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Liu Y, Huo K, Tan B, He X, Wu Q, Li ZJ. Metabolic engineering of Halomonas bluephagenesis for the production of ethylene glycol and glycolate from xylose. J Biotechnol 2024:S0168-1656(24)00269-4. [PMID: 39413879 DOI: 10.1016/j.jbiotec.2024.10.006] [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: 05/10/2024] [Revised: 09/09/2024] [Accepted: 10/12/2024] [Indexed: 10/18/2024]
Abstract
Halophilic Halomonas bluephagenesis, a natural producer of poly-3-hydroxybutyrate (PHB), was metabolically engineered to synthesize ethylene glycol and glycolate from xylose. Xylose utilization was achieved by overexpressing either the xylonate pathway or the ribulose-1-phosphate pathway. The key genes encoding for xylonate dehydratase and 2-keto-3-deoxy-xylonate aldolase in the xylonate pathway were screened. With further overexpressing aldehyde reductase gene yjgB, ethylene glycol accumulation was improved to 0.91g/L, accompanied with 1.48g/L of PHB accumulation. The disruption of native glycolate oxidase was found to be essential for glycolate production, and the defective recombinant strain produced 0.80g/L glycolate with 1.14g/L PHB in shake flask cultures. These results indicated that H. bluephagenesis has the potential to produce diverse metabolic chemicals from xylose.
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Affiliation(s)
- Yuzhong Liu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Kai Huo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Biwei Tan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xulin He
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qiong Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng-Jun Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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2
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Zhang S, Wang J, Chen Y, Zheng Z, Xu Z. Efficient secretion of an enzyme cocktail in Escherichia coli for hemicellulose degradation. Int J Biol Macromol 2024; 259:129205. [PMID: 38185299 DOI: 10.1016/j.ijbiomac.2024.129205] [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: 08/15/2023] [Revised: 11/18/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
The use of host to secrete several hemicellulase is a cost-effective way for hemicellulose degradation. In this study, the xylose utilization gene xylAB of Escherichia coli BL21 was knocked out, and the xylanase (N20Xyl), β-xylosidase (Xys), and feruloyl esterase (FaeLam) were co-expressed in this strain. By measuring the content of reducing sugars generated by enzymatic hydrolysis of wheat bran in the fermentation supernatant, the order of the three enzymes was screened to obtain the optimal recombinant strain of E. coli BL21/∆xylAB/pDIII-2. Subsequently, fermentation conditions including culture medium, inducer concentration, induction timing, metal ions, and glycine concentration were optimized. Then, different concentrations of wheat bran and xylan were added to the fermentation medium for degradation. The results showed that the extracellular reducing sugars content reached the highest value of 33.70 ± 0.46 g/L when 50 g/L xylan was added. Besides, the scavenging rates of hydroxyl radical by the fermentation supernatant was 81.0 ± 1.41 %, and the total antioxidant capacity reached 2.289 ± 0.55. Furthermore, it showed the growth promotion effect on different lactic acid bacteria. These results provided a basis for constructing E. coli strain to efficiently degrade hemicellulose, and the strain obtained has great potential application to transform hemicellulose into fermentable carbon source.
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Affiliation(s)
- Susu Zhang
- College of Life Science, Shandong Normal University, Jinan 250358, PR China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, PR China
| | - Jiapeng Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China; Department of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China
| | - Yunxia Chen
- College of Life Science, Shandong Normal University, Jinan 250358, PR China
| | - Ziyi Zheng
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China; Department of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China; Department of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, PR China.
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3
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Gu P, Li F, Huang Z, Gao J. Application of Acetate as a Substrate for the Production of Value-Added Chemicals in Escherichia coli. Microorganisms 2024; 12:309. [PMID: 38399713 PMCID: PMC10891810 DOI: 10.3390/microorganisms12020309] [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: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
At present, the production of the majority of valuable chemicals is dependent on the microbial fermentation of carbohydrate substrates. However, direct competition is a potential problem for microbial feedstocks that are also used within the food/feed industries. The use of alternative carbon sources, such as acetate, has therefore become a research focus. As a common organic acid, acetate can be generated from lignocellulosic biomass and C1 gases, as well as being a major byproduct in microbial fermentation, especially in the presence of an excess carbon source. As a model microorganism, Escherichia coli has been widely applied in the production of valuable chemicals using different carbon sources. Recently, several valuable chemicals (e.g., succinic acid, itaconic acid, isobutanol, and mevalonic acid) have been investigated for synthesis in E. coli using acetate as the sole carbon source. In this review, we summarize the acetate metabolic pathway in E. coli and recent research into the microbial production of chemical compounds in E. coli using acetate as the carbon source. Although microbial synthetic pathways for different compounds have been developed in E. coli, the production titer and yield are insufficient for commercial applications. Finally, we discuss the development prospects and challenges of using acetate for microbial fermentation.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai 264003, China;
