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Sun T, Zhao Y, Wang J, Kang W, Sun X, Sun Y, Chu M, Liu Z, Lu F, Li M. Increasing 1,4-Diaminobutane Production in Escherichia coli by Optimization of Cofactor PLP and NADPH Synthesis. Molecules 2024; 29:3094. [PMID: 38999045 PMCID: PMC11243127 DOI: 10.3390/molecules29133094] [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: 05/14/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
1,4-diaminobutane is widely used in the industrial production of polymers, pharmaceuticals, agrochemicals and surfactants. Owing to economic and environmental concerns, there has been a growing interest in using microbes to produce 1,4-diaminobutane. However, there is lack of research on the influence of cofactors pyridoxal phosphate (PLP) and NADPH on the synthesis of 1,4-diaminobutane. PLP serves as a cofactor of ornithine decarboxylase in the synthesis of 1,4-diaminobutane. Additionally, the synthesis of 1 mol 1,4-diaminobutane requires 2 mol NADPH, thus necessitating consideration of NADPH balance in the efficient synthesis of 1,4-diaminobutane by Escherichia coli. The aim of this study was to enhance the synthesis efficiency of 1,4-diaminobutane through increasing production of PLP and NADPH. By optimizing the expression of the genes associated with synthesis of PLP and NADPH in E. coli, cellular PLP and NADPH levels increased, and the yield of 1,4-diaminobutane also increased accordingly. Ultimately, using glucose as the primary carbon source, the yield of 1,4-diaminobutane in the recombinant strain NAP19 reached 272 mg/L·DCW, by increased 79% compared with its chassis strain.
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Affiliation(s)
- Tong Sun
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yongcan Zhao
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinjin Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenke Kang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiangxiang Sun
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanling Sun
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Meixue Chu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengyu Liu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ming Li
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, Tianjin 300457, China; (T.S.); (Y.Z.); (J.W.); (W.K.); (X.S.); (Y.S.); (M.C.); (Z.L.)
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
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Ali Z, Abdullah M, Yasin MT, Amanat K, Ahmad K, Ahmed I, Qaisrani MM, Khan J. Organic waste-to-bioplastics: Conversion with eco-friendly technologies and approaches for sustainable environment. ENVIRONMENTAL RESEARCH 2024; 244:117949. [PMID: 38109961 DOI: 10.1016/j.envres.2023.117949] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Petrochemical-based synthetic plastics poses a threat to humans, wildlife, marine life and the environment. Given the magnitude of eventual depletion of petrochemical sources and global environmental pollution caused by the manufacturing of synthetic plastics such as polyethylene (PET) and polypropylene (PP), it is essential to develop and adopt biopolymers as an environment friendly and cost-effective alternative to synthetic plastics. Research into bioplastics has been gaining traction as a way to create a more sustainable and eco-friendlier environment with a reduced environmental impact. Biodegradable bioplastics can have the same characteristics as traditional plastics while also offering additional benefits due to their low carbon footprint. Therefore, using organic waste from biological origin for bioplastic production not only reduces our reliance on edible feedstock but can also effectively assist with solid waste management. This review aims at providing an in-depth overview on recent developments in bioplastic-producing microorganisms, production procedures from various organic wastes using either pure or mixed microbial cultures (MMCs), microalgae, and chemical extraction methods. Low production yield and production costs are still the major bottlenecks to their deployment at industrial and commercial scale. However, their production and commercialization pose a significant challenge despite such potential. The major constraints are their production in small quantity, poor mechanical strength, lack of facilities and costly feed for industrial-scale production. This review further explores several methods for producing bioplastics with the aim of encouraging researchers and investors to explore ways to utilize these renewable resources in order to commercialize degradable bioplastics. Challenges, future prospects and Life cycle assessment of bioplastics are also highlighted. Utilizing a variety of bioplastics obtained from renewable and cost-effective sources (e.g., organic waste, agro-industrial waste, or microalgae) and determining the pertinent end-of-life option (e.g., composting or anaerobic digestion) may lead towards the right direction that assures the sustainable production of bioplastics.
