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研究生：	方文郁 Effendi, Sefli Sri Wahyu
論文名稱：	用合成生物學重新編程大腸桿菌Nissle打造穩健低碳之生物製造底盤 Reprogramming Escherichia coli Nissle using synthetic biology towards a robust chassis for the low-carbon footprint biomanufacturing
指導教授：	吳意珣 Ng, I-Son
學位類別：	博士 Doctor
系所名稱：	工學院 - 化學工程學系 Department of Chemical Engineering
論文出版年：	2024
畢業學年度：	112
語文別：	英文
論文頁數：	194
外文關鍵詞：	Escherichia coli, Nissle 1917, synthetic biology, recombinant protein, auxiliary modules, T7 RNA polymerase, p-coumaric acid, ferulic acid, carbonic anhydrase, non-native ribulose pathway, low-carbon footprint
相關次數：	點閱：40 下載：3
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The pressing need for climate change mitigation has focused on transitioning from traditional-based chemical manufacturing to sustainable process alternatives. Of bio-based materials, the phenolic group is one of the versatile fine chemicals. It had a remarkable value of $1.92 billion in 2022 due to its importance in the pharmaceutical and nutraceutical industries. However, the natural extraction of such compounds from plants involves chemical processes, endangers the environment, and causes land overexploitation. Recently, microbial cell factories (MCF) have emerged as an outright direction for a sustainable approach. With comprehensive genomic databases and genetic tools, Escherichia coli strains are gaining immense interest as robust chassis, thus expecting to be the next bio-successor for valued chemical synthesis.
p-coumaric acid (pCA) is a critical precursor in the biosynthetic route for varied phenolics. Nevertheless, in vivo production of pCA from carbon feedstock presents low yield and challenges due to the complexity of pathway manipulations and genetic regulatory designs. Regulating highly active tyrosine ammonia lyase from Rhodotorula toluroides (RtTAL) has been proposed to produce pCA from an inexpensive shortcut substrate (i.e., tyrosine) via in vitro whole-cell (WC) biocatalyst in a one-step reaction. Considered the function of pharmaceutical materials, a probiotic workhorse of E. coli Nissle (EcN) was used to produce pCA. EcN was engineered by fine-tuning the genetic design of T7 regulation, thus successfully converting tyrosine into pCA and degrading tyrosine excess in the simulated gut environment. As the versatile precursor, pCA was further utilized for producing ferulic acid (FA), a potent antioxidant agent. Due to the complex heterologous pathway, the FA pathway was dissociated into upstream and downstream modules for pCA transformation and FA synthesis, respectively. Unexpectedly, engineered EcN yielded poor FA titer due to trade-off phenomena between biomass and metabolites. In FA production, E. coli C43 strain accumulated a higher FA titer of 972.6 mg/L due to its capability to attenuate T7 orthogonality using a stepwise culture.
The spent coffee ground (SCG) was used as a starting material for producing pCA using solid-liquid extraction to repress the production cost of FA synthesis. The crude pCA was converted to FA using C43 strain in a one-pot reaction at the optimum conditions, thus acquiring 2.07 mM FA and 66.8% yield within 9 h. Due to possessing radical scavenging activities, FA extract was utilized as a booster for the growth of Cyanobacterium aponinum and its C-phycocyanin content, thus promoting the circular economy. Moreover, by using Life Cycle Assessment (LCA), FA biosynthesis from either tyrosine or pCA from SCG extract has the lowest environmental impact and greenhouse gas emissions when compared to a conventional chemical process.