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
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4
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Tan B, Zheng Y, Yan H, Liu Y, Li ZJ. Metabolic engineering of Halomonas bluephagenesis to metabolize xylose for poly-3-hydroxybutyrate production. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Han X, Liu J, Tian S, Tao F, Xu P. Microbial cell factories for bio-based biodegradable plastics production. iScience 2022; 25:105462. [DOI: 10.1016/j.isci.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Hua X, Zhang C, Han J, Xu Y. pH regulatory divergent point for the selective bio-oxidation of primary diols during resting cell catalysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:73. [PMID: 35773746 PMCID: PMC9248139 DOI: 10.1186/s13068-022-02171-5] [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: 03/15/2022] [Accepted: 06/09/2022] [Indexed: 11/12/2022]
Abstract
Background Hydroxyl acid is an important platform chemical that covers many industrial applications due to its dual functional modules. At present, the traditional technology for hydroxyl acid production mainly adopts the petroleum route with benzene, cyclohexane, butadiene and other non-renewable resources as raw materials which violates the development law of green chemistry. Conversely, it is well-known that biotechnology and bioengineering techniques possess several advantages over chemical methods, such as moderate reaction conditions, high chemical selectivity, and environmental-friendly. However, compared with chemical engineering, there are still some major obstacles in the industrial application of biotechnology. The critical issue of the competitiveness between bioengineering and chemical engineering is products titer and volume productivity. Therefore, based on the importance of hydroxyl acids in many fields, exploring a clean, practical and environmental-friendly preparation process of the hydroxyl acids is the core purpose of this study. Results To obtain high-purity hydroxyl acid, a microbiological regulation for its bioproduction by Gluconobacter oxydans was constructed. In the study, we found a critical point of chain length determine the end-products. Gluconobacter oxydans catalyzed diols with chain length ≤ 4, forming hydroxyl acids, and converting 1,5-pentylene glycol and 1,6-hexylene glycol to diacids. Based on this principle, we successfully synthesized 75.3 g/L glycolic acid, 83.2 g/L 3-hydroxypropionic acid, and 94.3 g/L 4-hydroxybutyric acid within 48 h. Furthermore, we directionally controlled the products of C5/C6 diols by adjusting pH, resulting in 102.3 g/L 5‑hydroxyvaleric acid and 48.8 g/L 6-hydroxycaproic acid instead of diacids. Combining pH regulation and cell-recycling technology in sealed-oxygen supply bioreactor, we prepared 271.4 g 5‑hydroxyvaleric acid and 129.4 g 6-hydroxycaproic acid in 6 rounds. Conclusions In this study, a green scheme of employing G. oxydans as biocatalyst for superior-quality hydroxyl acids (C2–C6) production is raised up. The proposed strategy commendably demonstrated a novel technology with simple pH regulation for high-value production of hydroxyl acids via green bioprocess developments. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02171-5.
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Affiliation(s)
- Xia Hua
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - ChenHui Zhang
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - Jian Han
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China.,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China.,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
| | - Yong Xu
- Key Laboratory of Forestry Genetics & Biotechnology (Nanjing Forestry University), Ministry of Education, Nanjing, 210037, People's Republic of China. .,Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, No. 159 Longpan Road, Nanjing, 210037, People's Republic of China. .,Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China.
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7
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Gao W, Yin Y, Wang P, Tan W, He M, Wen J. Production of fengycin from D-xylose through the expression and metabolic regulation of the Dahms pathway. Appl Microbiol Biotechnol 2022; 106:2557-2567. [PMID: 35362719 DOI: 10.1007/s00253-022-11871-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 02/14/2022] [Accepted: 03/05/2022] [Indexed: 12/01/2022]
Abstract
D-Xylose is a key component of lignocellulosic biomass and the second-most abundant carbohydrate on the planet. As one of the most powerful cyclo-lipopeptide antibiotics, fengycin displays strong wide-spectrum antifungal and antiviral, as well as potential anti-cancer activity. Pyruvate is a key metabolite linking the biosynthesis of fatty acids and amino acids, the precursors for fengycin. In this study, the genes encoding the Dahms xylose-utilization pathway were integrated into the amyE site of Bacillus subtilis 168, and based on the metabolic characteristics of the Dahms pathway, the acetate kinase (ackA) and lactate dehydrogenase (ldh) genes were knocked out. Then, the metabolic control module II was designed to convert glycolaldehyde, another intermediate of the Dahms pathway, in addition to pathways for the conversion of acetaldehyde into malic acid and oxaloacetic acid, resulting in strain BSU03. In the presence of module II, the content of acetic and lactic acid decreased significantly, and the xylose uptake efficiency increased. At the same time, the yield of fengycin increased by 87% compared to the original strain. Additionally, the underlying factors for the increase of fengycin titer were revealed through metabonomic analysis. This study therefore demonstrates that this regulation approach can not only optimize the intracellular fluxes for the Dahms pathway, but is also conducive to the synthesis of secondary metabolites similar to fengycin. KEY POINTS: • The expression and effect of the Dahms pathway on the synthesis of fengycin in Bacillus subtilis 168. • The expression of regulatory module II can promote the metabolic rate of the Dahms pathway and increase the synthesis of the fengycin.
