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Dodia H, Mishra V, Nakrani P, Muddana C, Kedia A, Rana S, Sahasrabuddhe D, Wangikar PP. Dynamic flux balance analysis of high cell density fed-batch culture of Escherichia coli BL21 (DE3) with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2024; 121:1394-1406. [PMID: 38214104 DOI: 10.1002/bit.28654] [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: 08/23/2023] [Revised: 12/08/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
Dynamic flux balance analysis (FBA) allows estimation of intracellular reaction rates using organism-specific genome-scale metabolic models (GSMM) and by assuming instantaneous pseudo-steady states for processes that are inherently dynamic. This technique is well-suited for industrial bioprocesses employing complex media characterized by a hierarchy of substrate uptake and product secretion. However, knowledge of exchange rates of many components of the media would be required to obtain meaningful results. Here, we performed spent media analysis using mass spectrometry coupled with liquid and gas chromatography for a fed-batch, high-cell density cultivation of Escherichia coli BL21(DE3) expressing a recombinant protein. Time course measurements thus obtained for 246 metabolites were converted to instantaneous exchange rates. These were then used as constraints for dynamic FBA using a previously reported GSMM, thus providing insights into how the flux map evolves through the process. Changes in tri-carboxylic acid cycle fluxes correlated with the increased demand for energy during recombinant protein production. The results show how amino acids act as hubs for the synthesis of other cellular metabolites. Our results provide a deeper understanding of an industrial bioprocess and will have implications in further optimizing the process.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vivek Mishra
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | | | | | - Anant Kedia
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Sneha Rana
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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2
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Matsuyama C, Seike T, Okahashi N, Niide T, Hara KY, Hirono-Hara Y, Ishii J, Shimizu H, Toya Y, Matsuda F. Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin. J Biosci Bioeng 2024; 137:187-194. [PMID: 38281859 DOI: 10.1016/j.jbiosc.2023.12.003] [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: 07/07/2023] [Revised: 11/18/2023] [Accepted: 12/04/2023] [Indexed: 01/30/2024]
Abstract
Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E. coli strains have distinct metabolic capacities. In this study, two proteins were overexpressed in four E. coli strains (MG1655(DE3), W3110(DE3), BL21star(DE3), and Rosetta(DE3)), and their effects on metabolic burden were investigated. Metabolomic analysis showed that E. coli strains overexpressing green fluorescent protein had decreased levels of several metabolites, with a positive correlation between the number of reduced metabolites and green fluorescent protein expression levels. Moreover, nucleic acid-related metabolites decreased, indicating a metabolic burden in the E. coli strains, and the growth rate and protein expression levels were improved by supplementation with the five nucleosides. In contrast, two strains overexpressing delta rhodopsin, a microbial membrane rhodopsin from Haloterrigena turkmenica, led to a metabolic burden and decrease in the amino acids Ala, Val, Leu, Ile, Thr, Phe, Asp, and Trp, which are the most frequent amino acids in the delta rhodopsin protein sequence. The metabolic burden caused by protein overexpression was influenced by the metabolic capacity of the host strains and the sequences of the overexpressed proteins. Detailed characterization of the effects of protein expression on the metabolic state of engineered cells using metabolomics will provide insights into improving the production of target compounds.
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Affiliation(s)
- Chinatsu Matsuyama
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Taisuke Seike
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
| | - Teppei Niide
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | | | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan.
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3
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Wen J, Chen C. From Energy Metabolic Change to Precision Therapy: a Holistic View of Energy Metabolism in Heart Failure. J Cardiovasc Transl Res 2024; 17:56-70. [PMID: 37450209 DOI: 10.1007/s12265-023-10412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
Heart failure (HF) is a complex and multifactorial disease that affects millions of people worldwide. It is characterized by metabolic disturbances of substrates such as glucose, fatty acids (FAs), ketone bodies, and amino acids, which lead to changes in cardiac energy metabolism pathways. These metabolic alterations can directly or indirectly promote myocardial remodeling, thereby accelerating the progression of HF, resulting in a vicious cycle of worsening symptoms, and contributing to the increased hospitalization and mortality among patients with HF. In this review, we summarized the latest researches on energy metabolic profiling in HF and provided the related translational therapeutic strategies for this devastating disease. By taking a holistic approach to understanding energy metabolism changes in HF, we hope to provide comprehensive insights into the pathophysiology of this challenging condition and identify novel precise targets for the development of more effective treatments.
