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Phégnon L, Pérochon J, Uttenweiler-Joseph S, Cahoreau E, Millard P, Létisse F. 6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway. FEBS J 2024. [PMID: 38982839 DOI: 10.1111/febs.17221] [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: 01/18/2024] [Revised: 04/03/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024]
Abstract
The metabolic networks of microorganisms are remarkably robust to genetic and environmental perturbations. This robustness stems from redundancies such as gene duplications, isoenzymes, alternative metabolic pathways, and also from non-enzymatic reactions. In the oxidative branch of the pentose phosphate pathway (oxPPP), 6-phosphogluconolactone hydrolysis into 6-phosphogluconate is catalysed by 6-phosphogluconolactonase (Pgl) but in the absence of the latter, the oxPPP flux is thought to be maintained by spontaneous hydrolysis. However, in Δpgl Escherichia coli, an extracellular pathway can also contribute to pentose phosphate synthesis. This raises question as to whether the intracellular non-enzymatic reaction can compensate for the absence of 6-phosphogluconolactonase and, ultimately, on the role of 6-phosphogluconolactonase in central metabolism. Our results validate that the bypass pathway is active in the absence of Pgl, specifically involving the extracellular spontaneous hydrolysis of gluconolactones to gluconate. Under these conditions, metabolic flux analysis reveals that this bypass pathway accounts for the entire flux into the oxPPP. This alternative metabolic route-partially extracellular-sustains the flux through the oxPPP necessary for cell growth, albeit at a reduced rate in the absence of Pgl. Importantly, these findings imply that intracellular non-enzymatic hydrolysis of 6-phosphogluconolactone does not compensate for the absence of Pgl. This underscores the crucial role of Pgl in ensuring the efficient functioning of the oxPPP.
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Affiliation(s)
- Léa Phégnon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Julien Pérochon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Edern Cahoreau
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), France
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Gong Y, Wang R, Ma L, Wang S, Li C, Xu Q. Optimization of trans-4-hydroxyproline synthesis pathway by rearrangement center carbon metabolism in Escherichia coli. Microb Cell Fact 2023; 22:240. [PMID: 37986164 PMCID: PMC10659092 DOI: 10.1186/s12934-023-02236-6] [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: 08/08/2023] [Accepted: 10/22/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND trans-4-Hydroxyproline (T-4-HYP) is a promising intermediate in the synthesis of antibiotic drugs. However, its industrial production remains challenging due to the low production efficiency of T-4-HYP. This study focused on designing the key nodes of anabolic pathway to enhance carbon flux and minimize carbon loss, thereby maximizing the production potential of microbial cell factories. RESULTS First, a basic strain, HYP-1, was developed by releasing feedback inhibitors and expressing heterologous genes for the production of trans-4-hydroxyproline. Subsequently, the biosynthetic pathway was strengthened while branching pathways were disrupted, resulting in increased metabolic flow of α-ketoglutarate in the Tricarboxylic acid cycle. The introduction of the NOG (non-oxidative glycolysis) pathway rearranged the central carbon metabolism, redirecting glucose towards acetyl-CoA. Furthermore, the supply of NADPH was enhanced to improve the acid production capacity of the strain. Finally, the fermentation process of T-4-HYP was optimized using a continuous feeding method. The rate of sugar supplementation controlled the dissolved oxygen concentrations during fermentation, and Fe2+ was continuously fed to supplement the reduced iron for hydroxylation. These modifications ensured an effective supply of proline hydroxylase cofactors (O2 and Fe2+), enabling efficient production of T-4-HYP in the microbial cell factory system. The strain HYP-10 produced 89.4 g/L of T-4-HYP in a 5 L fermenter, with a total yield of 0.34 g/g, the highest values reported by microbial fermentation, the yield increased by 63.1% compared with the highest existing reported yield. CONCLUSION This study presents a strategy for establishing a microbial cell factory capable of producing T-4-HYP at high levels, making it suitable for large-scale industrial production. Additionally, this study provides valuable insights into regulating synthesis of other compounds with α-ketoglutaric acid as precursor.