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Affiliation(s)
- Wenting Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Wei Tan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mingliang He
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China. .,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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8
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Jayakody LN, Chinmoy B, Turner TL. Trends in valorization of highly-toxic lignocellulosic biomass derived-compounds via engineered microbes. BIORESOURCE TECHNOLOGY 2022; 346:126614. [PMID: 34954359 DOI: 10.1016/j.biortech.2021.126614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 05/26/2023]
Abstract
Lignocellulosic biomass-derived fuels, chemicals, and materials are promising sustainable solutions to replace the current petroleum-based production. The direct microbial conversion of thermos-chemically pretreated lignocellulosic biomass is hampered by the presence of highly toxic chemical compounds. Also, thermo-catalytic upgrading of lignocellulosic biomass generates wastewater that contains heterogeneous toxic chemicals, a mixture of unutilized carbon. Metabolic engineering efforts have primarily focused on the conversion of carbohydrates in lignocellulose biomass; substantial opportunities exist to harness value from toxic lignocellulose-derived toxic compounds. This article presents the comprehensive metabolic routes and tolerance mechanisms to develop robust synthetic microbial cell factories to valorize the highly toxic compounds to advanced-platform chemicals. The obtained platform chemicals can be used to manufacture high-value biopolymers and biomaterials via a hybrid biochemical approach for replacing petroleum-based incumbents. The proposed strategy enables a sustainable bio-based materials economy by microbial biofunneling of lignocellulosic biomass-derived toxic molecules, an untapped biogenic carbon.
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Affiliation(s)
- Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
| | - Baroi Chinmoy
- Illinois Sustainable Technology Center, University of Illinois Urbana Champaign, IL, USA
| | - Timothy L Turner
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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9
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Lekshmi Sundar MS, Madhavan Nampoothiri K. An overview of the metabolically engineered strains and innovative processes used for the value addition of biomass derived xylose to xylitol and xylonic acid. BIORESOURCE TECHNOLOGY 2022; 345:126548. [PMID: 34906704 DOI: 10.1016/j.biortech.2021.126548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Xylose, the most abundant pentose sugar of the hemicellulosic fraction of lignocellulosic biomass, has to be utilized rationally for the commercial viability of biorefineries. An effective pre-treatment strategy for the release of xylose from the biomass and an appropriate microbe of the status of an Industrial strain for the utilization of this pentose sugar are key challenges which need special attention for the economic success of the biomass value addition to chemicals. Xylitol and xylonic acid, the alcohol and acid derivatives of xylose are highly demanded commodity chemicals globally with plenty of applications in the food and pharma industries. This review emphasis on the natural and metabolically engineered strains utilizing xylose and the progressive and innovative fermentation strategies for the production and subsequent recovery of the above said chemicals from pre-treated biomass medium.
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Affiliation(s)
- M S Lekshmi Sundar
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG Campus, Ghaziabad, Uttar Pradesh 201002, India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India.
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10
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Narisetty V, Cox R, Bommareddy R, Agrawal D, Ahmad E, Pant KK, Chandel AK, Bhatia SK, Kumar D, Binod P, Gupta VK, Kumar V. Valorisation of xylose to renewable fuels and chemicals, an essential step in augmenting the commercial viability of lignocellulosic biorefineries. SUSTAINABLE ENERGY & FUELS 2021; 6:29-65. [PMID: 35028420 PMCID: PMC8691124 DOI: 10.1039/d1se00927c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 05/30/2023]
Abstract
Biologists and engineers are making tremendous efforts in contributing to a sustainable and green society. To that end, there is growing interest in waste management and valorisation. Lignocellulosic biomass (LCB) is the most abundant material on the earth and an inevitable waste predominantly originating from agricultural residues, forest biomass and municipal solid waste streams. LCB serves as the renewable feedstock for clean and sustainable processes and products with low carbon emission. Cellulose and hemicellulose constitute the polymeric structure of LCB, which on depolymerisation liberates oligomeric or monomeric glucose and xylose, respectively. The preferential utilization of glucose and/or absence of the xylose metabolic pathway in microbial systems cause xylose valorization to be alienated and abandoned, a major bottleneck in the commercial viability of LCB-based biorefineries. Xylose is the second most abundant sugar in LCB, but a non-conventional industrial substrate unlike glucose. The current review seeks to summarize the recent developments in the biological conversion of xylose into a myriad of sustainable products and associated challenges. The review discusses the microbiology, genetics, and biochemistry of xylose metabolism with hurdles requiring debottlenecking for efficient xylose assimilation. It further describes the product formation by microbial cell factories which can assimilate xylose naturally and rewiring of metabolic networks to ameliorate xylose-based bioproduction in native as well as non-native strains. The review also includes a case study that provides an argument on a suitable pathway for optimal cell growth and succinic acid (SA) production from xylose through elementary flux mode analysis. Finally, a product portfolio from xylose bioconversion has been evaluated along with significant developments made through enzyme, metabolic and process engineering approaches, to maximize the product titers and yield, eventually empowering LCB-based biorefineries. Towards the end, the review is wrapped up with current challenges, concluding remarks, and prospects with an argument for intense future research into xylose-based biorefineries.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
| | - Rylan Cox
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- School of Aerospace, Transport and Manufacturing, Cranfield University Cranfield MK43 0AL UK
| | - Rajesh Bommareddy
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum Mohkampur Dehradun 248005 India
| | - Ejaz Ahmad
- Department of Chemical Engineering, Indian Institute of Technology (ISM) Dhanbad 826004 India
| | - Kamal Kumar Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo Lorena 12.602.810 Brazil
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University Seoul 05029 Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences Solan 173229 Himachal Pradesh India
| | - Parmeswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695 019 Kerala India
| | | | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
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11
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Understanding D-xylonic acid accumulation: a cornerstone for better metabolic engineering approaches. Appl Microbiol Biotechnol 2021; 105:5309-5324. [PMID: 34215905 DOI: 10.1007/s00253-021-11410-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 01/02/2023]
Abstract
The xylose oxidative pathway (XOP) has been engineered in microorganisms for the production of a wide range of industrially relevant compounds. However, the performance of metabolically engineered XOP-utilizing microorganisms is typically hindered by D-xylonic acid accumulation. It acidifies the media and perturbs cell growth due to toxicity, thus curtailing enzymatic activity and target product formation. Fortunately, from the growing portfolio of genetic tools, several strategies that can be adapted for the generation of efficient microbial cell factories have been implemented to address D-xylonic acid accumulation. This review centers its discussion on the causes of D-xylonic acid accumulation and how to address it through different engineering and synthetic biology techniques with emphasis given on bacterial strains. In the first part of this review, the ability of certain microorganisms to produce and tolerate D-xylonic acid is also tackled as an important aspect in developing efficient microbial cell factories. Overall, this review could shed some insights and clarity to those working on XOP in bacteria and its engineering for the development of industrially applicable product-specialist strains. KEY POINTS: D-Xylonic acid accumulation is attributed to the overexpression of xylose dehydrogenase concomitant with basal or inefficient expression of enzymes involved in D-xylonic acid assimilation. Redox imbalance and insufficient cofactors contribute to D-xylonic acid accumulation. Overcoming D-xylonic acid accumulation can increase product formation among engineered strains. Engineering strategies involving enzyme engineering, evolutionary engineering, coutilization of different sugar substrates, and synergy of different pathways could potentially address D-xylonic acid accumulation.
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12
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Bañares AB, Nisola GM, Valdehuesa KNG, Lee WK, Chung WJ. Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds. Crit Rev Biotechnol 2021; 41:649-668. [PMID: 33563072 DOI: 10.1080/07388551.2021.1873243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.
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Affiliation(s)
- Angelo B Bañares
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Grace M Nisola
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Kris N G Valdehuesa
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi, South Korea
| | - Wook-Jin Chung
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
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Enhanced glycolic acid yield through xylose and cellobiose utilization by metabolically engineered Escherichia coli. Bioprocess Biosyst Eng 2021; 44:1081-1091. [PMID: 33527231 DOI: 10.1007/s00449-020-02502-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Microbial biorefinery is a promising route toward sustainable production of glycolic acid (GA), a valuable raw material for various industries. However, inherent microbial GA production has limited substrate consumption using either D-xylose or D-glucose as carbon catabolite repression (CCR) averts their co-utilization. To bypass CCR, a GA-producing strain using D-xylose via Dahms pathway was engineered to allow cellobiose uptake. Unlike glucose, cellobiose was assimilated and intracellularly degraded without repressing D-xylose uptake. The final GA-producing E. coli strain (CLGA8) has an overexpressed cellobiose phosphorylase (cep94A) from Saccharophagus degradans 2-40 and an activated glyoxylate shunt pathway. Expression of cep94A improved GA production reaching the maximum theoretical yield (0.51 g GA g-1 xylose), whereas activation of glyoxylate shunt pathway enabled GA production from cellobiose, which further increased the GA titer (2.25 g GA L-1). To date, this is the highest reported GA yield from D-xylose through Dahms pathway in an engineered E. coli with cellobiose as co-substrate.
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14
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Li Y, Yang S, Ma D, Song W, Gao C, Liu L, Chen X. Microbial engineering for the production of C 2-C 6 organic acids. Nat Prod Rep 2021; 38:1518-1546. [PMID: 33410446 DOI: 10.1039/d0np00062k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C2-C6 organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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15
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Sundar MSL, Susmitha A, Rajan D, Hannibal S, Sasikumar K, Wendisch VF, Nampoothiri KM. Heterologous expression of genes for bioconversion of xylose to xylonic acid in Corynebacterium glutamicum and optimization of the bioprocess. AMB Express 2020; 10:68. [PMID: 32296988 PMCID: PMC7158973 DOI: 10.1186/s13568-020-01003-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/04/2020] [Indexed: 11/10/2022] Open
Abstract
In bacterial system, direct conversion of xylose to xylonic acid is mediated through NAD-dependent xylose dehydrogenase (xylB) and xylonolactonase (xylC) genes. Heterologous expression of these genes from Caulobacter crescentus into recombinant Corynebacterium glutamicum ATCC 13032 and C. glutamicum ATCC 31831 (with an innate pentose transporter, araE) resulted in an efficient bioconversion process to produce xylonic acid from xylose. Process parameters including the design of production medium was optimized using a statistical tool, Response Surface Methodology (RSM). Maximum xylonic acid of 56.32 g/L from 60 g/L xylose, i.e. about 76.67% of the maximum theoretical yield was obtained after 120 h fermentation from pure xylose with recombinant C. glutamicum ATCC 31831 containing the plasmid pVWEx1 xylB. Under the same condition, the production with recombinant C. glutamicum ATCC 13032 (with pVWEx1 xylB) was 50.66 g/L, i.e. 69% of the theoretical yield. There was no significant improvement in production with the simultaneous expression of xylB and xylC genes together indicating xylose dehydrogenase activity as one of the rate limiting factor in the bioconversion. Finally, proof of concept experiment in utilizing biomass derived pentose sugar, xylose, for xylonic acid production was also carried out and obtained 42.94 g/L xylonic acid from 60 g/L xylose. These results promise a significant value addition for the future bio refinery programs.![]()
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16
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Zhao Z, Xian M, Liu M, Zhao G. Biochemical routes for uptake and conversion of xylose by microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:21. [PMID: 32021652 PMCID: PMC6995148 DOI: 10.1186/s13068-020-1662-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.
