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研究生:鍾弘彥
研究生(外文):Hung-Yen Chung
論文名稱:石油降解菌PseudomonasstutzeriRMRCPAH5之奎林氧化還原酶基因選殖與表現預測
論文名稱(外文):The gene cloning and expression prediction of quinoline 2-oxidoreductase (Qor) in petroleum biodegradation bacteria-Pseudomonas stutzeri RMRC PAH5
指導教授:易逸波易逸波引用關係
指導教授(外文):Yet-Pole I
學位類別:碩士
校院名稱:國立雲林科技大學
系所名稱:環境與安全工程系碩士班
學門:工程學門
學類:環境工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:164
中文關鍵詞:選殖奎林氧化還原酶生物降解假單胞菌 stutzeri RMRC PAH5奎林
外文關鍵詞:Pseudomonas stutzeri RMRC PAH5Quinoline 2-oxidoreductaseQuinolineCloningBiodegradation
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奎林 (quinoline) 是一種由煤炭或石油等石化製程中所產生的含氮雜環碳氫化合物,對人體具毒性和致癌性。過去由台灣本土所篩選出之奎林降解菌株,往往僅針對生長最適化、酵素活性測試及代謝過程等生理作用機制進行探討,故對於奎林生物降解研究及其生化特性有較深入的了解,並累積了不少的成果;但是在分子生物層面則未有較深入的探討,所以本研究以建立基因選殖與表現的基本工具與系統為主要目的。實驗所選用之菌株係由嘉義中油煉製所所提供之 Pseudomonas stutzeri RMRC PAH5 ,此分解菌已被確認可將奎林當作唯一基質使用而達到降解之效果,以 HPLC 分析其降解程度高達 97 % 以上。
本研究著重於選殖出奎林降解時扮演重要角色之 quinoline 2-oxidoreductase 基因 (P.s. Qor) , 基因選殖方式以 PCR 搭配所設計之四對正反双股寡核苷酸 (S1/AS1) 、(S2/AS2) 、(Start/S1 up) 與 (AS2 down/Stop) 為引子,分別得到 PCR 產物 (S1/AS1):1.3 kb ,(S2/AS2):1.2 kb ,(Start/S1 up):0.34 kb 及 (AS2 down/Stop):1.8 kb 。進一步將產物純化後,以 T-A cloning 的方法轉殖至次選殖載體 yT&A vector ,篩選具正反應菌株並分別命名為 pHy-S1/AS1 、pHy-S2/AS2 、pHy-SS 和 pHy-AdS ,經定序結果顯示 P.s. Qor 全長為 3756 bp。
為構築完整的P.s. Qor全長,設計適當且具基因專一性引子 (gene specific primer, GSP) Qor Start 與 Qor Stop ,同樣以 PCR 的方式得到預期的序列長度後,轉形至 pGEM-T easy vector 次選殖載體中,進行正反應株快速篩選,證實所插入的片段為 Qor 基因序列。進一步針對所選殖的 P.s. Qor 進行序列分析,結果發現其基因序列包含可分別轉譯成三組完整且胺基酸序列有部分重疊的展讀區 (open reading fram, ORF) ,分別以P.s. QorM 、P.s. QorS 及 P.s. QorL 命名之,由比對結果發現 P.s. Qor 與 P. putida 86 Qor的胺基酸序列同質性高達 99% ,顯見於演化過程中 Qor 基因序列的變動不大,推測可能為一重要保留區域,若序列一經改變則活性可能會減少或消失。
所選殖的 Qor 片段序列上載至國家衛生研究院的 GCG 系統比對含鉬烴基化酶序列,其三個 P.s. Qor 片段序列具有高保留區域和不同的主要功能區。P.s QorM 的 ORF 有 867 bp ,可以轉譯出含有 288 胺基酸的蛋白質,推測 P.s. QorM 序列中可能包含 FAD cofactor ,但 FAD 輔因子結合位置並無高保留性。P.s. QorS 之 ORF為 513 bp ,相對轉譯後的胺基酸數為 168 ,P.s. QorS 胺基酸序列中含有 4 個為一組的半胱氨酸 (cysteines) 所組成之高保留性之主要功能 (motif) 區域,第一區的 4 個 cysteines 分別位於 48, 53, 56 和 68 的位置,此區的 motif序列排列方式為 (C-X4-C-G-X-C-Xn-C) ,另一區的 cysteines 則位於 107, 110, 142 與 144 的位置,其 motif序列排列方式則為 (C-G-X-C-X31-C-X-C) ,初步推測此結合部位主題區 (binding site motif) 含葉綠體型態之鐵硫蛋白次單元體。P.s. QorL 的 ORF 為 2367 bp ,可推衍成 788 個胺基酸,其胺基酸序列中推測含有鉬蕨素輔因子 (pterin molybdenum cofactor) 結合位置,其可能結合區共5處,分別位於 252~258 、369~380 、506~509 、542~548 以及 741~746 aa。
