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Nawab S, Zhang Y, Ullah MW, Lodhi AF, Shah SB, Rahman MU, Yong YC. Microbial host engineering for sustainable isobutanol production from renewable resources. Appl Microbiol Biotechnol 2024; 108:33. [PMID: 38175234 DOI: 10.1007/s00253-023-12821-9] [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: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Due to the limited resources and environmental problems associated with fossil fuels, there is a growing interest in utilizing renewable resources for the production of biofuels through microbial fermentation. Isobutanol is a promising biofuel that could potentially replace gasoline. However, its production efficiency is currently limited by the use of naturally isolated microorganisms. These naturally isolated microorganisms often encounter problems such as a limited range of substrates, low tolerance to solvents or inhibitors, feedback inhibition, and an imbalanced redox state. This makes it difficult to improve their production efficiency through traditional process optimization methods. Fortunately, recent advancements in genetic engineering technologies have made it possible to enhance microbial hosts for the increased production of isobutanol from renewable resources. This review provides a summary of the strategies and synthetic biology approaches that have been employed in the past few years to improve naturally isolated or non-natural microbial hosts for the enhanced production of isobutanol by utilizing different renewable resources. Furthermore, it also discusses the challenges that are faced by engineered microbial hosts and presents future perspectives to enhancing isobutanol production. KEY POINTS: • Promising potential of isobutanol to replace gasoline • Engineering of native and non-native microbial host for isobutanol production • Challenges and opportunities for enhanced isobutanol production.
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Affiliation(s)
- Said Nawab
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - YaFei Zhang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Adil Farooq Lodhi
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Syed Bilal Shah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mujeeb Ur Rahman
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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Jiang W, Cai Y, Sun S, Wang W, Tišma M, Baganz F, Hao J. Inactivation of hydrogenase-3 leads to enhancement of 1,3-propanediol and 2,3-butanediol production by Klebsiella pneumoniae. Enzyme Microb Technol 2024; 177:110438. [PMID: 38518554 DOI: 10.1016/j.enzmictec.2024.110438] [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: 02/15/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
Klebsiella pneumoniae can use glucose or glycerol as carbon sources to produce 1,3-propanediol or 2,3-butanediol, respectively. In the metabolism of Klebsiella pneumoniae, hydrogenase-3 is responsible for H2 production from formic acid, but it is not directly related to the synthesis pathways for 1,3-propanediol and 2,3-butanediol. In the first part of this research, hycEFG, which encodes subunits of the enzyme hydrogenase-3, was knocked out, so K. pneumoniae ΔhycEFG lost the ability to produce H2 during cultivation using glycerol as a carbon source. As a consequence, the concentration of 1,3-propanediol increased and the substrate (glycerol) conversion ratio reached 0.587 mol/mol. Then, K. pneumoniae ΔldhAΔhycEFG was constructed to erase lactic acid synthesis which led to the further increase of 1,3-propanediol concentration. A substrate (glycerol) conversion ratio of 0.628 mol/mol in batch conditions was achieved, which was higher compared to the wild type strain (0.545 mol/mol). Furthermore, since adhE encodes an alcohol dehydrogenase that catalyzes ethanol production from acetaldehyde, K. pneumoniae ΔldhAΔadhEΔhycEFG was constructed to prevent ethanol production. Contrary to expectations, this did not lead to a further increase, but to a decrease in 1,3-propanediol production. In the second part of this research, glucose was used as the carbon source to produce 2,3-butanediol. Knocking out hycEFG had distinct positive effect on 2,3-butanediol production. Especially in K. pneumoniae ΔldhAΔadhEΔhycEFG, a substrate (glucose) conversion ratio of 0.730 mol/mol was reached, which is higher compared to wild type strain (0.504 mol/mol). This work suggests that the inactivation of hydrogenase-3 may have a global effect on the metabolic regulation of K. pneumoniae, leading to the improvement of the production of two industrially important bulk chemicals, 1,3-propanediol and 2,3-butanediol.