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Affiliation(s)
- Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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17
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Bator I, Wittgens A, Rosenau F, Tiso T, Blank LM. Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products. Front Bioeng Biotechnol 2020; 7:480. [PMID: 32010683 PMCID: PMC6978631 DOI: 10.3389/fbioe.2019.00480] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas putida KT2440 is a well-established chassis in industrial biotechnology. To increase the substrate spectrum, we implemented three alternative xylose utilization pathways, namely the Isomerase, Weimberg, and Dahms pathways. The synthetic operons contain genes from Escherichia coli and Pseudomonas taiwanensis. For isolating the Dahms pathway in P. putida KT2440 two genes (PP_2836 and PP_4283), encoding an endogenous enzyme of the Weimberg pathway and a regulator for glycolaldehyde degradation, were deleted. Before and after adaptive laboratory evolution, these strains were characterized in terms of growth and synthesis of mono-rhamnolipids and pyocyanin. The engineered strain using the Weimberg pathway reached the highest maximal growth rate of 0.30 h-1. After adaptive laboratory evolution the lag phase was reduced significantly. The highest titers of 720 mg L-1 mono-rhamnolipids and 30 mg L-1 pyocyanin were reached by the evolved strain using the Weimberg or an engineered strain using the Isomerase pathway, respectively. The different stoichiometries of the three xylose utilization pathways may allow engineering of tailored chassis for valuable bioproduct synthesis.
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Affiliation(s)
- Isabel Bator
- iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Andreas Wittgens
- Institute for Pharmaceutical Biotechnology, Ulm-University, Ulm, Germany
- Ulm Center for Peptide Pharmaceuticals, Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Synthesis of Macromolecules, Mainz, Germany
| | - Frank Rosenau
- Institute for Pharmaceutical Biotechnology, Ulm-University, Ulm, Germany
- Ulm Center for Peptide Pharmaceuticals, Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Synthesis of Macromolecules, Mainz, Germany
| | - Till Tiso
- iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Lars M. Blank
- iAMB - Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
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18
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Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose-xylose co-substrate. Nat Commun 2020; 11:279. [PMID: 31937786 PMCID: PMC6959354 DOI: 10.1038/s41467-019-14024-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022] Open
Abstract
Glucose and xylose are the major components of lignocellulose. Effective utilization of both sugars can improve the efficiency of bioproduction. Here, we report a method termed parallel metabolic pathway engineering (PMPE) for producing shikimate pathway derivatives from glucose–xylose co-substrate. In this method, we seek to use glucose mainly for target chemical production, and xylose for supplying essential metabolites for cell growth. Glycolysis and the pentose phosphate pathway are completely separated from the tricarboxylic acid (TCA) cycle. To recover cell growth, we introduce a xylose catabolic pathway that directly flows into the TCA cycle. As a result, we can produce 4.09 g L−1cis,cis-muconic acid using the PMPE Escherichia coli strain with high yield (0.31 g g−1 of glucose) and produce l-tyrosine with 64% of the theoretical yield. The PMPE strategy can contribute to the development of clean processes for producing various valuable chemicals from lignocellulosic resources. In lignocellulose biomass, microbes prefer consuming glucose over xylose, which affects target compound production. Here, the authors achieve simultaneous utilization of glucose and xylose for target chemical production and cell growth, respectively, and realize high-level production of shikimate pathway derivatives.
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19
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Bañares AB, Valdehuesa KNG, Ramos KRM, Nisola GM, Lee WK, Chung WJ. A pH-responsive genetic sensor for the dynamic regulation of D-xylonic acid accumulation in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:2097-2108. [PMID: 31900554 DOI: 10.1007/s00253-019-10297-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022]
Abstract
The xylose oxidative pathway (XOP) is continuously gaining prominence as an alternative for the traditional pentose assimilative pathways in prokaryotes. It begins with the oxidation of D-xylose to D-xylonic acid, which is further converted to α-ketoglutarate or pyruvate + glycolaldehyde through a series of enzyme reactions. The persistent drawback of XOP is the accumulation of D-xylonic acid intermediate that causes culture media acidification. This study addresses this issue through the development of a novel pH-responsive synthetic genetic controller that uses a modified transmembrane transcription factor called CadCΔ. This genetic circuit was tested for its ability to detect extracellular pH and to control the buildup of D-xylonic acid in the culture media. Results showed that the pH-responsive genetic sensor confers dynamic regulation of D-xylonic acid accumulation, which adjusts with the perturbation of culture media pH. This is the first report demonstrating the use of a pH-responsive transmembrane transcription factor as a transducer in a synthetic genetic circuit that was designed for XOP. This may serve as a benchmark for the development of other genetic controllers for similar pathways that involve acidic intermediates.