Quinoline, an aromatic N-heterocyclic chemical compound produced in coal tar and other petroleum producing processes, is a known toxicity and carcinogen to the human body. In the past, the research of quinoline biodegrading bacterial strain in Taiwan usually focused on the physiological mechanisms studies, such as enzyme activity test, optimal cultivation, and metabolism process. Although many achievements have been accumulated and a deeper understanding of biodegradation of quinoline and it’s biochemical characteristic has been accomplished, little has been done in the field of molecular biology. Therefore, the purpose of this study is to build a basic tool and selecting system for gene cloning and expression. The bacterial strain used in the experiment, Pseudomonas stutzeri RMRC PAH5, is provided by Chiayi Refining and Manufacturing Research Institute that can treat quinoline as sole substrate. The degradation rate of quinoline can reach over 97 % that has been confirmed by HPLC.
The highlight of this study is to clone the quinoline 2-oxidoreductase (Qor) gene from the Pseudomonas stutzeri RMRC PAH5 where the former play an important role in degrading quinoline. Four pairs of sense/antisense oligonucleotide (S1/AS1), (S2/AS2), (Start/S1 up) and (AS2 down/Stop) were designed and synthesized as primers for PCR method. The resulting products are (S1/AS1 ): 1.3 kb, (S2/AS2): 1.2 kb, (Start/S1 up): 0.34 Kb and (AS2 down/Stop): 1.8 kb separately. After purification, all the previous DNA fragment were inserted into the subcarrier, yT&A vector, by T-A cloning method. The positive colony after screening that include Qor as well as flanking regions were denominated as pHy-S1/AS1, pHy-S2/AS2, pHy-SS and pHy-AdS. It was shown that the total length of P.s.Qor is 3756 bp after gene sequence analysis.
The gene specific primers (GSP), Qor start and Qor stop, were properly designed in order to construct the complete full length of P.s. Qor. The expectative DNA fragment can be obtained via PCR method and be inserted into a subcloned pGEM-T easy vector to proceed fast screening. The result proves that insertion is P.s. Qor gene. The complete gene-coding region were identified through the gene sequence analysis. It was found the complete P.s. Qor gene is composed of three subunits with transcriptional order as qorM, qorS and qorL. By comparing the sequence of P.s. Qor with P. putida 86 Qor shows their significant homology is above 99%, which means abrupt change of Qor gene is not very often during the evolution. It is postulated this gene is a highly conservative area and it’s corresponding enzyme activation might be reduced or disappeared once it’s sequence has been changed.