Due to its acidophilic nature, the potential of EcN was further harnessed to port the CO2-fixing pathway, expecting to circumvent the deleterious CO2 emission during chemical biosynthesis. To reinforce heterotrophic CO2 fixation, intracellular CO2 availability was increased by engaging carbonic anhydrase from human II (hCAII) which was designated under dual promoters from E. coli sigma70 and heat shock protein, aiming to eliminate the inducer usage and stimulate hCAII activity under heat environments, respectively. EcN expressing solely optimized hCAII or lysine decarboxylase (CadA) acquired the highest precipitated CaCO3 of 70 mg or cadaverine titer of 22.99 g/L, respectively. Co-expression of hCAII with CadA in EcN simultaneously sequestered CO2 release up to 79.4% and recycled into biomass instead of cadaverine. On the other hand, reconstructing artificial CO2-fixing bypasses from autotrophs via ribose-1,5-bisphosphate (R15P) or ribulose-5-phosphate (Ru5P) successfully reinforces CO2 fixation in EcN. The functional application was conducted for simultaneous CO2 recycling during 5-aminolevulinic acid (5-ALA) production. Through pathway manipulation from xylose, the recycled flux toward the CO2-fixing pathway was strengthened, thus accumulating the highest biomass and 5-ALA titer via R15P and Ru5P routes, respectively.
In conclusion, major works in this study attempted to harness EcN as a promising chemical producer with low environmental impact in FA production and an efficient low-carbon footprint chassis in cadaverine and 5-ALA production. However, EcN still needs sophisticated engineering for certain metabolic regulations and chemicals.

Disclaimer on Author Copyright 	i
Abstract	ii
Acknowledgment	iv
Table of contents	v
List of figures	x
List of tables	xiv
Abbreviations	xvi
Chapter 1 Introduction	1
1	Preface and research motivation	1
2 Research scope and framework of dissertation	3
Chapter 2 Literature review	7
1 Escherichia coli as a versatile microbial cell factory	7
1.1 A treasure trove and current status	7
1.2 The distinctive of probiotic E. coli Nissle 1917 (EcN)	8
2 System metabolic engineering in cell factory	11
2.1 System biology	11
2.2 Synthetic biology	13
2.3 Evolutionary engineering and directed evolution	16
3 Peculiarities of metabolic pathways in E. coli	18
3.1 Native existing pathways	18
3.2 Non-native existing pathway	20
3.3 Selection of target products	22
4 Process operation of engineered E. coli	24
4.1 Batch fermentation	25
4.2 In vitro biosynthesis	25
4.2 Microbial consortia system	27
5 Low-carbon footprint platforms in the chemical biosynthesis chain	29
5.1 Carboxylation system	29
5.2 Artificial CO2-fixing utilization	30
Chapter 3 Materials and methods	32
1 Chemicals and materials	32
2 Experimental instruments	34
3 Experimental procedures	36
3.1 Genetic engineering strain and cultivation	36
3.1.1 Plasmid DNA extraction	36
3.1.2 Polymerase Chain Reaction (PCR)	36
3.1.3 Gel extraction and purification	37
3.1.4 Enzyme digestion	38
3.1.5 DNA ligation	38
3.1.6 Gene integration into the chromosome and resistance removal	38
3.1.7 Chemical competent cell preparation	39
3.1.8 Transformation of plasmid by heat shock in E. coli	39
3.1.9 Cell culture and induction	39
3.2 Protein analysis	40
3.2.1 Cell disruption	40
3.2.2 Protein quantification using the Bradford method	40
3.2.3 Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE)	40
3.3 Characterization techniques	41
3.3.1 Determination of plasmid copy number (PCN)	41
3.3.2 Examination of mRNA expression levels using qRT-PCR	42
3.3.3 High-Performance Liquid Chromatography (HPLC) analysis	42
Chapter 4 Robust whole-cell biocatalyst of engineered tyrosine ammonia lyase in Escherichia coli for p-Coumaric acid biotransformation	43
1 Background	43
2 Materials and methods	44
2.1 DNA synthesis and construction of TALs plasmid in E. coli	44
2.2 Characterization of TAL for pCA production via in vivo and in vitro	45
2.3 Enzyme purification and kinetic analysis	46
2.4 Reusability of whole-cell	46
3 Results and discussions	47
3.1 Gene selection and characterization via in vivo and in vitro assay	47