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Affiliation(s)
- Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea.
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20
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Francois JM, Alkim C, Morin N. Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:118. [PMID: 32670405 PMCID: PMC7341569 DOI: 10.1186/s13068-020-01744-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 1011 tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.
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Affiliation(s)
- Jean Marie Francois
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
| | - Ceren Alkim
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
| | - Nicolas Morin
- Toulouse Biotechnology Institute, CNRS, INRA, LISBP INSA, 135 Avenue de Rangueil, Toulouse Cedex 04, 31077 France
- Toulouse White Biotechnology (TWB, UMS INRA/INSA/CNRS), NAPA CENTER Bât B, 3 Rue Ariane 31520, Ramonville Saint-Agnes, France
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21
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Lee SS, Park J, Heo YB, Woo HM. Case study of xylose conversion to glycolate in Corynebacterium glutamicum: Current limitation and future perspective of the CRISPR-Cas systems. Enzyme Microb Technol 2020; 132:109395. [PMID: 31731968 DOI: 10.1016/j.enzmictec.2019.109395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 08/05/2019] [Indexed: 11/30/2022]
Abstract
RNA-guided genome engineering technologies have been developed for the advanced metabolic engineering of microbial cells to enhance the production of value-added chemicals in Corynebacterium glutamicum as an industrial host. Here, we described the biotransformation of xylose to glycolate using engineered Corynebacterium glutamicum, a well-known industrial amino acid producer. A synthetic pathway involving heterologous D-tagatose 3-epimerase and L-fuculose kinase/aldolase reactions was introduced in C. glutamicum, resulting in 9.9 ± 0.01 g/L glycolate from 20 g/L xylose at a yield of 0.51 g/g (equal to 1.0 mol/mol). Additional glyoxylate reduction pathway developed by CRISPR-Cas12a recombineering has been introduced and attempted to increase the maximum theoretical molar yield of 2.0 (mol/mol). Due to the limitation of the CRISPR-Cas12a recombineering with TTTV PAM sites, advanced CRISPR-Cas systems were suggested for the next-round metabolic engineering for improving the glycolate yield to overcome the current genome-editing tool for metabolic engineering in C. glutamicum.
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Affiliation(s)
- Seung Soo Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jaehyun Park
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.
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22
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Lee S, Choi JI, Woo HM. Bioconversion of Xylose to Ethylene Glycol and Glycolate in Engineered Corynebacterium glutamicum. ACS OMEGA 2019; 4:21279-21287. [PMID: 31867522 PMCID: PMC6921644 DOI: 10.1021/acsomega.9b02805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/20/2019] [Indexed: 05/05/2023]
Abstract
The biological production of two-carbon compounds (ethylene glycol (EG) and glycolate) has been studied for the sustainable supply of the compounds to the polymer, cosmetic, textile, and medical industries. Here, we demonstrated the bioconversion of xylose to either ethylene glycol (EG) or glycolate using engineered Corynebacterium glutamicum, a well-known industrial amino acid producer. A synthetic ribulose 1-phosphate (Ru1P) pathway involving heterologous d-tagatose 3-epimerase and l-fuculose kinase/aldolase reactions was introduced in C. glutamicum. Subsequently, heterologous expression of Escherichia coli YqhD reductase with the synthetic Ru1P pathway led to ethylene glycol production from xylose. Additional pathway engineering in C. glutamicum by mutating ald, which encodes an aldehyde dehydrogenase, abolished the by-product formation of glycolate during xylose conversion to EG at a yield of 0.75 mol per mol. In addition, the bioconversion of xylose to glycolate was achieved, and the almost maximum molar yield was 0.99 mol per mol xylose in C. glutamicum via the Ru1P pathway. Thus, the synthetic Ru1P pathway in C. glutamicum led bioconversion of xylose to either ethylene glycol or glycolate with high molar yields.