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Affiliation(s)
- Zain Ali
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan
| | - Muhammad Abdullah
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan
| | - Muhammad Talha Yasin
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan.
| | - Kinza Amanat
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan.
| | - Khurshid Ahmad
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No.1299, Sansha Road, Qingdao, Shandong Province, 266404, P.R. China.
| | - Ishfaq Ahmed
- Haide College, Ocean University of China, Laoshan Campus, Qingdao, Shandong Province, 266100, PR China
| | - Muther Mansoor Qaisrani
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan
| | - Jallat Khan
- Institute of Biological Sciences, Khwaja Fareed University of Engineering & Information Technology, 64200, Rahim Yar Khan, Pakistan; Institute of Chemistry, Khwaja Fareed University of Engineering and Information Technology (KFUEIT), 64200, Rahim Yar Khan, Pakistan.
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Boecker S, Espinel-Ríos S, Bettenbrock K, Klamt S. Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metab Eng 2022; 73:50-57. [DOI: 10.1016/j.ymben.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 05/21/2022] [Indexed: 11/29/2022]
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Design of stable and self-regulated microbial consortia for chemical synthesis. Nat Commun 2022; 13:1554. [PMID: 35322005 PMCID: PMC8943006 DOI: 10.1038/s41467-022-29215-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
Microbial coculture engineering has emerged as a promising strategy for biomanufacturing. Stability and self-regulation pose a significant challenge for the generation of intrinsically robust cocultures for large-scale applications. Here, we introduce the use of multi-metabolite cross-feeding (MMCF) to establish a close correlation between the strains and the design rules for selecting the appropriate metabolic branches. This leads to an intrinicially stable two-strain coculture where the population composition and the product titer are insensitive to the initial inoculation ratios. With an intermediate-responsive biosensor, the population of the microbial coculture is autonomously balanced to minimize intermediate accumulation. This static-dynamic strategy is extendable to three-strain cocultures, as demonstrated with de novo biosynthesis of silybin/isosilybin. This strategy is generally applicable, paving the way to the industrial application of microbial cocultures. Stability and tunability are two desirable properties of microbial consortia-based bioproduction. Here, the authors integrate a caffeate-responsive biosensor into two and three strains coculture system to achieve autonomous regulation of strain ratios for coniferol and silybin/isosiltbin production, respectively.
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Immethun CM, Kathol M, Changa T, Saha R. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris. Front Bioeng Biotechnol 2022; 10:800734. [PMID: 35372317 PMCID: PMC8966681 DOI: 10.3389/fbioe.2022.800734] [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: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfill its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris, including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms.
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Lu H, Yadav V, Bilal M, Iqbal HMN. Bioprospecting microbial hosts to valorize lignocellulose biomass - Environmental perspectives and value-added bioproducts. CHEMOSPHERE 2022; 288:132574. [PMID: 34656619 DOI: 10.1016/j.chemosphere.2021.132574] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 02/08/2023]
Abstract
Current biorefinery approaches comprehend diverse biomass feedstocks and various conversion techniques to produce a variety of high-value biochemicals and biofuels. Lignocellulose is among the most abundant, bio-renewable, and sustainable bioresources on earth. It is regarded as a prodigious alternative raw feedstock to produce a large number of chemicals and biofuels. Producing biofuels and platform chemicals from lignocellulosic biomasses represent advantages in terms of energy and environmental perspectives. Lignocellulose is a main structural constituent of non-woody and woody plants consisting of lignin, cellulose, and hemicellulose. Efficient exploitation of all these components is likely to play a considerable contribution to the economic viability of the processes since lignocellulosic biomass often necessitate pretreatment for liberating fermentable sugars and added value products that might serve as feedstocks for microbial strains to produce biofuels and biochemicals. Developing robust microbial culture and advancements in metabolic engineering approaches might lead to the rapid construction of cell factories for the effective biotechnological transformation of biomass feedstocks to produce biorefinery products. In this comprehensive review, we discuss the recent progress in the valorization of agro-industrial wastes as prospective microbial feedstocks to produce a spectrum of high-value products, such as microbial pigments, biopolymers, industrial biocatalysts, biofuels, biologically active compounds, bioplastics, biosurfactants, and biocontrol agents with therapeutic and industrial potentialities. Lignocellulosic biomass architecture, compositional aspects, revalorization, and pretreatment strategies are outlined for efficient conversion of lignocellulosic biomass. Moreover, metabolic engineering approaches are briefly highlighted to develop cell factories to make the lignocellulose biorefinery platforms appealing.
