基因改質酵母菌於整合性生物加工程序上之應用: 利用啤酒酵母菌全細胞催化劑水解半纖維素並生產酒精

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研究生：	Ian Dominic Flormata Tabanag Ian Dominic Flormata Tabanag
論文名稱：	基因改質酵母菌於整合性生物加工程序上之應用: 利用啤酒酵母菌全細胞催化劑水解半纖維素並生產酒精 ENGINEERING YEASTS FOR CONSOLIDATED BIOPROCESSING: BIOETHANOL PRODUCTION FROM HEMICELLULOSE BY SACCHAROMYCES CEREVISIAE WHOLE-CELL BIOCATALYSTS
指導教授：	蔡伸隆 Shen-Long Tsai
口試委員:	李振綱 Cheng-Kang Lee 何明樺 Ming-Hua Ho 蔡伸隆 Shen-Long Tsai 王勝仕 Steven S.S. Wang 沈若樸 Claire Roa-Pu Shen 蘭宜錚 Ethan I. Lan
學位類別：	博士 Doctor
系所名稱：	工程學院 - 化學工程系 Department of Chemical Engineering
論文出版年：	2018
畢業學年度：	106
語文別：	英文
論文頁數：	203
中文關鍵詞：	整合性生物加工程序、生質酒精、酵母菌、表面展示、木質纖維素、半纖維素
外文關鍵詞：	consolidated bioprocessing, bioethanol, yeast surface display, lignocellulosic biomass, hemicellulose
相關次數：	點閱：352 下載：1
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氣候變遷是我們在這個時代面臨的最大的問題之一。由於人口不斷增長，人類活動的增加導致我們大量消耗了不可再生的化石資源，以滿足我們日益增長的消費需求。隨之而來的是大量的溫室氣體釋放到大氣中，導致全球氣候變化，如長時間的乾旱與嚴重的洪水等。這些不好的影響給我們的生態系統帶來了突然的壓力，最終導致我們生物多樣性的喪失。為避免我們對不可再生的化石資源的使用依賴，我們有必要將目前的化石經濟轉變為可持續的生物經濟。以生物為基礎的經濟或生物經濟的核心即是將木質纖維素的生物質（一種不與食物競爭的植物原料）轉化成乙醇，這是一種廣泛使用於製造石化商品的平台化學品。由於木質纖維素複雜的生物化學組成，以其為原料的乙醇發酵是相當具有挑戰性的。由於基因修飾的酵母（例如釀酒酵母）具有可以從各種底物有效地產生大量乙醇的能力，因此被認為是用於此程序最理想的主力微生物。這種既能將木質纖維素生物質降解成可發酵糖，又能將可發酵糖代謝轉化成乙醇的理想微生物是整合性生物加工程序（CBP）策略的最終目標。
本研究的目的主要集中於木質纖維素中半纖維素成分的降解和利用，特別是木聚醣，因為它是半纖維素的主要多醣組分。由於天然釀酒酵母本身不具有在其結構中釋放和消耗木糖的能力，本研究藉由在釀酒酵母中表達異源半纖維素酶，並利用使用混合物實驗設計來描述不同的協同相互作用以確定木聚醣底物水解的最佳製劑，來達成有效的半纖維素降解。此外，透過酵母表面展示技術，本研究亦獲得多株酵母全細胞生物催化劑，藉以改善半纖維素酶混合物的水解活性。為使展示半纖維素酶的全細胞生物催化劑能消耗木糖，本研究亦透過代謝工程表達一最小基因以利木糖能獲得啤酒酵母細胞的使用與代謝。最終，由此研究產生的混合菌叢能夠成功地從兩種不同的木聚醣底物生長並產生乙醇。
本研究亦針對所建構的酵母菌對於木質纖維素底物的水解與生物乙醇生產效能進行與其他酵母表面展示系統之比較數據分析，由結果可以觀察到，在本研究中使用的表面顯示策略與用於從純半纖維素基質生產乙醇的其他表面顯示系統完全相同。此外，本文中的定性評估可作為評估不同酵母表面展示策略對木質纖維素生物質的有效降解、利用和乙醇生產的能力和潛力的重要參考依據。