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Affiliation(s)
- Seung
Soo Lee
- Department
of Food Science and Biotechnology, Sungkyunkwan
University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jong-il Choi
- Department
of Biotechnology and Bioengineering, Chonnam
National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Han Min Woo
- Department
of Food Science and Biotechnology, Sungkyunkwan
University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- E-mail: . Tel: +82 31 290 7808. Fax: +82 31 290 7882
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23
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Lachaux C, Frazao CJR, Krauβer F, Morin N, Walther T, François JM. A New Synthetic Pathway for the Bioproduction of Glycolic Acid From Lignocellulosic Sugars Aimed at Maximal Carbon Conservation. Front Bioeng Biotechnol 2019; 7:359. [PMID: 31850327 PMCID: PMC6900487 DOI: 10.3389/fbioe.2019.00359] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022] Open
Abstract
Glycolic acid is a two-carbon α-hydroxy acid with many applications in industrial sectors including packaging, fine chemistry, cosmetics, and pharmaceutics. Currently, glycolic acid is chemically manufactured from fossil resources. This chemical mode of production is raising some concerns regarding its use in health for personal care. Microbial production of GA stands as a remarkable challenge to meet these concerns, while responding to the increasing demand to produce bio-sourced products from renewable carbon resources. We here report on the design and expression of a novel non-natural pathway of glycolic acid in E. coli. The originality of this new pathway, termed "glycoptimus" relies on two pillars. On the one hand, it requires the overexpression of three naturally occurring E. coli genes, namely kdsD encoding a D-arabinose-5-P isomerase, fsaA encoding a class 1 aldolase that cleaves D-arabinose-5-P into glyceraldehyde-3-P and glycolaldehyde, and aldA coding for an aldehyde dehydrogenase that oxidizes glycoladehyde in glycolate. These three genes constitute the "glycoptimus module." On the other hand, the expression of these genes together with a reshaping of the central carbon metabolism should enable a production of glycolic acid from pentose and hexose at a molar ratio of 2.5 and 3, respectively, which corresponds to 50% increase as compared to the existing pathways. We demonstrated the 'in vivo' potentiality of this pathway using an E. coli strain, which constitutively expressed the glycoptimus module and whose carbon flow in glycolysis was blocked at the level of glyceraldehyde-3-P dehydrogenase reaction step. This engineered strain was cultivated on a permissive medium containing malate and D-glucose. Upon exhaustion of malate, addition of either D-glucose, D-xylose or L-arabinose led to the production of glycolic acid reaching about 30% of the maximum molar yield. Further improvements at the level of enzymes, strains and bioprocess engineering are awaited to increase yield and titer, rendering the microbial production of glycolic acid affordable for a cost-effective industrial process.
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Affiliation(s)
- Cléa Lachaux
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,TWB, Toulouse, France
| | - Cláudio J R Frazao
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Franziska Krauβer
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Nicolas Morin
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,TWB, Toulouse, France
| | - Thomas Walther
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,TWB, Toulouse, France
| | - Jean Marie François
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,TWB, Toulouse, France
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Bañares AB, Valdehuesa KNG, Ramos KRM, Nisola GM, Lee WK, Chung WJ. Discovering a novel d-xylonate-responsive promoter: the PyjhI-driven genetic switch towards better 1,2,4-butanetriol production. Appl Microbiol Biotechnol 2019; 103:8063-8074. [DOI: 10.1007/s00253-019-10073-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/11/2019] [Accepted: 07/31/2019] [Indexed: 01/12/2023]
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25
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Xu JZ, Ruan HZ, Chen XL, Zhang F, Zhang W. Equilibrium of the intracellular redox state for improving cell growth and L-lysine yield of Corynebacterium glutamicum by optimal cofactor swapping. Microb Cell Fact 2019; 18:65. [PMID: 30943966 PMCID: PMC6448238 DOI: 10.1186/s12934-019-1114-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
Background NAD(H/+) and NADP(H/+) are the most important redox cofactors in bacteria. However, the intracellular redox balance is in advantage of the cell growth and production of NAD(P)H-dependent products. Results In this paper, we rationally engineered glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and isocitrate dehydrogenase (IDH) to switch the nucleotide-cofactor specificity resulting in an increase in final titer [from 85.6 to 121.4 g L−1] and carbon yield [from 0.33 to 0.46 g (g glucose)−1] of l-lysine in strain RGI in fed-batch fermentation. To do this, we firstly analyzed the production performance of original strain JL-6, indicating that the imbalance of intracellular redox was the limiting factor for l-lysine production. Subsequently, we modified the native GAPDH and indicated that recombinant strain RG with nonnative NADP-GAPDH dramatically changed the intracellular levels of NADH and NADPH. However, l-lysine production did not significantly increase because cell growth was harmed at low NADH level. Lastly, the nonnative NAD-IDH was introduced in strain RG to increase the NADH availability and to equilibrate the intracellular redox. The resulted strain RGI showed the stable ratio of NADPH/NADH at about 1.00, which in turn improved cell growth (μmax. = 0.31 h−1) and l-lysine productivity (qLys, max. = 0.53 g g−1 h−1) as compared with strain RG (μmax. = 0.14 h−1 and qLys, max. = 0.42 g g−1 h−1). Conclusions This is the first report of balancing the intracellular redox state by switching the nucleotide-cofactor specificity of GAPDH and IDH, thereby improving cell growth and l-lysine production.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1114-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China.
| | - Hao-Zhe Ruan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Xiu-Lai Chen
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
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Li W, Chen J, Liu CX, Yuan QP, Li ZJ. Microbial production of glycolate from acetate by metabolically engineered Escherichia coli. J Biotechnol 2019; 291:41-45. [DOI: 10.1016/j.jbiotec.2018.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/06/2018] [Accepted: 12/27/2018] [Indexed: 11/16/2022]
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Salusjärvi L, Havukainen S, Koivistoinen O, Toivari M. Biotechnological production of glycolic acid and ethylene glycol: current state and perspectives. Appl Microbiol Biotechnol 2019; 103:2525-2535. [PMID: 30707252 PMCID: PMC6443609 DOI: 10.1007/s00253-019-09640-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/14/2022]
Abstract
Glycolic acid (GA) and ethylene glycol (EG) are versatile two-carbon organic chemicals used in multiple daily applications. GA and EG are currently produced by chemical synthesis, but their biotechnological production from renewable resources has received a substantial interest. Several different metabolic pathways by using genetically modified microorganisms, such as Escherichia coli, Corynebacterium glutamicum and yeast have been established for their production. As a result, the yield of GA and EG produced from sugars has been significantly improved. Here, we describe the recent advancement in metabolic engineering efforts focusing on metabolic pathways and engineering strategies used for GA and EG production.
