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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 李佳音 | zh_TW |
| dc.contributor.author | 張珊齊 | zh_TW |
| dc.contributor.author | San-Chi Chang | en |
| dc.date.accessioned | 2021-07-11T15:06:24Z | - |
| dc.date.available | 2024-08-19 | - |
| dc.date.copyright | 2019-08-20 | - |
| dc.date.issued | 2019 | - |
| dc.date.submitted | 2002-01-01 | - |
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N., & Lee, C. Y. (2000). Metal content and biochemical analyses of a recombinant collagenase PrtV from Vibrio parahaemolyticus. Microbiology and Immunology, 44(10), 805-813. Zhang, Y., Qiu, Y., Tan, Y., Guo, Z., Yang, R., & Zhou, D. (2012). Transcriptional regulation of opaR, qrr2–4 and aphA by the master quorum-sensing regulator OpaR in Vibrio parahaemolyticus. PLoS One, 7(4), e34622. Zhang, L. L., & Orth, K. (2013). Virulence determinants for Vibrio parahaemolyticus infection. Current Opinion in Microbiology, 16(1), 70-77. Zhu, J., Miller, M. B., Vance, R. E., Dziejman, M., Bassler, B. L., & Mekalanos, J. J. (2002). Quorum-sensing regulators control virulence gene expression in Vibrio cholerae. Proceedings of the National Academy of Sciences of the United States of America, 99(5), 3129-3134. Zhu, J., & Mekalanos, J. J. (2003). Quorum sensing-dependent biofilms enhance colonization in Vibrio cholerae. Developmental Cell, 5(4), 647-656 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/78598 | - |
| dc.description.abstract | 腸炎弧菌 (Vibrio parahaemolyticus) 為海洋細菌，當人類食用受腸炎弧菌污染的海鮮會造成腹瀉等腸胃疾病，是台灣重要的食物病原菌。本研究首先結合Mi-seq、PacBio和Sanger三種定序方法解序腸炎弧菌VP93基因體序列。VP93基因體由一大一小的兩個染色體所組成，全長5,095,022 bp，GC含量 45.26%，有4,709個ORF，第一個染色體長3,396,947 bp，GC 含量45.07%，存在3,181個ORF、31個rRNA、101個tRNA; 第二個染色體較小長1,698,075 bp，GC含量45.63%，存在1,528個ORF、3個rRNA、14個tRNA。當VP93生長至後對數期 (late-log phase) 時胞外蛋白酶的活性達到最高峰。蛋白酶參與弧菌屬菌株營養攝取及感染的機制，菌體透過定額感應系統感知群體密度及環境條件，可以調控菌體中基因的表現。染色質免疫沉澱之定序 (ChIP-seq) 資料顯示VP93基因體有838個OpaR結合序列，歸納OpaR保守性結合序列為ATCAATA。即時定量聚合酶連鎖反應 (qRT-PCR) 和報導基因實驗 (luxAB assay) 確認OpaR經由八個蛋白酶基因附近之OpaR結合位抑制LytM (VPA1649)、Mcp02 (VPA0755)、M6 protease (VP0907)、serine protease (VPA0449)、DegS (VP0432)、protease II (VPA1467)、periplasmic protease (VP2032) 基因表現，以及促進PrtA (VPA0227) 基因表現。電泳遷移 (EMSA) 和足跡 (footprinting) 實驗證實蛋白酶基因附近八個OpaR結合位之結合情形及序列。OpaR於蛋白酶基因之專一性結合序列可歸納為ATCGTTG。胞外鹼性絲胺酸蛋白酶 (PrtA) 具有溶血性和細胞毒性，PrtA主導腸炎弧菌VP93胞外蛋白酶的活性。prtA和上游的反向基因ldh共用啟動子之-10序列。轉錄起始點實驗 (ARF-TSS) 證實ldh和prtA的轉錄起始點分別位於轉譯起始點上游－78的A和－198的G。OpaR於prtA上游有兩個結合位，一個在－269至－246處，另一個位於－88至－68處。其中－269至－246的OpaR結合位重疊於prtA的啟動子之－35序列。本論文提出定額感應調控子OpaR在腸炎弧菌蛋白酶基因的調控中扮演著重要的角色。由臺灣分離之腸炎弧菌VP93基因體解序、OpaR直接調控組 (direct regulon) 及蛋白酶基因調控機制各項研究結果，為海洋弧菌之相關研究領域提供嶄新資訊，對於蛋白酶調控機制提出不同的視野及研究手法。 | zh_TW |