Climate change is one of the biggest problems we are facing in this era. The increase in human activity due to our ever growing population led us to deplete our non-renewable fossil resources, to satisfy our increased demand of consumer goods derived from them. Along the way, vast amounts of greenhouse gases are released into the atmosphere, inducing a global climate change that cause severe weather changes in the atmosphere (e.g. prolonged droughts, severe flooding). These adverse effects present a sudden pressure to our ecosystems thus leading to an eventual loss of our biodiversity. Because of our incessant use of fossil resources, there is a need for us to shift from our current fossil-based economy into a sustainable bio-based economy. The bio-based economy or bioeconomy is centred on the conversion of lignocellulosic biomass, a plant feedstock that doesn’t compete with food, into ethanol, a widely used platform chemical for manufacturing goods. Ethanol fermentation from this feedstock is quite challenging due to its complex biochemical composition and the ideal workhorse for this formidable process is a microorganism, preferably a modified yeast (e.g. Saccharomyces cerevisiae), which can efficiently yield high amounts of ethanol from a wide range of substrates. This ideal microorganism that can both degrade the lignocellulosic biomass into fermentable sugars, and metabolically convert the fermentable sugars into ethanol is the ultimate goal of the consolidated bioprocessing (CBP) strategy.
The aim of this work is focused on the degradation and utilization of the hemicellulose component (specifically xylan, which serves as a major polysaccharide component of hemicellulose and mainly consists of linked xylose residues) of lignocellulosic biomass since the yeast S. cerevisiae does not inherently possess the ability to both release and consume the xylose sugar in its structure. By expressing heterologous hemicellulases via secretion in S. cerevisiae, efficient hemicellulose degradation was investigated by using a mixture experimental design to describe the different synergistic interactions and to determine optimum formulations for the hydrolysis of xylan substrates. The hydrolytic activities of the hemicellulase mixtures were then improved via the yeast surface display technology to obtain yeast whole-cell biocatalysts. The whole-cell biocatalysts displaying hemicellulases were metabolically engineered to express the minimum genes to utilize xylose to obtain yeast cells that are capable of displaying hemicellulases and consume xylose. The resulting consortium of strains were then able to grow and produce ethanol from two different xylan substrates.
The proficiency of the yeast surface display strategy utilized in this work was then assessed with to other yeast surface display systems with respect to bioethanol production from a range of pure lignocellulose to pre-treated plant-based lignocellulosic substrates via comparative data analysis. It can be observed that the surface display strategy utilized in this work performs at par to other surface display systems utilized for the production of ethanol from pure hemicellulosic substrates. Furthermore, the qualitative assessment presented in this work can serve as a reference material on assessing the capability and potential of the different yeast surface display strategies on the efficient degradation, utilization, and ethanol production from lignocellulosic biomass.

