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研究生: 翁伯瑋
Weng, Po-Wei
論文名稱: 橙黃壺菌L-BL10 品系之基因轉殖平台建立
Establishment of genetic transformation protocol for Aurantiochytrium sp. strain L-BL10
指導教授: 陳逸民
Chen, Yi-Min
學位類別: 碩士
Master
系所名稱: 生物科學與科技學院 - 生物科技研究所
Institute of Biotechnology
論文出版年: 2014
畢業學年度: 102
語文別: 中文
論文頁數: 128
中文關鍵詞: 橙黃壺菌L-BL10 品系密碼子使用偏性基因轉殖
外文關鍵詞: Aurantiochytrium sp. L-BL10, codon usage bias, gene transfer
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  • 橙黃壺菌L-BL10 品系 (Aurantiochytrium sp. strain L-BL10) 為真核 微藻,其具有培養成本低廉、成長快速、以及具有無細胞壁世代 (阿米巴 細胞) 的優點,加上已完成初步的基因體分析,因此具有成為新一代真核 表現平台的潛力。
    本研究的目的,即為建立L-BL10 外源性基因表現之轉 殖平台。首先,藉由L-BL10 的基因體資料庫預測基因序列之密碼子使用 偏性;同時取得延長因子的啟動子、基因及終止子序列,以作為起始及 終止外源基因轉錄的元件;其次,分別選用綠色螢光蛋白基因以及遺傳 黴素抗性基因-紐奧黴素磷酸轉移酶II 基因,作為基因片匣中的報導基因 或篩選標誌;最後進行細胞轉化測試,搭配微脂粒或電穿孔法並測試以 不同微脂粒包覆核酸之比例或脈衝條件等。 本研究共統計16788 個密碼子使用偏性,其中UUA、CUA、AUA 以及 CGA 在對應於同胺基酸的密碼子中,其使用率小於1 %。在核酸構 築已完成延長因子啟動子、外源基因以及延長因子終止子等三個片段連 接成的基因片匣。最後,以電穿孔法及微脂粒法皆能成功將綠色螢光蛋 白基因組序列送入細胞中且能偵測到外源基因之mRNA,此外能在微脂 粒化轉細胞中觀察到具有綠色螢光訊號之藻細胞。

    Aurantiochytrium sp. strain L-BL10 is a eukaryotic microalgae that incurs lower culture costs, displays higher growth, and has lower rates of cell wall generation (amoeba cells) than other eukaryotes currently being used to express foreign proteins. The objective of this study was thus to construct a transgenic platform for exogenous gene expression in L-BL10. For this, we first designed nucleic acid constructs. L-BL10 genome databases were accessed during platform design to predict and correct codon usage bias within the gene sequences. We obtained housekeeping genes, which included: (1) the promoter and terminator sequences of the elongation factor 1-α (EF-1α) and (2) the sequences of 18s ribosomal DNA. Next, we selected green fluorescent protein (GFP) gene, red fluorescent protein (RFP) gene, and neomycin phosphotransferase II (NPT II) gene. Those genes replaced sequences of the elongation factor, thereby serving as the reporter genes or selection markers in gene cassettes. For these, we coated the nucleic acids with different proportions of Lipofectamine or performed electroporation under different pulsed conditions. From the 16 predicted gene sequences of L-BL10, we recorded 16,788 instances of codon usage bias, among which the usage rates of UUA, CUA, AUA, and CGA in corresponding codons of the same amino acid were less than 1%. We had already completed gene cassettes during nucleic acid construction. Finally, we successfully transferred GFP gene sequences into cells using electroporation and Lipofectamine, and we detected the mRNA of exogenous genes. In addition, we observed green fluorescent signals in the algal cells transformed using Lipofectamine.