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Affiliation(s)
- Jianpei Wen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Avenue, Wuhan, 430030, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China
| | - Chen Chen
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Avenue, Wuhan, 430030, China.
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, China.
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4
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Cordell WT, Avolio G, Takors R, Pfleger BF. Milligrams to kilograms: making microbes work at scale. Trends Biotechnol 2023; 41:1442-1457. [PMID: 37271589 DOI: 10.1016/j.tibtech.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
If biomanufacturing can become a sustainable route for producing chemicals, it will provide a critical step in reducing greenhouse gas emissions to fight climate change. However, efforts to industrialize microbial synthesis of chemicals have met with varied success, due, in part, to challenges in translating laboratory successes to industrial scale. With a particular focus on Escherichia coli, this review examines the lessons learned when studying microbial physiology and metabolism under conditions that simulate large-scale bioreactors and methods to minimize cellular waste through reduction of maintenance energy, optimizing the stress response and minimizing culture heterogeneity. With general strategies to overcome these challenges, biomanufacturing process scale-up could be de-risked and the time and cost of bringing promising syntheses to market could be reduced.
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Affiliation(s)
- William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gennaro Avolio
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Center Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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5
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Lee CY, Chen KW, Chiang CL, Kao HY, Yu HC, Lee HC, Chen WL. Improved production of β-carotene in light-powered Escherichia coli by co-expression of Gloeobacter rhodopsin expression. Microb Cell Fact 2023; 22:207. [PMID: 37817206 PMCID: PMC10563301 DOI: 10.1186/s12934-023-02212-0] [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: 05/25/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Providing sufficient and usable energy for the cell factory has long been a heated issue in biosynthesis as solar energy has never been rooted out from the strategy for improvement, and turning Escherichia coli (E. coli) into a phototrophic host has multiple captivating qualities for biosynthesis. In this study, β-carotene was a stable compound for production in E. coli with the expression of four enzymes (CrtE, CrtB, CrtI, CrtY) for production due to its light-harvesting feature as an antenna pigment and as an antioxidant and important precursor for human health. The expression of Gloeobacter rhodopsin (GR) in microbial organisms was proved to have potential for application. RESULTS The expression of fusion protein, GR-GFP, in E. coli showed visible GFP signal under fluorescent microscopy, and its in vivo proton pumping activity signal can be detected in induced photocurrent by electrodes on the chip under intervals of illumination. To assess the phototrophic synthesis ability of the host strain compared to wild-type and vector control strain in chemostat batch with illumination, the expression of red fluorescent protein (RFP) as a target protein showed its yield improvement in protein assay and also reflected its early dominance in RFP fluorescence signal during the incubation, whereas the synthesis of β-carotene also showed yield increase by 1.36-fold and 2.32-fold compared with its wildtype and vector control strain. To investigate the effect of GR-GFP on E. coli, the growth of the host showed early rise into the exponential phase compared to the vector control strain and glucose turnover rate was elevated in increased glucose intake rate and upregulation of ATP-related genes in glycolysis (PtsG, Pgk, Pyk). CONCLUSION We reported the first-time potential application of GR in the form of fusion protein GR-GFP. Expression of GR-GFP in E. coli improved the production of β-carotene and RFP. Our work provides a strain of E. coli harboring phototrophic metabolism, thus paving path to a more sustainable and scalable production of biosynthesis.
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Affiliation(s)
- Chao-Yu Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Kai-Wen Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Chih-Lu Chiang
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsuan-Yu Kao
- Department of Mechanical Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hao-Cheng Yu
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsiao-Ching Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Wen-Liang Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan.