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Affiliation(s)
- Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaoyu Cai
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shaoqi Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenqi Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Marina Tišma
- Josip Juraj Strossmayer University of Osijek, Faculty of Food Technology Osijek, Franje Kuhača 18, Osijek HR-31000, Croatia
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, PR China; Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Wang Q, Jiang W, Cai Y, Tišma M, Baganz F, Shi J, Lye GJ, Xiang W, Hao J. 2-Hydroxyisovalerate production by Klebsiella pneumoniae. Enzyme Microb Technol 2024; 172:110330. [PMID: 37866134 DOI: 10.1016/j.enzmictec.2023.110330] [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: 06/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023]
Abstract
2-Hydroxyisovalerate is a valuable chemical that can be used in the production of biodegradable polyesters. In nature, it was only produced at a very low level by Lactococcus lactis. 2-Ketoisovalerate is an intermediate metabolite of the branched-chain amino acid biosynthesis pathway, and Klebsiella pneumoniae ΔbudAΔldhA (Kp ΔbudAΔldhA) was a 2-ketoisovalerate producing strain. In this research, 2-hydroxyisovalerate was identified as a metabolite of Kp ΔbudAΔldhA, and its synthesis pathway was revealed. It was found that 2-ketoisovalerate and 2-hydroxyisovalerate were produced by Kp ΔbudA and Kp ΔbudAΔldhA, but not by Kp ΔbudAΔldhAΔilvD in which the 2-ketoisovalerate synthesis was blocked. budA, ldhA, and ilvD encode α-acetolactate decarboxylase, lactate dehydrogenase, and dihydroxy acid dehydratase, respectively. Thus, it was deduced that 2-hydroxyisovalerate was synthesized from 2-ketoisovalerate. Isoenzymes of ketopantoate reductase PanE, PanE2, and IlvC were suspected of being responsible for this reaction. Kinetic parameters of these enzymes were detected, and they all hold the 2-ketoisovalerate reductase activities. PanE and PanE2 use both NADH and NADPH as co-factors. While IlvC only uses NADH as a co-factor. Over-expression of panE, panE2, or ilvC in Kp ΔbudAΔldhA all enhanced the production of 2-hydroxyisovalerate. Accordingly, 2-hydroxyisovalerate levels were reduced by knocking out panE or panE2. In fed-batch fermentation, 14.41 g/L of 2-hydroxyisovalerate was produced by Kp ΔbudAΔldhA-panE, with a substrate conversion ratio of 0.13 g/g glucose.
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Affiliation(s)
- Qinghui Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, People's Republic of China; Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, People's Republic of China
| | - Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yaoyu Cai
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Marina Tišma
- Josip Juraj Strossmayer University of Osijek, Faculty of Food Technology Osijek, Franje Kuhača 18, Osijek HR-31000, Croatia
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, People's Republic of China
| | - Gary J Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, People's Republic of China
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, People's Republic of China; Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
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Carranza-Saavedra D, Torres-Bacete J, Blázquez B, Sánchez Henao CP, Zapata Montoya JE, Nogales J. System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock. Front Bioeng Biotechnol 2023; 11:1176445. [PMID: 37152640 PMCID: PMC10158823 DOI: 10.3389/fbioe.2023.1176445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Replacing traditional substrates in industrial bioprocesses to advance the sustainable production of chemicals is an urgent need in the context of the circular economy. However, since the limited degradability of non-conventional carbon sources often returns lower yields, effective exploitation of such substrates requires a multi-layer optimization which includes not only the provision of a suitable feedstock but the use of highly robust and metabolically versatile microbial biocatalysts. We tackled this challenge by means of systems metabolic engineering and validated Escherichia coli W as a promising cell factory for the production of the key building block chemical 2-ketoisovalerate (2-KIV) using whey as carbon source, a widely available and low-cost agro-industrial waste. First, we assessed the growth performance of Escherichia coli W on mono and disaccharides and demonstrated that using whey as carbon source enhances it significantly. Second, we searched the available literature and used metabolic modeling approaches to scrutinize the metabolic space of E. coli and explore its potential for overproduction of 2-KIV identifying as basic strategies the block of pyruvate depletion and the modulation of NAD/NADP ratio. We then used our model predictions to construct a suitable microbial chassis capable of overproducing 2-KIV with minimal genetic perturbations, i.e., deleting the pyruvate dehydrogenase and malate dehydrogenase. Finally, we used modular cloning to construct a synthetic 2-KIV pathway that was not sensitive to negative feedback, which effectively resulted in a rerouting of pyruvate towards 2-KIV. The resulting strain shows titers of up to 3.22 ± 0.07 g/L of 2-KIV and 1.40 ± 0.04 g/L of L-valine in 24 h using whey in batch cultures. Additionally, we obtained yields of up to 0.81 g 2-KIV/g substrate. The optimal microbial chassis we present here has minimal genetic modifications and is free of nutritional autotrophies to deliver high 2-KIV production rates using whey as a non-conventional substrate.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
| | - Blas Blázquez
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Claudia Patricia Sánchez Henao
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - José Edgar Zapata Montoya
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - Juan Nogales
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- *Correspondence: Juan Nogales,
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Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:41. [PMID: 35501883 PMCID: PMC9063327 DOI: 10.1186/s13068-022-02144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2022] [Indexed: 11/15/2022]
Abstract
Background Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. Results Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. Conclusions This research provides a new way to improve the efficiency of the biological route of isobutanol production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02144-8. Kp-IpdC is more efficient than KivD for 2-ketoisovalerate decarboxylation. Pyruvate decarboxylase activity is a limitation of Kp-IpdC. T290L variant exhibits a decreased pyruvate decarboxylase activity. Isobutanol production by K. pneumoniae T290L was improved.
