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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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2
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Beck SW, Ye DY, Hwang HG, Jung GY. Stepwise Flux Optimization for Enhanced GABA Production from Acetate in Escherichia coli. J Agric Food Chem 2024. [PMID: 38657224 DOI: 10.1021/acs.jafc.4c01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Strategic allocation of metabolic flux is essential for achieving a higher production performance in genetically engineered organisms. Flux optimization between cell growth and chemical production has led to the establishment of cost-effective chemical production methods in microbial cell factories. This effect is amplified when utilizing a low-cost carbon source. γ-Aminobutyric acid (GABA), crucial in pharmaceuticals and biodegradable polymers, can be efficiently produced from acetate, a cost-effective substrate. However, a balanced distribution of acetate-derived flux is essential for optimizing the production without hindering growth. In this study, we demonstrated GABA production from acetate using Escherichia coli by focusing on optimizing the metabolic flux at isocitrate and α-ketoglutarate nodes. Through a series of flux optimizations, the final strain produced 2.54 g/L GABA from 5.91 g/L acetate in 24 h (0.43 g/g yield). These findings suggest that delicate flux balancing with the application of a cheap substrate can contribute to cost-effective production of GABA.
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Affiliation(s)
- Sun Woo Beck
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam - Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
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3
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Nam SH, Ye DY, Hwang HG, Jung GY. Convergent Synthesis of Two Heterogeneous Fluxes from Glucose and Acetate for High-Yield Citramalate Production. J Agric Food Chem 2024; 72:5797-5804. [PMID: 38465388 DOI: 10.1021/acs.jafc.3c09466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Biological production of citramalate has garnered attention due to its wide application for food additives and pharmaceuticals, although improvement of yield is known to be challenging. When glucose is used as the sole carbon source, carbon loss through decarboxylation steps for providing acetyl-CoA from pyruvate is inevitable. To avoid this, we engineered a strain to co-utilize glucose and cost-effective acetate while preventing carbon loss for enhancing citramalate production. The production pathway diverged to independently supply the precursors required for the synthesis of citramalate from glucose and acetate, respectively. Moreover, the phosphotransferase system was inactivated and the acetate assimilation pathway and the substrate ratio were optimized to enable the simultaneous and efficient utilization of both carbon sources. This yielded results (5.0 g/L, 0.87 mol/mol) surpassing the yield and titer of the control strain utilizing glucose as the sole carbon source in flask cultures, demonstrating an economically efficient strain redesign strategy for synthesizing various products.
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Affiliation(s)
- Sung Hyun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Hwang Y, Hwang HG, Lee JY, Jung GY. Systematic Engineering of Genistein Biosynthetic Pathway through Genetic Regulators and Combinatorial Enzyme Screening. J Agric Food Chem 2024; 72:5842-5848. [PMID: 38441872 DOI: 10.1021/acs.jafc.3c09687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Microbial production of genistein, an isoflavonoid primarily found in soybeans, is gaining prominence in the food industry due to its significant nutritional and health benefits. However, challenges arise in redesigning strains due to intricate regulatory nodes between cell growth and genistein production and in systematically exploring core enzymes involving genistein biosynthesis. To address this, this study devised a strategy that simultaneously and precisely rewires flux at both acetyl-CoA and malonyl-CoA nodes toward genistein synthesis. In particular, naringenin, the primary precursor of genistein, was accumulated 2.6 times more than the unoptimized strain through transcriptional repressor-based genetic regulators. Building upon this, a combination of isoflavone synthase and cytochrome P450 reductase with the remarkable conversion of naringenin to genistein was screened from enzyme homologue libraries. The integrated metabolic engineering strategy yields the highest reported production (98 mg/L of genistein) to date, providing a framework for the biosynthesis of diverse flavonoids, including genistein.
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Affiliation(s)
- Yunhee Hwang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Lee HK, Woo S, Baek D, Min M, Jung GY, Lim HG. Direct and robust citramalate production from brown macroalgae using fast-growing Vibrio sp. dhg. Bioresour Technol 2024; 394:130304. [PMID: 38211713 DOI: 10.1016/j.biortech.2024.130304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
Brown macroalgae is a promising feedstock for biorefinery owing to its high biomass productivity and contents of carbohydrates such as alginate and mannitol. However, the limited availability of microbial platforms efficiently catabolizing the brown macroalgae sugars has restricted its utilization. In this study, the direct production of citramalate, an important industrial compound, was demonstrated from brown macroalgae by utilizing Vibrio sp. dhg, which has a remarkably efficient catabolism of alginate and mannitol. Specifically, citramalate synthase from Methanocaldococcus jannaschii was synthetically expressed, and competing pathways were removed to maximally redirect the carbon flux toward citramalate production. Notably, a resulting strain, VXHC, produced citramalate up to 9.8 g/L from a 20 g/L mixture of alginate and mannitol regardless of their ratios. Citramalate was robustly produced even when diverse brown macroalgae were provided directly. Collectively, this study showcased the high potential of brown macroalgae biorefinery using Vibrio sp. dhg.
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Affiliation(s)
- Hye Kyung Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dongyeop Baek
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myeongwon Min
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
| | - Hyun Gyu Lim
- Department of Biological Engineering, Inha University, 100 Inha-Ro, Michuhol-Gu, Incheon 22212, Korea.