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6
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Gould H, Cheung W, Finnigan JD, Muñoz-Muñoz J, Charnock SJ, Black GW. In Search of Complementary Extraction Methods for Comprehensive Coverage of the Escherichia coli Metabolome. Metabolites 2023; 13:1010. [PMID: 37755290 PMCID: PMC10535102 DOI: 10.3390/metabo13091010] [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: 08/07/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Escherichia coli is an invaluable research tool for many fields of biology, in particular for the production of recombinant enzymes. However, the activity of many such recombinant enzymes cannot be determined using standard biochemical assays, as often, the relevant substrates are not known, or the products produced are not detectable. Today, the biochemical footprints of such unknown enzyme activities can be revealed via the analysis of the metabolomes of the recombinant E. coli clones in which they are expressed, using sensitive technologies such as mass spectrometry. However, before any metabolites can be identified, it is necessary to achieve as high a coverage of the potential metabolites present within E. coli as possible. We have therefore analyzed a wide range of different extraction methods against the cell free extracts of various recombinant E. coli clones. The results were analyzed to determine the minimum number of extractions that achieved high recovery and coverage of metabolites. Two methods were selected for further analysis due to their ability to produce not only high numbers of ions, but also wide mass coverage and a high degree of complementarity. One extraction method uses acetonitrile and water, in a 4:1 ratio, which is then dried down and reconstituted in the chromatography running buffer prior to injection onto the chromatography column, and the other extraction method uses a combination of methanol, water and chloroform, in a 3:1:1 ratio, which is injected directly onto the chromatography column. These two extraction methods were shown to be complementary to each other, as regards the respective metabolites extracted, and to cover a large range of metabolites.
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Affiliation(s)
- Henry Gould
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - James D Finnigan
- Prozomix Limited, West End Industrial Estate, Haltwhistle NE49 9HA, UK
| | - José Muñoz-Muñoz
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Simon J Charnock
- Prozomix Limited, West End Industrial Estate, Haltwhistle NE49 9HA, UK
| | - Gary W Black
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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7
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Emani SS, Kan A, Storms T, Bonanno S, Law J, Ray S, Joshi NS. Periplasmic stress contributes to a trade-off between protein secretion and cell growth in Escherichia coli Nissle 1917. Synth Biol (Oxf) 2023; 8:ysad013. [PMID: 37601821 PMCID: PMC10439730 DOI: 10.1093/synbio/ysad013] [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: 12/29/2022] [Revised: 06/29/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
Maximizing protein secretion is an important target in the design of engineered living systems. In this paper, we characterize a trade-off between cell growth and per-cell protein secretion in the curli biofilm secretion system of Escherichia coli Nissle 1917. Initial characterization using 24-h continuous growth and protein production monitoring confirms decreased growth rates at high induction, leading to a local maximum in total protein production at intermediate induction. Propidium iodide (PI) staining at the endpoint indicates that cellular death is a dominant cause of growth reduction. Assaying variants with combinatorial constructs of inner and outer membrane secretion tags, we find that diminished growth at high production is specific to secretory variants associated with periplasmic stress mediated by outer membrane secretion and periplasmic accumulation of protein containing the outer membrane transport tag. RNA sequencing experiments indicate upregulation of known periplasmic stress response genes in the highly secreting variant, further implicating periplasmic stress in the growth-secretion trade-off. Overall, these results motivate additional strategies for optimizing total protein production and longevity of secretory engineered living systems Graphical Abstract.
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Affiliation(s)
| | - Anton Kan
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Timothy Storms
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Shanna Bonanno
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Jade Law
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sanhita Ray
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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8
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Calvanese M, Balestra C, Colarusso A, Lauro C, Riccardi C, Fondi M, Parrilli E, Tutino ML. Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125. Appl Microbiol Biotechnol 2023; 107:2469-2481. [PMID: 36912903 PMCID: PMC10033558 DOI: 10.1007/s00253-023-12448-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/23/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) is considered an interesting alternative host for the recombinant protein production, that can be explored when the conventional bacterial expression systems fail. Indeed, the manufacture of all the difficult-to-express proteins produced so far in this bacterial platform gave back soluble and active products. Despite these promising results, the low yield of recombinant protein production achieved is hampering the wider and industrial exploitation of this psychrophilic cell factory. All the expression plasmids developed so far in PhTAC125 are based on the origin of replication of the endogenous pMtBL plasmid and are maintained at a very low copy number. In this work, we set up an experimental strategy to select mutated OriR sequences endowed with the ability to establish recombinant plasmids at higher multiplicity per cell. The solution to this major production bottleneck was achieved by the construction of a library of psychrophilic vectors, each containing a randomly mutated version of pMtBL OriR, and its screening by fluorescence-activated cell sorting (FACS). The selected clones allowed the identification of mutated OriR sequences effective in enhancing the plasmid copy number of approximately two orders of magnitude, and the production of the recombinant green fluorescent protein was increased up to twenty times approximately. Moreover, the molecular characterization of the different mutant OriR sequences allowed us to suggest some preliminary clues on the pMtBL replication mechanism that deserve to be further investigated in the future. KEY POINTS: • Setup of an electroporation procedure for Pseudoalteromonas haloplanktis TAC125. • Two order of magnitude improvement of OriR-derived psychrophilic expression systems. • Almost twenty times enhancement in Green fluorescent protein production.