The amino acid sequence of P.s. Qor is compared with various molybdenum containing hydroxylases by GCG command mode of NHRI. It was found the three subunits of P.s. Qor amino acid sequence contains highly conserved areas and different binding motifs. The open reading frame (ORF) of P.s. QorM has 867 bp and it’s corresponding protein consists of 288 amino acid. The P.s. QorM probably may harbor the FAD cofactor, but no conserved area was found. The P.s. QorS has 513 bp ORF and it’s corresponding protein consists of 168 amino acid. The P.s. QorS includes two distinct motifs and each one of them contains four cysteines that arranged in a specific structure. The four cysteines of the first motif locate in the positions of 48, 53, 56, and 68 aa with a structure as (C-X4-C-G-X-C-Xn-C). The second motif has a structure of (C-G-X-C-X31-C-X-C) where it’s four cysteines locate in the positions of 107, 110, 142 and 144 aa. This latter motif presumably is the binding site of the typical plant-type 【2Fe-2S】ferredoxins. The 2368 bp coding region of the P.s QorL was translated to a 788 amino acid sequence and probably contains the binding sites of the pterin molybdenum cofactor. The putative binding sites locate at position of 252~258, 369~380, 506~509, 542~548 and 741~746 aa.
中文摘要Ⅰ
英文摘要Ⅲ
目錄Ⅵ
表目錄Ⅷ
圖目錄Ⅸ
第一章緒論1
1.1 研究背景與現況1
1.2研究目的10
1.3研究流程與架構12
第二章文獻回顧13
2.1 奎林之環境流佈特性及分解機制13
2.2 微生物降解奎林之相關研究15
2.3 奎林氧化還原酶在基因選殖之研究18
第三章研究方法19
3.1材料、藥品及儀器19
3.2菌種篩選與鑑定23
3.3DNA 的製備26
3.4DNA片段的製備與定量35
3.5質體 DNA 之轉形43
3.6核酸電泳分析49
3.7電腦分析51
第四章結果與討論52
4.1Pseudomonas stutzeri RMRC PAH5之菌種培養與染色體 DNA
抽取52
4.2Pseudomonas stutzeri RMRC PAH5 奎林氧化還原酶基因 (Qor)
的選殖56
4.2.1Qor 基因專一性引子的設計56
4.2.2Qor 基因片段之聚合酶連鎖反應 (PCR) 實驗56
4.2.3Qor 基因片段的篩選64
4.2.4Qor 基因的定序策略71
4.2.5全長之 Qor 基因的建構與篩選76
4.3奎林氧化還原酶 DNA 序列分析87
4.4奎林氧化還原酶的胺基酸序列分析88
第五章結論與展望116
參考文獻120
附錄126
表 目錄
表1-1台灣洩油事故機率3
表1-2 Quinoline(奎林)的物化與毒理性質8
表1-3 2, 3, 4-Methylquinoline之物性與化性之比較9
表1-4 11種篩選菌株分別於液態培養下對 quinoline 、benzanthracene 或 naphthalene 的生物降解能力11
表4-1六株本土性多環芳香烴降解菌對quinoline、benz[a]anthracene或naphthalene之降解能力a53
表4-2用於 Qor 基因選殖的合成引子58
表4-3Qor 基因選殖在 PCR 反應中操作條件表59
表4-4用於次選殖載體 yT&A 之colony PCR 的高特異性引子65
