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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Essential factors, advanced strategies, challenges, and approaches involved for efficient expression of recombinant proteins in Escherichia coli. Arch Microbiol 2024; 206:152. [PMID: 38472371 DOI: 10.1007/s00203-024-03871-2] [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: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Producing recombinant proteins is a major accomplishment of biotechnology in the past century. Heterologous hosts, either eukaryotic or prokaryotic, are used for the production of these proteins. The utilization of microbial host systems continues to dominate as the most efficient and affordable method for biotherapeutics and food industry productions. Hence, it is crucial to analyze the limitations and advantages of microbial hosts to enhance the efficient production of recombinant proteins on a large scale. E. coli is widely used as a host for the production of recombinant proteins. Researchers have identified certain obstacles with this host, and given the growing demand for recombinant protein production, there is an immediate requirement to enhance this host. The following review discusses the elements contributing to the manifestation of recombinant protein. Subsequently, it sheds light on innovative approaches aimed at improving the expression of recombinant protein. Lastly, it delves into the obstacles and optimization methods associated with translation, mentioning both cis-optimization and trans-optimization, producing soluble recombinant protein, and engineering the metal ion transportation. In this context, a comprehensive description of the distinct features will be provided, and this knowledge could potentially enhance the expression of recombinant proteins in E. coli.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Yuan D, Liu B, Yuan X, Feng L, Xu X, Zhu J, Chen Z, Xu R, Chen J, Xu G, Lin J, Yang L, Li M, Lian J, Wu M. Multisite Mutation of the Escherichia coli cAMP Receptor Protein: Enhancing Xylitol Biosynthesis by Activating Xylose Catabolism and Improving Strain Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37921650 DOI: 10.1021/acs.jafc.3c05445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The bioproduction of xylitol from hemicellulose hydrolysate has good potential for industrial development. However, xylitol productivity has always been limited due to corncob hydrolysate toxicity and glucose catabolic repression. To address these challenges, this work selected the S83 and S128 amino acid residues of the cyclic AMP receptor protein (CRP) as the modification target. By introducing multisite mutation in CRP, this approach successfully enhanced xylose catabolism and improved the strain's tolerance to corncob hydrolysate. The resulting mutant strain, designated as CPH (CRP S83H-S128P), underwent fermentation in a 20 L bioreactor with semicontinuous feeding of corncob hydrolysate. Remarkably, xylitol yield and xylitol productivity for 41 h fermentation were 175 and 4.32 g/L/h, respectively. Therefore, multisite CRP mutation was demonstrated as an efficient global regulatory strategy to effectively improve xylitol productivity from lime-pretreated corncob hydrolysates.
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Affiliation(s)
- Dongxu Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Bingbing Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xinsong Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230601, PR China
| | - Leilei Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xudong Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jialin Zhu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Zhengjie Chen
- Shandong Weiyan Biotechnology Co., Ltd, Binzhou 256660, PR China
| | - Renhao Xu
- Hangzhou No. 14 Middle School, Hangzhou 310006, PR China
| | - Jiao Chen
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
- Haizheng Pharmaceutical Co., Ltd, Taizhou 318000, PR China
| | - Gang Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd, Quzhou 324302, PR China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, PR China
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
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Campbell RP, Whittington AC, Zorio DAR, Miller BG. Recruitment of a Middling Promiscuous Enzyme Drives Adaptive Metabolic Evolution in Escherichia coli. Mol Biol Evol 2023; 40:msad202. [PMID: 37708398 PMCID: PMC10519446 DOI: 10.1093/molbev/msad202] [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: 04/18/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
A key step in metabolic pathway evolution is the recruitment of promiscuous enzymes to perform new functions. Despite the recognition that promiscuity is widespread in biology, factors dictating the preferential recruitment of one promiscuous enzyme over other candidates are unknown. Escherichia coli contains four sugar kinases that are candidates for recruitment when the native glucokinase machinery is deleted-allokinase (AlsK), manno(fructo)kinase (Mak), N-acetylmannosamine kinase (NanK), and N-acetylglucosamine kinase (NagK). The catalytic efficiencies of these enzymes are 103- to 105-fold lower than native glucokinases, ranging from 2,400 M-1 s-1 for the most active candidate, NagK, to 15 M-1 s-1 for the least active candidate, AlsK. To investigate the relationship between catalytic activities of promiscuous enzymes and their recruitment, we performed adaptive evolution of a glucokinase-deficient E. coli strain to restore glycolytic metabolism. We observed preferential recruitment of NanK via a trajectory involving early mutations that facilitate glucose uptake and amplify nanK transcription, followed by nonsynonymous substitutions in NanK that enhance the enzyme's promiscuous glucokinase activity. These substitutions reduced the native activity of NanK and reduced organismal fitness during growth on an N-acetylated carbon source, indicating that enzyme recruitment comes at a cost for growth on other substrates. Notably, the two most active candidates, NagK and Mak, were not recruited, suggesting that catalytic activity alone does not dictate evolutionary outcomes. The results highlight our lack of knowledge regarding biological drivers of enzyme recruitment and emphasize the need for a systems-wide approach to identify factors facilitating or constraining this important adaptive process.
