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Yang X, Wang H, Ding D, Fang H, Dong H, Zhang D. A hybrid RNA-protein biosensor for high-throughput screening of adenosylcobalamin biosynthesis. Synth Syst Biotechnol 2024; 9:513-521. [PMID: 38680948 PMCID: PMC11047186 DOI: 10.1016/j.synbio.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024] Open
Abstract
Genetically encoded circuits have been successfully utilized to assess and characterize target variants with desirable traits from large mutant libraries. Adenosylcobalamin is an essential coenzyme that is required in many intracellular physiological reactions and is widely used in the pharmaceutical and food industries. High-throughput screening techniques capable of detecting adenosylcobalamin productivity and selecting superior adenosylcobalamin biosynthesis strains are critical for the creation of an effective microbial cell factory for the production of adenosylcobalamin at an industrial level. In this study, we developed an RNA-protein hybrid biosensor whose input part was an endogenous RNA riboswitch to specifically respond to adenosylcobalamin, the inverter part was an orthogonal transcriptional repressor to obtain signal inversion, and the output part was a fluorescent protein to be easily detected. The hybrid biosensor could specifically and positively correlate adenosylcobalamin concentrations to green fluorescent protein expression levels in vivo. This study also improved the operating concentration and dynamic range of the hybrid biosensor by systematic optimization. An individual cell harboring the hybrid biosensor presented over 20-fold higher fluorescence intensity than the negative control. Then, using such a biosensor combined with fluorescence-activated cell sorting, we established a high-throughput screening platform for screening adenosylcobalamin overproducers. This study demonstrates that this platform has significant potential to quickly isolate high-productive strains to meet industrial demand and that the framework is acceptable for various metabolites.
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Affiliation(s)
- Xia Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongqin Ding
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Moon JH, Nam S, Jeung K, Noh MH, Jung GY. Biosensor-Assisted Engineering for Diverse Microbial Cellular Physiologies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39107094 DOI: 10.1021/acs.jafc.4c04619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Recent advancements in biosensor technology have revolutionized the field of microbial engineering, enabling efficient and precise optimization of strains for the production of valuable chemicals. This review comprehensively explores the innovative integration of biosensors to enhance microbial cell factories, with a particular emphasis on the crucial role of high-throughput biosensor-assisted screening. Biosensor-assisted approaches have enabled the identification of novel transporters, the elucidation of underlying transport mechanisms, and the fine-tuning of metabolic pathways for enhanced production. Furthermore, this review illustrates the utilization of biosensors for manipulating cellular behaviors, including interactions with environmental factors, and the reduction of nongenetic cell-to-cell variations. This review highlights the indispensable role of biosensors in advancing the field of microbial engineering through the modulation and exploitation of diverse cellular physiological processes.
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Affiliation(s)
- Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sunghyun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Kumyoung Jeung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Myung Hyun Noh
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan 44429, 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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3
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d'Oelsnitz S, Love JD, Ellington AD, Ross D. Ligify: Automated Genome Mining for Ligand-Inducible Transcription Factors. ACS Synth Biol 2024. [PMID: 39029917 DOI: 10.1021/acssynbio.4c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
Prokaryotic transcription factors can be repurposed into biosensors for the ligand-inducible control of gene expression, but the landscape of chemical ligands for which biosensors exist is extremely limited. To expand this landscape, we developed Ligify, a web application that leverages information in enzyme reaction databases to predict transcription factors that may be responsive to user-defined chemicals. Candidate transcription factors are then incorporated into automatically generated plasmid sequences that are designed to express GFP in response to the target chemical. Our benchmarking analyses demonstrated that Ligify correctly predicted 31/100 previously validated biosensors and highlighted strategies for further improvement. We then used Ligify to build a panel of genetic circuits that could induce a 47-fold, 5-fold, 9-fold, and 27-fold change in fluorescence in response to D-ribose, L-sorbose, isoeugenol, and 4-vinylphenol, respectively. Ligify should enhance the ability of researchers to quickly develop biosensors for an expanded range of chemicals and is publicly available at https://ligify.groov.bio.
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Affiliation(s)
- Simon d'Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Joshua D Love
- Independent Web Developer, Bentonville, Arkansas 72712, United States
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, Maryland 20878, United States
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4
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d'Oelsnitz S, Diaz DJ, Kim W, Acosta DJ, Dangerfield TL, Schechter MW, Minus MB, Howard JR, Do H, Loy JM, Alper HS, Zhang YJ, Ellington AD. Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nat Commun 2024; 15:2084. [PMID: 38453941 PMCID: PMC10920890 DOI: 10.1038/s41467-024-46356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
A major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer's medication galantamine, are complex plant secondary metabolites with recognized therapeutic value. Due to their difficult synthesis they are regularly sourced by extraction and purification from the low-yielding daffodil Narcissus pseudonarcissus. Here, we propose an efficient biosensor-machine learning technology stack for biocatalyst development, which we apply to engineer an Amaryllidaceae enzyme in Escherichia coli. Directed evolution is used to develop a highly sensitive (EC50 = 20 μM) and specific biosensor for the key Amaryllidaceae alkaloid branchpoint 4'-O-methylnorbelladine. A structure-based residual neural network (MutComputeX) is subsequently developed and used to generate activity-enriched variants of a plant methyltransferase, which are rapidly screened with the biosensor. Functional enzyme variants are identified that yield a 60% improvement in product titer, 2-fold higher catalytic activity, and 3-fold lower off-product regioisomer formation. A solved crystal structure elucidates the mechanism behind key beneficial mutations.
