetrahymena Ribozyme Internal Guide Sequence: Effects on Docking of the P1 Helix into the Catalytic Core and Correlation with Catalytic Activity. Biochemistry 35: 11493-11502.
Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D’Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, and K. M. Muller. 2002. The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, introns, and other RNAs. BMC Bioinformatics 3: 1-31.
Carr, K. 1993. Nobel goes to discoverers of “split genes”. Nature 365: 597.
Cavalier-Smith, T. 1991. Intron phylogeny: a new hypothesis. Trends Genet. 7: 145-148.
Cech, T. R. 1983. RNA splicing: Three Themes with Variations. Cell 34: 713-716.
Cech, T. R. 1985. Self-splicing RNA: Implications for evolution. Int. Rev. Cyt. 93: 3-22.
Cech, T. R. 1986. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44: 207-210.
Cech, T. R. 1989. Self-splicing and enzymatic activity of an intervening sequence RNA from Tetrahymena. Nobel lecture.
Cech, T. R. 1990. Self-splicing of group I introns. Annu. Rev. Biochem. 59: 543-568.
Chevalier, B. S., and B. L. Stoddard. 2001. Homing endonucleases: structural and unctional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29: 3757-3774.
Chu, F. K., G. F. Maley, F. Maley, and M. Belfort. 1984. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc. Natl. Acad. Sci. U. S. A. 81: 3049-3058.
Clark-Walker, G. D. 1992. Evolution of mitochondrial genomes in fungi. Int. Rev. Cytol. 141: 89-127.
Cochrane, J. C., and S. A. Strobel. 2008. Catalytic strategies of self-cleaving ribozymes. Acc. Chem. Res. 41: 1027-1035.
Cummings, D.J., K. L. McNally, J. M. Domenico, and E. T. Matsuura. 1990. The complete DNA sequence of the mitochondrial genome of Podospora nserine. Curr. Genet. 17: 375-402.
Davies, R. W., R. B. Waring, J. Ray, T. A.Brown, and C. Scazzocchio. 1982. Making ends meet: a model for RNA splicing in fungal mitochondria. Nature (London) 300: 719-724.
De La Salle, H., C. Jacq, and P. P. Slonimski. 1982. Critical sequences within mitochondrial introns: pleiotropic mRNA maturase and cis-dominant signals of the box intron controlling reductase and oxidase. Cell 28: 721-732.
Doudna, J. A., A. S. Gerber, J. M. Cherry, and J. A. Szostak. 1987. Genetic dissection of an RNA enzyme. Cold Spring Harbor Symp. Quant. Biol. 52: 173-180.
Dujon, B. 1989. Group I introns as mobile genetic elements: facts and mechanistic speculations. Gene 82: 91-114.
Erpenbeck, D., J. N. A. Hooper, and G. Worheide. 2006. CO1 phylogenies in diploblasts and the ‘Barcoding of Life’ — are we sequencing a suboptimal partition? Mol. Ecol. Notes 6: 550-553.
Forster, A.C., and R. H. Symons. 1987. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49: 211-220.

Fukami, H., C. A. Chen, C. Y. Chiou, and N. Knowlton. 2007. Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of Scleractinian corals. J. Mol. Evol. 64: 591-600.
Fukui, H., F. Diaz, S. Garcia, C. Moraes. 2007. Cytochrome c oxidase deficiency in neurons decreases both oxidative stress and amyloid formation in a mouse model of Alzheimer’s disease. Proc. Natl. Acad. Sci. U. S. A. 104: 14163-8.
Gilbert, W. 1978. Why genes in pieces. Nature 271: 501.
Gingrich, J. C. and R. B. Hallick. 1985. The Euglena gracilis chloroplaset ribulose-1,5-bisphosphate carboxylase gene. II. The spliced mRNA and its product. J. Biol. Chem. 260: 16162-16168.
Gogarten, J. P., A. G. Senejani, O. Zhaxybayeva, L. Olendzenski, and E. Hilario. 2002. Inteins: Structure, Function, and Evolution. Annu. Rev. Microbiol. 56: 263-287.