| dc.description.abstract | Vibrio paraheamolyticus is marine bacteria. It causes gastroenteritis and diarrhea when humans are infected with V. parahaemolyticus via consumption of raw contaminated seafood. V. parahaemolyticus is an important foodborn pathogen in Taiwan. In this study, we combine three sequencing methods, Mi-seq, PacBio and Sanger to assemble the VP93 genome. VP93 genome has two chromosomes, containing 5,095,022 bp, 4,709 ORFs and GC content is 45.26%. Chr1 was composed with 3,396,947 bp, 3,181 ORF, 31 rRNA, 101 tRNA and GC content is 45.07%. Chr2 has 1,698,075 bp, 1,528 ORF, 3 rRNA, 14 tRNA and GC content is 45.63%. Extracellular protease activity was highest during the late-log growth phase of VP93. Many protease genes have been shown to be required for nutrient intake and the infection mechanism of Vibrios. Quorum sensing (QS) is a bacterial communication system which uses extracellular chemicals as signals. Bacteria changed their behaviour and synchronised gene expression in a microbial community by QS. ChIP-seq data reveals 838 OpaR binding sites in VP93 genome. The conserved OpaR binding motif is ATCAATA. qRT-PCR and luxAB assay confirmed that OpaR repressed the gene expression of LytM, Mcp02, M6 protease, serine protease, DegS, protease II, periplasmic protease and promoteed prtA expression. EMSA and footprinting results defined the OpaR specific binding sequence of the eight protease genes. The protease specific binding motif of OpaR is ATCGTTG. PrtA is an extracellular serine protease of Vibrio parahaemolyticus and has haemolytic and cytotoxic activities. PrtA is the dominant of VP93 extracellular protease activity. prtA and opposite direction gene, ldh shared the －10 box of the promoter region. ARF-TSS proved that the transcription start site of ldh and prtA is on －78A and －198G position from their translation start site. OpaR bound to prtA upstream sequence at positions －269 to －246 and －88 to －68 from the prtA translational start site. －269 to －246 overlapped the －35 box of prtA promoter. In this study, we report that OpaR, a quorum sensing regulator play important roles in the protease regulation mechanism. The results of clarifying the genome sequence VP93 strain isolated from Taiwan, OpaR direct regulon, protease gene regulation provided novel information and research method on protease regulation of Vibrio research field. | en |
| dc.description.provenance | Made available in DSpace on 2021-07-11T15:06:24Z (GMT). No. of bitstreams: 1 ntu-108-D02623002-1.pdf: 8238896 bytes, checksum: 5b3f61d694fb4d1ac05316fee47a8aa9 (MD5) Previous issue date: 2019 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
誌謝 ii 中文摘要 iv 英文摘要 v 目錄 vi 表次 x 圖次 xi 附錄表次 xiii 附錄圖次 xiv 縮寫表 xv 第一章、前言及文獻回顧 1 一、腸炎弧菌(Vibrio parahaemolyticus) 1 1. 起源及特性 1 2. 基因體分析 1 3. 致病因子 2 二、弧菌屬胞外蛋白酶 3 1. 胞外絲胺酸蛋白酶 3 1-1霍亂弧菌胞外絲胺酸蛋白酶-VC1649 4 1-2創傷弧菌胞外絲胺酸蛋白酶-VvpS 4 1-3腸炎弧菌胞外絲胺酸蛋白酶 PrtA 5 2. 胞外金屬蛋白酶 5 2-1霍亂弧菌胞外金屬蛋白酶- HA/protease 6 2-2創傷弧菌胞外金屬蛋白酶-VvpE 6 2-3腸炎弧菌胞外金屬蛋白酶 PrtV 7 三、定額感應系統(Quorum Sensing System) 7 1. 弧菌屬定額感應系統 7 2. 定額感應系統之調控子 8 3. 腸炎弧菌定額感應系統主要調控子OpaR 9 第二章、腸炎弧菌VP93全基因體解序及分析 11 一、本章摘要 11 二、本章前言 12 三、材料與方法 12 1. 菌株 12 2. 培養條件 12 3. 引子序列 12 4. 儀器及藥品試劑 13 5. 染色體純化 13 6. 設計引子 13 7. 聚合酶連鎖反應(PCR) 14 8. DNA瓊脂膠體電泳 14 四、結果 15 1. 