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Affiliation(s)
- Simon d'Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Synthetic Biology HIVE, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel J Diaz
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Foundations of Machine Learning, University of Texas at Austin, Austin, TX, 78712, USA
| | - Wantae Kim
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel J Acosta
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Mason W Schechter
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew B Minus
- Department of Chemistry, Prairie View A&M University, 100 University Dr, Prairie View, TX, 77446, USA
| | - James R Howard
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hannah Do
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - James M Loy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
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Zhou Y, Zhou S, Lyons S, Sun H, Sweedler JV, Lu Y. Enhancing 2-Pyrone Synthase Efficiency by High-Throughput Mass-Spectrometric Quantification and In Vitro/In Vivo Catalytic Performance Correlation. Chembiochem 2024; 25:e202300849. [PMID: 38116888 DOI: 10.1002/cbic.202300849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Engineering efficient biocatalysts is essential for metabolic engineering to produce valuable bioproducts from renewable resources. However, due to the complexity of cellular metabolic networks, it is challenging to translate success in vitro into high performance in cells. To meet such a challenge, an accurate and efficient quantification method is necessary to screen a large set of mutants from complex cell culture and a careful correlation between the catalysis parameters in vitro and performance in cells is required. In this study, we employed a mass-spectrometry based high-throughput quantitative method to screen new mutants of 2-pyrone synthase (2PS) for triacetic acid lactone (TAL) biosynthesis through directed evolution in E. coli. From the process, we discovered two mutants with the highest improvement (46 fold) in titer and the fastest kcat (44 fold) over the wild type 2PS, respectively, among those reported in the literature. A careful examination of the correlation between intracellular substrate concentration, Michaelis-Menten parameters and TAL titer for these two mutants reveals that a fast reaction rate under limiting intracellular substrate concentrations is important for in-cell biocatalysis. Such properties can be tuned by protein engineering and synthetic biology to adopt these engineered proteins for the maximum activities in different intracellular environments.
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Affiliation(s)
- Yu Zhou
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX 78712, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
| | - Shuaizhen Zhou
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
| | - Scott Lyons
- Department of Molecular Bioscience, The University of Texas at Austin, 100 E 24th St, Austin, TX 78712, USA
| | - Haoran Sun
- Department of Molecular Bioscience, The University of Texas at Austin, 100 E 24th St, Austin, TX 78712, USA
| | - Jonathan V Sweedler
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX 78712, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
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6
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Du H, Liang Y, Li J, Yuan X, Tao F, Dong C, Shen Z, Sui G, Wang P. Directed Evolution of 4-Hydroxyphenylpyruvate Biosensors Based on a Dual Selection System. Int J Mol Sci 2024; 25:1533. [PMID: 38338812 PMCID: PMC10855707 DOI: 10.3390/ijms25031533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To screen for PobR mutants responsive to 4-hydroxyphenylpyruvate(HPP), we developed a dual selection system in E. coli. The positive selection of this system was used to enrich PobR mutants that identified the required ligands. The following negative selection eliminated or weakened PobR mutants that still responded to 4HB. Directed evolution of the PobR library resulted in a variant where PobRW177R was 5.1 times more reactive to 4-hydroxyphenylpyruvate than PobRWT. Overall, we developed an efficient dual selection system for directed evolution of biosensors.
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Affiliation(s)
- Hongxuan Du
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaoyao Liang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianing Li
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Xinyao Yuan
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Fenglin Tao
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Chengjie Dong
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Zekai Shen
- School of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
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Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023; 14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.
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Affiliation(s)
- Chenggang Xi
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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8
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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] [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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9
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Matsuoka Y, Fujie N, Nakano M, Koshiba A, Kondo A, Tanaka T. Triacetic acid lactone production using 2-pyrone synthase expressing Yarrowia lipolytica via targeted gene deletion. J Biosci Bioeng 2023; 136:320-326. [PMID: 37574415 DOI: 10.1016/j.jbiosc.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
An environmentally sustainable world can be realized by using microorganisms to produce value-added materials from renewable biomass. Triacetic acid lactone (TAL) is a high-value-added compound that is used as a precursor of various organic compounds such as food additives and pharmaceuticals. In this study, we used metabolic engineering to produce TAL from glucose using an oleaginous yeast Yarrowia lipolytica. We first introduced TAL-producing gene 2-pyrone synthase into Y. lipolytica, which enabled TAL production. Next, we increased TAL production by engineering acetyl-CoA and malonyl-CoA biosynthesis pathways by redirecting carbon flux to glycolysis. Finally, we optimized the carbon and nitrogen ratios in the medium, culminating in the production of 4078 mg/L TAL. The strategy presented in this study had the potential to improve the titer and yield of polyketide biosynthesis.
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Affiliation(s)
- Yuta Matsuoka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Naofumi Fujie
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Mariko Nakano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ayumi Koshiba
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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10
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Bhat S, Banerjee A, Alagesan S. AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS OMEGA 2023; 8:26806-26815. [PMID: 37546622 PMCID: PMC10399174 DOI: 10.1021/acsomega.3c01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Isoprene is a valuable platform chemical, which is produced by engineered microorganisms, albeit in low quantities. The amount of isoprene produced is usually measured by gas chromatography, which can be time-consuming and expensive. Alternatively, biosensors have evolved as a powerful tool for real-time high-throughput screening and monitoring of product synthesis. The AraC-pBAD-inducible system has been widely studied, evolved, and engineered to develop biosensors for small molecules. In our preliminary studies, the AraC-pBAD system was mildly induced at higher isoprene concentrations when arabinose was also available. Hence, in the present study, we designed and constructed a synthetic biosensor based on the AraC-pBAD system, wherein the ligand-binding domain of AraC was replaced with IsoA. On introducing this chimeric AraC-IsoA (AcIa) transcription factor with the native PBAD promoter system regulating rfp gene expression, fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were further enhanced by removing operator sequences and by substituting the native promoter (PAraC) with the strong tac promoter (Ptac). The chimeric sensor did not work in AraC knockout strains; however, functionality was restored by reintroducing AraC. Hence, AraC is essential for the functioning of our biosensor, while AcIa provides enhanced sensitivity and specificity for isoprene. However, insights into how AraC-AcIa interacts and the possible working mechanism remain to be explored. This study provides a prototype for developing chimeric AraC-based biosensors with proteins devoid of known dimerizing domains and opens a new avenue for further study and exploration.
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11
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Lin P, Fu Z, Liu X, Liu C, Bai Z, Yang Y, Li Y. Direct Utilization of Peroxisomal Acetyl-CoA for the Synthesis of Polyketide Compounds in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1599-1607. [PMID: 37172280 DOI: 10.1021/acssynbio.2c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Polyketides are a class of natural products with many applications but are mainly appealing as pharmaceuticals. Heterologous production of polyketides in the yeast Saccharomyces cerevisiae has been widely explored because of the many merits of this model eukaryotic microorganism. Although acetyl-CoA and malonyl-CoA, the precursors for polyketide synthesis, are distributed in several yeast subcellular organelles, only cytosolic synthesis of polyketides has been pursued in previous studies. In this study, we investigate polyketide synthesis by directly using acetyl-CoA in the peroxisomes of yeast strain CEN.PK2-1D. We first demonstrate that the polyketide flaviolin can be synthesized in this organelle upon peroxisomal colocalization of native acetyl-CoA carboxylase and 1,3,6,8-tetrahydroxynaphthalene synthase (a type III polyketide synthase). Next, using the synthesis of the polyketide triacetic acid lactone as an example, we show that (1) a new peroxisome targeting sequence, pPTS1, is more effective than the previously reported ePTS1 for peroxisomal polyketide synthesis; (2) engineering peroxisome proliferation is effective to boost polyketide production; and (3) peroxisomes provide an additional acetyl-CoA reservoir and extra space to accommodate enzymes so that utilizing the peroxisomal pathway plus the cytosolic pathway produces more polyketide than the cytosolic pathway alone. This research lays the groundwork for more efficient heterologous polyketide biosynthesis using acetyl-CoA pools in subcellular organelles.
