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研究生: 巫豐耀
Wu, Feng-Yau
論文名稱: 高溫厭氧對苯二甲酸降解微生物社群之全量蛋白質表現分析
Global Protein Expression in Terephthalate-degrading Communities under Thermophilic Conditions
指導教授: 吳哲宏
Wu, Jer-Horng
學位類別: 碩士
Master
系所名稱: 工學院 - 環境工程學系
Department of Environmental Engineering
論文出版年: 2012
畢業學年度: 100
語文別: 中文
論文頁數: 131
中文關鍵詞: MetaproteomicMethanosaetaPelotomucalumMethanogenesisFunctional analysisSyntrophic BiofilmTerephthalate
外文關鍵詞: Metaproteomic, Methanosaeta, Pelotomucalum, Methanogenesis, Functional analysis, Syntrophic Biofilm, Terephthalate
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  • 多源蛋白體學(Metaproteomics, or Proteomic Community Analysis)是研究複雜微生物社群在其環境中實際功能表現一項新穎的生物技術。本研究利用多源蛋白體學方法解析高溫厭氧微生物社群降解石化廢水中重要的苯環化合物成份,對苯二甲酸(Terephthalate, TA)產生甲烷所表現的功能,希望深入瞭解關鍵菌群在此生態系統分解對苯二甲酸並產生甲烷的行為,以作為進一步提升厭氧生物處理程序效能的參考。
    降解對苯二甲酸產生甲烷之高溫(50oC)厭氧微生物社群來實驗室自行架構的反應器,本系統以對苯二甲酸為唯一碳源與能量來源操作551 天後,在有機負荷達3 gTA/L/day 的高負荷,並達對苯二甲酸去除率99%與總有碳去除率95%的表現下,分析萃取自生物膜、顆粒污泥以及水溶液樣本中的蛋白體,樣本經過純化、分離以及消化後,利用高通量質譜儀分析混合胜肽的質量指紋,然後以建立的多源基因體資料庫(TA-degrading biofilm metagenomic database,TDBMD)分別在生物膜、顆粒污泥以及水溶液三種樣本中成功鑑定了921、2142及2224 編碼序列(coding sequence, CDS)所表現之蛋白質;若利用Swiss-prot 的UniprotKB 的公開資料庫,則可分別在生物膜、顆粒污泥以及水溶液三種樣本中鑑定到2736、6020 及6864 個蛋白質身分,以上鑑定結果顯示了本研究採用的方法結合高通量質譜儀應用於微生物社群蛋白體研究的可行性與潛力。
    進一步地將獲得的蛋白質資訊進行分類與統計,並從功能多樣性、微生物生態、生化代謝路徑和反應槽操作等多種角度切入,解析這些蛋白質表現所代表的意義。分析結果顯示就功能多樣性而言,利用TDBMD 可於生物膜、顆粒污泥以及水溶液三種樣本中鑑定711、1600 與1620 種蛋白質功能,而使用UniprotKB 則分別可鑑定2087、4613 與5426 種蛋白質功能,除了數量上的差異,三種樣本中表現蛋白的來源CDS 亦明顯不同。就微生物生態與代謝路徑而言,分析結果顯Pelotomucalum 負責降解苯二甲酸,且以趨化系統PAS domain S-box 感知環境變化而四處移動;Methanosaeta 則利用其代謝產物產生甲烷,傾向固定式的生長。根據基因體與蛋白體分析顯示,除了嗜乙酸甲烷化,Methanosaeta 亦表現嗜氫甲烷化反應的一系列蛋白,這是首次發現Methanosaeta會同時進行嗜乙酸與嗜氫甲烷化的代謝行為。這兩類菌群的蛋白質表現豐富度在三種樣本之中皆分別佔第二(7%~8%)及第一(16~27%),顯示其在生態系統中優勢性與高活性。整合上述之實驗結果,最後嘗試以蛋白質表現的角度說明微生物間的互動與解釋反應槽無預警當機之可能原因。本研究建立之多源蛋白體分析平台成功地解析降解對苯二甲酸產生甲烷之高溫厭氧微生物社群的功能蛋白表現,此方法亦可應用於其他環境之微生物社群研究。

    Metaproteomics (or Proteomic Community Analysis) is an emergingbiotechnology which could be used to study the functional expression of complexmicrobial communities in the environment. In this study, the thermophilic anaerobic microbial communities which degrade aromatic compound in petrochemical wastewater, , terephthalate was analyzed by Metaproteomics platform to reveal the functional expression of microbial populations when terepthalate (TA) was degraded
    into methane. By deeply studying the actual microbial behaviors in this ecosystem, it is anticipated that the results can serve as a reference to further improve the performance of anaerobic biological treatment processes.