    中文摘要 I 英文摘要 II 誌謝 V 目錄 VII 表目錄 X 圖目錄 XI 縮寫表 XIII 一、前言 1 1-1 基因轉殖之定義 1 1-2 開發基因轉殖平台之重要性與應用性 3 1-3 常見基因轉殖表現平台之比較 5 1-4 破囊壺菌之研究背景與轉殖優勢 7 1-5 橙黃壺菌BL10之相關研究 9 1-6 研究的目的及策略 10 二、材料與方法 12 2-1 藥品與儀器 12 2-2 實驗藻種來源、活化培養以及保存 14 2-2-1 藻種來源 14 2-2-2 藻種活化培養與保存 14 2-3 基因體定序及基因註解 15 2-4 開放式讀碼框預測與密碼子統計 15 2-5 延長因子序列選殖與定序 16 2-5-1 延長因子基因序列選殖策略 16 2-5-2 延長因子未轉譯區序列選殖與定序 22 2-5-3 延長因子啟動子及終結子序列選殖與定序 26 2-6 定序與拷貝數分析 28 2-7 篩選標記與基因之選定 29 2-7-1 抗生素敏感測試 29 2-7-2 篩選標記與報導基因序列之選殖與定序 31 2-8 表現基因組序列之連結設計 32 2-9 細胞轉化 39 2-9-1 微脂粒轉化平台之建立 39 2-9-2 電穿孔轉化平台之建立 41 2-10 統計分析 43 三、結果 44 3-1 開放式讀碼框預測與密碼子分析 44 3-2 延長因子序列選殖與分析 44 3-2-1 延長因子全長序列定序 44 3-2-2 延長因子啟動子與終結子序列轉殖與分析 45 3-3 核醣體核酸序列分析 46 3-4 抗生素敏感分析與抗性基因選殖 46 3-4-1 抗生素敏感分析 46 3-4-2 抗性基因與報導基因選殖 47 3-5 表現基因組序列構築 48 3-5-1 限制酶切位點分析結果 48 3-5-2 表現載體構築與選殖 48 3-6 微脂粒包覆效率 49 3-7 電穿孔轉化細胞前處理測試 49 3-8 細胞轉化之分子檢測 50 四、討論 51 五、參考文獻 56 六、附錄 126

    王嘉慧,藉由RNA干擾、蛋白合成抑制及突變株篩選改善橙黃壺菌 L-BL10品系脂肪酸組成,國立成功大學生物科技研究所碩士論文,2013。

    周思丞,探討橙黃壺菌BL10品系阿米巴細胞形成與遷移的機制,國立成功大學生物科技研究所碩士論文,2013。

    劉致寧,橙黃壺菌L-BL10品系之聚酮合成酶基因序列與表現分析,國立成功大學生物科技研究所碩士論文,2013。

    蘇昱銘,來自北台灣之海洋異營性微藻分離株: Aurantiochytrium sp. Strain BL10之生物特性研究,國立成功大學生物科技研究所碩士論文,2012。

    Aldor, I.S. and Keasling, J.D. Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates. Current Opinion in Biotechnology 14, 475-483, 2003.

    Amador, E., Martín, J.F., Castro, J.M. A Brevibacterium lactofermentum 16S rRNA gene used as target site for homologous recombination. Fems Microbiology Letters 185, 199-204, 2000.

    Andersen, D.C. and Krummen, L. Recombinant protein expression for therapeutic applications. Current Opinion in Biotechnology 13, 117-123, 2002.

    Arber, W. and Linn, S. DNA modification and restriction. Annual Review of Biochemistry 38, 467-500, 1969.

    Bahnweg, G. and Sparrow Jr, F.K. Four new species of Thraustochytrium from Antarctic regions, with notes on the distribution of zoosporic fungi in the Antarctic marine ecosystems. American Journal of Botany 61, 754-766, 1974.

    Baneyx, F. and Mujacic, M. Recombinant protein folding and misfolding in Escherichia coli. Nature Biotechnology 22, 1399-1408, 2004.