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Affiliation(s)
- Yu Gong
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Ruiqi Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Ling Ma
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Shuo Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Changgeng Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
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Recent Advances in the Hydroxylation of Amino Acids and Its Derivatives. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Hydroxy amino acids (HAAs) are of unique value in the chemical and pharmaceutical industry with antiviral, antifungal, antibacterial, and anticancer properties. At present, the hydroxylated amino acids most studied are tryptophan, lysine, aspartic acid, leucine, proline, etc., and some of their derivatives. The hydroxylation of amino acids is inextricably linked to the catalysis of various biological enzymes, such as tryptophan hydroxylase, L-pipecolic acid trans-4-hydroxylase, lysine hydroxylase, etc. Hydroxylase conspicuously increases the variety of amino acid derivatives. For the manufacture of HAAs, the high regioselectivity biocatalytic synthesis approach is favored over chemical synthesis. Nowadays, the widely used method is to transcribe the hydroxylation pathway of various amino acids, including various catalytic enzymes, into Corynebacterium glutamicum or Escherichia coli for heterologous expression and then produce hydroxyamino acids. In this paper, we systematically reviewed the biosynthetic hydroxylation of aliphatic, heterocyclic, and aromatic amino acids and introduced the basic research and application of HAAs.
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Naaz N, Choudhary S, Sharma N, Hasan N, Al Shaye NA, Abd El-Moneim D. Frequency and spectrum of M 2 mutants and genetic variability in cyto-agronomic characteristics of fenugreek induced by caffeine and sodium azide. FRONTIERS IN PLANT SCIENCE 2023; 13:1030772. [PMID: 36726682 PMCID: PMC9886007 DOI: 10.3389/fpls.2022.1030772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
Trigonella foenum graecum L. (Fenugreek) is a valuable medicinal plant cultivated for decades for its therapeutic characteristics. Still no pronounced improvement concerning wild form was accomplished as it is a self-pollinating crop. Induced mutagenesis is encouraged as a remarkable tool on this plant to circumvent the genetic bottleneck of cultivated germplasms. As a result, novel allelomorphic combinations for short-term agronomic attributes were developed. Fenugreek cultivar Pusa Early Bunching, selected for the present experiment, was mutagenized with five doses (0.2%, 0.4%, 0.6%, 0.8%, and 1.0%) of caffeine and sodium azide (SA) to evaluate its impact on the qualitative and quantitative traits of M1 and M2 generation conducted in a Complete Randomized Block Design (CRBD), replicated five times during 2019-2020 and 2020-2021, respectively. The frequency of induced phenotypic variations was assessed in M2 progenies, resulting in the identification and isolation of a broad spectrum of mutants with altered phenotypes. Mutagenic effectiveness and efficiency were found to be maximum at lower concentrations of the mutagen treatments and highest in SA, followed by caffeine. Various morphological mutants with modified characters were observed at different concentrations in M2 generation. The spectrum of mutations was wider in SA than in caffeine, as caffeine produced 51 while SA produced 54 individual mutants under seven major categories. The maximum frequency of morphological mutants was associated with leaf, followed by plant size, plant growth habit, pod, seed size, seed shape, and seed color. Morphological and structural variations in the guard cells of stomata and seeds were observed through scanning electron microscopy. The variations created in the economically important traits may enrich the genetic diversity of this plant species. Moreover, these morphological mutants may serve as a source of elite genes in further breeding programs of fenugreek.