    TA degrading communities were sampled from a lab-scale anaerobic bioreactor fed with TA as the sole substrate under thermophilic (50oC) conditions, after operation of 551 days. The TA loading has achieved 3 gTA/L/day and had 99% of TA removal efficiency and 95% of total organic carbon removal efficiency, when total proteins were extracted from the biofilm, granular sludge and solution.
    Protein was extracted, purified, fractionated, digested, and analyzed using nano-liquid chromagraphy equipped with high-throughput mass spectrometer. The mass profiles were identified by TDBMD (TA-degrading biofilm metagenomic database) and totally 921, 2142 and 2224 coding sequences were successfully identified from biofilm, granular sludge and solution, respectively; on the other hand, 2736, 6020 and 6864 coding sequences were successfully identified from UniProtKB. These results showed the power and potential of metaproteomic analysis used in this study.
    The result of protein identification was further analyzed for understanding functional diversity, microbial ecology and biochemical metabolic pathway associated with the bioreactor operation based on the physical meaning of protein expression. For the functional diversity, totally 711, 1600 and 1620 COGs were expressed in biofilm, sludge and solution with TDBMD as the database, while 2087,4613 and 5426 COGs were expressed with UniProtKB as the database. In addition to quantitative differences, the genes encoding for the proteins were also significantly different among three samples.
    For microbial ecology and metabolic pathways, the analytic results showed that Pelotomaculum sp. was the main microorganism responsible for the degradation of TA, and utilized PAS domain S-box to detect the environmental changes for chemotaxis. Methanosaeta can utilize the metabolites of Pelotomaculum to produce methane and tend to grow in biofilm and granular sludge. Based on genomic and proteomic analysis, Methanosaeta operated both hydrogenotrophic and acetotrophic methanogenesis pathways. To our knowledge, this is the first report discovering that Methanosaeta can utilize hydrogen to produce methane. The protein expression of Pelotomaculum and Methanosaeta among the three samples are accounted for the second (7% ~ 8%) and first (16% ~ 27%), respectively, showing the high activity in the syntrophic ecosystem.
    In conclusion, this study has demonstrated he microbial functional analysis by using the metaproteomic analysis and successfully applied to analyze protein expression of TA degrading communities. This method can be also applied to other microbial community studies.

    摘要.......................................................I Abstract ............................................... III 誌謝...................................................... V 目錄 .................................................... VI 圖目錄 ................................................... IX 表目錄 .................................................... X 第一章. 前言 .............................................. 1 1.1. 研究背景 ............................................. 1 1.2. 研究目的 ............................................. 2 1.3. 研究架構 ............................................. 3 第二章. 文獻回顧 ........................................... 5 2.1. 對苯二甲酸之工業應用與廢水特性 ........................... 5 2.2. 對苯二甲酸工業廢水之處理程序介紹 ......................... 6 2.2.1. 各種廢水處理介紹 .................................... 6 2.2.2. 廢水處理之趨勢 ...................................... 7 2.3. 以厭氧微生物程序處理對苯二甲酸廢水 ........................ 8 2.3.1. 處理程序發展簡介 ..................................... 8 2.3.2. 分解機制介紹 ........................................ 8 2.3.3. 微生物社群分析 ..................................... 10 2.3.4. 關鍵微生物分離 ..................................... 11 2.3.5. 中溫及高溫厭氧處理程序之比較 .......................... 11 2.3.6. 分解對苯二甲酸厭氧生物膜之Metagenomic 分析 ............ 12 2.3.7. 檢視基因功能表現之必要 ............................... 13 2.4. 蛋白質體學技術 ....................................... 15 2.4.1. 蛋白質體學之源起 ................................... 15 2.4.2. 質譜儀應用於蛋白質體學 .............................. 