Doctoral Dissertation Advisor Recommendation    ii
Qualification Form by Degree Examination Committee    iii
論文摘要    v
ABSTRACT    vii
Acknowledgement    ix
Table of Contents    xi
Index of Abbreviations    xv
Index of Tables    xvii
Index of Figures    xviii
Chapter 1 Introduction    1
1.1 Background of the Study    4
1.2 Objectives of the Study    6
1.3 Scope and Limitations    7
1.4 General Framework    7
Chapter 2 Review of Related Literature    13
2.1 Climate Change, Sustainability, and the Bio-based Economy    14
2.1.1 On Climate Change    14
2.1.2 The Question of Sustainability    17
2.1.3 The Bio-Based Economy    18
2.2 Lignocellulosic Biomass and Consolidated Bio-Processing    21
2.2.1 Lignocellulosic Biomass: The Key to the Bio-based Economy    21
2.2.1.1 On Biomass Feedstocks    21
2.2.1.2 Lignocellulosic Bioethanol Production    26
2.2.2 The Consolidated Bio-Processing Strategy    30
2.3 Hemicellulose and Its Enzymatic Degradation    34
2.4 On Enzymes and Enzyme Immobilization    36
2.5 From Lignocellulosic Biomass to Bioethanol: The Role of Yeast Surface Display in Consolidated BioProcessing    40
2.5.1 The Advancement of Yeast Surface Display    40
2.5.1.1 A Brief Description of the  Surface Display Technology    40
2.5.1.2 Yeast Surface Display    41
2.5.1.3 Strategies for the Yeast Surface Display of CBP-Related Enzymes    44
2.5.2 Yeast Surface Display Studies for Bioethanol Production from Lignocellulosic Biomass    47
2.5.2.1 Pure Cellulose Substrates    48
2.5.2.2 Pure Hemicellulose Substrates    57
2.5.2.3 Pre-Treated Lignocellulosic Substrates    61
2.5.3 Comparing the Various Yeast Surface Display Strategies for Bioethanol Fermentation from Lignocellulosic Biomass Substrates    66
2.5.3.1 Cellulosic Bioethanol Fermentation    67
2.5.3.2 Hemicelllulosic Bioethanol Fermentation    67
2.5.3.3 Bioethanol Fermentation from Pre-Treated Lignocellulosic Biomass    68
2.5.4 Avenues of Improvement for Bioethanol Production using Yeast Surface Display    74
2.5.4.1 On the Enzyme Functionality and Display Efficiency    75
2.5.4.2 On Substrate Transport    77
2.5.4.3 On Metabolic Engineering for Improved Ethanol Production    79
2.5.4.4 On Process Parameters    80
2.6 Summary    83
Chapter 3 Methodology    85
3.1 The Statistical Design of Experiments    86
3.1.1 Overview    86
3.1.2 The Mixture Experimental Design    89
3.1.2.1 The Canonical Polynomial Model for Mixture Experimental Designs    92
3.1.2.2 Analysis of Mixture Data    93
3.1 Materials and Methods    94
3.1.1 Strains and Media    94
3.1.2 Molecular Biology Techniques    95
3.1.3 Plasmid Construction and Transformation    96
3.1.4 Expression, Secretion, and Concentration of Hemicellulases by S. cerevisiae    98
3.1.5 Protein Characterization    99
3.1.6 Protein Assay    100
3.1.7 Enzyme Activity Assay    100
3.1.8 Mixture Experimental Design Setup    101
3.1.9 Mixed Culture Fermentation Experiments    101
Chapter 4 Results and Discussion    103
4.1 Results    104
4.1.1 Mixture Design Experiments    104
4.1.1.1 Hemicellulase Mixture Optimization for Xylan Hydrolysis    104
4.1.1.2 Hemicellulase Mixture Optimization for Arabinoxylan Hydrolysis    105
4.1.2 Hemicellulose Hydrolysis Experiments by Whole-Cell Biocatalysts Mixtures    110
4.1.3 A Simple Growth Assay for the Simultaneous Xylose Release and Utilization during Xylan Hydrolysis    112
4.1.4 Ethanol Fermentation of Xylan Substrates by Hemicellulase-Displaying, Xylose-Utilizing Yeast Strains    115
4.2 Discussion    117
4.2.1 Mixture Design Experiments    117
4.2.2 Whole-Cell Biocatalysts for the Hydrolysis of Xylan Substrates    118
4.2.3 Growth Assay for the Simultaneous Xylose Release and Utilization during Xylan Hydrolysis    119
4.2.4 Ethanol Fermentation of Xylan Substrates    119
4.2.5 Comparison to Other Xylan-Utilizing Strains/Studies    120
Chapter 5 Conclusions and Recommendations    123
5.1 Conclusions and Generalizations    124
5.2 Recommendations and Future Work    125
References    127
Appendix A    155
Tables    155
Figures    164
Appendix B: Supplementary Material 1    168
Molecular Cloning    168
Hemicellulase Characterization    171
Mixture Design Experiment Modelling Regression Results    173
Mixture Experimental Design    173
Experimental Data for Hydrolysis of Xylan Substrates with Calculated Degree of Synergy Values    174
Xylan Hydrolysis Model Regression Results    177
Arabinoxylan Hydrolysis Model Regression Results    179
Growth of Constructed Yeast Strains on Xylose Minimal Medium    182
Works Cited    183


                                

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