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Affiliation(s)
- Ryan P Campbell
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Diego A R Zorio
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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Carreón-Rodríguez OE, Gosset G, Escalante A, Bolívar F. Glucose Transport in Escherichia coli: From Basics to Transport Engineering. Microorganisms 2023; 11:1588. [PMID: 37375089 DOI: 10.3390/microorganisms11061588] [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: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Escherichia coli is the best-known model for the biotechnological production of many biotechnological products, including housekeeping and heterologous primary and secondary metabolites and recombinant proteins, and is an efficient biofactory model to produce biofuels to nanomaterials. Glucose is the primary substrate used as the carbon source for laboratory and industrial cultivation of E. coli for production purposes. Efficient growth and associated production and yield of desired products depend on the efficient sugar transport capabilities, sugar catabolism through the central carbon catabolism, and the efficient carbon flux through specific biosynthetic pathways. The genome of E. coli MG1655 is 4,641,642 bp, corresponding to 4702 genes encoding 4328 proteins. The EcoCyc database describes 532 transport reactions, 480 transporters, and 97 proteins involved in sugar transport. Nevertheless, due to the high number of sugar transporters, E. coli uses preferentially few systems to grow in glucose as the sole carbon source. E. coli nonspecifically transports glucose from the extracellular medium into the periplasmic space through the outer membrane porins. Once in periplasmic space, glucose is transported into the cytoplasm by several systems, including the phosphoenolpyruvate-dependent phosphotransferase system (PTS), the ATP-dependent cassette (ABC) transporters, and the major facilitator (MFS) superfamily proton symporters. In this contribution, we review the structures and mechanisms of the E. coli central glucose transport systems, including the regulatory circuits recruiting the specific use of these transport systems under specific growing conditions. Finally, we describe several successful examples of transport engineering, including introducing heterologous and non-sugar transport systems for producing several valuable metabolites.
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Affiliation(s)
- Ofelia E Carreón-Rodríguez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
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5
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Sajid S, Salas LH, Rafiq M, Lund T, Jørgensen MG, Honoré B, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. Physiological response in E. coli to YdgR overexpression depends on whether the protein has an intact function. Biochem Biophys Res Commun 2023; 661:42-49. [PMID: 37087797 DOI: 10.1016/j.bbrc.2023.04.032] [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: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Membrane transport proteins are essential for the transport of a wide variety of molecules across the cell membrane to maintain cellular homeostasis. Generally, these transport proteins can be overexpressed in a suitable host (bacteria, yeast, or mammalian cells), and it is well documented that overexpression of membrane proteins alters the global metabolomic and proteomic profiles of the host cells. In the present study, we investigated the physiological consequences of overexpression of a membrane transport protein YdgR that belongs to the POT/PTR family from E. coli by using the lab strain BL21 (DE3)pLysS in its functional and attenuated mutant YdgR-E33Q. We found significant differences between the omics (metabolomics and proteomics) profiles of the cells expressing functional YdgR as compared to cells expressing attenuated YdgR, e.g., upregulation of several uncharacterized y-proteins and enzymes involved in the metabolism of peptides and amino acids. Furthermore, molecular network analysis suggested a relatively higher presence of proline-containing tripeptides in cells expressing functional YdgR. We envisage that an in-depth investigation of physiological alterations due to protein over-expression may be used for the deorphanization of the y-gene transportome.