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Affiliation(s)
- Pingxin Lin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhenhao Fu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Chunli Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
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12
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Feng L, Xu J, Ye C, Gao J, Huang L, Xu Z, Lian J. Metabolic Engineering of Pichia pastoris for the Production of Triacetic Acid Lactone. J Fungi (Basel) 2023; 9:jof9040494. [PMID: 37108948 PMCID: PMC10145311 DOI: 10.3390/jof9040494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Triacetic acid lactone (TAL) is a promising renewable platform polyketide with broad biotechnological applications. In this study, we constructed an engineered Pichia pastoris strain for the production of TAL. We first introduced a heterologous TAL biosynthetic pathway by integrating the 2-pyrone synthase encoding gene from Gerbera hybrida (Gh2PS). We then removed the rate-limiting step of TAL synthesis by introducing the posttranslational regulation-free acetyl-CoA carboxylase mutant encoding gene from S. cerevisiae (ScACC1*) and increasing the copy number of Gh2PS. Finally, to enhance intracellular acetyl-CoA supply, we focused on the introduction of the phosphoketolase/phosphotransacetylase pathway (PK pathway). To direct more carbon flux towards the PK pathway for acetyl-CoA generation, we combined it with a heterologous xylose utilization pathway or endogenous methanol utilization pathway. The combination of the PK pathway with the xylose utilization pathway resulted in the production of 825.6 mg/L TAL in minimal medium with xylose as the sole carbon source, with a TAL yield of 0.041 g/g xylose. This is the first report on TAL biosynthesis in P. pastoris and its direct synthesis from methanol. The present study suggests potential applications in improving the intracellular pool of acetyl-CoA and provides a basis for the construction of efficient cell factories for the production of acetyl-CoA derived compounds.
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Affiliation(s)
- Linjuan Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Junhao Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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13
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Otoupal PB, Geiselman GM, Oka AM, Barcelos CA, Choudhary H, Dinh D, Zhong W, Hwang H, Keasling JD, Mukhopadhyay A, Sundstrom E, Haushalter RW, Sun N, Simmons BA, Gladden JM. Advanced one-pot deconstruction and valorization of lignocellulosic biomass into triacetic acid lactone using Rhodosporidium toruloides. Microb Cell Fact 2022; 21:254. [PMID: 36482295 PMCID: PMC9733078 DOI: 10.1186/s12934-022-01977-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rhodosporidium toruloides is capable of co-utilization of complex carbon sources and robust growth from lignocellulosic hydrolysates. This oleaginous yeast is therefore an attractive host for heterologous production of valuable bioproducts at high titers from low-cost, deconstructed biomass in an economically and environmentally sustainable manner. Here we demonstrate this by engineering R. toruloides to produce the polyketide triacetic acid lactone (TAL) directly from unfiltered hydrolysate deconstructed from biomass with minimal unit process operations. RESULTS Introduction of the 2-pyrone synthase gene into R. toruloides enabled the organism to produce 2.4 g/L TAL from simple media or 2.0 g/L from hydrolysate produced from sorghum biomass. Both of these titers are on par with titers from other better-studied microbial hosts after they had been heavily engineered. We next demonstrate that filtered hydrolysates produced from ensiled sorghum are superior to those derived from dried sorghum for TAL production, likely due to the substantial organic acids produced during ensiling. We also demonstrate that the organic acids found in ensiled biomass can be used for direct synthesis of ionic liquids within the biomass pretreatment process, enabling consolidation of unit operations of in-situ ionic liquid synthesis, pretreatment, saccharification, and fermentation into a one-pot, separations-free process. Finally, we demonstrate this consolidation in a 2 L bioreactor using unfiltered hydrolysate, producing 3.9 g/L TAL. CONCLUSION Many steps involved in deconstructing biomass into fermentable substrate can be combined into a distinct operation, and directly fed to cultures of engineered R. toruloides cultures for subsequent valorization into gram per liter titers of TAL in a cost-effective manner.
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Affiliation(s)
- Peter B. Otoupal
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Gina M. Geiselman
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Asun M. Oka
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Carolina A. Barcelos
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Hemant Choudhary
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Duy Dinh
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Wenqing Zhong
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - HeeJin Hwang
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
| | - Jay D. Keasling
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA ,grid.5170.30000 0001 2181 8870Center for Biosustainability, Danish Technical University, Lyngby, Denmark ,grid.458489.c0000 0001 0483 7922Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Aindrila Mukhopadhyay
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Eric Sundstrom
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Robert W. Haushalter
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Ning Sun
- grid.184769.50000 0001 2231 4551Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Blake A. Simmons
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - John M. Gladden
- grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA USA ,grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA ,Agile BioFoundry, Department of Energy, Emeryville, CA USA
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14
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Shilling PJ, Khananisho D, Cumming J, Söderström B, Daley DO. Signal Amplification of araC pBAD Using a Standardised Translation Initiation Region. Synth Biol (Oxf) 2022; 7:ysac009. [PMID: 35903559 PMCID: PMC9316229 DOI: 10.1093/synbio/ysac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
araC pBAD is a genetic fragment that regulates the expression of the araBAD operon in bacteria, which is required for the metabolism of L-arabinose. It is widely used in bioengineering applications because it can drive regulatable and titratable expression of genes and genetic pathways in microbial cell factories. A notable limitation of araC pBAD is that it generates a low signal when induced with high concentrations of L-arabinose (the maximum ON state). Herein we have amplified the maximum ON state of araC pBAD by coupling it to a synthetically evolved translation initiation region (TIREVOL). The coupling maintains regulatable and titratable expression from araC pBAD and yet increases the maximal ON state by >5-fold. The general principle demonstrated in the study can be applied to amplify the signal from similar genetic modules.