3.2 Effect of protein partners and cultural temperature on RtTAL activity	49
3.3 Effect of fusion partner TrxA-tag	51
3.4 Purification and kinetic parameters of RtTAL	52
3.5 Reusability of whole-cell biocatalysts	53
4 Conclusion	55
Chapter 5 Reprogramming T7RNA polymerase in Escherichia coli Nissle 1917 under specific lac operon for efficient p-Coumaric Acid production	56
1 Background	56
2 Materials and methods	57
2.1 Plasmid construction	57
2.2 X-gal plate for β-galactosidase detection	58
2.3 Fluorescence intensity measurement	59
2.4 Acid resistance assay	59
2.5 In vitro simulated gastric assay	59
3 Results and discussions	60
3.1 New insight into lac operon of EcN and its derivatives	60
3.2 Genetic behavior of T7RNAP integrated at Lambda and HK022 sites	62
3.3 Heterologous expression of RtTAL in ET7 chassis	64
3.4 Optimization of enzymatic activity with GroELS and medium condition	67
3.5 Chassis durability in acid conditions and simulated gut fluids (SGF) system	70
4 Conclusion	72
Chapter 6 High value ferulic acid biosynthesis using modular design in engineered Escherichia coli chassis	73
1 Background	73
2 Materials and methods	74
2.1 DNA synthesis and construction of expression plasmids	74
2.2 One-pot and stepwise synthesis of ferulic acid from tyrosine	74
2.3 Determination of intracellular ATP level	75
3 Results and discussions	75
3.1 Optimization of pCA synthetic pathway	75
3.2 Modular design of FA synthetic pathway	77
3.3 Efficiency of cofactors supply via in vitro and in vivo	79
3.4 Enzymatic cascade reaction for FA biosynthesis in a one-pot system	80
3.5 Enhanced FA production via stepwise culture	82
4 Conclusion	84
Chapter 7 Sustainable and one-pot bioconversion of spent coffee grounds to ferulic acid for Cyanobacterium aponinum cultivation enhancement	85
1 Background	85
2 Materials and methods	86
2.1 Materials preparation	86
2.2 Kinetic modeling of solid-liquid extraction	86
2.3 One-pot bioconversion of FA from SCG extracts	87
2.4 Analytical assay of pCA and FA production	88
2.5 Antioxidant assays	88
2.6 Purification of FA	89
2.7 FA utilization for Cyanobacteria aponinum culture	90
2.8 Life cycle assessment (LCA) of FA production	90
3 Results and discussions	90
3.1 Validation of extraction kinetic model	90
3.2 Growth kinetics and FA production in semi–in–vivo biosynthesis	92
3.3 Optimization of one-pot FA biosynthesis via in vitro	94
3.4 Antioxidant activity of pCA and FA	96
3.5 Purification of FA using ion-exchang resin	97
3.6 Functional utilization of FA in Cyanobacteria culture and Life Cycle Assessment	98
4 Conclusion	101
Chapter 8 Simultaneous carbon dioxide sequestration and utilization for cadaverine production using dual promoters in engineered Escherichia coli strains	102
1 Background	102
2 Materials and methods	103
2.1 Preparation and construction of expression plasmids in E. coli	103
2.2 Cultivation condition	104
2.3 CO2 hydration activity and biomineralization analysis	105
2.4 Quantification of biomass, carbon content, and CO2 release	105
3 Results and discussions	106
3.1 Efficiency of the single and dual promoters for sfGFP	106
3.2 Proof-of-function by expression of hCAII in different E. coli strains	108
3.3 Concurrent CO2 utilization and cadaverine production	111
3.4 CO2 sequestration of recombinant E. coli strains	113
4 Conclusion	115
Chapter 9 Non-native pathway engineering CO2 assimilation in Escherichia coli Nissle for 5-ALA synthesis	116
1 Background	116
2 Materials and methods	117
2.1 Plasmid construction	117
2.2 Culture conditions	119
2.3 Calculation of the CO2 assimilation capability by element analysis	119
2.4 Analysis of 5-ALA production	119
3 Results and discussions	120
3.1 Genetic design of artificial CO2-assimilating pathways via ribulose route	120
3.2 Comparative efficiency of CO2-fixing strains for 5-ALA production	122
3.3 Fine-tuning carbon flux using CRISPRi	124
4 Conclusion	127
Chapter 10 Concluding remarks and perspectives	128
References	131
Appendix	160
Achievements	172
                                    

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