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Filipiak W, Żuchowska K, Marszałek M, Depka D, Bogiel T, Warmuzińska N, Bojko B. GC-MS profiling of volatile metabolites produced by Klebsiella pneumoniae. Front Mol Biosci 2022; 9:1019290. [PMID: 36330222 PMCID: PMC9623108 DOI: 10.3389/fmolb.2022.1019290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
Currently used methods for diagnosing ventilator-associated pneumonia (VAP) are complex, time-consuming and require invasive procedures while empirical antibacterial therapy applies broad spectrum antibiotics that may promote antimicrobial resistance. Hence, novel and fast methods based on alternative markers are needed for VAP detection and differentiation of causative pathogens. Pathogenic bacteria produce a broad range of volatile organic compounds (VOCs), some of which may potentially serve as biomarkers for microorganism identification. Additionally, monitoring of dynamically changing VOCs concentration profiles may indicate emerging pneumonia and allow timely implementation of appropriate antimicrobial treatment. This study substantially extends the knowledge on bacterial metabolites providing the unambiguous identification of volatile metabolites produced by carbapenem-resistant and susceptible strains of Klebsiella pneumoniae (confirmed with pure standards in addition to mass spectra match) but also revealing their temporary concentration profiles (along the course of pathogen proliferation) and dependence on the addition of antibiotic (imipenem) to bacteria. Furthermore, the clinical strains of K. pneumoniae isolated from bronchoalveolar lavage specimens collected from mechanically ventilated patients were investigated to reveal, whether bacterial metabolites observed in model experiments with reference strains could be relevant for wild pathogens as well. In all experiments, the headspace samples from bacteria cultures were collected on multibed sorption tubes and analyzed by GC-MS. Sampling was done under strictly controlled conditions at seven time points (up to 24 h after bacteria inoculation) to follow the dynamic changes in VOC concentrations, revealing three profiles: release proportional to bacteria load, temporary maximum and uptake. Altogether 32 VOCs were released by susceptible and 25 VOCs by resistant strain, amongst which 2-pentanone, 2-heptanone, and 2-nonanone were significantly higher for carbapenem-resistant KPN. Considerably more metabolites (n = 64) were produced by clinical isolates and in higher diversity compared to reference KPN strains.
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Affiliation(s)
- Wojciech Filipiak
- Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
- *Correspondence: Wojciech Filipiak,
| | - Karolina Żuchowska
- Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Marta Marszałek
- Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Dagmara Depka
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Tomasz Bogiel
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Natalia Warmuzińska
- Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Barbara Bojko
- Department of Pharmacodynamics and Molecular Pharmacology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
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Evaluation of Metabolic Engineering Strategies on 2-Ketoisovalerate Production by Escherichia coli. Appl Environ Microbiol 2022; 88:e0097622. [PMID: 35980178 PMCID: PMC9469723 DOI: 10.1128/aem.00976-22] [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] [Indexed: 11/20/2022] Open
Abstract
As an important metabolic intermediate, 2-ketoisovalerate has significant potential in the pharmaceutical and biofuel industries. However, a low output through microbial fermentation inhibits its industrial application. The microbial production of 2-ketoisovalerate is representative whereby redox imbalance is generated with two molecules of NADH accumulated and an extra NADPH required to produce one 2-ketoisovalerate from glucose. To achieve efficient 2-ketoisovalerate production, metabolic engineering strategies were evaluated in Escherichia coli. After deleting the competing routes, overexpressing the key enzymes for 2-ketoisovalerate production, tuning the supply of NADPH, and recycling the excess NADH through enhancing aerobic respiration, a 2-ketoisovalerate titer and yield of 46.4 g/L and 0.644 mol/mol glucose, respectively, were achieved. To reduce the main by-product of isobutanol, the activity and expression of acetolactate synthase were modified. Additionally, a protein degradation tag was fused to pyruvate dehydrogenase (PDH) to curtail the conversion of pyruvate precursor into acetyl-CoA and the generation of NADH. The resulting strain, 050TY/pCTSDTQ487S-RBS55, was initially incubated under aerobic conditions to attain sufficient cell mass and then transferred to a microaerobic condition to degrade PDH and inhibit the remaining activity of PDH. Intracellular redox imbalance was relieved with titer, productivity and yield of 2-ketoisovalerate improved to 55.8 g/L, 2.14 g/L h and 0.852 mol/mol glucose. These results revealed metabolic engineering strategies for the production of a redox-imbalanced fermentative metabolite with high titer, productivity, and yield. IMPORTANCE An efficient microbial strain was constructed for 2-ketoisovalerate synthesis. The positive effect of the leuA deletion on 2-ketoisovalerate production was found. An optimal combination of overexpressing the target genes was obtained by adjusting the positions of the multiple enzymes on the plasmid frame and the presence of terminators, which could also be useful for the production of downstream products such as isobutanol and l-valine. Reducing the isobutanol by-product by engineering the acetolactate synthase called for special attention to decreasing the promiscuous activity of the enzymes involved. Redox-balancing strategies such as tuning the expression of the chromosomal pyridine nucleotide transhydrogenase, recycling NADH under aerobic cultivation, switching off PDH by degradation, and inhibiting the expression and activity under microaerobic conditions were proven effective for improving 2-ketoisovalerate production. The degradation of PDH and inhibiting this enzyme's expression would serve as a means to generate a wide range of products from pyruvate.