定序品質分析-MiSeq (二代) &PacBio (三代) 15 2. MiSeq修剪(trim)和PacBio校正(correct) 16 3. De novo 序列組裝 16 4. Sanger定序Chr1-gap和Chr2-gap 16 5. 合併PacBio序列組裝VP93基因體 17 6. rRNA、tRNA 及ORF預測 17 7. 全基因體Gene Ontology (GO)分析 18 8. 全基因體COGs和KEGG分析 18 9. VP93和其他腸炎弧菌菌株之基因體比較 18 五、討論 19 六、結論 20 第三章、染色質免疫沉澱之定序分析定額感應調控子OpaR結合位 21 一、本章摘要 21 二、本章前言 22 三、材料與方法 23 1. 菌株及質體 23 2. 引子 23 3. 培養條件 23 4. 儀器及藥品試劑 23 5. 生物資訊分析 24 6. 染色體純化 24 7. DNA瓊脂膠體電泳 24 8. 質體小量製備 24 9. 膠體純化DNA片段 25 10. 聚合酶連鎖反應 (PCR) 25 11. DNA 之限制酶截切反應 25 12. 接合作用(ligation) 26 13. 大腸桿菌勝任細胞製備 26 14. 大腸桿菌熱休克轉型作用 26 15. 接合生殖(Conjugation)與篩選方式 27 16. FLAG-OpaR/VP93菌株建構 27 17. 西方墨點法 28 18. 染色質免疫沉澱(ChIP) 28 19. 染色質免疫沉澱之即時定量聚合酶連鎖反應(ChIP-qPCR) 29 四、結果 29 1. 建構並確認FLAG-OpaR的表現情形 29 2. 染色質免疫沉澱(ChIP)之DNA剪切(shearing)條件 30 3. 染色質免疫沉澱(ChIP)之FLAG抗體結合條件 30 4. ChIP-seq DNA片段品質確認及次世代定序 (ChIP-Seq) 31 5. ChIP-Seq 結果分析受OpaR直接調控的基因分類 32 6. OpaR的保守性結合序列 32 五、討論 33 六、結論 34 第四章、腸炎弧菌定額感應調控子OpaR直接調控八個蛋白酶 35 一、本章摘要 35 二、本章前言 35 三、材料與方法 36 1. 菌株 36 2. 質體及引子 36 3. 培養條件 37 4. 儀器及藥品試劑 37 5. 生物資訊學 37 6. 製備腸炎弧菌勝任細胞 37 7. 腸炎弧菌的轉型作用 37 8. 報導基因實驗 (luxAB reporter assay) 38 9. 細菌之RNA萃取 38 10. 去除RNA樣品中的DNA 39 11. RNA反轉錄作用 39 12. 即時定量聚合酶連鎖反應(q-PCR) 40 13. His-tag 蛋白純化方法 40 14. 蛋白質的定量 40 15. 蛋白質的膠體電泳 41 16. 電泳遷移實驗(EMSA) 41 17. 足跡實驗(footprinting) 43 18. 統計分析方法 44 四、結果 44 1. OpaR結合於八個蛋白酶基因附近 44 2. 蛋白酶基因於不同生長時期之表現情形 44 3. OpaR對於蛋白酶基因的調控情形 45 4. OpaR於八個蛋白酶基因之結合情形 (EMSA) 45 5. OpaR於蛋白酶基因之結合位序列 (footprinting) 46 6. OpaR於蛋白酶基因之專一性結合序列 46 7. 八個蛋白酶基因之特性 47 五、討論 47 六、結論 48 第五章、定額感應調控因子OpaR於prtA-ldh 基因間結合位分析 49 一、本章摘要 49 二、本章前言 49 三、材料與方法 50 1. 菌株 50 2. 質體及引子 50 3. 培養條件 50 4. 儀器及藥品試劑 50 5. 生物資訊學網站 51 6. 生長曲線測定 51 7. 胞外蛋白酶純化與濃縮 51 8. 胞外蛋白酶活性測試 52 9. 轉錄起始點的分析(ARF-TSS) 52 10. 報導基因實驗(luxAB assay) 52 11. 足跡實驗(footprinting) 53 四、結果 53 1. PrtA主導VP93之胞外蛋白酶活性 53 2. OpaR調控 prtA啟動子 53 3. prtA和ldh啟動子分析 54 4. OpaR於prtA上游之結合序列 54 5. OpaR於ldh和prtA基因間的角色 55 五、討論 55 六、結論 56 第六章、總結 57 第七章、未來展望 59 一、OpaR於VP93基因體中鞭毛基因結合位分析 59 二、RpoS 結合於prtA 上游啟動子區域 59 三、OpaR和RNAP結合並調控prtA 表現 60 四、PrtA 胺基酸序列及分泌途徑探討 60 五、PrtA結構分析 61 參考文獻 62 | - |
| dc.language.iso | zh_TW | - |
| dc.title | 腸炎弧菌基因體分析及OpaR調控蛋白酶基因之研究 | zh_TW |
| dc.title | Vibrio parahaemolyticus genome analysis and protease regulation of quorum sensing regulator OpaR | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 107-2 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.oralexamcommittee | 林奐妤;徐駿森;羅凱尹;徐丞志 | zh_TW |
| dc.contributor.oralexamcommittee | ;;; | en |
| dc.subject.keyword | 腸炎弧菌,定額感應系統,金屬蛋白?,絲胺酸蛋白?,胞外蛋白?, | zh_TW |
| dc.subject.keyword | Vibrio paraheamolyticus,quorum sensing,OpaR,metalloprotease,serine protease,extracellular protease,ChIP-seq, | en |
| dc.relation.page | 154 | - |
| dc.identifier.doi | 10.6342/NTU201902885 | - |
| dc.rights.note | 未授權 | - |
| dc.date.accepted | 2019-08-14 | - |
| dc.contributor.author-college | 生物資源暨農學院 | - |
| dc.contributor.author-dept | 農業化學系 | - |
| dc.date.embargo-lift | 2029-08-08 | - |
| 顯示於系所單位： | 農業化學系 | |
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