Graphical Abstract
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Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - James Cumming
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney , Sydney, New South Wales, Australia
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
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15
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Cao M, Tran VG, Qin J, Olson A, Mishra S, Schultz JC, Huang C, Xie D, Zhao H. Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnol Bioeng 2022; 119:2529-2540. [PMID: 35701887 PMCID: PMC9540541 DOI: 10.1002/bit.28159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/16/2022] [Accepted: 06/12/2022] [Indexed: 12/19/2022]
Abstract
The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.
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Affiliation(s)
- Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Andrew Olson
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John C Schultz
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chunshuai Huang
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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16
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Enriching intracellular macrolides in Escherichia coli improved the sensitivity of bioluminescent sensing systems. Talanta 2022; 249:123626. [PMID: 35696977 DOI: 10.1016/j.talanta.2022.123626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022]
Abstract
A repressor protein MphR and an enhanced green fluorescent protein (eGFP) were used to construct a bioluminescent sensing system for macrolide analysis in Escherichia coli host cells. We deleted TolC, an efflux pump for macrolides in E. coli, to promote the intracellular accumulation of macrolides. The binding constant (K1/2) of the sensing system constructed in an E. coli strain was decreased up to 33-fold with deleted TolC, and its sensitivity to the macrolides erythromycin, azithromycin, roxithromycin, and pikromycin was increased. The limit of detection of the bioluminescent sensing system for serum azithromycin was 4.1 nM. The ability to detect serum azithromycin concentrations was confirmed by analyzing photographs using ImageJ software. We also developed a novel sensing system for the immune suppressor FK506, another macrolide that is frequently prescribed. Deleting TolC also significantly improved the sensitivity of this sensing system. Bioluminescent sensing systems constructed in TolC mutants were sensitive to various macrolides, indicating their potential for clinical application with hand-held devices.
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17
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Liang Y, Luo J, Yang C, Guo S, Zhang B, Chen F, Su K, Zhang Y, Dong Y, Wang Z, Fu H, Sui G, Wang P. Directed evolution of the PobR allosteric transcription factor to generate a biosensor for 4-hydroxymandelic acid. World J Microbiol Biotechnol 2022; 38:104. [PMID: 35501522 DOI: 10.1007/s11274-022-03286-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
Hydroxy-mandelic acid (HMA) is widely applied in pharmaceuticals, food and cosmetics. In this study, we aimed to develop an allosteric transcription factors (aTFs) based biosensor for HMA. PobR, an aTF for HMA analog 4-hydroxybenzoic acid, was used to alter its selectivity and create novel aTFs responsive to HMA by directed evolution. We established a PobR mutant library with a capacity of 550,000 mutants using error-prone PCR and Megawhop PCR. Through our screening, two mutants were obtained with responsiveness to HMA. Analysis of each missense mutation indicating residues 122-126 were involved in its PobR ligand specificity. These results showed the effectiveness of directed evolution in switching the ligand specificity of a biosensor and improving HMA production.
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Affiliation(s)
- YaoYao Liang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Juan Luo
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Chenhao Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Shuning Guo
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Bowen Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Fengqianrui Chen
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Kairui Su
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yulong Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yi Dong
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zhihao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Hongda Fu
- NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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18
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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19
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Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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20
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Machado LFM, Dixon N. Directed Evolution of Transcription Factor-Based Biosensors for Altered Effector Specificity. Methods Mol Biol 2022; 2461:175-193. [PMID: 35727451 DOI: 10.1007/978-1-0716-2152-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transcription factor-based biosensors are important tools in Synthetic Biology for the sensing of industrially valuable molecules and clinically important metabolites, therefore presenting applications in the bioremediation, industrial biotechnology, and biomedical fields. The directed evolution of allosteric transcription factors (aTFs) with the aim of altering effector specificity has the potential for the development of new biosensors to detect natural and nonnatural molecules, expanding the scope of available aTF-based biosensors. In this chapter, we delineate a general method for the directed evolution of aTFs. The theory of library design is discussed, along with the detailed methodology for an improved transformation of combined libraries, and the experimental search space by counterselection using fluorescence-activated cell sorting (FACS) is presented.
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21
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Kaczmarek JA, Prather KLJ. Effective use of biosensors for high-throughput library screening for metabolite production. J Ind Microbiol Biotechnol 2021; 48:6339276. [PMID: 34347108 PMCID: PMC8788864 DOI: 10.1093/jimb/kuab049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022]
Abstract
The development of fast and affordable microbial production from recombinant pathways is a challenging endeavor, with targeted improvements difficult to predict due to the complex nature of living systems. To address the limitations in biosynthetic pathways, much work has been done to generate large libraries of various genetic parts (promoters, RBSs, enzymes, etc.) to discover library members that bring about significantly improved levels of metabolite production. To evaluate these large libraries, high throughput approaches are necessary, such as those that rely on biosensors. There are various modes of operation to apply biosensors to library screens that are available at different scales of throughput. The effectiveness of each biosensor-based method is dependent on the pathway or strain to which it is applied, and all approaches have strengths and weaknesses to be carefully considered for any high throughput library screen. In this review, we discuss the various approaches used in biosensor screening for improved metabolite production, focusing on transcription factor-based biosensors.
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Affiliation(s)
- Jennifer A Kaczmarek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
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22
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Abstract
Enzymes are represented across a vast space of protein sequences and structural forms and have activities that far exceed the best chemical catalysts; however, engineering them to have novel or enhanced activity is limited by technologies for sensing product formation. Here, we describe a general and scalable approach for characterizing enzyme activity that uses the metabolism of the host cell as a biosensor by which to infer product formation. Since different products consume different molecules in their synthesis, they perturb host metabolism in unique ways that can be measured by mass spectrometry. This provides a general way by which to sense product formation, to discover unexpected products and map the effects of mutagenesis. The testing of engineered enzymes represents a bottleneck. Here the authors report a screening method combining microfluidics and mass spectrometry, to map the catalysis of a mutated enzyme, characterise the range of products generated and recover the sequences of variants with desired activities.