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Affiliation(s)
- Salvia Sajid
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Lilia Hernandez Salas
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Torben Lund
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Bent Honoré
- Department of Biomedicine, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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Sangtani R, Nogueira R, Yadav AK, Kiran B. Systematizing Microbial Bioplastic Production for Developing Sustainable Bioeconomy: Metabolic Nexus Modeling, Economic and Environmental Technologies Assessment. JOURNAL OF POLYMERS AND THE ENVIRONMENT 2023; 31:2741-2760. [PMID: 36811096 PMCID: PMC9933833 DOI: 10.1007/s10924-023-02787-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 06/12/2023]
Abstract
The excessive usage of non-renewable resources to produce plastic commodities has incongruously influenced the environment's health. Especially in the times of COVID-19, the need for plastic-based health products has increased predominantly. Given the rise in global warming and greenhouse gas emissions, the lifecycle of plastic has been established to contribute to it significantly. Bioplastics such as polyhydroxy alkanoates, polylactic acid, etc. derived from renewable energy origin have been a magnificent alternative to conventional plastics and reconnoitered exclusively for combating the environmental footprint of petrochemical plastic. However, the economically reasonable and environmentally friendly procedure of microbial bioplastic production has been a hard nut to crack due to less scouted and inefficient process optimization and downstream processing methodologies. Thereby, meticulous employment of computational tools such as genome-scale metabolic modeling and flux balance analysis has been practiced in recent times to understand the effect of genomic and environmental perturbations on the phenotype of the microorganism. In-silico results not only aid us in determining the biorefinery abilities of the model microorganism but also curb our reliance on equipment, raw materials, and capital investment for optimizing the best conditions. Additionally, to accomplish sustainable large-scale production of microbial bioplastic in a circular bioeconomy, extraction, and refinement of bioplastic needs to be investigated extensively by practicing techno-economic analysis and life cycle assessment. This review put forth state-of-the-art know-how on the proficiency of these computational techniques in laying the foundation of an efficient bioplastic manufacturing blueprint, chiefly focusing on microbial polyhydroxy alkanoates (PHA) production and its efficacy in outplacing fossil based plastic products.
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Affiliation(s)
- Rimjhim Sangtani
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, 453552, Indore, India
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management, Leibniz Universität Hannover, Hannover, Germany
| | - Asheesh Kumar Yadav
- CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, Odisha 751013 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Bala Kiran
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, 453552, Indore, India
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Zhang ZX, Nong FT, Wang YZ, Yan CX, Gu Y, Song P, Sun XM. Strategies for efficient production of recombinant proteins in Escherichia coli: alleviating the host burden and enhancing protein activity. Microb Cell Fact 2022; 21:191. [PMID: 36109777 PMCID: PMC9479345 DOI: 10.1186/s12934-022-01917-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli, one of the most efficient expression hosts for recombinant proteins (RPs), is widely used in chemical, medical, food and other industries. However, conventional expression strains are unable to effectively express proteins with complex structures or toxicity. The key to solving this problem is to alleviate the host burden associated with protein overproduction and to enhance the ability to accurately fold and modify RPs at high expression levels. Here, we summarize the recently developed optimization strategies for the high-level production of RPs from the two aspects of host burden and protein activity. The aim is to maximize the ability of researchers to quickly select an appropriate optimization strategy for improving the production of RPs.
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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9
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Han JH, Jung ST, Oh MK. Improved Yield of Recombinant Protein via Flagella Regulator Deletion in Escherichia coli. Front Microbiol 2021; 12:655072. [PMID: 33790884 PMCID: PMC8005581 DOI: 10.3389/fmicb.2021.655072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Protein production requires a significant amount of intracellular energy. Eliminating the flagella has been proposed to help Escherichia coli improve protein production by reducing energy consumption. In this study, the gene encoding a subunit of FlhC, a master regulator of flagella assembly, was deleted to reduce the expression of flagella-related genes. FlhC knockout in the ptsG-deleted strain triggered significant growth retardation with increased ATP levels and a higher NADPH/NADP+ ratio. Metabolic flux analysis using a 13C-labeled carbon substrate showed increased fluxes toward the pentose phosphate and tricarboxylic acid cycle pathways in the flhC- and ptsG-deleted strains. Introduction of a high copy number plasmid or overexpression of the recombinant protein in this strain restored growth rate without increasing glucose consumption. These results suggest that the metabolic burden caused by flhC deletion was resolved by recombinant protein production. The recombinant enhanced green fluorescent protein yield per glucose consumption increased 1.81-fold in the flhC mutant strain. Thus, our study demonstrates that high-yield production of the recombinant protein was achieved with reduced flagella formation.