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Affiliation(s)
- Neha Naaz
- Department of Botany, Aligarh Muslim University, Aligarh, UP, India
| | - Sana Choudhary
- Department of Botany, Aligarh Muslim University, Aligarh, UP, India
| | - Nidhi Sharma
- Department of Botany, Aligarh Muslim University, Aligarh, UP, India
| | - Nazarul Hasan
- Department of Botany, Aligarh Muslim University, Aligarh, UP, India
| | - Najla A. Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
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Engineering Escherichia coli for Efficient Aerobic Conversion of Glucose to Malic Acid through the Modified Oxidative TCA Cycle. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Malic acid is a versatile building-block chemical that can serve as a precursor of numerous valuable products, including food additives, pharmaceuticals, and biodegradable plastics. Despite the present petrochemical synthesis, malic acid, being an intermediate of the TCA cycle of a variety of living organisms, can also be produced from renewable carbon sources using wild-type and engineered microbial strains. In the current study, Escherichia coli was engineered for efficient aerobic conversion of glucose to malic acid through the modified oxidative TCA cycle resembling that of myco- and cyanobacteria and implying channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation. The formation of succinate semialdehyde was enabled in the core strain MAL 0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP, ∆aceBAK, ∆glcB) by the expression of Mycobacterium tuberculosis kgd gene. The secretion of malic acid by the strain was ensured, resulting from the deletion of the mdh, maeA, maeB, and mqo genes. The Bacillus subtilis pycA gene was expressed in the strain to allow pyruvate to oxaloacetate conversion. The corresponding recombinant was able to synthesise malic acid from glucose aerobically with a yield of 0.65 mol/mol. The yield was improved by the derepression in the strain of the electron transfer chain and succinate dehydrogenase due to the enforcement of ATP hydrolysis and reached 0.94 mol/mol, amounting to 94% of the theoretical maximum. The implemented strategy offers the potential for the development of highly efficient strains and processes of bio-based malic acid production.
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
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Skorokhodova AY, Gulevich AY, Debabov VG. Engineering Escherichia coli for efficient aerobic conversion of glucose to fumaric acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00703. [PMID: 35145886 PMCID: PMC8801760 DOI: 10.1016/j.btre.2022.e00703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022]
Abstract
Escherichia coli was engineered for efficient aerobic conversion of glucose to fumaric acid. A novel design for biosynthesis of the target product through the modified TCA cycle rather than via glyoxylate shunt, implying oxaloacetate formation from pyruvate and artificial channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation, was implemented. The main fumarases were inactivated in the core strain MSG1.0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP) by the deletion of the fumA, fumB, and fumC genes. The Bacillus subtilis pycA gene was expressed in the strain to ensure pyruvate to oxaloacetate conversion. The Mycobacterium tuberculosis kgd gene was expressed to enable succinate semialdehyde formation. The resulting strain was able to convert glucose to fumaric acid with a yield of 0.86 mol/mol, amounting to 86% of the theoretical maximum. The results demonstrated the high potential of the implemented strategy for development of efficient strains for bio-based fumaric acid production.
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Affiliation(s)
- Alexandra Yu. Skorokhodova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Andrey Yu. Gulevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Vladimir G. Debabov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
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8
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Kloska S, Pałczyński K, Marciniak T, Talaśka T, Nitz M, Wysocki BJ, Davis P, Wysocki TA. Queueing theory model of Krebs cycle. Bioinformatics 2021; 37:2912-2919. [PMID: 33724355 DOI: 10.1093/bioinformatics/btab177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Queueing theory can be effective in simulating biochemical reactions taking place in living cells, and the article paves a step toward development of a comprehensive model of cell metabolism. Such a model could help to accelerate and reduce costs for developing and testing investigational drugs reducing number of laboratory animals needed to evaluate drugs. RESULTS The article presents a Krebs cycle model based on queueing theory. The model allows for tracking of metabolites concentration changes in real time. To validate the model, a drug-induced inhibition affecting activity of enzymes involved in Krebs cycle was simulated and compared with available experimental data. AVAILABILITYAND IMPLEMENTATION The source code is freely available for download at https://github.com/UTP-WTIiE/KrebsCycleUsingQueueingTheory, implemented in C# supported in Linux or MS Windows. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylwester Kloska
- Faculty of Medicine, Nicolaus Copernicus University Ludwik Rydygier Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Tomasz Talaśka
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Marissa Nitz
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE 68182, USA
| | - Beata J Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Paul Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Tadeusz A Wysocki
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland.,Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE 68182, USA
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Zhang Z, Liu P, Su W, Zhang H, Xu W, Chu X. Metabolic engineering strategy for synthetizing trans-4-hydroxy-L-proline in microorganisms. Microb Cell Fact 2021; 20:87. [PMID: 33882914 PMCID: PMC8061225 DOI: 10.1186/s12934-021-01579-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/13/2021] [Indexed: 11/14/2022] Open
Abstract
Trans-4-hydroxy-L-proline is an important amino acid that is widely used in medicinal and industrial applications, particularly as a valuable chiral building block for the organic synthesis of pharmaceuticals. Traditionally, trans-4-hydroxy-L-proline is produced by the acidic hydrolysis of collagen, but this process has serious drawbacks, such as low productivity, a complex process and heavy environmental pollution. Presently, trans-4-hydroxy-L-proline is mainly produced via fermentative production by microorganisms. Some recently published advances in metabolic engineering have been used to effectively construct microbial cell factories that have improved the trans-4-hydroxy-L-proline biosynthetic pathway. To probe the potential of microorganisms for trans-4-hydroxy-L-proline production, new strategies and tools must be proposed. In this review, we provide a comprehensive understanding of trans-4-hydroxy-L-proline, including its biosynthetic pathway, proline hydroxylases and production by metabolic engineering, with a focus on improving its production.