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23
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Zhao N, Song J, Zhang H, Lin Y, Han S, Huang Y, Zheng S. Development of a Transcription Factor-Based Diamine Biosensor in Corynebacterium glutamicum. ACS Synth Biol 2021; 10:3074-3083. [PMID: 34662101 DOI: 10.1021/acssynbio.1c00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diamines serve as major platform chemicals that can be employed to a variety of industrial scenarios, particularly as monomers for polymer synthesis. High-throughput sensors for diamine biosynthesis can greatly improve the biological production of diamines. Here, we identified and characterized a transcription factor-driven biosensor for putrescine and cadaverine in Corynebacterium glutamicum. The transcriptional TetR-family regulatory protein CgmR (CGL2612) is used for the specific detection of diamine compounds. This study also improved the dynamic range and the sensitivity to putrescine by systematically optimizing genetic components of pSenPut. By a single cell-based screening strategy for a library of CgmR with random mutations, this study obtained the most sensitive variant CgmRI152T, which possessed an experimentally determined limit of detection (LoD) of ≤0.2 mM, a K of 11.4 mM, and a utility of 720. Using this highly sensitive putrescine biosensor pSenPutI152T, we demonstrated that CgmRI152T can be used as a sensor to detect putrescine produced biologically in a C. glutamicum system. This high sensitivity and the range of CgmR will be an influential tool for rewiring metabolic circuits and facilitating the directed evolution of recombinant strains toward the biological synthesis of diamine compounds.
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Affiliation(s)
- Nannan Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jie Song
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Hao Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, P. R. China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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24
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Zhang J, Pang Q, Wang Q, Qi Q, Wang Q. Modular tuning engineering and versatile applications of genetically encoded biosensors. Crit Rev Biotechnol 2021; 42:1010-1027. [PMID: 34615431 DOI: 10.1080/07388551.2021.1982858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.
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Affiliation(s)
- Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingxiao Pang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
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25
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Bowman EK, Wagner JM, Yuan SF, Deaner M, Palmer CM, D'Oelsnitz S, Cordova L, Li X, Craig FF, Alper HS. Sorting for secreted molecule production using a biosensor-in-microdroplet approach. Proc Natl Acad Sci U S A 2021; 118:e2106818118. [PMID: 34475218 PMCID: PMC8433520 DOI: 10.1073/pnas.2106818118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Sorting large libraries of cells for improved small molecule secretion is throughput limited. Here, we combine producer/secretor cell libraries with whole-cell biosensors using a microfluidic-based screening workflow. This approach enables a mix-and-match capability using off-the-shelf biosensors through either coencapsulation or pico-injection. We demonstrate the cell type and library agnostic nature of this workflow by utilizing single-guide RNA, transposon, and ethyl-methyl sulfonate mutagenesis libraries across three distinct microbes (Escherichia coli, Saccharomyces cerevisiae, and Yarrowia lipolytica), biosensors from two organisms (E. coli and S. cerevisiae), and three products (triacetic acid lactone, naringenin, and L-DOPA) to identify targets improving production/secretion.
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Affiliation(s)
- Emily K Bowman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Shuo-Fu Yuan
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Claire M Palmer
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Simon D'Oelsnitz
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712
| | - Lauren Cordova
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Xin Li
- Sphere Fluidics Limited, Cambridge CB21 6GP, United Kingdom
| | - Frank F Craig
- Sphere Fluidics Limited, Cambridge CB21 6GP, United Kingdom
| | - Hal S Alper
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712;
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
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26
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Flachbart LK, Gertzen CGW, Gohlke H, Marienhagen J. Development of a Biosensor Platform for Phenolic Compounds Using a Transition Ligand Strategy. ACS Synth Biol 2021; 10:2002-2014. [PMID: 34369151 DOI: 10.1021/acssynbio.1c00165] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The time-consuming and laborious characterization of protein or microbial strain designs limits the development of high-performance biocatalysts for biotechnological applications. Here, transcriptional biosensors emerged as valuable tools as they allow for rapid characterization of several thousand variants within a very short time. However, for many molecules of interest, no specific transcriptional regulator determining a biosensor's specificity is available. We present an approach for rapidly engineering biosensor specificities using a semirational transition ligand approach combined with fluorescence-activated cell sorting. In this two-step approach, a biosensor is first evolved toward a more relaxed-ligand specificity before using the resulting variant as the starting point in a second round of directed evolution toward high specificity for several chemically different ligands. By following this strategy, highly specific biosensors for 4-hydroxybenzoic acid, p-coumaric acid, 5-bromoferulic acid, and 6-methyl salicylic acid were developed, starting from a biosensor for the intracellular detection of trans-cinnamic acid.
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Affiliation(s)
- Lion Konstantin Flachbart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Christoph Gerhard Wilhelm Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
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27
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Zou Y, Li C, Zhang R, Jiang T, Liu N, Wang J, Wang X, Yan Y. Exploring the Tunability and Dynamic Properties of MarR-PmarO Sensor System in Escherichia coli. ACS Synth Biol 2021; 10:2076-2086. [PMID: 34319697 DOI: 10.1021/acssynbio.1c00245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transcriptional factor-based biosensors (TFBs) have been widely used in dynamic pathway control or high-throughput screening. Here, we systematically explored the tunability of a salicylic acid responsive regulator MarR from Escherichia coli aiming to explore its engineering potential. The effect of endogenous MarR in E. coli on the MarR-PmarO biosensor system was investigated. Furthermore, to investigate the function of marO binding boxes in this biosensor system, a series of hybrid promoters were constructed by placing the marO binding boxes in the strong constitutive pL promoter. The engineered hybrid promoters became responsive to MarR and salicylic acid. To further study the influence of each nucleotide in the marO box on MarR binding, we employed dynamic modeling to simulate the interaction and binding energy between each nucleotide in the marO boxes with the corresponding residues on MarR. Guided by the results of the simulation, we introduced mutations to key positions on the hybrid promoters and investigated corresponding dynamic performance. Two promoter variants I12AII4T and I12AII14T that exhibited improved responsive strengths and shifted dynamic ranges were obtained, which can be beneficial for future metabolic engineering research.
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Affiliation(s)
- Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Ning Liu
- School of Environmental, Civil, Agricultural, and Mechanical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Xianqiao Wang
- School of Environmental, Civil, Agricultural, and Mechanical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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28
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Cui S, Lv X, Xu X, Chen T, Zhang H, Liu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways. ACS Synth Biol 2021; 10:1587-1597. [PMID: 34213900 DOI: 10.1021/acssynbio.1c00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The dynamic regulation of metabolic pathways is based on changes in external signals and endogenous changes in gene expression levels and has extensive applications in the field of synthetic biology and metabolic engineering. However, achieving dynamic control is not trivial, and dynamic control is difficult to obtain using simple, single-level, control strategies because they are often affected by native regulatory networks. Therefore, synthetic biologists usually apply the concept of logic gates to build more complex and multilayer genetic circuits that can process various signals and direct the metabolic flux toward the synthesis of the molecules of interest. In this review, we first summarize the applications of dynamic regulatory systems and genetic circuits and then discuss how to design multilayer genetic circuits to achieve the optimal control of metabolic fluxes in living cells.
