合成生物學為一跨領域工程概念，將系統生物學、基因工程、機械工程、資訊理論、物理學及電腦模擬等等結合於生物科學，達成對環境友善且永續的工程策略以應用於醫、農、食品、化學等不同產業。近年來隨著基因體學、轉錄體學及代謝體學的發展，更多資訊及技術加速合成生物學在生物製造的可行性及機會。
由於石油的濫用與大量石油衍生產品，造成溫室效應與極端氣候，成為最受注重且急迫的環境問題。達成碳中和、淨零碳排、或負碳排是未來化學工程的使命與責任之一。於此，本論文旨在利用合成生物學與代謝工程，於微生物中建立低碳足跡生物合成高價值化學品。
五胺基酮戊酸 (5-aminolevulinic acid, ALA) 為生物體內之必須代謝物，在正常細胞能往下合成血基質 (heme)，而在癌症細胞內則會以原紫質 IX (protoporphyrin IX)累積，能應用於癌症之光動力療法形成超氧活性物質 (ROS) 引發癌細胞凋亡。本文選用具有高血紅素合成能力的非模式菌株希瓦氏菌 (Shewanella oneidensis MR-1)，以C4 及 C5 代謝路徑調控及合成生物學技術增強 ALA 生產。在 C5 途徑中，首先應用 CRISPR 干擾 (CRISPRi) 調升 TCA 循環中的碳通量、降低向血紅素的碳流出，結果在減弱關鍵基因 hemB 的表達後提升2倍5-ALA產量。在C4 途徑中，共表達葡萄糖激酶 GlK 與葡萄糖運輸蛋白 GalP 增強 MR-1 的葡萄糖利用效率。藉由將 T7 RNA 聚合酶、分子伴侶蛋白GroELS及莢膜紅細菌 (Rhodobacter capsulatus) 的ALA合成酶，獲得 M::TRG 菌株產207 mg/L ALA，與原菌相比可有效提高 145 倍的 ALA 產量。
為了建立一高效且低碳足跡之 ALA 合成方法，本文選用大腸桿菌 (Escherichia coli) 表達 1,5-二磷酸核酮糖羧化酶/加氧酶 (RuBisCo) 及磷酸核酮激酶 (Prk)，藉由卡爾循環將二氧化碳 (CO2) 回收作為細胞生長和 ALA 合成的碳源。研究發現分子伴侶蛋白、稀有 tRNA、 ALAS 輔因子磷酸吡哆醛 (PLP) 的提供、整合到基因組等技術都有效提高產量。最後以饋料策略在最佳工程菌株可生產 14.3 g/L ALA。在低碳足跡方面，結合 RuBisCo、Prk、ALAS、pdxY 與 pRARE 五個重要基因元件，成功減少了 53.8% 的CO2排放量且生產 7.8 g/L ALA。將 ALA 應用於抗菌光動力療法 (aPDT)，在三種病原菌的殺菌效率皆可達到 100% 殺菌率。
除了五胺基酮戊酸，乙醇酸 (glycolic acid, GA) 是最小的果酸分子，可應用於醫美產品及經聚合形成可降解之生物塑膠用於藥物釋放，而備受關注。因此，本文首次使用基因工程大腸桿菌並引入低碳足跡的方式生產 GA。以葡萄糖為碳源，微調 TCA 循環和乙醛酸分流 (glyoxylate shunt) 中的基因，GA 產率為 0.21 g/g，生產率為 0.08 g/L/h。為了維持細胞中輔因子 NADPH 的生成及平衡，我們將丙酮丁醇梭菌 (Clostridium acetobutylicum) 的甘油醛 3-磷酸脫氫酶 (gapC) 整合於大腸桿菌基因組中，剔除葡萄糖-6-磷酸-1-脫氫酶 (zwf) 以平衡細胞氧化還原狀態；在增強 CO2利用上，表達磷酸烯醇丙酮酸羧化酶 (ppc) 和丙酮酸羧化酶 (pyc) 引入更多碳流入 TCA 循環，在饋料發酵中成功提升 GA 產量和生產率至 11.9 g/L 和 0.23 g/L/h，同時降低 41% CO2 排放量。GA 可由縮合聚合反應合成聚乙醇酸，由傅里葉轉換紅外光譜 (FTIR) 和差示掃描量熱法 (DSC) 特性分析證明PGA合成成功，且熔點提高到217oC。
本論文闡明 CRISPRi 技術在希瓦氏菌中對 ALA 合成的血紅素合成途徑的調控，提出一種具備 RuBisCo 及高活性 ALAS 的大腸桿菌以達成低碳足跡之 ALA 生產。我們也發現在大腸桿菌中表達羧化酶 (carboxylase) 可有利細胞內使用CO2，獲得低碳排的 GA 生產製程。未來可將已開發的基因菌株應用在更多化學品合成，實現低碳排放且環境友好的高值化學品生產。

Synthetic biology is a multidisciplinary concept of engineering which combines systems biology, genetic and mechanical engineering, physics, and computer science with biological aspect to achieve the ecofriendly and sustainable strategies for pharmaceutical medical, agricultural, foods and chemicals and other industries. In recent years, with the development of genomics, transcriptomics, metabolomics and bioinformation, the advanced biotechnologies have accelerated the feasibility and opportunities of synthetic biology in biomanufacturing. Due to the abuse of petroleum and a great amount of petroleum derivatives, the greenhouse effect and extreme climate change have become the most critical and environmental problems. Chemical engineering is now in the transition state from release carbon to achieve net zero carbon emissions, or negative carbon emissions. This dissertation aims to establish low-carbon-footprint biosynthesis of high-value chemicals in microorganisms using synthetic biology and metabolic engineering.