Gonzalez, P., G. Barroso, and J. Labarere. 1999. Molecular gene organization and secondary structure of the mitochondrial large subunit ribosomal RNA from the cultivated Basidiomycota Agrocybe aegerita: a 13 kb gene possessing six unusual nucleotide extensions and eight introns. Nucleic Acids Res. 27: 1754-1761.
Grabowski, P. J., S. R. Seiler, and P. A. Sharp. 1985. A multicomponent complex is involved in the splicing of messenger RNA precursors. Cell 42: 345-353.
Guerrier-Takada, C., K. Gardiner, T. Marsh, N. Pace, S. Altman. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849-857.
Guo, F., and T. R. Cech. 2002. Evolution of Tetrahymena ribozyme mutants with increased structural stability. Nat. Struct. Biol. 9: 855-861.
Hall, D. H., C. M. Povinelli, K. Ehrenman, J. Pedersen-Lane, F. Chu, and M. Belfort. 1987. Two domains for splicing in the intron of the phage T4 td gene established by non-directed mutagenesis. Cell 48: 63-71.
Hall, T. 2001. BioEdit: BioEdit version 5.0.6. Department of Microbiology, North Carolina State University, USA.
Haugen, P., D. M. Simon, and D. Bhattacharya. 2005. The natural history of group I introns. Trends. Genet. 21: 111-119.
Heilman-Miller, S. L., and S. A. Woodson. 2003. Effect of transcription on folding of the Tetrahymena ribozyme. RNA 9: 722-733.
Hoch, I., C. Berens, E. Westhof, R. Schroeder. 1998. Antibiotic inhibition of RNA catalysis:neomycin B binds to the catalytic core of the td group I intron displacing essential metal ions. J. Mol. Biol. 282: 557-569.
Hur, M., W. J. Geese, and R. B. Waring. 1997. Self-splicing activity of the mitochondrial group-I introns from Aspergillus nidulans and related introns from other species. Curr. Genet. 6: 399-407.
Jayaguru, P., and M. Raghunathan. 2007. Group I intron renders differential susceptibility of Candida albicans to Bleomycin. Mol. Biol. Rep. 34: 11-17.
Johnson, I. M., C. Kesavan, S. Usha, R. Malathi. 2009. Analysis of group I intron splicing in the presence of naturally occurring methylxanthines. Clinica. Chimica. Acta. 400: 74-76.
Joyce, G. F., and T. Inoue. 1987. Structure of the catalytic core of the Tetrahymena ribozyme as demonstrated by reactive abbreviated formsof the molecule. Nucleic Acids Res. 15: 9825-9840.
Jung, C., S. Shin, and I. K. Park. 2005. Pyridoxal phosphate inhibits the group I intron splicing. Mol. Cell Biochem. 280:17-23.
Kaine, B. P., R. Gupta, and C. R. Woese. 1983. Putative introns in tRNA genes of prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 80: 3309-3312.
Kim, J. Y., and I. K. Park. 2000. The flavin coenzymes: a new class of group I intron inhibitors. Biochim. Biophys. Acta. 1475: 56-61.
Kim, S. H., and T. R. Cech. 1987. Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena. Proc. Natl. Acad. Sci. U. S. A. 84: 8788-8792.
Kruger, K., P. J. Grabowski, A. J. Zaun, J. Sands, D. E. Gottschling, and T. R. Cech. 1982. Self-splicing RNA: autoexcision and autocyclization of the rRNA intervening sequence of Tetrahymena. Cell 31: 147-157.
Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5: 150–163.
Kuo, M. Y., L. Sharmeen, G. Dinter-Gottlieb, J. Taylor. 1988. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol. 62: 4439-4444.
Kushner, S. R. 1978. in Genet Engineering, eds. Boyer, H. B. & Nicosia, S. (Elsevier North-Holland, Amsterdam). pp. 17-23.
Laggerbauer, B., F. L. Murphy, and T. R. Cech. 1994. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13: 2669-2676.
Lamb, M. R., P. Q. Anziano, K. R. Glaus, D. K. Hanson, H. J. Klapper, P. S. Perlman, and H. R. Mahler. 1983. Functional domains in introns: RNA processing intermediates in cis and trans-acting mutants in the penultimate intron of the mitochondrial gene for cytochrome b. J. Biol. Chem. 258: 1991-1999.