    Barclay, W., Weaver, C., Metz, J. Development of a docosahexaenoic acid production technology using Schizochytrium: a historical perspective. Single Cell Oils 41, 36-52, 2005.

    Bardor, M., Faveeuw, C., Fitchette, A.C., Gilbert, D., Galas, L., Trottein, F., Faye, L., Lerouge, P. Immunoreactivity in mammals of two typical plant glyco-epitopes, core α (1,3)-fucose and core xylose. Glycobiology 13, 427-434, 2003.

    Bayne, A.C.V., Boltz, D., Owen, C., Betz, Y., Maia, G., Azadi, P., Archer, H.S., Zirkle, R., Lippmeier, J.C. Vaccination against influenza with recombinant hemagglutinin expressed by Schizochytrium sp. confers protective immunity. PloS One 8, e61790, 2013.

    Boehm, R. Bioproduction of therapeutic proteins in the 21st century and the role of plants and plant cells as production platforms. Annals of the New York Academy of Sciences 1102, 121-134, 2007.

    Bumbak, F., Cook, S., Zachleder, V., Hauser, S., Kovar, K. Best practices in heterotrophic high-cell-density microalgal processes: achievements, potential and possible limitations. Applied Microbiology and Biotechnology 91, 31-46, 2011.

    Cavalier, S.T., Allsopp, M., Chao, E.E. Thraustochytrids are chromists, not Fungi: 18s rRNA signatures of Heterokonta. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 346, 387-397, 1994.

    Chaung, K.C., Chu, C.Y., Su, Y.M., Chen, Y.M. Effect of culture conditions on growth, lipid content, and fatty acid composition of Aurantiochytrium mangrovei strain BL10. AMB Express 2, 1-11, 2012.

    Cheng, R.B., Lin, X.Z., Wang, Z.K., Yang, S.J., Rong, H., Ma, Y. Establishment of a transgene expression system for the marine microalga Schizochytrium by 18S rDNA-targeted homologous recombination. World Journal of Microbiology and Biotechnology 27, 737-741, 2011.

    Chung, B.Y.W., Simons, C., Firth, A.E., Brown, C.M., Hellens, R.P. Effect of 5'UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7, 120, 2006.

    Cohen, S.N. and Chang, A.C.Y. Recircularization and Autonomous Replication of a Sheared R-Factor DNA Segment in Escherichia coli Transformants. Proceedings of the National Academy of Sciences 70, 1293-1297, 1973.

    Coleman, A.W. The Autofluorescent flagellum: a new phylogenetic enigma. Journal of Phycology 24, 118-120, 1988.

    Copeland, N., G., Jenkins, N., A., Court, D., L. Recombineering: a powerful new tool for mouse functional genomics. Nature Reviews Genetics 2, 769-779, 2001.

    Dalby, B., Cates, S., Harris, A., Ohki, E.C., Tilkins, M.L., Price, P.J., Ciccarone, V.C. Advanced transfection with Lipofectamine 2000 reagent: primary neurons, siRNA, and high-throughput applications. Methods 33, 95-103, 2004.

    Decker, E., L. and Reski, R. The moss bioreactor. Current Opinion in Plant Biology 7, 166-170, 2004.

    Einerhand, M.P., Antoniou, M., Zolotukhin, S., Muzyczka, N., Berns, K.I., Grosveld, F., Valerio, D. Regulated high-level human beta-globin gene expression in erythroid cells following recombinant adeno-associated virus-mediated gene transfer. Gene Therapy 2, 336-343, 1995.

    Elbrächter, M. Green autofluorescence-a new taxonomic feature for living dinoflagellate cysts and vegetative cells. Review of Palaeobotany and Palynology 84, 101-105, 1994.

    Endy, D. Foundations for engineering biology. Nature 438, 449-453, 2005.

    Fromont-Racine, M., Rain, J.C., Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genetics 16, 277-282, 1997.