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Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
| | - Cecilia Balestra
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Oceanography Division - OGS, Trieste, Italy
| | - Andrea Colarusso
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie d'Oro, 305-00136, Rome, Italy
| | - Christopher Riccardi
- Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, 50018, Florence, Italy
| | - Marco Fondi
- Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, 50018, Florence, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, Federico II University of Naples, Complesso Universitario Monte S.- Angelo, Via Cintia, 80126, Naples, Italy.
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9
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García-Calvo L, Rane DV, Everson N, Humlebrekk ST, Mathiassen LF, Mæhlum AHM, Malmo J, Bruheim P. Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2023.1142226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used host for recombinant protein production, both as an industrial expression platform and as a model system at laboratory scale. The recombinant protein production industry generates proteins with direct applications as biopharmaceuticals and in technological processes central to a plethora of fields. Despite the increasing economic significance of recombinant protein production, and the importance of E. coli as an expression platform and model organism, only few studies have focused on the central carbon metabolic landscape of E. coli during high-level recombinant protein production. In the present work, we applied four targeted CapIC- and LC-MS/MS methods, covering over 60 metabolites, to perform an in-depth metabolite profiling of the effects of high-level recombinant protein production in strains derived from E. coli BL21, carrying XylS/Pm vectors with different characteristics. The mass-spectrometric central carbon metabolite profiling was complemented with the study of growth kinetics and protein production in batch bioreactors. Our work shows the robustness in E. coli central carbon metabolism when introducing increased plasmid copy number, as well as the greater importance of induction of recombinant protein production as a metabolic challenge, especially when strong promoters are used.
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10
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Baez A, Sharma AK, Bryukhanov A, Anderson ED, Rudack L, Olivares-Hernández R, Quan D, Shiloach J. Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures while upregulating anaerobic respiratory chains. N Biotechnol 2022; 71:11-20. [PMID: 35777694 PMCID: PMC9444934 DOI: 10.1016/j.nbt.2022.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 10/31/2022]
Abstract
Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 μM) is characterized by lower biomass yield, higher acetate accumulation and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, previous studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. Here, the effect of iron availability on the energy metabolism of E. coli has been investigated. It was established that aerobic cultures growing under limiting iron conditions showed lower ATP yield per glucose, lower growth rate and lower TCA cycle activity and respiration, at the same time as increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independent of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiratory chain. In conditions of iron excess, some iron-requiring terminal reductases of the respiratory chain, that were thought to function only under anaerobiosis, were used by the E. coli, when in aerobic conditions, to maintain high respiratory activity. This allowed it to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase and catalase) and the iron-sulfur cluster repair systems.
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Affiliation(s)
- Antonino Baez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - Ashish K Sharma
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - Andrey Bryukhanov
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University (MSU), Moscow, Russia
| | - Eric D Anderson
- Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - Leba Rudack
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe, 05348 Mexico City, Mexico
| | - David Quan
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA.