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Wang Q, Gu J, Shu L, Jiang W, Mojovic L, Knezevic-Jugovic Z, Shi J, Baganz F, Lye GJ, Xiang W, Hao J. Blocking the 2,3-butanediol synthesis pathway of Klebsiella pneumoniae resulted in L-valine production. World J Microbiol Biotechnol 2022; 38:81. [PMID: 35348886 DOI: 10.1007/s11274-022-03266-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Klebsiella pneumoniae is a 2,3-butanediol producing bacterium. Nevertheless, a design and construction of L-valine production strain was studied in this paper. The first step of 2,3-butanediol synthesis and branched-chain amino acid synthesis pathways share the same step of α-acetolactate synthesis from pyruvate. However, the two pathways are existing in parallel and do not interfere with each other in the wild-type strain. A knockout of budA blocked the 2,3-butanediol synthesis pathway and resulted in the L-valine production. The budA coded an α-acetolactate decarboxylase and catalyzed the acetoin formation from α-acetolactate. Furthermore, blocking the lactic acid synthesis by knocking out of ldhA, which is encoding a lactate dehydrogenase, improved the L-valine synthesis. 2-Ketoisovalerate is the precursor of L-valine, it is also an intermediate of the isobutanol synthesis pathway, while indole-3-pyruvate decarboxylase (ipdC) is responsible for isobutyraldehyde formation from 2-ketoisovalerate. Production of L-valine has been improved by knocking out of ipdC. On the other side, the ilvE, encoding a transaminase B, reversibly transfers one amino group from glutamate to α-ketoisovalerate. Overexpression of ilvE exhibited a distinct improvement of L-valine production. The brnQ encodes a branched-chain amino acid transporter, and L-valine production was further improved by disrupting brnQ. It is also revealed that weak acidic and aerobic conditions favor L-valine production. Based on these findings, L-valine production by metabolically engineered K. pneumonia was examined. In fed-batch fermentation, 22.4 g/L of L-valine was produced by the engineered K. pneumoniae ΔbudA-ΔldhA-ΔipdC-ΔbrnQ-ilvE after 55 h of cultivation, with a substrate conversion ratio of 0.27 mol/mol glucose.
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Affiliation(s)
- Qinghui Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.,Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Jinjie Gu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Lin Shu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Ljiljana Mojovic
- Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | | | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Gary J Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China. .,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
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Lakshmi NM, Binod P, Sindhu R, Awasthi MK, Pandey A. Microbial engineering for the production of isobutanol: current status and future directions. Bioengineered 2021; 12:12308-12321. [PMID: 34927549 PMCID: PMC8809953 DOI: 10.1080/21655979.2021.1978189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fermentation-derived alcohols have gained much attention as an alternate fuel due to its minimal effects on atmosphere. Besides its application as biofuel it is also used as raw material for coating resins, deicing fluid, additives in polishes, etc. Among the liquid alcohol type of fuels, isobutanol has more advantage than ethanol. Isobutanol production is reported in native yeast strains, but the production titer is very low which is about 200 mg/L. In order to improve the production, several genetic and metabolic engineering approaches have been carried out. Genetically engineered organism has been reported to produce maximum of 50 g/L of isobutanol which is far more than the native strain without any modification. In bacteria mostly last two steps in Ehrlich pathway, catalyzed by enzymes ketoisovalerate decarboxylase and alcohol dehydrogenase, are heterologously expressed to improve the production. Native Saccharomyces cerevisiae can produce isobutanol in negligible amount since it possesses the pathway for its production through valine degradation pathway. Further modifications in the existing pathways made the improvement in isobutanol production in many microbial strains. Fermentation using cost-effective lignocellulosic biomass and an efficient downstream process can yield isobutanol in environment friendly and sustainable manner. The present review describes the various genetic and metabolic engineering practices adopted to improve the isobutanol production in microbial strains and its downstream processing.