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Affiliation(s)
- Jae-Ho Han
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
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Jung H, Han J, Oh M. Improved production of 2,3-butanediol and isobutanol by engineering electron transport chain in Escherichia coli. Microb Biotechnol 2021; 14:213-226. [PMID: 32954676 PMCID: PMC7888471 DOI: 10.1111/1751-7915.13669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
The electron transport chain (ETC) is one of the major energy generation pathways in microorganisms under aerobic condition. Higher yield of ATP can be achieved through oxidative phosphorylation with consumption of NADH than with substrate level phosphorylation. However, most value-added metabolites are in an electrochemically reduced state, which requires reducing equivalent NADH as a cofactor. Therefore, optimal production of value-added metabolites should be balanced with ETC in terms of energy production. In this study, we attempted to reduce the activity of ETC to secure availability of NADH. The ETC mutants exhibited poor growth rate and production of fermentative metabolites compared to parental strain. Introduction of heterologous pathways for synthesis of 2,3-butanediol and isobutanol to ETC mutants resulted in increased titres and yields of the metabolites. ETC mutants yielded higher NADH/NAD+ ratio but similar ATP content than that by the parental strain. Furthermore, ETC mutants operated fermentative metabolism pathways independent of oxygen supply in large-scale fermenter, resulting in increased yield and titre of 2,3-butanediol. Thus, engineering of ETC is a useful metabolic engineering approach for production of reduced metabolites.
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Affiliation(s)
- Hwi‐Min Jung
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
| | - Jae‐Ho Han
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
| | - Min‐Kyu Oh
- Department of Chemical and Biological EngineeringKorea University145 Anam‐ro, Seongbuk‐guSeoul02841Korea
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11
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Li L, Liu Z, Jiang H, Mao X. Biotechnological production of lycopene by microorganisms. Appl Microbiol Biotechnol 2020; 104:10307-10324. [PMID: 33097966 DOI: 10.1007/s00253-020-10967-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 12/16/2022]
Abstract
Lycopene is a dark red carotenoid belonging to C40 terpenoids and is widely found in a variety of plants, especially ripe red fruits and vegetables. Lycopene has been shown to reduce the risk of prostate cancer, other cancers, and cardiovascular disease. It is one of the most widely used carotenoids in the healthcare product market. Currently, commercially available lycopene is mainly extracted from tomatoes. However, production of lycopene from plants is costly and environmentally unfriendly. To date, there have been many reports on the biosynthesis of lycopene by microorganisms, providing another route for lycopene production. This review discusses the lycopene biosynthetic pathway and natural and engineered lycopene-accumulating microorganisms, as well as their production of lycopene. The effects of different metabolic engineering strategies on lycopene accumulation are also considered. Furthermore, this work presents perspectives concerning the microbial production of lycopene, especially trends to construct microbial cell factories for lycopene production. KEY POINTS: • Recent achievements in the lycopene biosynthesis in microorganisms. • Review of lycopene biosynthetic metabolism engineering strategy. • Discuss the current challenges and prospects of using microorganisms to produce lycopene.
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Affiliation(s)
- Lei Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Hong Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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12
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Im D, Hong J, Gu B, Sung C, Oh M. 13
C Metabolic Flux Analysis of
Escherichia coli
Engineered for Gamma‐Aminobutyrate Production. Biotechnol J 2020; 15:e1900346. [DOI: 10.1002/biot.201900346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Dae‐Kyun Im
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Jaeseung Hong
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Boncheol Gu
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Changmin Sung
- Doping Control CenterKorea Institute of Science and Technology 5 Hwarang‐ro 14‐gil, Seongbuk‐gu Seoul 02792 Korea
| | - Min‐Kyu Oh
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
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Mauri M, Gouzé JL, de Jong H, Cinquemani E. Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs. PLoS Comput Biol 2020; 16:e1007795. [PMID: 32282794 PMCID: PMC7179936 DOI: 10.1371/journal.pcbi.1007795] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/23/2020] [Accepted: 03/18/2020] [Indexed: 01/20/2023] Open
Abstract
Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species. In nature, microorganisms occur in communities comprising a variety of mutually interacting species. Established through evolution, these interactions allow for the survival and growth of microorganisms in their natural environment, and give rise to complex dynamics that could not be exhibited by any of the species in isolation. The richness of microbial community dynamics has been leveraged to outperform individual species in biotechnological production processes and other processes of high societal value. Yet, in view of their complexity, natural communities are difficult to study and control. In order to overcome these issues, a rapidly growing research field concerns the rational design and engineering of synthetic microbial consortia. Despite the great potential of synthetic microbial consortia, and significant efforts devoted to their mathematical modelling and analysis, a detailed understanding of how enhanced production can be achieved, and at what cost, is still unavailable. In this work, based on a quantitative model of a prototypical synthetic microbial consortium, we determine precise conditions under which a consortium outperforms individual species in the production of a recombinant protein. Moreover, we identify the inherent trade-offs between productivity and efficiency of substrate utilization.