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11
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Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide. J Microbiol 2022; 60:960-967. [DOI: 10.1007/s12275-022-2122-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
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12
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Li Z, Nees M, Bettenbrock K, Rinas U. Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microb Cell Fact 2022; 21:67. [PMID: 35449049 PMCID: PMC9027384 DOI: 10.1186/s12934-022-01787-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/26/2022] [Indexed: 12/20/2022] Open
Abstract
Background Escherichia coli adapted to carbon-limiting conditions is generally geared for energy-efficient carbon utilization. This includes also the efficient utilization of glucose, which serves as a source for cellular building blocks as well as energy. Thus, catabolic and anabolic functions are balanced under these conditions to minimize wasteful carbon utilization. Exposure to glucose excess interferes with the fine-tuned coupling of anabolism and catabolism leading to the so-called carbon overflow metabolism noticeable through acetate formation and eventually growth inhibition. Results Cellular adaptations towards sudden but timely limited carbon excess conditions were analyzed by exposing slow-growing cells in steady state glucose-limited continuous culture to a single glucose pulse. Concentrations of metabolites as well as time-dependent transcriptome alterations were analyzed and a transcriptional network analysis performed to determine the most relevant transcription and sigma factor combinations which govern these adaptations. Down-regulation of genes related to carbon catabolism is observed mainly at the level of substrate uptake and downstream of pyruvate and not in between in the glycolytic pathway. It is mainly accomplished through the reduced activity of CRP-cAMP and through an increased influence of phosphorylated ArcA. The initiated transcriptomic change is directed towards down-regulation of genes, which contribute to active movement, carbon uptake and catabolic carbon processing, in particular to down-regulation of genes which contribute to efficient energy generation. Long-term changes persisting after glucose depletion and consumption of acetete encompassed reduced expression of genes related to active cell movement and enhanced expression of genes related to acid resistance, in particular acid resistance system 2 (GABA shunt) which can be also considered as an inefficient bypass of the TCA cycle. Conclusions Our analysis revealed that the major part of the trancriptomic response towards the glucose pulse is not directed towards enhanced cell proliferation but towards protection against excessive intracellular accumulation of potentially harmful concentration of metabolites including among others energy rich compounds such as ATP. Thus, resources are mainly utilized to cope with “overfeeding” and not for growth including long-lasting changes which may compromise the cells future ability to perform optimally under carbon-limiting conditions (reduced motility and ineffective substrate utilization). Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01787-4.
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Affiliation(s)
- Zhaopeng Li
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany
| | - Markus Nees
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany. .,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany.
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Bhave D, Tautz D. Effects of the Expression of Random Sequence Clones on Growth and Transcriptome Regulation in Escherichia coli. Genes (Basel) 2021; 13:genes13010053. [PMID: 35052392 PMCID: PMC8775113 DOI: 10.3390/genes13010053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 02/04/2023] Open
Abstract
Comparative genomic analyses have provided evidence that new genetic functions can emerge out of random nucleotide sequences. Here, we apply a direct experimental approach to study the effects of plasmids harboring random sequence inserts under the control of an inducible promoter. Based on data from previously described experiments dealing with the growth of clones within whole libraries, we extracted specific clones that had shown either negative, neutral or positive effects on relative cell growth. We analyzed these individually with respect to growth characteristics and the impact on the transcriptome. We find that candidate clones for negative peptides lead to growth arrest by eliciting a general stress response. Overexpression of positive clones, on the other hand, does not change the exponential growth rates of hosts, and they show a growth advantage over a neutral clone when tested in direct competition experiments. Transcriptomic changes in positive clones are relatively moderate and specific to each clone. We conclude from our experiments that random sequence peptides are indeed a suitable source for the de novo evolution of genetic functions.
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Du F, Liu YQ, Xu YS, Li ZJ, Wang YZ, Zhang ZX, Sun XM. Regulating the T7 RNA polymerase expression in E. coli BL21 (DE3) to provide more host options for recombinant protein production. Microb Cell Fact 2021; 20:189. [PMID: 34565359 PMCID: PMC8474846 DOI: 10.1186/s12934-021-01680-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023] Open
Abstract
Escherichia coli is the most widely used bacterium in prokaryotic expression system for the production of recombinant proteins. In BL21 (DE3), the gene encoding the T7 RNA polymerase (T7 RNAP) is under control of the strong lacUV5 promoter (PlacUV5), which is leakier and more active than wild-type lac promoter (PlacWT) under certain growth conditions. These characteristics are not advantageous for the production of those recombinant proteins with toxic or growth-burdened. On the one hand, leakage expression of T7 RNAP leads to rapid production of target proteins under non-inducing period, which sucks resources away from cellular growth. Moreover, in non-inducing or inducing period, high expression of T7 RNAP production leads to the high-production of hard-to-express proteins, which may all lead to loss of the expression plasmid or the occurrence of mutations in the expressed gene. Therefore, more BL21 (DE3)-derived variant strains with rigorous expression and different expression level of T7 RNAP should be developed. Hence, we replaced PlacUV5 with other inducible promoters respectively, including arabinose promoter (ParaBAD), rhamnose promoter (PrhaBAD), tetracycline promoter (Ptet), in order to optimize the production of recombinant protein by regulating the transcription level and the leakage level of T7 RNAP. Compared with BL21 (DE3), the constructed engineered strains had higher sensitivity to inducers, among which rhamnose and tetracycline promoters had the lowest leakage ability. In the production of glucose dehydrogenase (GDH), a protein that causes host autolysis, the engineered strain BL21 (DE3::ara) exhibited higher biomass, cell survival rate and foreign protein expression level than that of BL21 (DE3). In addition, these engineered strains had been successfully applied to improve the production of membrane proteins, including E. coli cytosine transporter protein (CodB), the E. coli membrane protein insertase/foldase (YidC), and the E. coli F-ATPase subunit b (Ecb). The engineered strains constructed in this paper provided more host choices for the production of recombinant proteins.