5-aminolevulinic acid (ALA) is an essential metabolite in living organisms. It can be converted to synthesize heme in normal cells; however, it is converted to protoporphyrin IX and accumulated in cancer cells, and then causes apoptosis with reactive oxygen species in photodynamic therapy for cancer treatment. Herein, a non-model strain Shewanella oneidensis MR-1 with strong heme synthesis ability was selected for ALA production by regulating C4 and C5 metabolic pathways through synthetic biology techniques. In the C5 pathway, CRISPR interference (CRISPRi) was first applied to increase the carbon flux in the TCA cycle and reduced the carbon outflow to heme in MR-1, resulting in a 2-fold increment on 5-ALA production after reducing the expression of the key gene hemB. In the C4 pathway, the co-expression of glucokinase GlK and glucose transporter GalP enhanced the glucose utilization efficiency of MR-1. By combining T7 RNA polymerase, chaperone GroELS and ALA synthase from Rhodobacter capsulatus, the M::TRG strain was constructed and produced 207 mg/L ALA, which was a 145-times increase compared with that of the original strain.
To formulate a high-efficiency and low-carbon-footprint method for ALA synthesis, Escherichia coli was selected to express 1,5-bisphosphate ribulose carboxylase/oxygenase (RuBisCo) and phosphorribulose kinase (Prk) for carbon dioxide (CO2) recycle as a carbon source for cell growth and ALA synthesis via the Calvin cycle. In this section, we observed that techniques such as molecular chaperones, rare tRNAs, provision of the ALAS cofactor pyridoxal phosphate (PLP), and integration into the genome are showed significant improvement on ALA production. Finally, 14.3 g/L ALA was produced in the engineered strain with optimal feeding strategy. In terms of low carbon footprint, the combination of five critical genes RuBisCo, Prk, ALAS, pdxY and pRARE successfully reduced CO2 emissions by 53.8% and 7.8 g/L ALA was produced. Finally, we applied ALA to antimicrobial photodynamic therapy (aPDT), achieving 100 killing-rate on the elimination of three pathogens.
Aside from ALA, glycolic acid (GA) is the simplest molecule of hydroxycarboxylic acids. GA can be used in medical aesthetic products and polymerized to form biodegradable polymerase for drug release, attracting intensive attention in recent years. In this section, a genetically engineered E. coli was constructed to produce GA through a low carbon footprint approach for the first time. By applying glucose as the carbon source and fine-tuning the genes in the TCA cycle and glyoxylate shunt, the GA yield reached 0.21 g/g-glucose with the productivity at 0.08 g/L/h. To improve the production of NADPH and maintain the redox balance in cells, the glyceraldehyde 3-phosphate dehydrogenase (gapC) from Clostridium acetobutylicum was integrated into E. coli genome while the glucose-6-phosphate-1-dehydrogenase (zwf) was deleted. For the enhancement of CO2 utilization, phosphoenolpyruvate carboxylase (ppc) and pyruvate carboxylase (pyc) were expressed to introduce more carbon flux into TCA cycle for GA production, reaching 11.9 g/L and 0.23 g/L/h of titer and productivity in a fed-batch fermentation, as well as to reduce CO2 emissions by 41%. GA was then synthesized into polyglycolic acid through polycondensation, and the successful polymerization was verified by analysis of Fourier Transform Infrared Spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC), showing melting point at 217oC of PGA.
This dissertation elucidated the regulation of the heme synthesis pathway for ALA synthesis by CRISPRi technology in Shewanella and proposed an engineered E. coli with RuBisCo and highly active ALAS for ALA production with a low carbon footprint. We also demonstrated that the expression of carboxylase in E. coli showed benefits to the utilization of CO2, obtaining a low carbon emission process for GA production. In the future, the genetically developed strains can be applied to the synthesis of diverse chemicals, achieving low-carbon emission for sustainable production of high-value chemicals in industries.

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