    Garcia, O., Escalante, F.M.E., Bashan, L.E., Bashan, Y. Heterotrophic cultures of microalgae: metabolism and potential products. Water Research 45, 11-36, 2011.

    Gerngross, T.U. Advances in the production of human therapeutic proteins in yeasts and filamentous fungi. Nature Biotechnology 22, 1409-1414, 2004.

    Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F.J., Burton, J.N., Walker, B.J., Sharpe, T., Hall, G., Shea, T.P., Sykes, S. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences 108, 1513-1518, 2011.

    Gong, Y., Hu, H., Gao, Y., Xu, X., Gao, H. Microalgae as platforms for production of recombinant proteins and valuable compounds: progress and prospects. Journal of Industrial Microbiology and Biotechnology 38, 1879-1890, 2011.

    Grandjean, M., Girod, P.A., Calabrese, D., Kostyrko, K., Wicht, M., Yerly, F., Mazza, C., Beckmann, J.S., Martinet, D., Mermod, N. High-level transgene expression by homologous recombination-mediated gene transfer. Nucleic Acids Research 39, e104-e104, 2011.

    Griesbeck, C., Kobl, I., Heitzer, M. Chlamydomonas reinhardtii. Molecular Biotechnology 34, 213-223, 2006.

    Heitzer, M., Eckert, A., Fuhrmann, M., Griesbeck, C., Influence of codon bias on the expression of foreign genes in microalgae. Springer, New York, 46-53, 2007.

    Honda, D., Yokochi, T., Nakahara, T., Erata, M., Higashihara, T. Schizochytrium limacinum sp. nov., a new thraustochytrid from a mangrove area in the west Pacific Ocean. Mycological Research 102, 439-448, 1998.

    Horton, R.M., Cai, Z.L., Ho, S.N., Pease, L.R. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques 8, 528-535, 1990.

    Ikonomou, L., Schneider, Y.J., Agathos, S.N. Insect cell culture for industrial production of recombinant proteins. Applied Microbiology and Biotechnology 62, 1-20, 2003.

    Kaul, S., Koo, H.L., Jenkins, J., Rizzo, M., Rooney, T., Tallon, L.J., Feldblyum, T., Nierman, W., Benito, M.I., Lin, X.Y. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815, 2000.

    Kawai, H. A flavin-like autofluorescent substance in the posterior flagellum of golden and brown algae. Journal of Phycology 24, 114-117, 1988.

    Kazama, F.Y. Ultrastructure of Thraustochytrium sp. zoospores. IV. External morphology with notes on the zoospores of Schizochytrium sp. Mycologia 66, 272-280, 1974.

    Key, S., Ma, J., K. C., Drake, P.M.W. Genetically modified plants and human health. Journal of the Royal Society of Medicine 101, 290-298, 2008.

    Kopczynski, M., Lenzer, T., Oum, K., Seehusen, J., Seidel, M.T., Ushakov, V.G. Ultrafast transient lens spectroscopy of various C 40 carotenoids: lycopene, β-carotene,(3'R, 3'R)-zeaxanthin,(3'R, 3'R, 6'R)-lutein, echinenone, canthaxanthin, and astaxanthin. Physical Chemistry Chemical Physics 7, 2793-2803, 2005.

    Laird, P.W., Zijderveld, A., Linders, K., Rudnicki, M.A., Jaenisch, R., Berns, A. Simplified mammalian DNA isolation procedure. Nucleic Acids Research 19, 4293, 1991.

    Lavie, L., Maldener, E., Brouha, B., Meese, E.U., Mayer, J. The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity. Genome Research 14, 2253-2260, 2004.

    León-Bañares, R., González-Ballester, D., Galván, A., Fernández, E. Transgenic microalgae as green cell-factories. Trends in Biotechnology 22, 45-52, 2004.

    Lehnman, I.R. DNA ligase: structure, mechanism, and function. Science 186, 790-797, 1974.