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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Ye DY, Moon JH, Jung GY. Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids. J Agric Food Chem 2023; 71:10916-10931. [PMID: 37458388 DOI: 10.1021/acs.jafc.3c02156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
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8
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. Adv Mater 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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Jeung K, Kim S, Yeon Lee J, Yeol Jung G. Optimization of mevalonate production using acetate by precursor balancing and flux redistribution in Escherichia coli. J IND ENG CHEM 2023. [DOI: 10.1016/j.jiec.2022.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Hwang HG, Milito A, Yang JS, Jang S, Jung GY. Riboswitch-guided chalcone synthase engineering and metabolic flux optimization for enhanced production of flavonoids. Metab Eng 2023; 75:143-152. [PMID: 36549411 DOI: 10.1016/j.ymben.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/05/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Flavonoids are a group of secondary metabolites from plants that have received attention as high value-added pharmacological substances. Recently, a robust and efficient bioprocess using recombinant microbes has emerged as a promising approach to supply flavonoids. In the flavonoid biosynthetic pathway, the rate of chalcone synthesis, the first committed step, is a major bottleneck. However, chalcone synthase (CHS) engineering was difficult because of high-level conservation and the absence of effective screening tools, which are limited to overexpression or homolog-based combinatorial strategies. Furthermore, it is necessary to precisely regulate the metabolic flux for the optimum availability of malonyl-CoA, a substrate of chalcone synthesis. In this study, we engineered CHS and optimized malonyl-CoA availability to establish a platform strain for naringenin production, a key molecular scaffold for various flavonoids. First, we engineered CHS through synthetic riboswitch-based high-throughput screening of rationally designed mutant libraries. Consequently, the catalytic efficiency (kcat/Km) of the optimized CHS enzyme was 62% higher than that of the wild-type enzyme. In addition to CHS engineering, we designed genetic circuits using transcriptional repressors to fine-tune the malonyl-CoA availability. The best mutant with synergistic effects of the engineered CHS and the optimized genetic circuit produced 98.71 mg/L naringenin (12.57 mg naringenin/g glycerol), which is the highest naringenin concentration and yield from glycerol in similar culture conditions reported to date, a 2.5-fold increase compared to the parental strain. Overall, this study provides an effective strategy for efficient production of flavonoids.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, South Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, South Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, South Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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Kim S, Lee HK, Jung GY. Identification Process and Physiological Properties of Transporters of Carboxylic Acids in Escherichia coli. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0305-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Woo S, Moon JH, Sung J, Baek D, Shon YJ, Jung GY. Recent Advances in the Utilization of Brown Macroalgae as Feedstock for Microbial Biorefinery. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0301-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kang CW, Lim HG, Won J, Cha S, Shin G, Yang JS, Sung J, Jung GY. Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production. Nat Commun 2022; 13:6506. [PMID: 36344561 PMCID: PMC9640620 DOI: 10.1038/s41467-022-34190-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
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Affiliation(s)
- Chae Won Kang
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Hyun Gyu Lim
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jaehyuk Won
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Sanghak Cha
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Giyoung Shin
- grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jae-Seong Yang
- grid.423637.70000 0004 1763 5862Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193 Spain
| | - Jaeyoung Sung
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Gyoo Yeol Jung
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea ,grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
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Kim D, Noh MH, Park M, Kim I, Ahn H, Ye DY, Jung GY, Kim S. Enzyme activity engineering based on sequence co-evolution analysis. Metab Eng 2022; 74:49-60. [PMID: 36113751 DOI: 10.1016/j.ymben.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The utility of engineering enzyme activity is expanding with the development of biotechnology. Conventional methods have limited applicability as they require high-throughput screening or three-dimensional structures to direct target residues of activity control. An alternative method uses sequence evolution of natural selection. A repertoire of mutations was selected for fine-tuning enzyme activities to adapt to varying environments during the evolution. Here, we devised a strategy called sequence co-evolutionary analysis to control the efficiency of enzyme reactions (SCANEER), which scans the evolution of protein sequences and direct mutation strategy to improve enzyme activity. We hypothesized that amino acid pairs for various enzyme activity were encoded in the evolutionary history of protein sequences, whereas loss-of-function mutations were avoided since those are depleted during the evolution. SCANEER successfully predicted the enzyme activities of beta-lactamase and aminoglycoside 3'-phosphotransferase. SCANEER was further experimentally validated to control the activities of three different enzymes of great interest in chemical production: cis-aconitate decarboxylase, α-ketoglutaric semialdehyde dehydrogenase, and inositol oxygenase. Activity-enhancing mutations that improve substrate-binding affinity or turnover rate were found at sites distal from known active sites or ligand-binding pockets. We provide SCANEER to control desired enzyme activity through a user-friendly webserver.
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Affiliation(s)
- Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, South Korea
| | - Hyunsoo Ahn
- Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea; Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
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Ye DY, Noh MH, Moon JH, Milito A, Kim M, Lee JW, Yang JS, Jung GY. Kinetic compartmentalization by unnatural reaction for itaconate production. Nat Commun 2022; 13:5353. [PMID: 36097012 PMCID: PMC9468356 DOI: 10.1038/s41467-022-33033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Physical compartmentalization of metabolism using membranous organelles in eukaryotes is helpful for chemical biosynthesis to ensure the availability of substrates from competitive metabolic reactions. Bacterial hosts lack such a membranous system, which is one of the major limitations for efficient metabolic engineering. Here, we employ kinetic compartmentalization with the introduction of an unnatural enzymatic reaction by an engineered enzyme as an alternative strategy to enable substrate availability from competitive reactions through kinetic isolation of metabolic pathways. As a proof of concept, we kinetically isolate the itaconate synthetic pathway from the tricarboxylic acid cycle in Escherichia coli, which is natively separated by mitochondrial membranes in Aspergillus terreus. Specifically, 2-methylcitrate dehydratase is engineered to alternatively catalyze citrate and kinetically secure cis-aconitate for efficient production using a high-throughput screening system. Itaconate production can be significantly improved with kinetic compartmentalization and its strategy has the potential to be widely applicable.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Alfonsina Milito
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea. .,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Kim DH, Hwang HG, Jung GY. Optimum flux rerouting for efficient production of naringenin from acetate in engineered Escherichia coli. Biotechnol Biofuels 2022; 15:90. [PMID: 36056377 PMCID: PMC9440541 DOI: 10.1186/s13068-022-02188-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/20/2022] [Indexed: 11/13/2022]
Abstract
Background Microbial production of naringenin has received much attention owing to its pharmaceutical applicability and potential as a key molecular scaffold for various flavonoids. In the microbial fermentation, a cheap and abundant feedstock is required to achieve an economically feasible bioprocess. From this perspective, utilizing acetate for naringenin production could be an effective strategy, with the advantages of both low-cost and abundant feedstock. For the efficient production of naringenin using acetate, identification of the appropriate regulatory node of carbon flux in the biosynthesis of naringenin from acetate would be important. While acetyl-CoA is a key precursor for naringenin production, carbon flux between the TCA cycle and anaplerosis is effectively regulated at the isocitrate node through glyoxylate shunt in acetate metabolism. Accordingly, appropriate rerouting of TCA cycle intermediates from anaplerosis into naringenin biosynthesis via acetyl-CoA replenishment would be required. Results This study identified the isocitrate and oxaloacetate (OAA) nodes as key regulatory nodes for the naringenin production using acetate. Precise rerouting at the OAA node for enhanced acetyl-CoA was conducted, avoiding extensive loss of OAA by fine-tuning the expression of pckA (encoding phosphoenolpyruvate carboxykinase) with flux redistribution between naringenin biosynthesis and cell growth at the isocitrate node. Consequently, the flux-optimized strain exhibited a significant increase in naringenin production, a 27.2-fold increase (with a 38.3-fold increase of naringenin yield on acetate) over that by the unoptimized strain, producing 97.02 mg/L naringenin with 21.02 mg naringenin/g acetate, which is a competitive result against those in previous studies on conventional substrates, such as glucose. Conclusions Collectively, we demonstrated efficient flux rerouting for maximum naringenin production from acetate in E. coli. This study was the first attempt of naringenin production from acetate and suggested the potential of biosynthesis of various flavonoids derived from naringenin using acetate. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02188-w.