16 2.4.3. 質譜儀分析模式 ..................................... 18 2.4.4. 質譜儀類型簡介 ..................................... 19 2.4.5. 蛋白質分離技術 ..................................... 23 2.4.6. 應用蛋白質體學探討環境微生物功能表現 ................... 26 2.4.7. Metaproteomic 之發展與應用..........................27 第三章. 材料與方法 ........................................ 29 3.1. 樣本來源 ............................................ 29 3.1.1. 樣本來源與取出條件 .................................. 29 3.2. 蛋白質萃取與定量 ...................................... 30 3.2.1. 蛋白質萃取 ........................................ 30 3.2.1.1. 生物膜蛋白與污泥蛋白萃取 ........................... 30 3.2.1.2. 水溶性蛋白萃取 ................................... 30 3.2.2. 蛋白質定量 ........................................ 31 3.3. 蛋白質之分離與消化 .................................... 31 3.3.1. 使用SDS-PAGE 進行蛋白質分離 ......................... 32 3.3.1.1. SDS-PAGE ....................................... 32 3.3.1.2. 膠體內蛋白質染色 .................................. 32 3.3.1.3. 膠體內消化 ...................................... 33 3.3.2. 使用HPLC 進行蛋白質分離 ............................. 34 3.3.2.1. 溶液中消化 ...................................... 34 3.3.2.2. HPLC 分離胜肽 ................................... 34 3.4. 胜肽純化 ............................................ 35 3.5. 高通量質譜儀分析 ..................................... 35 3.5.1. 質譜儀分析 ........................................ 35 3.6. 蛋白質鑑定 .......................................... 36 3.6.1. 蛋白質序列之來源 ................................... 36 3.6.2. 蛋白質鑑定 ........................................ 36 3.7. 生物資訊分析 ........................................ 37 3.7.1. 蛋白質身分註解 ..................................... 37 3.7.1.1. 生物來源與E.C.number ............................ 37 3.7.1.2. KO number ..................................... 38 3.7.1.3. COG、Pfam 與TIGRfams ........................... 38 3.7.2. 蛋白質功能分類與分析 ................................ 38 3.7.3. 鑑定結果之初步統計 .................................. 39 3.7.4. 蛋白質來源分析 ..................................... 39 3.7.5. 代謝途徑分析 ....................................... 39 第四章. 結果 ............................................. 40 4.1. 蛋白質之萃取與定量 ................................... 40 4.2. 蛋白質分離 .......................................... 42 4.2.1. SDS-PAGE 分離蛋白質與膠體內消化 ..................... 42 4.2.2. HPLC 分離蛋白質與溶液中消化 ......................... 43 4.3. 比較HPLC 分離法與SDS-PAGE 分離法 ...................... 44 4.4. 質譜儀分析 .......................................... 45 4.5. 蛋白質鑑定與註解 ..................................... 46 4.5.1. 蛋白質鑑定數量 ..................................... 46 4.6. 蛋白質功能分析 ....................................... 48 4.6.1. COG 功能分類結果.................................... 49 4.6.1.1. Information storage and processing ............. 52 4.6.1.2. Cellular processes and signaling ............... 53 4.6.1.3. Metabolism ..................................... 57 4.6.1.4. Poorly characterized ........................... 57 4.6.2. 以COG 分類比較使用不同基因庫分析之結果.................. 58 4.6.3. 以COG 分類結果比較三種樣本之差異....................... 63 4.7. 蛋白質的微生物來源 .................................... 70 4.8. 蛋白質參與之代謝 ...................................... 72 4.8.1. 對苯二甲酸之降解途徑 ................................ 72 4.8.2. 甲烷生成途徑 ....................................... 80 4.8.3. Uncultured OP5 與二氧化碳固定 ...................... 92 第五章. 綜合討論 .......................................... 97 5.1. 綜合討論 ............................................ 97 5.1.1. 蛋白質體技術應用於分析微生物社群 ...................... 97 5.1.2. 高溫厭氧對苯二甲酸降解微生物社群之蛋白質表現 ............ 98 5.1.2.1. Pelotomaculum ................................. 99 5.1.2.2. Methanogens .................................. 108 5.1.2.3. OP5 .......................................... 114 5.1.2.4. 假設蛋白質 ..................................... 116 5.1.3. 高溫厭氧對苯二甲酸降解微生物社群生態 .................. 121 第六章. 結論與建議 ....................................... 123 6.1 結論 ............................................... 123 6.2 建議 ............................................... 124 第七章. 參考文獻 ......................................... 126 自述 ................................................... 131

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