1
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Ackermann YS, de Witt J, Mezzina MP, Schroth C, Polen T, Nikel PI, Wynands B, Wierckx N. Bio-upcycling of even and uneven medium-chain-length diols and dicarboxylates to polyhydroxyalkanoates using engineered Pseudomonas putida. Microb Cell Fact 2024; 23:54. [PMID: 38365718 PMCID: PMC10870600 DOI: 10.1186/s12934-024-02310-7] [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: 11/16/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Bio-upcycling of plastics is an emerging alternative process that focuses on extracting value from a wide range of plastic waste streams. Such streams are typically too contaminated to be effectively processed using traditional recycling technologies. Medium-chain-length (mcl) diols and dicarboxylates (DCA) are major products of chemically or enzymatically depolymerized plastics, such as polyesters or polyethers. In this study, we enabled the efficient metabolism of mcl-diols and -DCA in engineered Pseudomonas putida as a prerequisite for subsequent bio-upcycling. We identified the transcriptional regulator GcdR as target for enabling metabolism of uneven mcl-DCA such as pimelate, and uncovered amino acid substitutions that lead to an increased coupling between the heterologous β-oxidation of mcl-DCA and the native degradation of short-chain-length DCA. Adaptive laboratory evolution and subsequent reverse engineering unravelled two distinct pathways for mcl-diol metabolism in P. putida, namely via the hydroxy acid and subsequent native β-oxidation or via full oxidation to the dicarboxylic acid that is further metabolized by heterologous β-oxidation. Furthermore, we demonstrated the production of polyhydroxyalkanoates from mcl-diols and -DCA by a single strain combining all required metabolic features. Overall, this study provides a powerful platform strain for the bio-upcycling of complex plastic hydrolysates to polyhydroxyalkanoates and leads the path for future yield optimizations.
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Affiliation(s)
- Yannic S Ackermann
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Jan de Witt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Mariela P Mezzina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christoph Schroth
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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2
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Pearson AN, Thompson MG, Kirkpatrick LD, Ho C, Vuu KM, Waldburger LM, Keasling JD, Shih PM. The pGinger Family of Expression Plasmids. Microbiol Spectr 2023; 11:e0037323. [PMID: 37212656 PMCID: PMC10269703 DOI: 10.1128/spectrum.00373-23] [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: 01/24/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023] Open
Abstract
The pGinger suite of expression plasmids comprises 43 plasmids that will enable precise constitutive and inducible gene expression in a wide range of Gram-negative bacterial species. Constitutive vectors are composed of 16 synthetic constitutive promoters upstream of red fluorescent protein (RFP), with a broad-host-range BBR1 origin and a kanamycin resistance marker. The family also has seven inducible systems (Jungle Express, Psal/NahR, Pm/XylS, Prha/RhaS, LacO1/LacI, LacUV5/LacI, and Ptet/TetR) controlling RFP expression on BBR1/kanamycin plasmid backbones. For four of these inducible systems (Jungle Express, Psal/NahR, LacO1/LacI, and Ptet/TetR), we created variants that utilize the RK2 origin and spectinomycin or gentamicin selection. Relevant RFP expression and growth data have been collected in the model bacterium Escherichia coli as well as Pseudomonas putida. All pGinger vectors are available via the Joint BioEnergy Institute (JBEI) Public Registry. IMPORTANCE Metabolic engineering and synthetic biology are predicated on the precise control of gene expression. As synthetic biology expands beyond model organisms, more tools will be required that function robustly in a wide range of bacterial hosts. The pGinger family of plasmids constitutes 43 plasmids that will enable both constitutive and inducible gene expression in a wide range of nonmodel Proteobacteria.
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Affiliation(s)
- Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liam D. Kirkpatrick
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cindy Ho
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Khanh M. Vuu
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lucas M. Waldburger
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
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3
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Hanko EKR, Joosab Noor Mahomed TA, Stoney RA, Breitling R. TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors. ACS Synth Biol 2023; 12:1497-1507. [PMID: 37053505 DOI: 10.1021/acssynbio.2c00679] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Transcription factors responsive to small molecules are essential elements in synthetic biology designs. They are often used as genetically encoded biosensors with applications ranging from the detection of environmental contaminants and biomarkers to microbial strain engineering. Despite our efforts to expand the space of compounds that can be detected using biosensors, the identification and characterization of transcription factors and their corresponding inducer molecules remain labor- and time-intensive tasks. Here, we introduce TFBMiner, a new data mining and analysis pipeline that enables the automated and rapid identification of putative metabolite-responsive transcription factor-based biosensors (TFBs). This user-friendly command line tool harnesses a heuristic rule-based model of gene organization to identify both gene clusters involved in the catabolism of user-defined molecules and their associated transcriptional regulators. Ultimately, biosensors are scored based on how well they fit the model, providing wet-lab scientists with a ranked list of candidates that can be experimentally tested. We validated the pipeline using a set of molecules for which TFBs have been reported previously, including sensors responding to sugars, amino acids, and aromatic compounds, among others. We further demonstrated the utility of TFBMiner by identifying a biosensor for S-mandelic acid, an aromatic compound for which a responsive transcription factor had not been found previously. Using a combinatorial library of mandelate-producing microbial strains, the newly identified biosensor was able to distinguish between low- and high-producing strain candidates. This work will aid in the unraveling of metabolite-responsive microbial gene regulatory networks and expand the synthetic biology toolbox to allow for the construction of more sophisticated self-regulating biosynthetic pathways.