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Affiliation(s)
- Zhenyu Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Wenqian Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang People’s Republic of China
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Jiang L, Pang J, Yang L, Li W, Duan L, Zhang G, Luo Y. Engineering endogenous l-proline biosynthetic pathway to boost trans-4-hydroxy-l-proline production in Escherichia coli. J Biotechnol 2021; 329:104-117. [PMID: 33539894 DOI: 10.1016/j.jbiotec.2021.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
Non-proteinogenic trans-4-hydroxy-l-proline (t4HYP), a crucial naturally occurred amino acid, is present in most organisms. t4HYP is a regio- and stereo-selectively hydroxylated product of l-proline and a valuable building block for pharmaceutically important intermediates/ingredients synthesis. Microbial production of t4HYP has aroused extensive investigations because of its low-cost and environmentally benign features. Herein, we reported metabolic engineering of endogenous l-proline biosynthetic pathway to enhance t4HYP production in trace l-proline-producing Escherichia coli BL21(DE3) (21-S0). The genes responsible for by-product formation from l-proline, pyruvate, acetyl-CoA, and isocitrate in the biosynthetic network of 21-S0 were knocked out to channel the metabolic flux towards l-proline biosynthesis. PdhR was knocked out to remove its negative regulation and aceK was deleted to ensure isocitrate dehydrogenase's activity and to increase NADPH/NADP+ level. The other genes for l-proline biosynthesis were enhanced by integration of strong promoters and 5'-untranslated regions. The resulting engineered E. coli strains 21-S1 ∼ 21-S9 harboring a codon-optimized proline 4-hydroxylase-encoding gene (P4H) were grown and fermented. A titer of 4.82 g/L of t4HYP production in 21-S6 overexpressing P4H was obtained at conical flask level, comparing with the starting 21-S0 (26 mg/L). The present work paves an efficient metabolic engineering way for higher t4HYP production in E. coli.
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Affiliation(s)
- Liangzhen Jiang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; College of Pharmacy and Biological Engineering, Chengdu University, 2025 Chengluo Avenue, Chengdu 610106, People's Republic of China
| | - Jing Pang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Lixia Yang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Lili Duan
- College of Food Science and Technology, Sichuan Tourism University, 459 Hongling Road, Chengdu 610100, People's Republic of China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, 9 Section 4, Renmin Road South, Chengdu 610041, People's Republic of China; State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
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Brandenburg F, Theodosiou E, Bertelmann C, Grund M, Klähn S, Schmid A, Krömer JO. Trans-4-hydroxy-L-proline production by the cyanobacterium Synechocystis sp. PCC 6803. Metab Eng Commun 2020; 12:e00155. [PMID: 33511031 PMCID: PMC7815826 DOI: 10.1016/j.mec.2020.e00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 01/21/2023] Open
Abstract
Cyanobacteria play an important role in photobiotechnology. Yet, one of their key central metabolic pathways, the tricarboxylic acid (TCA) cycle, has a unique architecture compared to most heterotrophs and still remains largely unexploited. The conversion of 2-oxoglutarate to succinate via succinyl-CoA is absent but is by-passed by several other reactions. Overall, fluxes under photoautotrophic growth conditions through the TCA cycle are low, which has implications for the production of chemicals. In this study, we investigate the capacity of the TCA cycle of Synechocystis sp PCC 6803 for the production of trans-4-hydroxy-L-proline (Hyp), a valuable chiral building block for the pharmaceutical and cosmetic industries. For the first time, photoautotrophic Hyp production was achieved in a cyanobacterium expressing the gene for the L-proline-4-hydroxylase (P4H) from Dactylosporangium sp. strain RH1. Interestingly, while elevated intracellular Hyp concentrations could be detected in the recombinant Synechocystis strains under all tested conditions, detectable Hyp secretion into the medium was only observed when the pH of the medium exceeded 9.5 and mostly in the late phases of the cultivation. We compared the rates obtained for autotrophic Hyp production with published sugar-based production rates in E. coli. The land-use efficiency (space-time yield) of the phototrophic process is already in the same order of magnitude as the heterotrophic process considering sugar farming as well. But, the remarkable plasticity of the cyanobacterial TCA cycle promises the potential for a 23–55 fold increase in space-time yield when using Synechocystis. Altogether, these findings contribute to a better understanding of bioproduction from the TCA cycle in photoautotrophs and broaden the spectrum of chemicals produced in metabolically engineered cyanobacteria. Phototrophic production of trans-4-hydroxy-L-prolin. pH dependency of product accumulation in Synechocystis PCC6803. Comparative analysis of land use efficiency in phototrophs & heterotrophs.
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Schirmer M, Wink K, Ohla S, Belder D, Schmid A, Dusny C. Conversion Efficiencies of a Few Living Microbial Cells Detected at a High Throughput by Droplet-Based ESI-MS. Anal Chem 2020; 92:10700-10708. [DOI: 10.1021/acs.analchem.0c01839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Martin Schirmer
- Helmholtz Centre for Environmental Research−UFZ Leipzig, Leipzig 04318, Germany
| | - Konstantin Wink
- Institute of Analytical Chemistry, Leipzig University, Leipzig 04103, Germany
| | - Stefan Ohla
- Institute of Analytical Chemistry, Leipzig University, Leipzig 04103, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Leipzig 04103, Germany
| | - Andreas Schmid
- Helmholtz Centre for Environmental Research−UFZ Leipzig, Leipzig 04318, Germany
| | - Christian Dusny
- Helmholtz Centre for Environmental Research−UFZ Leipzig, Leipzig 04318, Germany
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13
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Chen X, Yi J, Song W, Liu J, Luo Q, Liu L. Chassis engineering of Escherichia coli for trans-4-hydroxy-l-proline production. Microb Biotechnol 2020; 14:392-402. [PMID: 32396278 PMCID: PMC7936311 DOI: 10.1111/1751-7915.13573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial production of trans-4-hydroxy-l-proline (Hyp) offers significant advantages over conventional chemical extraction. However, it is still challenging for industrial production of Hyp due to its low production efficiency. Here, chassis engineering was used for tailoring Escherichia coli cellular metabolism to enhance enzymatic production of Hyp. Specifically, four proline 4-hydroxylases (P4H) were selected to convert l-proline to Hyp, and the recombinant strain overexpressing DsP4H produced 32.5 g l-1 Hyp with α-ketoglutarate addition. To produce Hyp without α-ketoglutarate addition, α-ketoglutarate supply was enhanced by rewiring the TCA cycle and l-proline degradation pathway, and oxygen transfer was improved by fine-tuning heterologous haemoglobin expression. In a 5-l fermenter, the engineered strain E. coliΔsucCDΔputA-VHb(L) -DsP4H showed a significant increase in Hyp titre, conversion rate and productivity up to 49.8 g l-1 , 87.4% and 1.38 g l-1 h-1 respectively. This strategy described here provides an efficient method for production of Hyp, and it has a great potential in industrial application.