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Abstract
The untranslated region (UTR) of prokaryotic mRNA contains riboswitches, which are gene regulating modules. Riboswitches can be used as biosensors to regulate the expression of a gene or an operon depending on the intracellular level of a target molecule and consequently modulate the cellular responses. In evolutionary engineering, riboswitch-based biosensors have been widely applied for high-throughput screening or selection of target phenotypes. Evolutionary approaches can overcome the limitations of rational approaches in metabolic engineering. Previous studies have reported synthetic riboswitches equipped with novel aptamers and marker genes based on a deep understanding of the operation mechanism of the riboswitch. Here, we introduce the development process of novel synthetic riboswitches for applications in metabolic engineering.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon, Korea
- Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Korea
- Research Center for Bio Materials & Process Development, Incheon National University, Incheon, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.
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Kim S, Jin SH, Lim HG, Lee B, Kim J, Yang J, Seo SW, Lee CS, Jung GY. Synthetic cellular communication-based screening for strains with improved 3-hydroxypropionic acid secretion. Lab Chip 2021; 21:4455-4463. [PMID: 34651155 DOI: 10.1039/d1lc00676b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although cellular secretion is important in industrial biotechnology, its assessment is difficult due to the lack of efficient analytical methods. This study describes a synthetic cellular communication-based microfluidic platform for screening strains with the improved secretion of 3-hydroxypropionic acid (3-HP), an industry-relevant platform chemical. 3-HP-secreting cells were compartmentalized in droplets, with receiving cells equipped with a genetic circuit that converts the 3-HP secretion level into an easily detectable signal. This platform was applied to identify Escherichia coli genes that enhance the secretion of 3-HP. As a result, two genes (setA, encoding a sugar exporter, and yjcO, encoding a Sel1 repeat-containing protein) found by this platform enhance the secretion of 3-HP and its production. Given the increasing design capability for chemical-detecting cells, this platform has considerable potential in identifying efflux pumps for not only 3-HP but also many important chemicals.
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Affiliation(s)
- Seungjin Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
| | - Si Hyung Jin
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
| | - Byungjin Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Jaesung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Seok JY, Han YH, Yang JS, Yang J, Lim HG, Kim SG, Seo SW, Jung GY. Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite. Cell Rep 2021; 36:109589. [PMID: 34433019 DOI: 10.1016/j.celrep.2021.109589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae-Seong Yang
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
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Lee JY, Cha S, Lee JH, Lim HG, Noh MH, Kang CW, Jung GY. Plug-in repressor library for precise regulation of metabolic flux in Escherichia coli. Metab Eng 2021; 67:365-372. [PMID: 34333137 DOI: 10.1016/j.ymben.2021.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
In metabolic engineering, enhanced production of value-added chemicals requires precise flux control between growth-essential competing and production pathways. Although advances in synthetic biology have facilitated the exploitation of a number of genetic elements for precise flux control, their use requires expensive inducers, or more importantly, needs complex and time-consuming processes to design and optimize appropriate regulator components, case-by-case. To overcome this issue, we devised the plug-in repressor libraries for target-specific flux control, in which expression levels of the repressors were diversified using degenerate 5' untranslated region (5' UTR) sequences employing the UTR Library Designer. After we validated a wide expression range of the repressor libraries, they were applied to improve the production of lycopene from glucose and 3-hydroxypropionic acid (3-HP) from acetate in Escherichia coli via precise flux rebalancing to enlarge precursor pools. Consequently, we successfully achieved optimal carbon fluxes around the precursor nodes for efficient production. The most optimized strains were observed to produce 2.59 g/L of 3-HP and 11.66 mg/L of lycopene, which were improved 16.5-fold and 2.82-fold, respectively, compared to those produced by the parental strains. These results indicate that carbon flux rebalancing using the plug-in library is a powerful strategy for efficient production of value-added chemicals in E. coli.
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Affiliation(s)
- Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Ji Hoon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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Gwon DA, Seok JY, Jung GY, Lee JW. Biosensor-Assisted Adaptive Laboratory Evolution for Violacein Production. Int J Mol Sci 2021; 22:ijms22126594. [PMID: 34205463 PMCID: PMC8233975 DOI: 10.3390/ijms22126594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Violacein is a naturally occurring purple pigment, widely used in cosmetics and has potent antibacterial and antiviral properties. Violacein can be produced from tryptophan, consequently sufficient tryptophan biosynthesis is the key to violacein production. However, the complicated biosynthetic pathways and regulatory mechanisms often make the tryptophan overproduction challenging in Escherichia coli. In this study, we used the adaptive laboratory evolution (ALE) strategy to improve violacein production using galactose as a carbon source. During the ALE, a tryptophan-responsive biosensor was employed to provide selection pressure to enrich tryptophan-producing cells. From the biosensor-assisted ALE, we obtained an evolved population of cells capable of effectively catabolizing galactose to tryptophan and subsequently used the population to obtain the best violacein producer. In addition, whole-genome sequencing of the evolved strain identified point mutations beneficial to the overproduction. Overall, we demonstrated that the biosensor-assisted ALE strategy could be used to rapidly and selectively evolve the producers to yield high violacein production.
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Affiliation(s)
- Da-ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea; (D.G.); (G.Y.J.)
| | - Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea;
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea; (D.G.); (G.Y.J.)
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea;
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea; (D.G.); (G.Y.J.)