    Lewis, T., Mooney, B., McMeekin, T.A., Nichols, P.D. New Australian microbial sources of polyunsaturated fatty acids. Chemistry in Australia 65, 37-39, 1998.

    Li, J. and Wang, W. Detailed assessment of homology detection using different substitution matrices. Chinese Science Bulletin 51, 1538-1545, 2006.

    Lopes, T.S., Klootwijk, J., Veenstra, A.E., van der Aar, P.C., van Heerikhuizen, H., Raué, H.A., Planta, R.J. High-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: a new vector for high-level expression. Gene 79, 199-206, 1989.

    Magaña, J.A. and Calderón, A.M. Risk assessment of genetically modified crops for nutrition and health. Nutrition Reviews 67, 1-16, 2009.

    Maiorella, B., Inlow, D., Shauger, A., Harano, D. Large-scale insect cell-culture for recombinant protein production. Nature Biotechnology 6, 1406-1410, 1988.

    Matsumoto, T., Wu, J.Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K. The map-based sequence of the rice genome. Nature 436, 793-800, 2005.

    Mayfield, S.P., Manuell, A.L., Chen, S., Wu, J., Tran, M., Siefker, D., Muto, M., Marin-Navarro, J. Chlamydomonas reinhardtii chloroplasts as protein factories. Current Opinion in Biotechnology 18, 126-133, 2007.

    Mcgarvey, P. and Kaper, J.M. A simple and rapid method for screening transgenic plants using the PCR. Biotechniques 11, 428-432, 1991.

    Melo, E.O., Canavessi, A.M.O., Franco, M.M., Rumpf, R. Animal transgenesis: state of the art and applications. Journal of Applied Genetics 48, 47-61, 2007.

    Mittler, R. Oxidative stress, antioxidants and stress tolerance. Trends in Plant Science 7, 405-410, 2002.

    Mogilna, N. and Magufwa, A. Genetic modified foods: advantages and disadvantages. Economics for Ecology 15, 97-100, 2009.

    Motulsky, H.J. Prism 5 Statistics Guide, 2007. GraphPad Software 31, 39-42, 2007.

    Naganuma, T. Abundance of thraustochytrids in coastal plankton. Marine Ecology Progress Series 162, 105-110, 1998.

    Old, R.W., Principles of gene manipulation: an introduction to genetic engineering. University of California Press, California, 98-104, 1981.

    Pavlou, A.K. and Reichert, J.M. Recombinant protein therapeutics-success rates, market trends and values to 2010. Nature Biotechnology 22, 1513-1519, 2004.

    Pevsner, J., Bioinformatics and functional genomics. John Wiley & Sons, Massachusetts, 297-302, 2009.

    Pinkert, C.A., Transgenic animal technology: a laboratory handbook. Gulf Professional Publishing, California, 146-154, 2002.

    Radakovits, R., Jinkerson, R.E., Darzins, A.l., Posewitz, M.C. Genetic engineering of algae for enhanced biofuel production. Eukaryotic Cell 9, 486-501, 2010.

    Ragauskas, A.J., Williams, C.K., Davison, B.H., Britovsek, G., Cairney, J., Eckert, C.A., Frederick, W.J., Hallett, J.P., Leak, D.J., Liotta, C.L. The path forward for biofuels and biomaterials. Science 311, 484-489, 2006.

    Raghukumar, S. Schizochytrium mangrovei sp. nov., a thraustochytrid from mangroves in India. Transactions of the British Mycological Society 90, 627-631, 1988.

    Raghukumar, S. Ecology of the marine protists, the Labyrinthulomycetes (Thraustochytrids and Labyrinthulids). European Journal of Protistology 38, 127-145, 2002.

    Raja, R., Hemaiswarya, S., Kumar, N.A., Sridhar, S., Rengasamy, R. A perspective on the biotechnological potential of microalgae. Critical Reviews in Microbiology 34, 77-88, 2008.

