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論文名稱(外文):Optimal design of 2S-naringenin and p-coumaryl alcohol products in E. coli
外文關鍵詞:iAF1260 model2S-naringeninp-coumaryl alcoholGene regulation
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目前已知的植物天然產物(plant nature products)超過二十萬種,其中有些具有藥理活性或重要的生物特性。本研究主要探討兩種植物天然產物:柚皮素(2S-naringenin)和香豆醇(p-coumaryl alcohol)。柚皮素屬於黃酮類化合物,具有抗炎、抗菌、抗癌作用;香豆醇為木質素主要前驅物之一,也常被應用在工業合成上。此研究利用模擬代謝工程,找尋最適化設計使目標產物達最大化。分別建立了兩個csae,第一個case利用大腸桿菌iAF1260模型,加入生產柚皮素的類黃酮代謝途徑(Flavanone pathway)和相關基因(TAL、4CL、CHS、CHI);第二個case利用大腸桿菌iAF1260模型,加入生產香豆醇植物的苯丙烷代謝途徑(Phenylpropanoid pathway)和相關基因(TAL、4CL、CCR、CAD)。透過重建網路模型可得到突變後大腸桿菌模型,再利用通量均衡分析方法(Flux balance analysis, FBA)的計算,和使用巢狀式混合差值演化(Nested Hybrid Differential Evolution ; NHDE)與通量封包(Flux envelope)作分析,可得知生產柚皮素所需要氧氣通量為20 mmol gDW-1h-1,且當上調控基因TAL為0.6,可得到最大柚皮素產量;生產香豆醇所需要氧氣通量為15 mmol gDW-1h-1,且當上調控基因TAL為0.6,可得到最大香豆醇產量。
Currently, there are more than two hundred thousand kinds of known plant natural products, some of which have pharmacological activity or important biological properties. This study focused on two plant natural products: 2S-naringenin and p-coumaryl alcohol. 2S-naringenin belongs to flavonoids and it has anti-inflammatory, anti-bacterial and anti-cancer effect; p-coumaryl alcohol is one of precursors of lignin and it is also used in the industrial synthesis applications. The methods of microbial production are becoming more important. Microbial metabolic engineering means by modifying metabolic pathways to make microorganisms demonstrate desired characteristics. Two cases were built, the case 1 used iAF1260 model of E. coli, then added the flavonoid metabolic pathway about 2S-naringenin and related genes (TAL, 4CL, CHS, CHI) ; the case 2 also used iAF1260 model of E. coli, then added phenylpropanoid metabolic pathway about p-coumaryl alcohol and related genes (TAL, 4CL, CCR, CAD). Genes and other information from the previous literature were reconstructed in iAF1260 model. And then calculated flux balance by the analysis method (Flux balance analysis, FBA) and used Nested Hybrid Differential Evolution(NHDE) and Flux envelope. The result of the first case, 2S-naringenin produced need oxygen flux of 20 mmol gDW-1h-1 and when the regulation of gene TAL was 0.6, to obtain the maximum yield; the second case, p-coumaryl alcohol produced need oxygen flux of 15 mmol gDW-1h-1 and when the regulation of gene TAL was 0.6, to obtain the maximum yield.
致謝 I
摘要 II
Abstract III
目錄 V
表目錄 VIII
圖目錄 IX
第一章 緒論 1
1.1 前言 1
1.2 文獻回顧 5
1.3 研究動機 7
1.4 組織章節 8
第二章 生物資料庫及工具程式簡介 9
1.2 生物資料庫簡介 9
2.1.1 Biochemically , Genomically and Genetically(BIGG) 9
2.1.2 Kyoto Encyclopedia of Genes and Genomes(KEGG) 10
2.1.3 BRaunschweig Enzyme DAtabase (BRENDA) 11
2.2 工具程式簡介 14
2.2.1 Model Transformation Program(MTP) 14
2.2.2 General Algebraic Modeling System(GAMS) 15
第三章 代謝網路模型與分析方法 18
3.1 前言 18
3.2代謝網路模型 19
3.2.1 iAF1260代謝模型 19
3.2.2 加入異源代謝途徑重建iAF1260模型 19
3.3 基本設定與計算方法介紹 25
3.3.1 最佳化目標函數 25
3.3.2 計算方法介紹 26
第四章 結果與討論 41
4.1 氧氣攝取量影響 41
4.2 調控重組基因影響 44
4.3 酵素調控強度與目標函數影響 48
第五章 結論與未來研究方向 52
5.1 結論 52
5.2未來研究方向 53
第六章 參考文獻 54
附錄A 57

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