Lambowitz, A. M., and M. Belfort. 1993. Intron as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
Lambowitz, A. M., and P. S. Perlman. 1990. Involvement of aminoazyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15: 440-444.
Le Campion-Alsumard, T., S. Golubic, and K. Priess. 1995. Fungi in corals: symbiosis or disease: interaction between polyps and fungi causes pearl-like skeleton biomineralization. Mar. Ecol. Prog. Ser. 117: 137-147.
Lehnert, V., L. Jaeger, F. Michel, and E. Westhof. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3: 993-1009.
Lewin. 2004. Genes VIII. Pearson Prentice Hall Pearson Education, Inc. U. S. A. pp. 697-750.
Li, Z., and Y. Zhang. 2005. Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup. Nucleic Acids Res. 33: 2118-2128.
Liu, Y., and M. J. Leibowitz. 1995. Bidirectional effectors of a group I intron ribozyme. Nucleic Acids Res. 23: 1284-1291.
López-Victoria, M., and S. Zea. 2004. Storm-mediated coral colonization by an excavating Caribbean sponge. Clim. Res. 26: 251-256.
Lunt, D. H., D. X. Zhang, J. M. Szymura, and G. M. Hewltt. 1996. The insect cytochrome oxidase I gene: evolutionary patterns and conserved primers for phylogenetic studies. Insect. Mol. Biol. 5: 153-165.
McDonald, J. I., J. N. A. Hooper, and K. A. McGuinness. 2002. Environmentally influenced variability in the morphology of Cinachyrella australiensis (Carter 1886) (Porifera：Spirophorida：Tetillidae). Mar. Freshwater Res. 53: 79-84.
Michel, F., and D. Cummings. 1985. Analysis of Class I introns in a mitochondrial plasmid associated with senescence of Podospora nserine reveals extraordinary resemblance to the Tetrahymena ribosomal intron. Curr. Genet. 10: 69-79.
Michel, F., and E. Westhof. 1990. Modelling of the Three-dimensional Architecture of Group I Catalytic Introns Based on Comparative Sequence Analysis. J. Mol. Biol. 216: 585-610.
Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. pp. 352-354.
Mohr, G., A. Zhang, J. A. Gianelos, M. Belfort, and A. M. Lambowitz. 1992. The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69: 483-494.
Muscarella, D. E., and V. M. Vogt. 1993. A mobile group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 1023-1033.
Nielsen, H., and J. Engberg. 1985. Sequence comparisons of the rDNA introns from six different species of Tetrahymena. Nucleic Acids Res. 13: 7445-7455.
Nielsen, H., T. Fiskaa, A. B. Birgisdottir, P. Haugen, C. Einvik, and S. Johansen. 2003. The ability to form full-length intron RNA circles is a general property of nuclear group I introns. RNA 9: 1464-1475.
Nikolcheeva, T., and S. A. Woodson. 1999. Facilitation of Group I Splicing in Vivo: Misfolding of the Tetrahymena IVS and the Role of Ribosomal RNA Exons. J. Mol. Biol. 292: 557-567.
Oda K., K. Yamato, E. Ohta, Y. Nakamura, M. Takemura, N. Nozato, K. Akashi, T. Kanegae, Y. Ogura, T. Kohchi, and K. Ohyama. 1992. Gene organization deduced from the complete sequence of the liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of the plant mitochondrial genome. J. Mol. Biol. 223: 1-7.
Park, I. K., and J. K. Kim. 2001. NAD+ inhibits the self-splicing of the group 1 intron. Biochem. Biophys. Res. Commun. 281: 206-211.
Price, J. V., and T. R. Cech. 1985. Coupling of Tetrahymena Ribosomal RNA Splicing to β-Galactosidase Expression in Escherichia coli. Science 228: 719-722.
Price, J. V., and T. R. Cech. 1988. Determination of the 3’ splice site for self-splicing of the Tetrahymena pre-RNA. Genes Dev. In press.
Prody, G. A., J. T. Bakos, J. M. Buzayan, I. R. Schyneider, and G. Breuning. 1986. Autolytic processing of dimeric plant virus satellite RNA. Science 231: 1577-1580.