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea;
- Correspondence:
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Hwang Y, Kim SG, Jang S, Kim J, Jung GY. Signal amplification and optimization of riboswitch-based hybrid inputs by modular and titratable toehold switches. J Biol Eng 2021; 15:11. [PMID: 33741029 PMCID: PMC7977183 DOI: 10.1186/s13036-021-00261-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synthetic biological circuits are widely utilized to control microbial cell functions. Natural and synthetic riboswitches are attractive sensor modules for use in synthetic biology applications. However, tuning the fold-change of riboswitch circuits is challenging because a deep understanding of the riboswitch mechanism and screening of mutant libraries is generally required. Therefore, novel molecular parts and strategies for straightforward tuning of the fold-change of riboswitch circuits are needed. RESULTS In this study, we devised a toehold switch-based modulator approach that combines a hybrid input construct consisting of a riboswitch and transcriptional repressor and de-novo-designed riboregulators named toehold switches. First, the introduction of a pair of toehold switches and triggers as a downstream signal-processing module to the hybrid input for coenzyme B12 resulted in a functional riboswitch circuit. Next, several optimization strategies that focused on balancing the expression levels of the RNA components greatly improved the fold-change from 260- to 887-fold depending on the promoter and host strain. Further characterizations confirmed low leakiness and high orthogonality of five toehold switch pairs, indicating the broad applicability of this strategy to riboswitch tuning. CONCLUSIONS The toehold switch-based modulator substantially improved the fold-change compared to the previous sensors with only the hybrid input construct. The programmable RNA-RNA interactions amenable to in silico design and optimization can facilitate further development of RNA-based genetic modulators for flexible tuning of riboswitch circuitry and synthetic biosensors.
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Affiliation(s)
- Yunhee Hwang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, South Korea
- Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, South Korea
| | - Jongmin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea.
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Cha S, Lim HG, Kwon S, Kim DH, Kang CW, Jung GY. Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals. Metab Eng 2021; 64:146-153. [PMID: 33571657 DOI: 10.1016/j.ymben.2021.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/22/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Carbon monoxide (CO) is a promising carbon source for producing value-added biochemicals via microbial fermentation. However, its microbial conversion has been challenging because of difficulties in genetic engineering of CO-utilizing microorganisms and, more importantly, maintaining CO consumption which is negatively affected by the toxicity of CO and accumulated byproducts. To overcome these issues, we devised mutualistic microbial consortia, co-culturing Eubacterium limosum and genetically engineered Escherichia coli for the production of 3-hydroxypropionic acid (3-HP) and itaconic acid (ITA). During the co-culture, E. limosum assimilated CO and produced acetate, a toxic by-product, while E. coli utilized acetate as a sole carbon source. We found that this mutualistic interaction dramatically stabilized and improved CO consumption of E. limosum compared to monoculture. Consequently, the improved CO consumption allowed successful production of 3-HP and ITA from CO. This study is the first demonstration of value-added biochemical production from CO using a microbial consortium. Moreover, it suggests that synthetic mutualistic microbial consortium can serve as a powerful platform for the valorization of CO.
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Affiliation(s)
- Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Seokmu Kwon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Dong-Hwan Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Noh MH, Lim HG, Moon D, Park S, Jung GY. Auxotrophic Selection Strategy for Improved Production of Coenzyme B 12 in Escherichia coli. iScience 2020; 23:100890. [PMID: 32086013 PMCID: PMC7033360 DOI: 10.1016/j.isci.2020.100890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 02/02/2023] Open
Abstract
The production of coenzyme B12 using well-characterized microorganisms, such as Escherichia coli, has recently attracted considerable attention to meet growing demands of coenzyme B12 in various applications. In the present study, we designed an auxotrophic selection strategy and demonstrated the enhanced production of coenzyme B12 using a previously engineered coenzyme B12-producing E. coli strain. To select a high producer, the coenzyme B12-independent methionine synthase (metE) gene was deleted in E. coli, thus limiting its methionine synthesis to only that via coenzyme B12-dependent synthase (encoded by metH). Following the deletion of metE, significantly enhanced production of the specific coenzyme B12 validated the coenzyme B12-dependent auxotrophic growth. Further precise tuning of the auxotrophic system by varying the expression of metH substantially increased the cell biomass and coenzyme B12 production, suggesting that our strategy could be effectively applied to E. coli and other coenzyme B12-producing strains. The auxotrophic selection strategy was applied to coenzyme B12 production Coenzyme B12-independent methionine synthase was deleted for auxotroph system The auxotrophic strategy could significantly enhance the coenzyme B12 production Optimization of the auxotroph system further enhanced the coenzyme B12 production
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Affiliation(s)
- Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Daeyeong Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-Ro, Ulju-gun, Ulsan, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea.
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26
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Jung HM, Im DK, Lim JH, Jung GY, Oh MK. Metabolic perturbations in mutants of glucose transporters and their applications in metabolite production in Escherichia coli. Microb Cell Fact 2019; 18:170. [PMID: 31601271 PMCID: PMC6786474 DOI: 10.1186/s12934-019-1224-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 09/29/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Most microorganisms have evolved to maximize growth rate, with rapid consumption of carbon sources from the surroundings. However, fast growing phenotypes usually feature secretion of organic compounds. For example, E. coli mainly produced acetate in fast growing condition such as glucose rich and aerobic condition, which is troublesome for metabolic engineering because acetate causes acidification of surroundings, growth inhibition and decline of production yield. The overflow metabolism can be alleviated by reducing glucose uptake rate. RESULTS As glucose transporters or their subunits were knocked out in E. coli, the growth and glucose uptake rates decreased and biomass yield was improved. Alteration of intracellular metabolism caused by the mutations was investigated with transcriptome analysis and 13C metabolic flux analysis (13C MFA). Various transcriptional and metabolic perturbations were identified in the sugar transporter mutants. Transcription of genes related to glycolysis, chemotaxis, and flagella synthesis was downregulated, and that of gluconeogenesis, Krebs cycle, alternative transporters, quorum sensing, and stress induced proteins was upregulated in the sugar transporter mutants. The specific production yields of value-added compounds (enhanced green fluorescent protein, γ-aminobutyrate, lycopene) were improved significantly in the sugar transporter mutants. CONCLUSIONS The elimination of sugar transporter resulted in alteration of global gene expression and redirection of carbon flux distribution, which was purposed to increase energy yield and recycle carbon sources. When the pathways for several valuable compounds were introduced to mutant strains, specific yield of them were highly improved. These results showed that controlling the sugar uptake rate is a good strategy for ameliorating metabolite production.