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Affiliation(s)
- Fei Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yun-Qi Liu
- Nanjing Foreign Language School, Nanjing, People's Republic of China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zi-Jia Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yu-Zhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China.
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Weber J, Li Z, Rinas U. Recombinant protein production provoked accumulation of ATP, fructose-1,6-bisphosphate and pyruvate in E. coli K12 strain TG1. Microb Cell Fact 2021; 20:169. [PMID: 34446023 PMCID: PMC8394631 DOI: 10.1186/s12934-021-01661-9] [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: 06/11/2021] [Accepted: 08/16/2021] [Indexed: 12/03/2022] Open
Abstract
Background Recently it was shown that production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress comparable to a carbon overfeeding response. Opposite to original expectations generation of energy as well as catabolic provision of precursor metabolites were excluded as limiting factors for growth and protein production. On the contrary, accumulation of ATP and precursor metabolites revealed their ample formation but insufficient withdrawal as a result of protein production mediated constraints in anabolic pathways. Thus, not limitation but excess of energy and precursor metabolites were identified as being connected to the protein production associated metabolic burden. Results Here we show that the protein production associated accumulation of energy and catabolic precursor metabolites is not unique to E. coli BL21(DE3) but also occurs in E. coli K12. Most notably, it was demonstrated that the IPTG-induced production of hFGF-2 using a tac-promoter based expression vector in the E. coli K12 strain TG1 was leading to persistent accumulation of key regulatory molecules such as ATP, fructose-1,6-bisphosphate and pyruvate. Conclusions Excessive energy generation, respectively, accumulation of ATP during recombinant protein production is not unique to the BL21(DE3)/T7 promoter based expression system but also observed in the E. coli K12 strain TG1 using another promoter/vector combination. These findings confirm that energy is not a limiting factor for recombinant protein production. Moreover, the data also show that an accelerated glycolytic pathway flux aggravates the protein production associated “metabolic burden”. Under conditions of compromised anabolic capacities cells are not able to reorganize their metabolic enzyme repertoire as required for reduced carbon processing.
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Affiliation(s)
- Jan Weber
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Zhaopeng Li
- Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany. .,Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany.
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Impact of the Expression System on Recombinant Protein Production in Escherichia coli BL21. Front Microbiol 2021; 12:682001. [PMID: 34234760 PMCID: PMC8257044 DOI: 10.3389/fmicb.2021.682001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production for medical, academic, or industrial applications is essential for our current life. Recombinant proteins are obtained mainly through microbial fermentation, with Escherichia coli being the host most used. In spite of that, some problems are associated with the production of recombinant proteins in E. coli, such as the formation of inclusion bodies, the metabolic burden, or the inefficient translocation/transport system of expressed proteins. Optimizing transcription of heterologous genes is essential to avoid these drawbacks and develop competitive biotechnological processes. Here, expression of YFP reporter protein is evaluated under the control of four promoters of different strength (PT7lac, Ptrc, Ptac, and PBAD) and two different replication origins (high copy number pMB1′ and low copy number p15A). In addition, the study has been carried out with the E. coli BL21 wt and the ackA mutant strain growing in a rich medium with glucose or glycerol as carbon sources. Results showed that metabolic burden associated with transcription and translation of foreign genes involves a decrease in recombinant protein expression. It is necessary to find a balance between plasmid copy number and promoter strength to maximize soluble recombinant protein expression. The results obtained represent an important advance on the most suitable expression system to improve both the quantity and quality of recombinant proteins in bioproduction engineering.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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