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Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Juyang Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Shaoxing Baiyin Biotechnology Co. Ltd, Shaoxing, 312000, China
| | - Wei Song
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
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14
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Lee HW, Park JH, Kim WK, Lee JG, Lee JS, Ahn JO, Lee EG, Lee HW. Engineered Escherichia coli strains as platforms for biological production of isoprene. FEBS Open Bio 2020; 10:780-788. [PMID: 32135038 PMCID: PMC7193156 DOI: 10.1002/2211-5463.12829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 11/12/2022] Open
Abstract
Volatile compounds can be produced by fermentation from genetically engineered microorganisms. Escherichia coli strains are mainly used for isoprene production owing to their higher titers; however, this has thus far been confined to only strains BL21, BL21 (DE3), Rosetta, and BW25113. Here, we tested four groups of E. coli strains for improved isoprene production, including K-12 (DH5α, BW25113, W3110, MG1655, XL1-Blue, and JM109), B [Rosetta (DE3), BL21, and BL21 (DE3)], Crooks C, and Waksman W strains. The isoprene productivity of BL21 and MG1655 was remarkably higher than that of the others in 5-L fermentation, and scale-up fermentation (300 L) of BL21 was successfully performed. This system shows potential for biobased production of fuel and volatile compounds in industrial applications.
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Affiliation(s)
- Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Won-Kyo Kim
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jin-Gyeom Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Ju-Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea
| | - Jung-Oh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
| | - Eun-Gyo Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
| | - Hong-Weon Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioprocess Engineering, University of Science and Technology (UST) of Korea, Daejeon, Korea
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15
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Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nat Microbiol 2019; 4:2109-2117. [PMID: 31451773 DOI: 10.1038/s41564-019-0536-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/08/2019] [Indexed: 01/19/2023]
Abstract
Growth rate and metabolic state of bacteria have been separately shown to affect antibiotic efficacy1-3. However, the two are interrelated as bacterial growth inherently imposes a metabolic burden4; thus, determining individual contributions from each is challenging5,6. Indeed, faster growth is often correlated with increased antibiotic efficacy7,8; however, the concurrent role of metabolism in that relationship has not been well characterized. As a result, a clear understanding of the interdependence between growth and metabolism, and their implications for antibiotic efficacy, are lacking9. Here, we measured growth and metabolism in parallel across a broad range of coupled and uncoupled conditions to determine their relative contribution to antibiotic lethality. We show that when growth and metabolism are uncoupled, antibiotic lethality uniformly depends on the bacterial metabolic state at the time of treatment, rather than growth rate. We further reveal a critical metabolic threshold below which antibiotic lethality is negligible. These findings were general for a wide range of conditions, including nine representative bactericidal drugs and a diverse range of Gram-positive and Gram-negative species (Escherichia coli, Acinetobacter baumannii and Staphylococcus aureus). This study provides a cohesive metabolic-dependent basis for antibiotic-mediated cell death, with implications for current treatment strategies and future drug development.
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16
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Liu X. Hydrolysing the soluble protein secreted by Escherichia coli in trans-4-hydroxy-L-proline fermentation increased dissolve oxygen to promote high-level trans-4-hydroxy-L-proline production. Bioengineered 2019; 10:52-58. [PMID: 30955438 PMCID: PMC6527073 DOI: 10.1080/21655979.2019.1600966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Trans-4-hydroxy-L-proline (Hyp) production by Escherichia coli (E. coli) in fermentation is a high-oxygen-demand process. E. coli secretes large amounts of soluble protein, especially in the anaphase of fermentation, which is an important factor leading to inadequate oxygen supply. And acetic acid that is the major by-product of Hyp production accumulates under low dissolved oxygen (DO). To increase DO and achieve high-level Hyp production, soluble protein was hydrolysed by adding protease in Hyp fermentation. The optimal protease, concentration, and addition time were trypsin, 0.2 g/L, and 18 h, respectively. With the addition of trypsin, the soluble protein in Hyp fermentation decreased by 43.5%. The DO could be maintained at 20–30% throughout fermentation. Hyp production and glucose conversion rate were 45.3 g/L and 18.1%, which were increases of 24.1% and 8.4%, respectively. The accumulation of acetic acid was decreased by 52.1%. The metabolic flux of Hyp was increased by 44.2% and the flux of acetate was decreased by 51.0%.