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Affiliation(s)
- Erik K R Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Tariq A Joosab Noor Mahomed
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Ruth A Stoney
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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4
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Zhou GJ, Zhang F. Applications and Tuning Strategies for Transcription Factor-Based Metabolite Biosensors. BIOSENSORS 2023; 13:428. [PMID: 37185503 PMCID: PMC10136082 DOI: 10.3390/bios13040428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023]
Abstract
Transcription factor (TF)-based biosensors are widely used for the detection of metabolites and the regulation of cellular pathways in response to metabolites. Several challenges hinder the direct application of TF-based sensors to new hosts or metabolic pathways, which often requires extensive tuning to achieve the optimal performance. These tuning strategies can involve transcriptional or translational control depending on the parameter of interest. In this review, we highlight recent strategies for engineering TF-based biosensors to obtain the desired performance and discuss additional design considerations that may influence a biosensor's performance. We also examine applications of these sensors and suggest important areas for further work to continue the advancement of small-molecule biosensors.
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Affiliation(s)
- Gloria J. Zhou
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA;
- Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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5
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Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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6
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Hartline CJ, Zhang F. The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors. ACS Synth Biol 2022; 11:2247-2258. [PMID: 35700119 PMCID: PMC9994378 DOI: 10.1021/acssynbio.2c00143] [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: 11/30/2022]
Abstract
Metabolite biosensors based on metabolite-responsive transcription factors are key synthetic biology components for sensing and precisely controlling cellular metabolism. Biosensors are often designed under laboratory conditions but are deployed in applications where cellular growth rate differs drastically from its initial characterization. Here we asked how growth rate impacts the minimum and maximum biosensor outputs and the dynamic range, which are key metrics of biosensor performance. Using LacI, TetR, and FadR-based biosensors in Escherichia coli as models, we find that the dynamic range of different biosensors have different growth rate dependencies. We developed a kinetic model to explore how tuning biosensor parameters impact the dynamic range growth rate dependence. Our modeling and experimental results revealed that the effects to dynamic range and its growth rate dependence are often coupled, and the metabolite transport mechanisms shape the dynamic range-growth rate response. This work provides a systematic understanding of biosensor performance under different growth rates, which will be useful for predicting biosensor behavior in broad synthetic biology and metabolic engineering applications.
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Affiliation(s)
- Christopher J Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Division of Biology & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
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7
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Kang Z, Zhang M, Gao K, Zhang W, Meng W, Liu Y, Xiao D, Guo S, Ma C, Gao C, Xu P. An L-2-hydroxyglutarate biosensor based on specific transcriptional regulator LhgR. Nat Commun 2021; 12:3619. [PMID: 34131130 PMCID: PMC8206213 DOI: 10.1038/s41467-021-23723-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
l-2-Hydroxyglutarate (l-2-HG) plays important roles in diverse physiological processes, such as carbon starvation response, tumorigenesis, and hypoxic adaptation. Despite its importance and intensively studied metabolism, regulation of l-2-HG metabolism remains poorly understood and none of regulator specifically responded to l-2-HG has been identified. Based on bacterial genomic neighborhood analysis of the gene encoding l-2-HG oxidase (LhgO), LhgR, which represses the transcription of lhgO in Pseudomonas putida W619, is identified in this study. LhgR is demonstrated to recognize l-2-HG as its specific effector molecule, and this allosteric transcription factor is then used as a biorecognition element to construct an l-2-HG-sensing FRET sensor. The l-2-HG sensor is able to conveniently monitor the concentrations of l-2-HG in various biological samples. In addition to bacterial l-2-HG generation during carbon starvation, biological function of the l-2-HG dehydrogenase and hypoxia induced l-2-HG accumulation are also revealed by using the l-2-HG sensor in human cells. L-2-hydroxyglutarate (L-2-HG) is an important metabolite but its regulation is poorly understood. Here the authors report an L-2-HG FRET biosensor based on the allosteric transcription factor, LhgR, to monitor L-2-HG in cells and biological samples.
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Affiliation(s)
- Zhaoqi Kang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Manman Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, People's Republic of China
| | - Kaiyu Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Wen Zhang
- Center for Gene and Immunotherapy, The Second Hospital of Shandong University, Jinan, People's Republic of China
| | - Wensi Meng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Dan Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Shiting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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8
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Ding N, Zhou S, Deng Y. Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology. ACS Synth Biol 2021; 10:911-922. [PMID: 33899477 DOI: 10.1021/acssynbio.0c00252] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transcription-factor-based biosensors (TFBs) are often used for metabolite detection, adaptive evolution, and metabolic flux control. However, designing TFBs with superior performance for applications in synthetic biology remains challenging. Specifically, natural TFBs often do not meet real-time detection requirements owing to their slow response times and inappropriate dynamic ranges, detection ranges, sensitivity, and selectivity. Furthermore, designing and optimizing complex dynamic regulation networks is time-consuming and labor-intensive. This Review highlights TFB-based applications and recent engineering strategies ranging from traditional trial-and-error approaches to novel computer-model-based rational design approaches. The limitations of the applications and these engineering strategies are additionally reviewed.
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Affiliation(s)
- Nana Ding
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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9
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Jiang Y, Sheng Q, Wu XY, Ye BC, Zhang B. l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process. Crit Rev Biotechnol 2020; 41:172-185. [PMID: 33153325 DOI: 10.1080/07388551.2020.1844625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.
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Affiliation(s)
- Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Qi Sheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
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10
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Gordillo Sierra AR, Alper HS. Progress in the metabolic engineering of bio-based lactams and their ω-amino acids precursors. Biotechnol Adv 2020; 43:107587. [DOI: 10.1016/j.biotechadv.2020.107587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 01/08/2023]
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11
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High-throughput screening for efficient microbial biotechnology. Curr Opin Biotechnol 2020; 64:141-150. [DOI: 10.1016/j.copbio.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 01/25/2023]
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12
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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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