    Rosenberg, J.N., Oyler, G.A., Wilkinson, L., Betenbaugh, M.J. A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Current Opinion in Biotechnology 19, 430-436, 2008.

    Ruxton, G.D. The unequal variance t-test is an underused alternative to Student's t-test and the Mann-Whitney U test. Behavioral Ecology 17, 688-690, 2006.

    Sakaguchi, K., Matsuda, T., Kobayashi, T., Ohara, J.I., Hamaguchi, R., Abe, E., Nagano, N., Hayashi, M., Ueda, M., Honda, D. Versatile transformation system that is applicable to both multiple transgene expression and gene targeting for Thraustochytrids. Applied and Environmental Microbiology 78, 3193-3202, 2012.

    Sanger, F., Nicklen, S., Coulson, A. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74, 5463-5467, 1977.

    Scolari, F., Siciliano, P., Gabrieli, P., Gomulski, L.M., Bonomi, A., Gasperi, G., Malacrida, A.R. Safe and fit genetically modified insects for pest control: from lab to field applications. Genetica 139, 41-52, 2011.

    Song, L., Nakaar, V., Kavita, U., Price, A., Huleatt, J., Tang, J., Jacobs, A., Liu, G., Huang, Y., Desai, P. Efficacious recombinant influenza vaccines produced by high yield bacterial expression: a solution to global pandemic and seasonal needs. PLoS One 3, e2257, 2008.

    Sparrow, F.K. Biological observations on the marine fungi of Woods Hole waters. The Biological Bulletin 70, 236-263, 1936.

    Steinbrenner, J. and Sandmann, G. Transformation of the green alga Haematococcus pluvialis with a phytoene desaturase for accelerated astaxanthin biosynthesis. Applied and Environmental Microbiology 72, 7477-7484, 2006.

    Swartz, J.R. Advances in Escherichia coli production of therapeutic proteins. Current Opinion in Biotechnology 12, 195-201, 2001.

    Tang, Y.Z. and Dobbs, F.C. Green autofluorescence in dinoflagellates, diatoms, and other microalgae and its implications for vital staining and morphological studies. Applied and Environmental Microbiology 73, 2306-2313, 2007.

    Weathers, P.J., Towler, M.J., Xu, J. Bench to batch: advances in plant cell culture for producing useful products. Applied Microbiology and Biotechnology 85, 1339-1351, 2010.

    Wildt, S. and Gerngross, T.U. The humanization of N-glycosylation pathways in yeast. Nature Reviews Microbiology 3, 119-128, 2005.

    Williams, D.C., Van Frank, R.M., Muth, W.L., Burnett, J.P. Cytoplasmic inclusion bodies in Escherichia coli producing biosynthetic human insulin proteins. Science 215, 687-689, 1982.

    Wilson, I.B., Zeleny, R., Kolarich, D., Staudacher, E., Stroop, C.J., Kamerling, J.P., Altmann, F. Analysis of Asn-linked glycans from vegetable foodstuffs: widespread occurrence of Lewis a, core alpha 1,3-linked fucose and xylose substitutions. Glycobiology 11, 261-274, 2001.

    Wurm, F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nature Biotechnology 22, 1393-1398, 2004.

    Xi, H., Yu, Y., Fu, Y., Foley, J., Halees, A., Weng, Z. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Research 17, 798-806, 2007.

    Yang, H.L., Lu, C.K., Chen, S.F., Chen, Y.M., Chen, Y.M. Isolation and characterization of Taiwanese heterotrophic microalgae: screening of strains for docosahexaenoic acid (DHA) production. Marine Biotechnology 12, 173-185, 2010.

    Zhang, H., Wang, W., Quan, C., Fan, S. Engineering considerations for process development in mammalian cell cultivation. Current Pharmaceutical Biotechnology 11, 103-112, 2010.

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