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Affiliation(s)
- Nair M Lakshmi
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India.,Academy of Scientific and Innovative Research (Acsir), Ghaziabad, Uttar Pradesh India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West a & F University, Yangling, Shaanxi China
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research (Csir-iitr), Lucknow India.,Centre for Energy and Environmental Sustainability, Lucknow Uttar Pradesh, India
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10
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Sellés Vidal L, Murray JW, Heap JT. Versatile selective evolutionary pressure using synthetic defect in universal metabolism. Nat Commun 2021; 12:6859. [PMID: 34824282 PMCID: PMC8616928 DOI: 10.1038/s41467-021-27266-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
The non-natural needs of industrial applications often require new or improved enzymes. The structures and properties of enzymes are difficult to predict or design de novo. Instead, semi-rational approaches mimicking evolution entail diversification of parent enzymes followed by evaluation of isolated variants. Artificial selection pressures coupling desired enzyme properties to cell growth could overcome this key bottleneck, but are usually narrow in scope. Here we show diverse enzymes using the ubiquitous cofactors nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) can substitute for defective NAD regeneration, representing a very broadly-applicable artificial selection. Inactivation of Escherichia coli genes required for anaerobic NAD regeneration causes a conditional growth defect. Cells are rescued by foreign enzymes connected to the metabolic network only via NAD or NADP, but only when their substrates are supplied. Using this principle, alcohol dehydrogenase, imine reductase and nitroreductase variants with desired selectivity modifications, and a high-performing isopropanol metabolic pathway, are isolated from libraries of millions of variants in single-round experiments with typical limited information to guide design.
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Affiliation(s)
- Lara Sellés Vidal
- grid.7445.20000 0001 2113 8111Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ UK ,grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - James W. Murray
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - John T. Heap
- grid.7445.20000 0001 2113 8111Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ UK ,grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK ,grid.4563.40000 0004 1936 8868School of Life Sciences, The University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
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11
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Shomar H, Bokinsky G. Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need. Molecules 2021; 26:molecules26226930. [PMID: 34834021 PMCID: PMC8617995 DOI: 10.3390/molecules26226930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein-protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
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Affiliation(s)
- Helena Shomar
- INSERM U722, Faculté de Médecine, Université de Paris, Site Xavier Bichat, 75018 Paris, France
- Correspondence: (H.S.); (G.B.)
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Correspondence: (H.S.); (G.B.)
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12
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Carranza-Saavedra D, Sánchez Henao CP, Zapata Montoya JE. Kinetic analysis and modeling of L-valine production in fermentation batch from E. coli using glucose, lactose and whey as carbon sources. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 31:e00642. [PMID: 34150530 PMCID: PMC8193114 DOI: 10.1016/j.btre.2021.e00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022]
Abstract
In this study the effect of the carbon source on L-valine production kinetics using genetically modified E. coli was researched. Glucose, lactose, Whey (W) and deproteinized whey (DW) were tested as carbon sources, keeping the carbon/nitrogen (C/N) ratio constant. Biomass generation and substrate consumption were modeled with Contois and Mass Conservation models, respectively, whereas Mass Conservation Balance and Luedeking-Piret models were used for product obtaining. Results showed that L-valine production is partially associated to growth, with values of 0.485 g L-valine/(g dry cell weight.h), and a product loss effect at a specific rate (β) of 0.019 g L-valine/(g dry cell weight.h) with W. The yield of this product increased 36 % using W concerning glucose or lactose as carbon sources. On the other hand, Mass Balance and Luedeking-Piret models adjust properly to experimental data (R2 >0.90). In conclusion whey is a promising substrate for obtaining L-valine using genetically-modified E. coli.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Grupo Nutrición y Tecnología de Alimentos, Universidad de Antioquia, Medellín 050010, Colombia
- Departamento de Producción y Sanidad Vegetal, Facultad de Ingeniería Agronómica, Universidad Del Tolima, Ibagué 730006299, Colombia
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13
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Sun S, Wang Y, Shu L, Lu X, Wang Q, Zhu C, Shi J, Lye GJ, Baganz F, Hao J. Redirection of the central metabolism of Klebsiella pneumoniae towards dihydroxyacetone production. Microb Cell Fact 2021; 20:123. [PMID: 34187467 PMCID: PMC8243499 DOI: 10.1186/s12934-021-01608-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022] Open
Abstract