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Affiliation(s)
- Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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Tafur Rangel AE, Oviedo AG, Mojica FC, Gómez JM, Gónzalez Barrios AF. Development of an integrating systems metabolic engineering and bioprocess modeling approach for rational strain improvement. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. ACS Synth Biol 2021; 10:3379-3395. [PMID: 34762392 PMCID: PMC8870144 DOI: 10.1021/acssynbio.1c00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Microbes are being
engineered for an increasingly large and diverse
set of applications. However, the designing of microbial genomes remains
challenging due to the general complexity of biological systems. Adaptive
Laboratory Evolution (ALE) leverages nature’s problem-solving
processes to generate optimized genotypes currently inaccessible to
rational methods. The large amount of public ALE data now represents
a new opportunity for data-driven strain design. This study describes
how novel strain designs, or genome sequences not yet observed in
ALE experiments or published designs, can be extracted from aggregated
ALE data and demonstrates this by designing, building, and testing
three novel Escherichia coli strains with fitnesses
comparable to ALE mutants. These designs were achieved through a meta-analysis
of aggregated ALE mutations data (63 Escherichia coli K-12 MG1655 based ALE experiments, described by 93 unique environmental
conditions, 357 independent evolutions, and 13 957 observed
mutations), which additionally revealed global ALE mutation trends
that inform on ALE-derived strain design principles. Such informative
trends anticipate ALE-derived strain designs as largely gene-centric,
as opposed to noncoding, and composed of a relatively small number
of beneficial variants (approximately 6). These results demonstrate
how strain design efforts can be enhanced by the meta-analysis of
aggregated ALE data.
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Affiliation(s)
- Patrick V. Phaneuf
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - James T. Yurkovich
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Lei Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sebastian Schulz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Muyao Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Emre Ozdemir
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Rebecca M. Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O. Palsson
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Adam M. Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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Wei L, Zhao J, Wang Y, Gao J, Du M, Zhang Y, Xu N, Du H, Ju J, Liu Q, Liu J. Engineering of Corynebacterium glutamicum for high-level γ-aminobutyric acid production from glycerol by dynamic metabolic control. Metab Eng 2021; 69:134-146. [PMID: 34856366 DOI: 10.1016/j.ymben.2021.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/28/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022]
Abstract
Synthetic biology seeks to reprogram microbial cells for efficient production of value-added compounds from low-cost renewable substrates. A great challenge of chemicals biosynthesis is the competition between cell metabolism and target product synthesis for limited cellular resource. Dynamic regulation provides an effective strategy for fine-tuning metabolic flux to maximize chemicals production. In this work, we created a tunable growth phase-dependent autonomous bifunctional genetic switch (GABS) by coupling growth phase responsive promoters and degrons to dynamically redirect the carbon flux for metabolic state switching from cell growth mode to production mode, and achieved high-level GABA production from low-value glycerol in Corynebacterium glutamicum. A ribosome binding sites (RBS)-library-based pathway optimization strategy was firstly developed to reconstruct and optimize the glycerol utilization pathway in C. glutamicum, and the resulting strain CgGly2 displayed excellent glycerol utilization ability. Then, the initial GABA-producing strain was constructed by deleting the GABA degradation pathway and introducing an exogenous GABA synthetic pathway, which led to 5.26 g/L of GABA production from glycerol. In order to resolve the conflicts of carbon flux between cell growth and GABA production, we used the GABS to reconstruct the GABA synthetic metabolic network, in which the competitive modules of GABA biosynthesis, including the tricarboxylic acid (TCA) cycle module and the arginine biosynthesis module, were dynamically down-regulated while the synthetic modules were dynamically up-regulated after sufficient biomass accumulation. Finally, the resulting strain G7-1 accumulated 45.6 g/L of GABA with a yield of 0.4 g/g glycerol, which was the highest titer of GABA ever reported from low-value glycerol. Therefore, these results provide a promising technology to dynamically balance the metabolic flux for the efficient production of other high value-added chemicals from a low-value substrate in C. glutamicum.