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Affiliation(s)
- Shixiu Cui
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Taichi Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai’an 271000, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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29
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Chen B, Xie Z, Peng F, Li S, Yang J, Wu T, Fan H, Zhang Z, Hou M, Li S, Liu H, Han B. Production of Piperidine and δ-Lactam Chemicals from Biomass-Derived Triacetic Acid Lactone. Angew Chem Int Ed Engl 2021; 60:14405-14409. [PMID: 33825278 DOI: 10.1002/anie.202102353] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/23/2021] [Indexed: 12/28/2022]
Abstract
Piperidine and δ-Lactam chemicals have wide application, which are currently produced from fossil resource in industry. Production of this kind of chemicals from lignocellulosic biomass is of great importance, but is challenging and the reported routes give low yield. Herein, we demonstrate the strategy to synthesize 2-methyl piperidine (MP) and 6-methylpiperidin-2-one (MPO) from biomass-derived triacetic acid lactone (TAL) that is produced microbially from glucose. In this route, TAL was firstly converted into 4-hydroxy-6-methylpyridin-2(1H)-one (HMPO) through facile aminolysis, subsequently HMPO was selectively transformed into MP or MPO over Ru catalysts supported on beta zeolite (Ru/BEA-X, X is the molar ratio of Si to Al) via the tandem reaction. It was found that the yield of MP could reach 76.5 % over Ru/BEA-60 in t-BuOH, and the yield of MPO could be 78.5 % in dioxane. Systematic studies reveal that the excellent catalytic performance of Ru/BEA-60 was closely correlated with the cooperative effects between active metal and acidic zeolite with large pore geometries. The related reaction pathway was studied on the basis of control experiments.
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Affiliation(s)
- Bingfeng Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhenbing Xie
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Fangfang Peng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shaopeng Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junjuan Yang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Tianbin Wu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Honglei Fan
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhaofu Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Minqiang Hou
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shumu Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huizhen Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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30
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Chen B, Xie Z, Peng F, Li S, Yang J, Wu T, Fan H, Zhang Z, Hou M, Li S, Liu H, Han B. Production of Piperidine and δ‐Lactam Chemicals from Biomass‐Derived Triacetic Acid Lactone. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bingfeng Chen
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Zhenbing Xie
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemistry and Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Fangfang Peng
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Shaopeng Li
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Junjuan Yang
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Tianbin Wu
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Honglei Fan
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Zhaofu Zhang
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Minqiang Hou
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Shumu Li
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Huizhen Liu
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemistry and Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemistry and Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
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31
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Abstract
One of the most prominent features of genetically encoded biosensors (GEBs) is their evolvability-the ability to invent new sensory functions using mutations. Among the GEBs, the transcription factor-based biosensors (TF-biosensors) is the focus of this review. We also discuss how this class of sensors can be highly evolvable and how we can exploit it. With an established platform for directed evolution, researchers can create, or evolve, new TF-biosensors. Directed evolution experiments have revealed the TF-biosensors' evolvability, which is based partially on their characteristic physicochemical properties.
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Affiliation(s)
- Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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32
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
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Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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34
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Zhang X, He Y, Wu Z, Liu G, Tao Y, Jin JM, Chen W, Tang SY. Whole-Cell Biosensors Aid Exploration of Vanillin Transmembrane Transport. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3114-3123. [PMID: 33666081 DOI: 10.1021/acs.jafc.0c07886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transcriptional regulatory protein (TRP)-based whole-cell biosensors are widely used nowadays. Here, they were demonstrated to have great potential application in screening cell efflux and influx pumps for small molecules. First, a vanillin whole-cell biosensor was developed by altering the specificity of a TRP, VanR, and strains with improved vanillin productions that were selected from a random genome mutagenesis library by using this biosensor as a high-throughput screening tool. A high intracellular vanillin concentration was found to accumulate due to the inactivation of the AcrA protein, indicating the involvement of this protein in vanillin efflux. Then, the application of this biosensor was extended to explore efflux and influx pumps, combined with directed genome evolution. Elevated intracellular vanillin levels resulting from efflux pump inactivation or influx pump overexpression could be rapidly detected by the whole-cell biosensor, markedly facilitating the identification of genome targets related to small-molecule transmembrane transport, which is of great importance in metabolic engineering.
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Affiliation(s)
- Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang He
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Zhe Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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35
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Transcription factor-based biosensors: a molecular-guided approach for natural product engineering. Curr Opin Biotechnol 2021; 69:172-181. [PMID: 33493842 DOI: 10.1016/j.copbio.2021.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/21/2020] [Accepted: 01/10/2021] [Indexed: 12/13/2022]
Abstract
Natural products and their derivatives offer a rich source of chemical and biological diversity; however, traditional engineering of their biosynthetic pathways to improve yields and access to unnatural derivatives requires a precise understanding of their enzymatic processes. High-throughput screening platforms based on allosteric transcription-factor based biosensors can be leveraged to overcome the screening bottleneck to enable searching through large libraries of pathway/strain variants. Herein, the development and application of engineered allosteric transcription factor-based biosensors is described that enable optimization of precursor availability, product titers, and downstream product tailoring for advancing the natural product bioeconomy. We discuss recent successes for tailoring biosensor design, including computationally-based approaches, and present our future outlook with the integration of cell-free technologies and de novo protein design for rapidly generating biosensor tools.
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36
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Sajjad H, Prebihalo EA, Tolman WB, Reineke TM. Ring opening polymerization of β-acetoxy-δ-methylvalerolactone, a triacetic acid lactone derivative. Polym Chem 2021. [DOI: 10.1039/d1py00561h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report here the synthesis and polymerization of a novel disubstituted valerolactone, β-acetoxy-δ-methylvalerolactone, derived from the renewable feedstock triacetic acid lactone (TAL).