Background Klebsiella pneumoniae is a bacterium that can be used as producer for numerous chemicals. Glycerol can be catabolised by K. pneumoniae and dihydroxyacetone is an intermediate of this catabolism pathway. Here dihydroxyacetone and glycerol were produced from glucose by this bacterium based a redirected glycerol catabolism pathway. Results tpiA, encoding triosephosphate isomerase, was knocked out to block the further catabolism of dihydroxyacetone phosphate in the glycolysis. After overexpression of a Corynebacterium glutamicum dihydroxyacetone phosphate dephosphorylase (hdpA), the engineered strain produced remarkable levels of dihydroxyacetone (7.0 g/L) and glycerol (2.5 g/L) from glucose. Further increase in product formation were obtained by knocking out gapA encoding an iosenzyme of glyceraldehyde 3-phosphate dehydrogenase. There are two dihydroxyacetone kinases in K. pneumoniae. They were both disrupted to prevent an inefficient reaction cycle between dihydroxyacetone phosphate and dihydroxyacetone, and the resulting strains had a distinct improvement in dihydroxyacetone and glycerol production. pH 6.0 and low air supplement were identified as the optimal conditions for dihydroxyacetone and glycerol production by K, pneumoniae ΔtpiA-ΔDHAK-hdpA. In fed batch fermentation 23.9 g/L of dihydroxyacetone and 10.8 g/L of glycerol were produced after 91 h of cultivation, with the total conversion ratio of 0.97 mol/mol glucose. Conclusions This study provides a novel and highly efficient way of dihydroxyacetone and glycerol production from glucose. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01608-0.
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Affiliation(s)
- Shaoqi Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yike Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Lin Shu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiyang Lu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Qinghui Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Chenguang Zhu
- School of Life Science, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Gary J Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China. .,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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14
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Yoo JI, Sohn YJ, Son J, Jo SY, Pyo J, Park SK, Choi JI, Joo JC, Kim HT, Park SJ. Recent advances in the microbial production of C4 alcohols by metabolically engineered microorganisms. Biotechnol J 2021; 17:e2000451. [PMID: 33984183 DOI: 10.1002/biot.202000451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The heavy global dependence on petroleum-based industries has led to serious environmental problems, including climate change and global warming. As a result, there have been calls for a paradigm shift towards the use of biorefineries, which employ natural and engineered microorganisms that can utilize various carbon sources from renewable resources as host strains for the carbon-neutral production of target products. PURPOSE AND SCOPE C4 alcohols are versatile chemicals that can be used directly as biofuels and bulk chemicals and in the production of value-added materials such as plastics, cosmetics, and pharmaceuticals. C4 alcohols can be effectively produced by microorganisms using DCEO biotechnology (tools to design, construct, evaluate, and optimize) and metabolic engineering strategies. SUMMARY OF NEW SYNTHESIS AND CONCLUSIONS In this review, we summarize the production strategies and various synthetic tools available for the production of C4 alcohols and discuss the potential development of microbial cell factories, including the optimization of fermentation processes, that offer cost competitiveness and potential industrial commercialization.
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Affiliation(s)
- Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jiwon Pyo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Su Kyeong Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Engineering, Interdisciplinary Program of Bioenergy and Biomaterials, Chonnam National University, Gwangju, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyenggi-do, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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15
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Yang Y, Zhang Z, Lu X, Gu J, Wang Y, Yao Y, Liao X, Shi J, Lye G, Baganz F, Hao J. Production of 2,3-dihydroxyisovalerate by Enterobacter cloacae. Enzyme Microb Technol 2020; 140:109650. [PMID: 32912674 DOI: 10.1016/j.enzmictec.2020.109650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023]
Abstract
2,3-Dihydroxyisovalerate is an intermediate of the valine synthesis pathway. However, neither natural microorganisms nor valine producing engineered strains have been reported yet to produce this chemical. Based on the 2,3-butanediol synthesis pathway, a biological route of 2,3-dihydroxyisovalerate production was developed using a budA and ilvD disrupted Klebsiella pneumoniae strain in our previous research. We hypothesised, that other 2,3-butanediol producing bacteria could be used for 2,3-dihydroxyisovalerate production. Here a budA disrupted Enterobacter cloacae was constructed, and this strain exhibited a high 2,3-dihydroxyisovalerate producing ability. Disruption of ilvD in E. cloacae ΔbudA further increased 2,3-dihydroxyisovalerate level. The disruption of budA, encoding an acetolactate decarboxylase, resulted in the acetolactate synthesized in the 2,3-butanediol synthesis pathway to flow into the valine synthesis pathway. The additional disruption of ilvD, encoding a dihydroxy acid dehydratase, prevented the 2,3-dihydroxyisovalerate to be further metabolized in the valine synthesis pathway. Thus, the disruption of both budA and ilvD in 2,3-butanediol producing strains might be an universal strategy for 2,3-dihydroxyisovalerate accumulation. After optimization of the medium components and culture parameters 31.2 g/L of 2,3-dihydroxyisovalerate was obtained with a productivity of 0.41 g/L h and a substrate conversion ratio of 0.56 mol/mol glucose in a fed-batch fermentation. This approach provides an economic way for 2,3-dihydroxyisovalerate production.