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Affiliation(s)
- Xiaocui Liu
- a School of Life Sciences of Shanxi Datong University , Datong Shanxi , China
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17
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Affiliation(s)
- Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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18
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Zhang HL, Zhang C, Pei CH, Han MN, Xu ZD, Li CH, Li W. Efficient production of trans
-4-Hydroxy-l
-proline from glucose by metabolic engineering of recombinant Escherichia coli. Lett Appl Microbiol 2018; 66:400-408. [DOI: 10.1111/lam.12864] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/28/2018] [Accepted: 02/04/2018] [Indexed: 01/16/2023]
Affiliation(s)
- H.-L. Zhang
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
| | - C. Zhang
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
| | - C.-H. Pei
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
| | - M.-N. Han
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
| | - Z.-D. Xu
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
| | - C.-H. Li
- HeBei Brant Pharmaceutical Co., Ltd.; Shingjiazhuang China
| | - W. Li
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education; College of Chemistry and Environmental Science; Hebei University; Baoding China
- HeBei Brant Pharmaceutical Co., Ltd.; Shingjiazhuang China
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19
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Chen K, Pang Y, Zhang B, Feng J, Xu S, Wang X, Ouyang P. Process optimization for enhancing production of cis-4-hydroxy-L-proline by engineered Escherichia coli. Microb Cell Fact 2017; 16:210. [PMID: 29166916 PMCID: PMC5700529 DOI: 10.1186/s12934-017-0821-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/12/2017] [Indexed: 02/06/2023] Open
Abstract
Background Understanding the bioprocess limitations is critical for the efficient design of biocatalysts to facilitate process feasibility and improve process economics. In this study, a proline hydroxylation process with recombinant Escherichia coli expressing l-proline cis-4-hydroxylase (SmP4H) was investigated. The factors that influencing the metabolism of microbial hosts and process economics were focused on for the optimization of cis-4-hydroxy-l-proline (CHOP) production. Results In recombinant E. coli, SmP4H synthesis limitation was observed. After the optimization of expression system, CHOP production was improved in accordance with the enhanced SmP4H synthesis. Furthermore, the effects of the regulation of proline uptake and metabolism on whole-cell catalytic activity were investigated. The improved CHOP production by repressing putA gene responsible for l-proline degradation or overexpressing l-proline transporter putP on CHOP production suggested the important role of substrate uptake and metabolism on the whole-cell biocatalyst efficiency. Through genetically modifying these factors, the biocatalyst activity was significantly improved, and CHOP production was increased by twofold. Meanwhile, to further improve process economics, a two-strain coupling whole-cell system was established to supply co-substrate (α-ketoglutarate, α-KG) with a cheaper chemical l-glutamate as a starting material, and 13.5 g/L of CHOP was successfully produced. Conclusions In this study, SmP4H expression, and l-proline uptake and degradation, were uncovered as the hurdles for microbial production of CHOP. Accordingly, the whole-cell biocatalysts were metabolically engineered for enhancing CHOP production. Meanwhile, a two-strain biotransformation system for CHOP biosynthesis was developed aiming at supplying α-KG more economically. Our work provided valuable insights into the design of recombinant microorganism to improve the biotransformation efficiency that catalyzed by Fe(II)/α-KG-dependent dioxygenase. Electronic supplementary material The online version of this article (10.1186/s12934-017-0821-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Pang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Bowen Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Jiao Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China.