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Affiliation(s)
- Laura Salusjärvi
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044 VTT, Espoo, Finland.
| | - Sami Havukainen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Outi Koivistoinen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Mervi Toivari
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, 02044 VTT, Espoo, Finland
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28
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Cabulong RB, Valdehuesa KNG, Bañares AB, Ramos KRM, Nisola GM, Lee WK, Chung WJ. Improved cell growth and biosynthesis of glycolic acid by overexpression of membrane-bound pyridine nucleotide transhydrogenase. J Ind Microbiol Biotechnol 2018; 46:159-169. [PMID: 30554290 DOI: 10.1007/s10295-018-2117-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/27/2018] [Indexed: 01/07/2023]
Abstract
The non-conventional D-xylose metabolism called the Dahms pathway which only requires the expression of at least three enzymes to produce pyruvate and glycolaldehyde has been previously engineered in Escherichia coli. Strains that rely on this pathway exhibit lower growth rates which were initially attributed to the perturbed redox homeostasis as evidenced by the lower intracellular NADPH concentrations during exponential growth phase. NADPH-regenerating systems were then tested to restore the redox homeostasis. The membrane-bound pyridine nucleotide transhydrogenase, PntAB, was overexpressed and resulted to a significant increase in biomass and glycolic acid titer and yield. Furthermore, expression of PntAB in an optimized glycolic acid-producing strain improved the growth and product titer significantly. This work demonstrated that compensating for the NADPH demand can be achieved by overexpression of PntAB in E. coli strains assimilating D-xylose through the Dahms pathway. Consequently, increase in biomass accumulation and product concentration was also observed.
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Affiliation(s)
- Rhudith B Cabulong
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
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29
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Kim D, Woo HM. Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories. Appl Microbiol Biotechnol 2018; 102:9471-9480. [PMID: 30238140 DOI: 10.1007/s00253-018-9353-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 11/29/2022]
Abstract
The goal of sustainable production of biochemicals and biofuels has driven the engineering of microbial cell as factories that convert low-value substrates to high-value products. Xylose is the second most abundant sugar substrate in lignocellulosic hydrolysates. We analyzed the mechanisms of xylose metabolism using genome sequencing data of 492 industrially relevant bacterial species in the mini-review. The analysis revealed the xylose isomerase and Weimberg pathways as the major routes across diverse routes of bacterial xylose metabolism. In addition, we discuss recent developments in metabolic engineering of xylose metabolism in industrial microorganisms. Genome-scale analyses have revealed xylose pathway-specific flux landscapes. Overall, a comprehensive understanding of bacterial xylose metabolism could be useful for the feasible development of microbial cell factories.
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Affiliation(s)
- Donghyuk Kim
- School of Energy and Chemical Engineering and School of Biological Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan, 44919, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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30
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Valdehuesa KNG, Ramos KRM, Nisola GM, Bañares AB, Cabulong RB, Lee WK, Liu H, Chung WJ. Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms. Appl Microbiol Biotechnol 2018; 102:7703-7716. [PMID: 30003296 DOI: 10.1007/s00253-018-9186-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/25/2022]
Abstract
The D-xylose oxidative pathway (XOP) has recently been employed in several recombinant microorganisms for growth or for the production of several valuable compounds. The XOP is initiated by D-xylose oxidation to D-xylonolactone, which is then hydrolyzed into D-xylonic acid. D-Xylonic acid is then dehydrated to form 2-keto-3-deoxy-D-xylonic acid, which may be further dehydrated then oxidized into α-ketoglutarate or undergo aldol cleavage to form pyruvate and glycolaldehyde. This review introduces a brief discussion about XOP and its discovery in bacteria and archaea, such as Caulobacter crescentus and Haloferax volcanii. Furthermore, the current advances in the metabolic engineering of recombinant strains employing the XOP are discussed. This includes utilization of XOP for the production of diols, triols, and short-chain organic acids in Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum. Improving the D-xylose uptake, growth yields, and product titer through several metabolic engineering techniques bring some of these recombinant strains close to industrial viability. However, more developments are still needed to optimize the XOP pathway in the host strains, particularly in the minimization of by-product formation.
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Affiliation(s)
- Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Rhudith B Cabulong
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, People's Republic of China.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 17058, Republic of Korea.
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31
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Metabolic engineering of Escherichia coli for the production of L-malate from xylose. Metab Eng 2018; 48:25-32. [DOI: 10.1016/j.ymben.2018.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/08/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022]
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