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Affiliation(s)
- Hwi-Min Jung
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841 South Korea
| | - Dae-Kyun Im
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841 South Korea
| | - Jae Hyung Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841 South Korea
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Wang R, Cress BF, Yang Z, Hordines JC, Zhao S, Jung GY, Wang Z, Koffas MAG. Design and Characterization of Biosensors for the Screening of Modular Assembled Naringenin Biosynthetic Library in Saccharomyces cerevisiae. ACS Synth Biol 2019; 8:2121-2130. [PMID: 31433622 DOI: 10.1021/acssynbio.9b00212] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A common challenge in the assembly and optimization of plant natural product biosynthetic pathways in recombinant hosts is the identification of gene orthologues that will result in best production titers. Here, we describe the modular assembly of a naringenin biosynthetic pathway in Saccharomyces cerevisiae that was facilitated by optimized naringenin-inducible prokaryotic transcription activators used as biosensors. The biosensors were designed and developed in S. cerevisiae by a multiparametric engineering strategy, which further was applied for the in vivo, high-throughput screening of the established yeast library. The workflow for assembling naringenin biosynthetic pathways involved Golden gate-directed combinatorial assembly of genes and promoters, resulting in a strain library ideally covering 972 combinations in S. cerevisiae. For improving the performance of our screening biosensor, a series of fundamental components was optimized, affecting the efficiency of the biosensor such as nuclear localization signal (NLS), the detector module and the effector module. One biosensor (pTDH3_NLS_FdeR-N_tPGK1-pGPM1-fdeO_mcherry_tTDH1-MV2) showed better performance, defined as better dynamic range and sensitivity than others established in this study as well as other previously reported naringenin biosensors. Using this biosensor, we were able to identify a recombinant S. cerevisiae strain as the most efficient candidate for the production of naringenin from the established naringenin biosynthetic library. This approach can be exploited for the optimization of other metabolites derived from the flavonoid biosynthetic pathways and more importantly employed in the characterization of putative flavonoid biosynthetic genes.
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Affiliation(s)
- Rufeng Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica , Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Brady F Cress
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Zheng Yang
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - John C Hordines
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Shujuan Zhao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica , Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Gyoo Yeol Jung
- Department of Chemical Engineering , Pohang University of Science and Technology , Pohang , Gyeongbuk 37673 , Korea
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica , Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
- Department of Biological Sciences , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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28
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Kim SG, Noh MH, Lim HG, Jang S, Jang S, Koffas MAG, Jung GY. Molecular parts and genetic circuits for metabolic engineering of microorganisms. FEMS Microbiol Lett 2019; 365:5059574. [PMID: 30052915 DOI: 10.1093/femsle/fny187] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
Microbial conversion of biomass into value-added biochemicals is a highly sustainable process compared to petroleum-based production. In this regard, microorganisms have been engineered via simple overexpression or deletion of metabolic genes to facilitate the production. However, the producer microorganisms require complex regulatory circuits to maximize productivity and performance. To address this issue, diverse genetic circuits have been developed that allow cells to minimize their metabolic burden, overcome metabolic imbalances and respond to a dynamically changing environment. In this review, we briefly explain the basic strategy for constructing genetic circuits by assembling molecular parts such as input, operation and output modules. Next, we describe recent applications of the circuits in the metabolic engineering of microorganisms to improve biochemical production. Beyond those achievements, genetic circuits will facilitate more innovative approaches to future strain development through mining and engineering new genetic elements and improving the complexity of genetic circuit design.
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Affiliation(s)
- Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Mattheos A G Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy 12180, USA
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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Abstract
Caprolactam is a monomer used for the synthesis of nylon-6, and a recombinant microbial strain for biobased production of nylon-6 was recently developed. An intracellular biosensor for caprolactam can facilitate high-throughput metabolic engineering of recombinant microbial strains. Because of the mixed production of caprolactam and valerolactam in the recombinant strain, a caprolactam biosensor should be highly specific for caprolactam. However, a highly specific caprolactam sensor has not been reported. Here, we developed an artificial riboswitch that specifically responds to caprolactam. This riboswitch was prepared using a coupled in vitro- in vivo selection strategy with a heterogeneous pool of RNA aptamers obtained from in vitro selection to construct a riboswitch library used in in vivo selection. The caprolactam riboswitch successfully discriminated caprolactam from valerolactam. Moreover, the riboswitch was activated by 3.36-fold in the presence of 50 mM caprolactam. This riboswitch enabled caprolactam-dependent control of cell growth, which will be useful for improving caprolactam production and is a valuable tool for metabolic engineering.
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Affiliation(s)
- Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Dae-Kyun Im
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-Ro, Seongbuk-Gu, Seoul 02841, Korea
| | - Taek Jin Kang
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, 30 Pildong-Ro 1-Gil, Jung-Gu, Seoul 04620, Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-Ro, Seongbuk-Gu, Seoul 02841, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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30
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Lim HG, Kwak DH, Park S, Woo S, Yang JS, Kang CW, Kim B, Noh MH, Seo SW, Jung GY. Vibrio sp. dhg as a platform for the biorefinery of brown macroalgae. Nat Commun 2019; 10:2486. [PMID: 31171782 PMCID: PMC6554313 DOI: 10.1038/s41467-019-10371-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Although brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability to metabolize one of the principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate alginate. Based on systematic characterization of the genomic information of Vibrio sp. dhg, we establish a genetic toolbox for its engineering. We also demonstrate its ability to rapidly produce ethanol, 2,3-butanediol, and lycopene from brown macroalgae sugar mixture with high productivities and yields. Collectively, Vibrio sp. dhg can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals.
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Affiliation(s)
- Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Dong Hun Kwak
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sungwoo Park
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Jae-Seong Yang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
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31
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Yang J, Kim B, Kim GY, Jung GY, Seo SW. Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype. Biotechnol Biofuels 2019; 12:113. [PMID: 31086565 PMCID: PMC6506968 DOI: 10.1186/s13068-019-1460-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
With the increased attention on bio-based industry, demands for techniques that enable fast and effective strain improvement have been dramatically increased. Evolutionary engineering, which is less dependent on biological information, has been applied to strain improvement. Currently, synthetic biology has made great innovations in evolutionary engineering, particularly in the development of synthetic tools for phenotypic perturbation. Furthermore, discovering biological parts with regulatory roles and devising novel genetic circuits have promoted high-throughput screening and selection. In this review, we first briefly explain basics of synthetic biology tools for mutagenesis and screening of improved variants, and then describe how these strategies have been improved and applied to phenotypic engineering. Evolutionary engineering using advanced synthetic biology tools will enable further innovation in phenotypic engineering through the development of novel genetic parts and assembly into well-designed logic circuits that perform complex tasks.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
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32
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Jo M, Noh MH, Lim HG, Kang CW, Im DK, Oh MK, Jung GY. Precise tuning of the glyoxylate cycle in Escherichia coli for efficient tyrosine production from acetate. Microb Cell Fact 2019; 18:57. [PMID: 30890173 PMCID: PMC6423740 DOI: 10.1186/s12934-019-1106-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/09/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Acetate is one of promising feedstocks owing to its cheap price and great abundance. Considering that tyrosine production is gradually shifting to microbial production method, its production from acetate can be attempted to further improve the economic feasibility of its production. RESULTS Here, we engineered a previously reported strain, SCK1, for efficient production of tyrosine from acetate. Initially, the acetate uptake and gluconeogenic pathway were amplified to maximize the flux toward tyrosine. As flux distribution between glyoxylate and TCA cycles is critical for efficient precursor supplementation, the activity of the glyoxylate cycle was precisely controlled by expression of isocitrate lyase gene under different-strength promoters. Consequently, the engineered strain with optimal flux distribution produced 0.70 g/L tyrosine with 20% of the theoretical maximum yield which are 1.6-fold and 1.9-fold increased values of the parental strain. CONCLUSIONS Tyrosine production from acetate requires precise tuning of the glyoxylate cycle and we obtained substantial improvements in production titer and yield by synthetic promoters and 5' untranslated regions (UTRs). This is the first demonstration of tyrosine production from acetate. Our strategies would be widely applicable to the production of various chemicals from acetate in future.