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Affiliation(s)
- Yang Yang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; School of Life Science, Shanghai University, Shanghai 200444, PR China
| | - Zhongxi Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; School of Life Science, Shanghai University, Shanghai 200444, PR China
| | - Xiyang Lu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China
| | - Jinjie Gu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yike Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; School of Life Science, Shanghai University, Shanghai 200444, PR China
| | - Yao Yao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xianyan Liao
- School of Life Science, Shanghai University, Shanghai 200444, PR China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; School of Life Science and Technology, ShanghaiTech University, PR China
| | - Gary Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK.
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, PR China; Department of Biochemical Engineering, University College London, Gordon Street, London WC1H 0AH, UK.
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Pei S, Ruan X, Liu J, Song W, Chen X, Luo Q, Liu L, Wu J. Enhancement of α-ketoisovalerate production by relieving the product inhibition of l-amino acid deaminase from Proteus mirabilis. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Lu X, Yao Y, Yang Y, Zhang Z, Gu J, Mojovic L, Knezevic-Jugovic Z, Baganz F, Lye G, Shi J, Hao J. Ethylene glycol and glycolic acid production by wild-type Escherichia coli. Biotechnol Appl Biochem 2020; 68:744-755. [PMID: 32683722 DOI: 10.1002/bab.1987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ethylene glycol and glycolic acid are bulk chemicals with a broad range of applications. The ethylene glycol and glycolic acid biosynthesis pathways have been produced by microorganisms and used as a biological route for their production. Unlike the methods that use xylose or glucose as carbon sources, xylonic acid was used as a carbon source to produce ethylene glycol and glycolic acid in this study. Amounts of 4.2 g/L of ethylene glycol and 0.7 g/L of glycolic acid were produced by a wild-type Escherichia coli W3110 within 10 H of cultivation with a substrate conversion ratio of 0.5 mol/mol. Furthermore, E. coli strains that produce solely ethylene glycol or glycolic acid were constructed. 10.3 g/L of glycolic acid was produced by E. coli ΔyqhD+aldA, and the achieved conversion ratio was 0.56 mol/mol. Similarly, the E. coli ΔaldA+yqhD produced 8.0 g/L of ethylene glycol with a conversion ratio of 0.71 mol/mol. Ethylene glycol and glycolic acid production by E. coli on xylonic acid as a carbon source provides new information on the biosynthesis pathway of these products and opens a novel way of biomass utilization.