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Affiliation(s)
- Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jinhua Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yiran Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jinshan Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhua Du
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yue Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huanmin Du
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Qingdai Liu
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Efficient Conversion of Glycerol to Ethanol by an Engineered Saccharomyces cerevisiae Strain. Appl Environ Microbiol 2021; 87:e0026821. [PMID: 34524902 DOI: 10.1128/aem.00268-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycerol is an eco-friendly solvent that enhances plant biomass decomposition via glycerolysis in many pretreatment methods. Nonetheless, inefficient conversion of glycerol to ethanol by natural Saccharomyces cerevisiae limits its use in these processes. In this study, we have developed an efficient glycerol-converting yeast strain by genetically modifying the oxidation of cytosolic NAD (NADH) by an O2-dependent dynamic shuttle and abolishing both glycerol phosphorylation and biosynthesis in S. cerevisiae strain D452-2, as well as by vigorous expression of whole genes in the dihydroxyacetone (DHA) pathway (Candida utilis glycerol facilitator, Ogataea polymorpha glycerol dehydrogenase, endogenous dihydroxyacetone kinase, and triosephosphate isomerase). The engineered strain showed conversion efficiencies (CE) up to 0.49 g ethanol/g glycerol (98% of theoretical CE), with a production rate of >1 g liter-1 h-1 when glycerol was supplemented in a single fed-batch fermentation in a rich medium. Furthermore, the engineered strain converted a mixture of glycerol and glucose into bioethanol (>86 g/liter) with 92.8% CE. To the best of our knowledge, this is the highest reported titer of bioethanol produced from glycerol and glucose. Notably, we developed a glycerol-utilizing transformant from a parent strain which cannot utilize glycerol as a sole carbon source. The developed strain converted glycerol to ethanol with a productivity of 0.44 g liter-1 h-1 on minimal medium under semiaerobic conditions. Our findings will promote the utilization of glycerol in eco-friendly biorefineries and integrate bioethanol and plant oil industries. IMPORTANCE With the development of efficient lignocellulosic biorefineries, glycerol has attracted attention as an eco-friendly biomass-derived solvent that can enhance the dissociation of lignin and cell wall polysaccharides during the pretreatment process. Coconversion of glycerol with the sugars released from biomass after glycerolysis increases the resources for ethanol production and lowers the burden of component separation. However, low conversion efficiency from glycerol and sugars limits the industrial application of this process. Therefore, the generation of an efficient glycerol-fermenting yeast will promote the applicability of integrated biorefineries. Hence, metabolic flux control in yeast grown on glycerol will lead to the generation of cell factories that produce chemicals, which will boost biodiesel and bioethanol industries. Additionally, the use of glycerol-fermenting yeast will reduce global warming and generation of agricultural waste, leading to the establishment of a sustainable society.
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Clomburg JM, Cintolesi A, Gonzalez R. In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Microb Biotechnol 2021; 15:289-304. [PMID: 34699695 PMCID: PMC8719807 DOI: 10.1111/1751-7915.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2 , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Angela Cintolesi
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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12
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Banu JR, Kumar G, Chattopadhyay I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 2021; 11:429. [PMID: 34603908 DOI: 10.1007/s13205-021-02962-x] [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] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
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Affiliation(s)
- J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
| | - Gopalakrishnan Kumar
- Faculty of Science and Technology, Institute of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Forus, Box 8600, 4036 Stavanger, Norway
| | - Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
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13
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Lad BC, Coleman SM, Alper HS. Microbial valorization of underutilized and nonconventional waste streams. J Ind Microbiol Biotechnol 2021; 49:6371101. [PMID: 34529075 PMCID: PMC9118980 DOI: 10.1093/jimb/kuab056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022]
Abstract
The growing burden of waste disposal coupled with natural resource scarcity has renewed interest in the remediation, valorization, and/or repurposing of waste. Traditional approaches such as composting, anaerobic digestion, use in fertilizers or animal feed, or incineration for energy production extract very little value out of these waste streams. In contrast, waste valorization into fuels and other biochemicals via microbial fermentation is an area of growing interest. In this review, we discuss microbial valorization of nonconventional, aqueous waste streams such as food processing effluents, wastewater streams, and other industrial wastes. We categorize these waste streams as carbohydrate-rich food wastes, lipid-rich wastes, and other industrial wastes. Recent advances in microbial valorization of these nonconventional waste streams are highlighted, along with a discussion of the specific challenges and opportunities associated with impurities, nitrogen content, toxicity, and low productivity.