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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20
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Cascades in Compartments: En Route to Machine-Assisted Biotechnology. Angew Chem Int Ed Engl 2017; 56:13574-13589. [DOI: 10.1002/anie.201703806] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
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21
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Kaskaden in Kompartimenten: auf dem Weg zu maschinengestützter Biotechnologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703806] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
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22
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Theodosiou E, Breisch M, Julsing MK, Falcioni F, Bühler B, Schmid A. An artificial TCA cycle selects for efficient α-ketoglutarate dependent hydroxylase catalysis in engineered Escherichia coli. Biotechnol Bioeng 2017; 114:1511-1520. [PMID: 28266022 DOI: 10.1002/bit.26281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/13/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023]
Abstract
Amino acid hydroxylases depend directly on the cellular TCA cycle via their cosubstrate α-ketoglutarate (α-KG) and are highly useful for the selective biocatalytic oxyfunctionalization of amino acids. This study evaluates TCA cycle engineering strategies to force and increase α-KG flux through proline-4-hydroxylase (P4H). The genes sucA (α-KG dehydrogenase E1 subunit) and sucC (succinyl-CoA synthetase β subunit) were alternately deleted together with aceA (isocitrate lyase) in proline degradation-deficient Escherichia coli strains (ΔputA) expressing the p4h gene. Whereas, the ΔsucCΔaceAΔputA strain grew in minimal medium in the absence of P4H, relying on the activity of fumarate reductase, growth of the ΔsucAΔaceAΔputA strictly depended on P4H activity, thus coupling growth to proline hydroxylation. P4H restored growth, even when proline was not externally added. However, the reduced succinyl-CoA pool caused a 27% decrease of the average cell size compared to the wildtype strain. Medium supplementation partially restored the morphology and, in some cases, enhanced proline hydroxylation activity. The specific proline hydroxylation rate doubled when putP, encoding the Na+ /l-proline transporter, was overexpressed in the ΔsucAΔaceAΔputA strain. This is in contrast to wildtype and ΔputA single-knock out strains, in which α-KG availability obviously limited proline hydroxylation. Such α-KG limitation was relieved in the ΔsucAΔaceAΔputA strain. Furthermore, the ΔsucAΔaceAΔputA strain was used to demonstrate an agar plate-based method for the identification and selection of active α-KG dependent hydroxylases. This together with the possibility to waive selection pressure and overcome α-KG limitation in respective hydroxylation processes based on living cells emphasizes the potential of TCA cycle engineering for the productive application of α-KG dependent hydroxylases. Biotechnol. Bioeng. 2017;114: 1511-1520. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Eleni Theodosiou
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Marina Breisch
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Mattijs K Julsing
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Francesco Falcioni
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
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23
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Zhang Y, Cai J, Shang X, Wang B, Liu S, Chai X, Tan T, Zhang Y, Wen T. A new genome-scale metabolic model of Corynebacterium glutamicum and its application. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:169. [PMID: 28680478 PMCID: PMC5493880 DOI: 10.1186/s13068-017-0856-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/22/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Corynebacterium glutamicum is an important platform organism for industrial biotechnology to produce amino acids, organic acids, bioplastic monomers, and biofuels. The metabolic flexibility, broad substrate spectrum, and fermentative robustness of C. glutamicum make this organism an ideal cell factory to manufacture desired products. With increases in gene function, transport system, and metabolic profile information under certain conditions, developing a comprehensive genome-scale metabolic model (GEM) of C. glutamicum ATCC13032 is desired to improve prediction accuracy, elucidate cellular metabolism, and guide metabolic engineering. RESULTS Here, we constructed a new GEM for ATCC13032, iCW773, consisting of 773 genes, 950 metabolites, and 1207 reactions. Compared to the previous model, iCW773 supplemented 496 gene-protein-reaction associations, refined five lumped reactions, balanced the mass and charge, and constrained the directionality of reactions. The simulated growth rates of C. glutamicum cultivated on seven different carbon sources using iCW773 were consistent with experimental values. Pearson's correlation coefficient between the iCW773-simulated and experimental fluxes was 0.99, suggesting that iCW773 provided an accurate intracellular flux distribution of the wild-type strain growing on glucose. Furthermore, genetic interventions for overproducing l-lysine, 1,2-propanediol and isobutanol simulated using OptForceMUST were in accordance with reported experimental results, indicating the practicability of iCW773 for the design of metabolic networks to overproduce desired products. In vivo genetic modifications of iCW773-predicted targets resulted in the de novo generation of an l-proline-overproducing strain. In fed-batch culture, the engineered C. glutamicum strain produced 66.43 g/L l-proline in 60 h with a yield of 0.26 g/g (l-proline/glucose) and a productivity of 1.11 g/L/h. To our knowledge, this is the highest titer and productivity reported for l-proline production using glucose as the carbon resource in a minimal medium. CONCLUSIONS Our developed iCW773 serves as a high-quality platform for model-guided strain design to produce industrial bioproducts of interest. This new GEM will be a successful multidisciplinary tool and will make valuable contributions to metabolic engineering in academia and industry.
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Affiliation(s)
- Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jingyi Cai
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianwei Tan
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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