表4-5用於 Qor 基因定序時的 nested 退化性引子71
表4-6 Qor 全長序列選殖之 PCR 反應條件表78
圖 目錄
圖1-1環境中石化污染物之污染來源5
圖1-2石化污染物在環境中所遭遇之物理性、化學性與生物性命運6
圖1-3各類含氮雜環化合物 (NAHs) 之結構9
圖1-4研究工作內容與流程圖12
圖2-1奎林經由coumarin 代謝途徑的初步降解反應過程17
圖3-1 Qiagene 之 Dneasy Mini Spin Column29
圖3-2 Genemark 之 spin column31
圖3-3 Bio-RAD 之 PCR Kleen spin Column39
圖3-4 Qiagene 之 MinElute column41
圖3-5圖 3-5 鑄膠槽內的洋菜膠體完成品51
圖3-6置於電泳槽的洋菜膠體51
圖4-1石油降解菌 Pseudomonas stutzeri RMRC PAH5 的生長曲線圖54
圖4-2 Pseudomonas stutzeri RMRC PAH5 之染色體 DNA的膠體電泳圖55
圖4-3以Pseudomonas stutzeri RMRC PAH5的染色體 DNA 當作模板,S1 (sense) 與 AS1 (antisense) 寡核苷酸為引子之 PCR 產物膠體電泳圖60
圖4-4以Pseudomonas stutzeri. RMRC PAH5的染色體 DNA 當作模板,S2 (sense) 與 AS2 (antisense) 寡核苷酸為引子之 PCR 產物膠體電泳圖61
圖4-5以Pseudomonas stutzeri. RMRC PAH5的染色體 DNA 當作模板,Start (sense) 與 S1 up (antisense) 寡核苷酸為引子之 PCR 產物膠體電泳圖62
圖4-6以Pseudomonas stutzeri. RMRC PAH5的染色體 DNA 當作模板,AS2 down (sense) 與 Stop (antisense) 寡核苷酸為引子之 PCR 產物膠體電泳圖63
圖4-7以Pseudomonas sp. RMRC PAH5 的 染色體 DNA 當作模板,不同高保留性序列為引子之 PCR 產物經回收純化後之膠體電泳圖66
圖4-8奎林氧化還原酶基因 (Qor) 之質體片段以高特異性序列為引子的colony PCR 產物之膠體電泳圖67
圖4-9奎林氧化還原酶基因 (Qor) 之質體片段以高特異性序列為引子的colony PCR 產物之膠體電泳圖68
圖4-10奎林氧化還原酶基因 (Qor) 之質體片段以高特異性序列為引子的colony PCR 產物之膠體電泳圖69
圖4-11奎林氧化還原酶基因 (Qor) 之質體片段以高特異性序列為引子的colony PCR 產物之膠體電泳圖70
圖4-12奎林氧化還原酶基因 (Qor) 序列校正策略圖72
圖4-13 Pseudomonas stutzeri RMRC PAH5 所選殖的Qor 基因 DNA 排列和限酶圖譜78
圖4-14質體 pHy-S1/AS1 之限制酶單一切點圖譜79
圖4-15質體 pHy-S2/AS2 之限制酶單一切點圖譜80
圖4-16質體 pHy-SS 之限制酶單一切點圖譜81
圖4-17質體 pHy-AdS 之限制酶單一切點圖譜82
圖4-18質體 pHy-S1/AS1 與 pHy-S2/AS2 以Bam HI 及 Pvu I 限制酶切割後之膠體電泳圖83
圖4-19以Pseudomonas sp. RMRC PAH5的 chromosomal DNA 當作模板,Start (sense) 與 Stop (antisense) 寡核苷酸為引子之 PCR 產物膠體電泳圖84
圖4-20奎林氧化還原酶 (Qor) 基因序列全長之質體以快速篩選法所得產物之膠體電泳圖85
圖4-21基因重組質體 pHy-Oor23 之限制酶單一切點圖譜86
圖4-22 Pseudomonas stutzeri RMRC PAH5 奎林分解菌的 QorM 基因序列與胺基酸序列90
圖4-23 Pseudomonas stutzeri RMRC PAH5 奎林分解菌的 QorS 基因序列與胺基酸序列95
圖4-24 Pseudomonas stutzeri RMRC PAH5 奎林分解菌的 QorL 基因序列與胺基酸序列98
圖4-25 P.stutzeri RMRC PAH5 QorS 與 P.putida 86 QorS 之胺基酸序列比對112
圖4-26 P.stutzeri RMRC PAH5 QorM 與 P.putida 86 QorM 之胺基酸序列比對113
圖4-27 P.stutzeri RMRC PAH5 QorL 與 P.putida 86 QorL 之胺基酸序列比對115
圖4-28表現質體 pHy-Qor 的構築策略119
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