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Affiliation(s)
- Xiyang Lu
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China
| | - Yao Yao
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China
| | - Yang Yang
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China
| | - Zhongxi Zhang
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China
| | - Jinjie Gu
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, People's Republic of China
| | - Ljiljana Mojovic
- Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | | | - Frank Baganz
- Department of Biochemical Engineering, University College London, London, UK
| | - Gary Lye
- Department of Biochemical Engineering, University College London, London, UK
| | - Jiping Shi
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, People's Republic of China
| | - Jian Hao
- Lab of Biorefinery, Chinese Academy of Sciences, Shanghai Advanced Research Institute, Pudong, Shanghai, People's Republic of China.,Department of Biochemical Engineering, University College London, London, UK
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Chen Q, Wu H, Ji M, Xie Y, Li S, Li Y, Shi J, Sun J. Engineering a colanic acid biosynthesis pathway in E. coli for manufacturing 2’-fucosyllactose. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Wu H, Li S, Ji M, Chen Q, Shi J, Blamey JM, Sun J. Improvement of polyhydroxybutyrate production by deletion of csrA in Escherichia coli. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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2,3-Dihydroxyisovalerate production by Klebsiella pneumoniae. Appl Microbiol Biotechnol 2020; 104:6601-6613. [PMID: 32519119 DOI: 10.1007/s00253-020-10711-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 02/28/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023]
Abstract
2,3-Dihydroxyisovalerate is an intermediate of valine and leucine biosynthesis pathway; however, no natural microorganism has been found yet that can accumulate this compound. Klebsiella pneumoniae is a useful bacterium that can be used as a workhorse for the production of a range of industrially desirable chemicals. Dihydroxy acid dehydratase, encoded by the ilvD gene, catalyzes the reaction of 2-ketoisovalerate formation from 2,3-dihydroxyisovalerate. In this study, an ilvD disrupted strain was constructed which resulted in the inability to synthesize 2-ketoisovalerate, yet accumulate 2,3-dihydroxyisovalerate in its culture broth. 2,3-Butanediol is the main metabolite of K. pneumoniae and its synthesis pathway and the branched-chain amino acid synthesis pathway share the same step of the α-acetolactate synthesis. By knocking out the budA gene, carbon flow into the branched-chain amino acid synthesis pathway was upregulated, which resulted in a distinct increase in 2,3-dihydroxyisovalerate levels. Lactic acid was identified as a by-product of the process and by blocking the lactic acid synthesis pathway, a further increase in 2,3-dihydroxyisovalerate levels was obtained. The culture parameters of 2,3-dihydroxyisovalerate fermentation were optimized, which include acidic pH and medium level oxygen supplementation to favor 2,3-dihydroxyisovalerate synthesis. At optimal conditions (pH 6.5, 400 rpm), 36.5 g/L of 2,3-dihydroxyisovalerate was produced in fed-batch fermentation over 45 h, with a conversion ratio of 0.49 mol/mol glucose. Thus, a biological route of 2,3-dihydroxyisovalerate production with high conversion ratio and final titer was developed, providing a basis for an industrial process. Key Points • A biological route of 2,3-dihydroxyisovalerate production was setup. • Disruption of budA causes 2,3-dihydroxuisovalerate accumulation in K. pneumoniae. • Disruption of ilvD prevents 2,3-dihydroxyisovalerate reuse by the cell. • 36.5 g/L of 2,3-dihydroxyisovalerate was obtained in fed-batch fermentation.
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Mazzoli R, Olson D. Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose. ADVANCES IN APPLIED MICROBIOLOGY 2020; 113:111-161. [PMID: 32948265 DOI: 10.1016/bs.aambs.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.
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Wu H, Chen S, Ji M, Chen Q, Shi J, Sun J. Activation of colanic acid biosynthesis linked to heterologous expression of the polyhydroxybutyrate pathway in Escherichia coli. Int J Biol Macromol 2019; 128:752-760. [DOI: 10.1016/j.ijbiomac.2019.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 01/31/2023]
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Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metab Eng 2019; 52:324-340. [DOI: 10.1016/j.ymben.2018.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/25/2018] [Indexed: 10/27/2022]
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Recent Advances in the Metabolic Engineering of Klebsiella pneumoniae: A Potential Platform Microorganism for Biorefineries. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0346-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Wu W, Zhao Q, Che S, Jia H, Liang H, Zhang H, Liu R, Zhang Q, Bartlam M. Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae. Biochem Biophys Res Commun 2019; 509:154-160. [PMID: 30580999 DOI: 10.1016/j.bbrc.2018.12.094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 10/27/2022]
Abstract
Acetolactate decarboxylase (ALDC) is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin), an important physiological metabolite excreted by microbes. Although the enzyme is widely present in microorganisms, few atomic structures and functions of ALDC have been reported to date. Here we report the crystal structure of ALDC from Klebsiella pneumoniae KP (KpALDC). KpALDC crystallizes in space group P3121 with one monomer per asymmetric unit. Analytical ultracentrifugation data shows that KpALDC forms a stable dimer but can exist as a tetramer in solution. A Zn2+ ion is coordinated by three strictly-conserved histidines (His198, His200 and His211) and a conserved glutamate (Glu69), but the C-terminal tail that forms part of the active site in ALDC enzymes is disordered. A complex structure with ethane-1,2-diol shows a unusual mode of binding, whereby the ligand does not coordinate the Zn2+ ion. MicroScale Thermophoresis analysis shows that KpALDC binds Zn2+ ions, but no binding of Mg2+, Ca2+ and Mn2+ ions was detected.
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Affiliation(s)
- Wenyue Wu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qi Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Haizhu Jia
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hao Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China; College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Exploring the combinatorial space of complete pathways to chemicals. Biochem Soc Trans 2018; 46:513-522. [DOI: 10.1042/bst20170272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol.
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