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Affiliation(s)
- Minji Jo
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Dae-Kyun Im
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea. .,Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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Song J, Lee M, Kim T, Na J, Jung Y, Jung GY, Kim S, Park N. A RNA producing DNA hydrogel as a platform for a high performance RNA interference system. Nat Commun 2018; 9:4331. [PMID: 30337586 PMCID: PMC6193956 DOI: 10.1038/s41467-018-06864-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
RNA interference (RNAi) is a mechanism in which small interfering RNA (siRNA) silences a target gene. Herein, we describe a DNA hydrogel capable of producing siRNA and interfering with protein expression. This RNAi-exhibiting gel (termed I-gel for interfering gel) consists of a plasmid carrying the gene transcribing siRNA against the target mRNA as part of the gel scaffold. The RNAi efficiency of the I-gel has been confirmed by green fluorescent protein (GFP) expression assay and RNA production quantification. The plasmid stability in the I-gel results in an 8-times higher transcription efficiency than that of the free plasmid. We further applied the I-gel to live cells and confirmed its effect in interfering with the GFP expression. The I-gel shows higher RNAi effect than plasmids in free form or complexed with Lipofectamine. This nanoscale hydrogel, which is able to produce RNA in a cell, provides a platform technology for efficient RNAi system.
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Affiliation(s)
- Jaejung Song
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
| | - Minhyuk Lee
- Department of Chemistry, Myongji University, 116 Myongji Ro, Yongin, 17058, Gyeonggi-do, South Korea
| | - Taeyoung Kim
- Department of Chemistry, Myongji University, 116 Myongji Ro, Yongin, 17058, Gyeonggi-do, South Korea
| | - Jeongkyeong Na
- Department of Chemical Engineering, POSTECH, 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
| | - Yebin Jung
- Department of Chemistry, POSTECH, 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
- Department of Chemical Engineering, POSTECH, 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
| | - Sungjee Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
- Department of Chemistry, POSTECH, 77 Cheongam Ro, Nam Gu, 37673, Pohang, South Korea
| | - Nokyoung Park
- Department of Chemistry, Myongji University, 116 Myongji Ro, Yongin, 17058, Gyeonggi-do, South Korea.
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Park YM, Lim SY, Shin SJ, Kim CH, Jeong SW, Shin SY, Bae NH, Lee SJ, Na J, Jung GY, Lee TJ. A film-based integrated chip for gene amplification and electrochemical detection of pathogens causing foodborne illnesses. Anal Chim Acta 2018; 1027:57-66. [DOI: 10.1016/j.aca.2018.03.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
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35
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Gupta M, Zha J, Zhang X, Jung GY, Linhardt RJ, Koffas MAG. Production of Deuterated Cyanidin 3- O-Glucoside from Recombinant Escherichia coli. ACS Omega 2018; 3:11643-11648. [PMID: 30320269 PMCID: PMC6173498 DOI: 10.1021/acsomega.8b01134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Anthocyanins are plant secondary metabolites that, despite their chemical instability, have found many applications as natural food colorants. They are also known for their beneficial health effects because of their antioxidant and anticancer properties. More stable versions of these molecules, particularly at neutral pH conditions, are required to study the anthocyanin pharmacokinetic properties and obtain effective therapeutic results. In the present report, a cost-effective technique was developed to prepare the deuterated anthocyanin using recombinant Escherichia coli as a production host and deuterated glycerol and D2O in the culture media. This approach resulted in the formation of endogenous deuterated uridine 5'-diphosphate-glucose that was further incorporated by the recombinant anthocyanin pathway, resulting in the formation of deuterated cyanidin 3-O-glucoside (C3G). The deuterium exchange of O-D and C-D were studied by liquid chromatography (LC)-mass spectrometry and NMR analysis. The labeled C3G, purified by high-performance LC showed a stable nature at pH 7.0 as compared to nondeuterated C3G.
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Affiliation(s)
- Mamta Gupta
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic
Institute, Troy, New York 12180, United States
- Department
of Botany and Environment Studies, DAV University, Jalandhar 144 001, Punjab, India
| | - Jian Zha
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic
Institute, Troy, New York 12180, United States
| | - Xing Zhang
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic
Institute, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department of Chemical Engineering and School of Interdisciplinary Bioscience
and Bioengineering, Pohang University of
Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Robert J. Linhardt
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic
Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic
Institute, Troy, New York 12180, United States
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Jang S, Jang S, Noh MH, Lim HG, Jung GY. Novel Hybrid Input Part Using Riboswitch and Transcriptional Repressor for Signal Inverting Amplifier. ACS Synth Biol 2018; 7:2199-2204. [PMID: 30092633 DOI: 10.1021/acssynbio.8b00213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genetic circuits are composed of input, logic, and output parts. Construction of complex circuits for practical applications requires numerous tunable genetic parts. However, the limited diversity and complicated tuning methods used for the input parts hinders the scalability of genetic circuits. Therefore, a new type of input part is required that responds to diverse signals and enables easy tuning. Here, we developed RNA-protein hybrid input parts that combine a riboswitch and orthogonal transcriptional repressors. The hybrid inputs successfully regulated the transcription of an output in response to the input signal detected by the riboswitch and resulted in signal inversion because of the expression of transcriptional repressors. Dose-response parameters including fold-change and half-maximal effective concentration were easily modulated and amplified simply by changing the promoter strength. Furthermore, the hybrid input detected both exogenous and endogenous signals, indicating potential applications in metabolite sensing. This hybrid input part could be highly extensible considering the rich variety of components.