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Affiliation(s)
- Hussnain Sajjad
- Department of Chemistry and Center for Sustainable Polymers, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA
| | - Emily A. Prebihalo
- Department of Chemistry and Center for Sustainable Polymers, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA
| | - William B. Tolman
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Campus Box 1134, St Louis, MO 63130-4899, USA
| | - Theresa M. Reineke
- Department of Chemistry and Center for Sustainable Polymers, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, USA
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37
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Kim J, Hoang Nguyen Tran P, Lee SM. Current Challenges and Opportunities in Non-native Chemical Production by Engineered Yeasts. Front Bioeng Biotechnol 2021; 8:594061. [PMID: 33381497 PMCID: PMC7767886 DOI: 10.3389/fbioe.2020.594061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Yeasts are promising industrial hosts for sustainable production of fuels and chemicals. Apart from efficient bioethanol production, yeasts have recently demonstrated their potential for biodiesel production from renewable resources. The fuel-oriented product profiles of yeasts are now expanding to include non-native chemicals with the advances in synthetic biology. In this review, current challenges and opportunities in yeast engineering for sustainable production of non-native chemicals will be discussed, with a focus on the comparative evaluation of a bioethanol-producing Saccharomyces cerevisiae strain and a biodiesel-producing Yarrowia lipolytica strain. Synthetic pathways diverging from the distinctive cellular metabolism of these yeasts guide future directions for product-specific engineering strategies for the sustainable production of non-native chemicals on an industrial scale.
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Affiliation(s)
- Jiwon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Biotechnology, Korea University, Seoul, South Korea
| | - Phuong Hoang Nguyen Tran
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, South Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, South Korea.,Green School, Korea University, Seoul, South Korea
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38
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Yang H, Lu L, Chen X. An overview and future prospects of sialic acids. Biotechnol Adv 2020; 46:107678. [PMID: 33285252 DOI: 10.1016/j.biotechadv.2020.107678] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022]
Abstract
Sialic acids (Sias) are negatively charged functional monosaccharides present in a wide variety of natural sources (plants, animals and microorganisms). Sias play an important role in many life processes, which are widely applied in the medical and food industries as intestinal antibacterials, antivirals, anti-oxidative agents, food ingredients, and detoxification agents. Most Sias are composed of N-acetylneuraminic acid (Neu5Ac, >99%), and Sia is its most commonly used name. In this article, we review Sias in terms of their structures, applications, determination methods, metabolism, and production strategies. In particular, we summarise and compare different production strategies, including extraction from natural sources, chemical synthesis, polymer decomposition, enzymatic synthesis, whole-cell catalysis, and de novo biosynthesis via microorganism fermentation. We also discuss research on their physiological functions and applications, barriers to efficient production, and strategies for overcoming these challenges. We focus on efficient de novo biosynthesis strategies for Neu5Ac via microbial fermentation using novel synthetic biology tools and methods that may be applied in future. This work provides a comprehensive overview of recent advances on Sias, and addresses future challenges regarding their functions, applications, and production.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Liping Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; College of life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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39
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Wang Z, Doshi A, Chowdhury R, Wang Y, Maranas CD, Cirino PC. Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. Protein Eng Des Sel 2020; 33:5993570. [DOI: 10.1093/protein/gzaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
We previously described the design of triacetic acid lactone (TAL) biosensor ‘AraC-TAL1’, based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a ‘decoy’ ligand during negative selection, resulting in the isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the iterative protein redesign and optimization computational framework was employed, followed by 2 rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.
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Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Aarti Doshi
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
| | - Ratul Chowdhury
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Yixi Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Costas D Maranas
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
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40
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Muhammad A, Feng X, Rasool A, Sun W, Li C. Production of plant natural products through engineered Yarrowia lipolytica. Biotechnol Adv 2020; 43:107555. [DOI: 10.1016/j.biotechadv.2020.107555] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
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41
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Engineering and application of a biosensor with focused ligand specificity. Nat Commun 2020; 11:4851. [PMID: 32978386 PMCID: PMC7519686 DOI: 10.1038/s41467-020-18400-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/20/2020] [Indexed: 02/01/2023] Open
Abstract
Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering approach using a FACS-based screening/counterscreening strategy to generate an l-lysine insensitive LysG-based biosensor. This biosensor can be used to isolate l-histidine-producing strains by FACS, showing that TR engineering towards a more focused ligand spectrum can expand the scope of application of such metabolite sensors. Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.
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42
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43
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Li C, Zhang R, Wang J, Wilson LM, Yan Y. Protein Engineering for Improving and Diversifying Natural Product Biosynthesis. Trends Biotechnol 2020; 38:729-744. [PMID: 31954530 PMCID: PMC7274900 DOI: 10.1016/j.tibtech.2019.12.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 01/26/2023]
Abstract
Proteins found in nature have traditionally been the most frequently used biocatalysts to produce numerous natural products ranging from commodity chemicals to pharmaceuticals. Protein engineering has emerged as a powerful biotechnological toolbox in the development of metabolic engineering, particularly for the biosynthesis of natural products. Recently, protein engineering has become a favored method to improve enzymatic activity, increase enzyme stability, and expand product spectra in natural product biosynthesis. This review summarizes recent advances and typical strategies in protein engineering, highlighting the paramount role of protein engineering in improving and diversifying the biosynthesis of natural products. Future prospects and research directions are also discussed.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Ruihua Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jian Wang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Lauren Marie Wilson
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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44
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Tan Z, Clomburg JM, Cheong S, Qian S, Gonzalez R. A polyketoacyl-CoA thiolase-dependent pathway for the synthesis of polyketide backbones. Nat Catal 2020. [DOI: 10.1038/s41929-020-0471-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Qiu C, Zhai H, Hou J. Biosensors design in yeast and applications in metabolic engineering. FEMS Yeast Res 2020; 19:5645237. [PMID: 31778177 DOI: 10.1093/femsyr/foz082] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Engineering microbial cell factories is a potential approach of sustainable production of chemicals, fuels and pharmaceuticals. However, testing the production of molecules in high throughput is still a time-consuming and laborious process since product synthesis usually does not confer a clear phenotype. Therefore, it is necessary to develop new techniques for fast high-producer screening. Genetically encoded biosensors are considered to be promising devices for high-throughput analysis owing to their ability to sense metabolites and couple detection to an actuator, thereby facilitating the rapid detection of small molecules at single-cell level. Here, we review recent advances in the design and engineering of biosensors in Saccharomyces cerevisiae, and their applications in metabolic engineering. Three types of biosensor are introduced in this review: transcription factor based, RNA-based and enzyme-coupled biosensors. The studies to improve the features of biosensors are also described. Moreover, we summarized their metabolic engineering applications in dynamic regulation and high producer selection. Current challenges in biosensor design and future perspectives on sensor applications are also discussed.