Raghukumar, C., and S. Raghukumar. 1991. Fungal invasion of massive corals. Mar. Ecol. 12: 251-260.
Reyes, V. M. and J. Abelson. 1988. Substrate recognition and splice site determination in yeast tRNA splicing. Cell 55: 719-730.
Roman, J., and S. A. Woodson. 1998. Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl. Acad. Sci. U. S. A. 95: 2134-2139.
Roman, J., M. N. Rubin, and S. A. Woodson. 1999. Sequence specificity of in vivo reverse splicing of the Tetrahymena group I intron. RNA 5: 1-13.
Rot, C., I. Goldfarb, M. Ilan, and D. Huchon. 2006. Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. BMC Evol. Biol. 6: 71.
Salehi-Ashtiani, K., A. Luptak, A. Litovchick, J. W. Szostak. 2006. A genomewide search for ribozymes reveals an HDV-like sequences in thehuman CPEB3 gene. Science 313: 1788-1792.
Sambrook J., T. Maniatis, and E. F. Fritsch. 1982. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory. New York pp. 1.74-1.86.
Saville, V. J., and R. A. Collins. 1990. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora ribozymes. Cell 61: 685-696.
Schönberg, C. H. L., and C. R. Wilkinson. 2001. Induced colonization of corals by a clionid bioeroding sponge. Coral Reefs 20: 69-76.
Shick, J. M. 1991. A functional biology of sea anemone. London: Chapman & Hall. pp. 395.
Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic Note: A place for DNA-DNA reassociation and 16S rRNA sequence analysisin the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849.
Suh, S. O., J. W. Spatafora, G. R. S. Ochiel, H. C. Evans, and M. Blackwell. 1998. Molecular phylogenetic study of a termite pathogen Cordycepioideus bisporus. Mycologia 90: 611-617.
Suh, S. O., K. G. Jones, and M. Blackwell. 1999. A group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: evidence for a new major class of group I introns. J. Mol. Evol. 48: 493-500.
Szewczak, A. A., and T. R. Cech. 1997. An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis. RNA 3: 838-849.
Tanner, K., and T. R. Cech. 1987. Guanosine binding required for cyclization of the self-splicing intervening sequence ribonucleic acid from Tetrahymena thermophila. Biochemistry 26: 3330-3340.
Tanner, M. A., E. M. Anderson, R. R. Gutell, and T. R. Cech. 1997. Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. RNA 3: 1037-1051.
Tanner, N. K., and T. R. Cech. 1985. Self-catalyzed cyclization of the intervening sequence RNA of Tetrahymena: inhibition by intercalating dyes. Nucleic Acids Res. 13: 7741-7758.
Teixeira, A., A. Tehiri-Alaoul, S. West, S. Thomas, A. Ramadass, Martianovl, M. Dye, W. James, N. J. Proudfoot, and A. Akoulitchev. 2004. Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotestranscription termination. Nature 432: 526-530.
Thompson, A. J., and D. L. Herrin. 1994. A chloroplast group I intron undergoes the first step of reverse splicing into host cytoplasmic 5.8 S rRNA. Implications for intron-mediated RNA recombination, intron transposition and 5.8 S rRNA structure. J. Mol. Biol. 236: 455-468.
Trinkl, H., and K. Wolf. 1986. The mosaic cox1 gene in the mitochondrial genome of Schizosaccharomyces prome: Minimal structural requirements and evolution of group I introns. Gene 45: 289-297.
Turmel, M., V. Cote, C. Otis, J. P. Mercier, M. W. Gray, K. M. Lonergan, and C. Lemieux. 1995. Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol. 12: 533-545.
Usha, S., I. M. Johnson, and R. Malathi. 2006. Possible inhibition of group I intron RNA by resveratrol and genistein. J. Biomol. Struct. Dyn. 24: 25-32.
Vicens, Q., P. J. Paukstelis, E. Westhof, A. M. Lambowitz, and T. R. Cech. 2009. Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA 14: 2013-2029.
Vieira, J., and J. Messing. 1982. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19: 259-268.
von Ahsen, U., and R. Schroeder. 1991. Streptomycin inhibits splicing of group I introns by competition with the guanosine substrate. Nucleic Acids Res. 19: 2261-2265.