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Affiliation(s)
- Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
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Abstract
CRISPR interference (CRISPRi) is widely utilized for regulation of target gene expression by repressing transcription. Simple design rules for the single guide RNA (sgRNA) and multiplexity won this method immense popularity. However, quantitative control of the expression levels at varying degrees in a dynamic manner using CRISPRi has been regarded difficult. To deal with this limitation, Fontana et al. modulated the expression levels of the components of CRISPRi, the deactivated Cas9 (dCas9), and the sgRNAs, using various constitutive or inducible promoters (Fontana et al., Biotechnol. J. 2018, 13, 1800069). They found that the expression level of sgRNA is the key to controlling CRISPRi. Modulation of sgRNA expression levels enabled quantitative tuning of the CRISPRi-regulated gene expression level. This approach is expected to be easily applied to diverse applications owing to its simplicity compared to the conventional approaches that modified target sequence or changed the expression level of dCas9.
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Affiliation(s)
- Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Korea
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Kang CW, Lim HG, Yang J, Noh MH, Seo SW, Jung GY. Synthetic auxotrophs for stable and tunable maintenance of plasmid copy number. Metab Eng 2018; 48:121-128. [PMID: 29864582 DOI: 10.1016/j.ymben.2018.05.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
Abstract
Although plasmid-based expression systems have advantages in multi-copy expression of genes, heterogeneity of plasmid copy number (PCN) in individual cells is inevitable even with the addition of antibiotics. Here, we developed a synthetic auxotrophic system for stable and tunable maintenance of the PCN in Escherichia coli without addition of antibiotics. This auxotroph expresses infA, one of the essential genes encoding a translation initiation factor, on a plasmid instead of on the chromosome. With this system, the gene expression was stably maintained for 40 generations with minimized cell-to-cell variation under antibiotic-free conditions. Moreover, varying the expression level of infA enabled us to rationally tune the PCN by more than 5.6-fold. This antibiotic-free PCN control system significantly improved the production of itaconic acid and lycopene compared to the conventional system based on antibiotics (2-fold). Collectively, the developed strategy could be a platform for the production of value-added products in antibiotic-free cultivation.
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Affiliation(s)
- Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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Lim HG, Lee JH, Noh MH, Jung GY. Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals. J Agric Food Chem 2018; 66:3998-4006. [PMID: 29637770 DOI: 10.1021/acs.jafc.8b00458] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the great advantages of microbial fermentation is the capacity to convert various carbon compounds into value-added chemicals. In this regard, there have been many efforts to engineer microorganisms to facilitate utilization of abundant carbon sources. Recently, the potential of acetate as a feedstock has been discovered; efforts have been made to produce various biochemicals from acetate based on understanding of its metabolism. In this review, we discuss the potential sources of acetate and summarized the recent progress to improve acetate utilization with microorganisms. Furthermore, we also describe representative studies that engineered microorganisms for the production of biochemicals from acetate.
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Oh YR, Jung KA, Lee HJ, Jung GY, Park JM. A Novel 3,6-anhydro-L-galactose Dehydrogenase Produced by a Newly Isolated Raoultella ornithinolytica B6-JMP12. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0480-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Seok JY, Yang J, Choi SJ, Lim HG, Choi UJ, Kim KJ, Park S, Yoo TH, Jung GY. Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device. Metab Eng 2018; 47:113-120. [PMID: 29545147 DOI: 10.1016/j.ymben.2018.03.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/30/2022]
Abstract
3-Hydroxypropionic acid (3-HP) is an important platform chemical, and biological production of 3-HP from glycerol as a carbon source using glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) has been revealed to be effective because it involves a relatively simple metabolic pathway and exhibits higher yield and productivity than other biosynthetic pathways. Despite the successful attempts of 3-HP production from glycerol, the biological process suffers from problems arising from low activity and inactivation of the two enzymes. To apply the directed evolutionary approach to engineer the 3-HP production system, we constructed a synthetic selection device using a 3-HP-responsive transcription factor and developed a selection approach for screening 3-HP-producing microorganisms. The method was applied to an ALDH library, specifically aldehyde-binding site library of alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). Only two serial cultures resulted in enrichment of strains showing increased 3-HP production, and an isolated KGSADH variant enzyme exhibited a 2.79-fold higher catalytic efficiency toward its aldehyde substrate than the wild-type one. This approach will provide the simple and efficient tool to engineer the pathway enzymes in metabolic engineering.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-Ro 80, Buk-Ku, Daegu 702-701, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-Gil 50, Eonyang-Eup, Ulju-Gun, Ulsan 449419, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 Worldcup-Ro, Yeongtong-Gu, Suwon 16499, Republic of Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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Kim SG, Jang S, Lim JH, Jeon BS, Kim J, Kim KH, Sang BI, Jung GY. Optimization of hexanoic acid production in recombinant Escherichia coli by precise flux rebalancing. Bioresour Technol 2018; 247:1253-1257. [PMID: 29054557 DOI: 10.1016/j.biortech.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/01/2017] [Accepted: 10/05/2017] [Indexed: 05/12/2023]
Abstract
The aim of this study is to demonstrate that rebalancing of metabolic fluxes at acetyl-CoA branch node can substantially improve the titer and productivity of hexanoic acid in recombinant Escherichia coli strains. First, a hexanoic acid-producing E. coli strain was constructed by expressing genes encoding β-ketothiolase (BktB) from Cupriavidus necator and acetyl-CoA transferase (ACT) from Megasphaera sp. MH in a butyric acid producer strain. Next, metabolic flux was optimized at the acetyl-CoA branch node by fine-tuning the expression level of the gene for acetyl-CoA acetyltransferase (AtoB). Four synthetic 5'-untranslated regions were designed for atoB using UTR Designer to modulate the expression level of the gene. Notably, the productivity of the optimized strain (14.7 mg/L/h) was the highest among recombinant E. coli strains in literature when using a similar inoculum size for fermentation. These results show that fine-tuning the expression level of atoB is critical for production of hexanoic acid.