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Affiliation(s)
- Chenxi Qiu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Haotian Zhai
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, Shandong 266237, P. R. China
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46
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Srivastava RK, Akhtar N, Verma M, Imandi SB. Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnol Appl Biochem 2020; 67:852-874. [PMID: 32294277 DOI: 10.1002/bab.1927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/12/2020] [Indexed: 02/06/2023]
Abstract
Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high production cost of metabolites is a big challenge for most of the bioprocess industries and commercial production needs to be achieved. This issue can be solved to some extent by screening and developing the engineered microbial systems via reconstruction of the genome-scale metabolic model. The predicted genetic modification is applied for an increased flux in biosynthesis pathways toward the desired product. Wherein the resulting microbial strain is capable of converting a large amount of carbon substrate to the expected product with minimum by-product formation in the optimal operating conditions. Metabolic engineering efforts have also resulted in significant improvement of metabolite yields, depending on the nature of the products, microbial cell factory modification, and the types of substrate used. The objective of this review is to comprehend the state of art for the production of various primary metabolites by microbial strains system, focusing on the selection of efficient strain and genetic or pathway modifications, applied during strain engineering.
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Affiliation(s)
- Rajesh K Srivastava
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Nasim Akhtar
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Malkhey Verma
- Departments of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, India
| | - Sarat Babu Imandi
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
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47
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Yao J, He Y, Su N, Bharath SR, Tao Y, Jin JM, Chen W, Song H, Tang SY. Developing a highly efficient hydroxytyrosol whole-cell catalyst by de-bottlenecking rate-limiting steps. Nat Commun 2020; 11:1515. [PMID: 32251291 PMCID: PMC7090077 DOI: 10.1038/s41467-020-14918-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
Hydroxytyrosol is an antioxidant free radical scavenger that is biosynthesized from tyrosine. In metabolic engineering efforts, the use of the mouse tyrosine hydroxylase limits its production. Here, we design an efficient whole-cell catalyst of hydroxytyrosol in Escherichia coli by de-bottlenecking two rate-limiting enzymatic steps. First, we replace the mouse tyrosine hydroxylase by an engineered two-component flavin-dependent monooxygenase HpaBC of E. coli through structure-guided modeling and directed evolution. Next, we elucidate the structure of the Corynebacterium glutamicum VanR regulatory protein complexed with its inducer vanillic acid. By switching its induction specificity from vanillic acid to hydroxytyrosol, VanR is engineered into a hydroxytyrosol biosensor. Then, with this biosensor, we use in vivo-directed evolution to optimize the activity of tyramine oxidase (TYO), the second rate-limiting enzyme in hydroxytyrosol biosynthesis. The final strain reaches a 95% conversion rate of tyrosine. This study demonstrates the effectiveness of sequentially de-bottlenecking rate-limiting steps for whole-cell catalyst development. Whole-cell catalyst-based hydroxytyrosol production is low. Here, the authors increase the efficiency of its production in E. coli by de-bottlenecking two enzymatic steps catalyzed by monooxygenase and tyramine oxidase using structure-based enzyme redesign or in vivo-directed evolution with the aid of a newly developed biosensor.
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Affiliation(s)
- Jun Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yang He
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore
| | - Nannan Su
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore
| | | | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, China.
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, Singapore.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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48
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Han G, Xu N, Sun X, Chen J, Chen C, Wang Q. Improvement of l-Valine Production by Atmospheric and Room Temperature Plasma Mutagenesis and High-Throughput Screening in Corynebacterium glutamicum. ACS OMEGA 2020; 5:4751-4758. [PMID: 32201760 PMCID: PMC7081258 DOI: 10.1021/acsomega.9b02747] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
As one of the branched-chain amino acids, l-valine is an essential nutrient for most mammalian species. In this study, the l-valine producer Corynebacterium glutamicum ΔppcΔaceEΔalatΔpqo was first constructed. Additionally, an improved biosensor based on the Lrp-type transcriptional regulator and temperature-sensitive replication was built. Then, the C. glutamicum strain was mutagenized by atmospheric and room temperature plasma. A sequential three-step procedure was carried out to screen l-valine-producing strains, including the fluorescence-activated cell sorting (FACS), 96-well plate screening, and flask fermentation. The final mutant HL2-7 obtained by screening produced 3.20 g/L of l-valine, which was 21.47% higher than the titer produced by the starting strain. This study demonstrates that the l-valine-producing mutants can be successfully isolated based on the Lrp sensor system in combination with FACS screening after random mutagenesis.
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Affiliation(s)
- Guoqiang Han
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
| | - Ning Xu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, P. R. China
| | - Xieping Sun
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Jinzhao Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Chun Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Qing Wang
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
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49
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Li JW, Zhang XY, Wu H, Bai YP. Transcription Factor Engineering for High-Throughput Strain Evolution and Organic Acid Bioproduction: A Review. Front Bioeng Biotechnol 2020; 8:98. [PMID: 32140463 PMCID: PMC7042172 DOI: 10.3389/fbioe.2020.00098] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/03/2020] [Indexed: 01/15/2023] Open
Abstract
Metabolic regulation of gene expression for the microbial production of fine chemicals, such as organic acids, is an important research topic in post-genomic metabolic engineering. In particular, the ability of transcription factors (TFs) to respond precisely in time and space to various small molecules, signals and stimuli from the internal and external environment is essential for metabolic pathway engineering and strain development. As a key component, TFs are used to construct many biosensors in vivo using synthetic biology methods, which can be used to monitor the concentration of intracellular metabolites in organic acid production that would otherwise remain “invisible” within the intracellular environment. TF-based biosensors also provide a high-throughput screening method for rapid strain evolution. Furthermore, TFs are important global regulators that control the expression levels of key enzymes in organic acid biosynthesis pathways, therefore determining the outcome of metabolic networks. Here we review recent advances in TF identification, engineering, and applications for metabolic engineering, with an emphasis on metabolite monitoring and high-throughput strain evolution for the organic acid bioproduction.
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Affiliation(s)
- Jia-Wei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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50
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Zeng W, Guo L, Xu S, Chen J, Zhou J. High-Throughput Screening Technology in Industrial Biotechnology. Trends Biotechnol 2020; 38:888-906. [PMID: 32005372 DOI: 10.1016/j.tibtech.2020.01.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.
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Affiliation(s)
- Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Likun Guo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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