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Affiliation(s)
- Marco Mauri
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
| | - Jean-Luc Gouzé
- University Côte d’Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, 06902 Sophia-Antipolis, France
| | - Hidde de Jong
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
- * E-mail: (HdJ); (EC)
| | - Eugenio Cinquemani
- Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
- * E-mail: (HdJ); (EC)
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Hong J, Im DK, Oh MK. Investigating E. coli Coculture for Resveratrol Production with 13C Metabolic Flux Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3466-3473. [PMID: 32079399 DOI: 10.1021/acs.jafc.9b07628] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Resveratrol, a phytoalexin produced by plants, has several beneficial effects in humans. It can be produced using Escherichia coli by introducing only three heterologous genes: TAL, 4CL, and STS. However, the resveratrol synthesis pathway requires two precursors, tyrosine and acetyl-CoA, which are produced by two branched central metabolic pathways. Therefore, overexpression of these genes in E. coli results in the production of only trace amounts of resveratrol. In this study, we attempted to produce resveratrol via coculture of two engineered strains in which the two metabolic pathways are activated. The first strain was engineered to produce p-coumaric acid using tyrosine as a precursor, which can be synthesized by the pentose phosphate pathway. The second strain produced resveratrol by combining p-coumaric acid from the first strain and malonyl-CoA synthesized from acetyl-CoA, which is produced by the glycolytic pathway. In total, 55.7 mg/L of resveratrol was produced from 20 g/L of glucose via coculture of these two strains in glucose minimal medium without any supplements. The metabolic fluxes in each of the strains producing resveratrol were successfully investigated by 13C metabolic flux analysis. The results showed that the balance between the citric acid cycle and the malonyl-CoA supply node was important for resveratrol production.
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Affiliation(s)
- Jaeseung Hong
- Department of Chemical & Biological Engineering, Korea University, Anam-Ro 145, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Dae-Kyun Im
- Department of Chemical & Biological Engineering, Korea University, Anam-Ro 145, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Anam-Ro 145, Seongbuk-Gu, Seoul 02841, Republic of Korea
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Jin T, Käldström M, Benavides A, Rechulski MDK, Jarboe LR. Utilization of mechanocatalytic oligosaccharides by ethanologenic Escherichia coli as a model microbial cell factory. AMB Express 2020; 10:28. [PMID: 32016659 PMCID: PMC6997310 DOI: 10.1186/s13568-020-0965-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
Mechanocatalysis is a promising method for depolymerization of lignocellulosic biomass. Microbial utilization of the resulting oligosaccharides is one potential route of adding value to the depolymerized biomass. However, it is unclear how readily these oligosaccharides are utilized by standard cell factories. Here, we investigate utilization of cellulose subjected to mechanocatalytic depolymerization, using ethanologenic Escherichia coli as a model fermentation organism. The mechanocatalytic oligosaccharides supported ethanol titers similar to those observed when glucose was provided at comparable concentrations. Tracking of the various oligomers, using maltose (alpha-1,4) and cellobiose (beta-1,4) oligomers as representative standards of the orientation, but not linkage, of the glycosidic bond, suggests that the malto-like-oligomers are more readily utilized than cello-like-oligomers, consistent with poor growth with cellotetraose or cellopentaose as sole carbon source. Thus, mechanocatalytic oligosaccharides are a promising substrate for cell factories, and microbial utilization of these sugars could possibly be improved by addressing utilization of cello-like oligomers.
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Affiliation(s)
- Tao Jin
- Department of Chemical and Biological Engineering, Iowa State University, 4134 Biorenewables Research Laboratory, 617 Bissell Rd, Ames, IA, USA
| | - Mats Käldström
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Mulheim an der Ruhr, Germany
| | - Adriana Benavides
- Department of Chemical and Biological Engineering, Iowa State University, 4134 Biorenewables Research Laboratory, 617 Bissell Rd, Ames, IA, USA
- BioMAP REU Program, Ames, IA, USA
| | - Marcelo D Kaufman Rechulski
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Mulheim an der Ruhr, Germany
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, 4134 Biorenewables Research Laboratory, 617 Bissell Rd, Ames, IA, USA.
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