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Affiliation(s)
- Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jae Hyung Lim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Byoung Seung Jeon
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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43
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Noh MH, Lim HG, Woo SH, Song J, Jung GY. Production of itaconic acid from acetate by engineering acid-tolerant Escherichia coli
W. Biotechnol Bioeng 2017; 115:729-738. [DOI: 10.1002/bit.26508] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Myung Hyun Noh
- Department of Chemical Engineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
| | - Sung Hwa Woo
- Department of Chemical Engineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
| | - Jinyi Song
- Department of Chemical Engineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Nam-Gu Pohang Gyeongbuk Korea
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Park YS, Choi UJ, Nam NH, Choi SJ, Nasir A, Lee SG, Kim KJ, Jung GY, Choi S, Shim JY, Park S, Yoo TH. Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD +, for enhancing the production of 3-hydroxypropionic acid. Sci Rep 2017; 7:17155. [PMID: 29214999 PMCID: PMC5719400 DOI: 10.1038/s41598-017-15400-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/25/2017] [Indexed: 11/09/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD+ regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues. The residues in the binding sites for the substrates, 3-HPA and NAD+, were randomized, and the resulting libraries were screened for higher activity. Isolated KGSADH variants had significantly lower Km values for both the substrates. The enzymes also showed higher substrate specificities for aldehyde and NAD+, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain with one of the engineered KGSADH variants exhibited less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that with the wild-type KGSADH. The flask culture of the P. denitrificans strain with the mutant KGSADH resulted in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM).
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Un Jong Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Nguyen Hoai Nam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Sang Jin Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, Pusan, 46241, Korea
| | - Kyung Jin Kim
- School of Life Sciences, Kyungpook National University, Daegu, 41566, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea
| | - Jeung Yeop Shim
- Bio R&D Center, Noroo Holdings Co., Ltd, Suwon, 16229, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, Korea.
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Abstract
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist. Unlike the protein-based trans-regulating controllers, riboswitches can respond to their ligands faster and eliminate off-target effects. Here, we developed artificial riboswitches that activate gene expression in response to naringenin, an important flavonoid. RNA aptamers for naringenin were developed using SELEX and cloned upstream of a dual selectable marker gene to construct a riboswitch library. Two in vivo selection routes were applied separately to the library by supplementing naringenin at two different concentrations during enrichments to modulate the operational ranges of the riboswitches. The selected riboswitches were responsive to naringenin and activated gene expression up to 2.91-fold. Operational ranges of the riboswitches were distinguished on the basis of their selection route. Additionally, the specificity of the riboswitches was assessed, and their applicability as dynamic regulators was confirmed. Collectively, the naringenin riboswitches reported in this work will be valuable tools in metabolic engineering of microorganisms for the production of flavonoids.
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Affiliation(s)
- Sungho Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungyeon Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Yu Xiu
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing 100191, China
| | - Taek Jin Kang
- Department
of Chemical and Biochemical Engineering, Dongguk University, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 04620, Korea
| | - Sang-Hyeup Lee
- Department
of Life Chemistry, Catholic University of Daegu, Hayang-ro 13-13,
Hayang-eup, Gyeongsan, Gyeongbuk 38430, Korea
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institutee, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School
of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
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46
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Jang S, Jang S, Yang J, Seo SW, Jung GY. RNA-based dynamic genetic controllers: development strategies and applications. Curr Opin Biotechnol 2017; 53:1-11. [PMID: 29132120 PMCID: PMC7126020 DOI: 10.1016/j.copbio.2017.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
Unique properties of RNA lead to the development of RNA-based dynamic genetic controllers. Natural riboswitches are re-engineered to detect new molecules. RNA-based regulatory mechanisms are exploited to construct novel dynamic RNA controllers. Computational methods and in vitro–in vivo selection enable de novo design of dynamic RNA controllers. Dynamic RNA controllers are utilized for metabolic engineering and synthetic biology.
Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.
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Affiliation(s)
- Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1, Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1, Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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47
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Jang S, Jung GY. Systematic optimization of L-tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli. Biotechnol Bioeng 2017; 115:266-271. [PMID: 28892124 DOI: 10.1002/bit.26448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/08/2017] [Indexed: 12/31/2022]
Abstract
Riboswitches form a class of genetically encoded sensor-regulators and are considered as promising tools for monitoring various metabolites. Functional parameters of a riboswitch, like dynamic or operational range, should be optimized before the riboswitch is implemented in a specific application for monitoring the target molecule efficiently. However, optimization of a riboswitch was not straightforward and required detailed studies owing to its complex sequence-function relationship. Here, we present three approaches for tuning and optimization of functional parameters of a riboswitch using an artificial L-tryptophan riboswitch as an example. First, the constitutive expression level was adjusted to control the dynamic range of an L-tryptophan riboswitch. The dynamic range increased as the constitutive expression level increased. Then, the function of a riboswitch-encoded protein was utilized to connect the regulatory response of the riboswitch to another outcome for amplifying the dynamic range. Riboswitch-mediated control of the host cell growth enabled the amplification of the riboswitch response. Finally, L-tryptophan aptamers with different dissociation constants were employed to alter the operational range of the riboswitch. The dose-response curve was shifted towards higher L-tryptophan concentrations when an aptamer with higher dissociation constant was employed. All strategies were effective in modifying the distinct functional parameters of the L-tryptophan riboswitch, and they could be easily applied to optimization of other riboswitches owing to their simplicity.
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Affiliation(s)
- Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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Sankaranarayanan M, Somasundar A, Seol E, Chauhan AS, Kwon S, Jung GY, Park S. Production of 3-hydroxypropionic acid by balancing the pathway enzymes using synthetic cassette architecture. J Biotechnol 2017; 259:140-147. [DOI: 10.1016/j.jbiotec.2017.07.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 07/18/2017] [Accepted: 07/23/2017] [Indexed: 10/19/2022]
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Noh MH, Lim HG, Park S, Seo SW, Jung GY. Precise flux redistribution to glyoxylate cycle for 5-aminolevulinic acid production in Escherichia coli. Metab Eng 2017; 43:1-8. [DOI: 10.1016/j.ymben.2017.07.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/01/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
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Sung J, Kim S, Cabatbat JJT, Jang S, Jin YS, Jung GY, Chia N, Kim PJ. Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nat Commun 2017; 8:15393. [PMID: 28585563 PMCID: PMC5467172 DOI: 10.1038/ncomms15393] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
A system-level framework of complex microbe–microbe and host–microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut. The metabolic interactions between gut microbes and host cells play roles in human health. Here, Sung et al. present a literature-curated metabolic network of the human gut microbiota and three human cell types, together with a mathematical approach to identify distinct microbial and metabolic features in gut microbiomes.
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Affiliation(s)
- Jaeyun Sung
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Seunghyeon Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea.,Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.,The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy
| | | | - Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Surgery, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Biomedical Engineering, Mayo College, Rochester, Minnesota 55905, USA
| | - Pan-Jun Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea.,Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.,Department of Physics, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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