Wang, G., C. Barton, and F. G. Rodgers. Bacterial DNA decontamination for reverse transcription polymerase chain reaction (RT-PCR). J. Microbiol. Methods 51: 119-121.
Waring, R. B., C. Scazzocchio, T. A. Brown, and R. W. Davies. 1983. Close relationship between certain nuclear and mitochondrial introns. J. Mol. Biol. 167: 595-605.
Waring, R. B., J. A. Ray, S. W. Edwards, C. Scazzocchio, and R. W. Davies. 1985. The Tetrahymena rRNA intron self-splices in E.coli: in vivo evidence for the importance of key base-paired regions of RNA for RNA enzyme function. Cell 40: 371-380.
Watanabe, K. I., E. Megumi, I. Yuji, and O. Takeshi. 1998. Distinctive origins of group I introns found in the cox1 genes of three green algae. Gene 213: 1-7.
Weiss-Brummer, B., G. Rodel, R. J. Schweyen, and F. Kaudewitz. 1982. Expression of the split gene cob in yeast: evidence for precursor of a ‘maturase’ protein translated from intron 4 and preceding exons. Cell 29: 527-536.
Weiss-Brummer, B., J. Holl, R. J. Schweyen, G. R. Rodel, and F. Kaudewitz. 1983. Processing of yeast mitochondrial RNA: involvement of intramolecular hybrids in splicing of cob I4 RNA by mutation and reversion. Cell 33: 195-202.
Williamson, C.L., Tiemey, W.M., Kerker, B.J. and Burke, J.M. 1987. Site-directed mutagenesis of core sequence elements 9R’, 9L, 9R and 2 in self-splicing Tetrahymena pre-rRNA. J. Biol. Chem. 262: 14672-14682.
Wilson, A. C., R. L. Cann, S. M. Carr, M. George, U. B. Gyllensten, K. M. Helm-Bychowski, G. Higuchi, S. Higuchi, S. R. Palumbi, E. M. Prager, R. D. Sage, and M. Stroneking. 1985. Mitochondria DNA and two perspectives on evolutionary genetics. Biol. J. Linn. Soc. Lond. 26: 375-400.
Winkler, W. C., A. Nahvi, A. Roth, J. A. Collins, R. R. Breaker. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
Winter, A. J., G. van der Horst, and H. F. Tabak. 1988. Characterization of products derived from self-splicing of intron aI5α which is located in the mitochondrial COX1 gene of Saccharomyces cerevisiae. Nucleic Acids Res. 16: 3845-3861.
Wolff, G., G. Burger, B. F. Lang, and U. Kuck. 1993. Mitochondrial genes in the colourless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns. Nucleic Acids Res. 21: 719-726.
Woodson, S. A., and T. R. Cech. 1989. Reverse self-splicing of the Tetrahymena group I intron: Implication for the directionary of splicing and for intron transposition. Cell 57: 335-345.
Xiao, M., T. Li, X. Yuan, Y. Shang, F. Wang, S. Chen, and Y. Zhang. 2005. A peripheral element assembles the compact core structure essential for group I intron self-splicing. Nucleic Acids Res. 33: 4602-4611.
Zaug, A. J., J. R. Kent, and T. R. Cech. 1984. A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA. Science 224: 574-578.
Zhou, Y., C. Lu, Q. J. Wu, Y. Wang, Z. T. Sun, J. C. Deng, and Y. Zhang. 2007. GISSD: Group I intron sequence and structure database. Nucleic Acids Res. 1: 1-7.
吳瑞賢。2007。從台灣海峽隔離探討鯉科魚丹亞科魚類之族群演化暨台灣產五種珊瑚粒線體DNA之研究。國立中山大學海洋資源研究所。博士論文。
莊曜陽。2006。絲珊瑚屬的粒線體基因及其細胞色素氧化酶次單位I基因介入子之演化研究。國立台灣大學海洋研究所。碩士論文。
陳勇輝。1988。澳洲球形海綿 (Cinachyrella australiensis (Carter) 1886) 芽體與成體型態之研究。國立中山大學海洋生物研究所。碩士論文。
蕭聖代。2005。澳洲球形海綿完整粒線體DNA序列及分析研究。國立中山大學海洋資源研究所。碩士論文。