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Affiliation(s)
- Beena C Lad
- Department of Molecular Biosciences, The University of Texas at Austin, 100 East 24th Street Stop A5000, Austin, TX 78712 USA
| | - Sarah M Coleman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712 USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712 USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712 USA
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14
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Chan HS, Xiao K, Tsang TH, Zeng C, Wang B, Peng X, Wong PK. Bioremediation of Crude Glycerol by a Sustainable Organic-Microbe Hybrid System. Front Microbiol 2021; 12:654033. [PMID: 33967990 PMCID: PMC8103898 DOI: 10.3389/fmicb.2021.654033] [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: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Klebsiella pneumoniae with crude glycerol-utilizing and hydrogen (H2)-producing abilities was successfully isolated from return activated sludge from Shatin Sewage Treatment Works. The H2 production strategy used in this study was optimized with crude glycerol concentrations, and 1,020 μmol of H2 was generated in 3 h. An organic–microbe hybrid system was constructed with metal-free hydrothermal carbonation carbon (HTCC) microspheres to enhance the H2 production under visible light (VL) irradiation. Under optimized VL intensity and HTCC concentration, an elevation of 35.3% in H2 production can be obtained. Electron scavenger study revealed that the photogenerated electrons (e–) from HTCC contributed to the additional H2 production. The variation in intercellular intermediates, enzymatic activity, and reducing equivalents also suggested that the photogenerated e– interacted with K. pneumoniae cells to direct the metabolic flux toward H2 production. This study demonstrated the feasibility of using an organic–microbe hybrid system as a waste-to-energy technology.
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Affiliation(s)
- Ho Shing Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kemeng Xiao
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tsz Ho Tsang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Cuiping Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bo Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Po Keung Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China
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15
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Tafur Rangel AE, Ríos W, Mejía D, Ojeda C, Carlson R, Gómez Ramírez JM, González Barrios AF. In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. Front Genet 2021; 12:633073. [PMID: 33868371 PMCID: PMC8044919 DOI: 10.3389/fgene.2021.633073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, it is important to use tools that allow predicting gene deletions. An in silico experiment was performed to model and understand the metabolic engineering effects on the cell factory considering a second complexity level by transcriptomics data integration. In this study, a systems-based metabolic engineering target prediction was used to increase glycerol bioconversion to succinic acid based on Escherichia coli. Transcriptomics analysis suggests insights on how to increase cell glycerol utilization to further design efficient cell factories. Three E. coli models were used: a core model, a second model based on the integration of transcriptomics data obtained from growth in an optimized culture media, and a third one obtained after integration of transcriptomics data from adaptive laboratory evolution (ALE) experiments. A total of 2,402 strains were obtained with fumarase and pyruvate dehydrogenase being frequently predicted for all the models, suggesting these reactions as essential to increase succinic acid production. Finally, based on using flux balance analysis (FBA) results for all the mutants predicted, a machine learning method was developed to predict new mutants as well as to propose optimal metabolic engineering targets and mutants based on the measurement of the importance of each knockout's (feature's) contribution. Glycerol has become an interesting carbon source for industrial processes due to biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. The combination of transcriptome, systems metabolic modeling, and machine learning analyses revealed the versatility of computational models to predict key metabolic engineering targets in a less cost-, time-, and laborious-intensive process. These data provide a platform to improve the prediction of metabolic engineering targets to design efficient cell factories. Our results may also work as a guide and platform for the selection/engineering of microorganisms for the production of interesting chemical compounds.
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Affiliation(s)
- Albert Enrique Tafur Rangel
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
- Grupo de Investigación CINBIOS, Department of Microbiology, Universidad Popular del Cesar, Valledupar, Colombia
| | - Wendy Ríos
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Daisy Mejía
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Carmen Ojeda
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Ross Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Jorge Mario Gómez Ramírez
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
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16
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Soto-Varela ZE, Cabrera G, Romero A, Cantero D, Valle A, Bolivar J. Identification of Enzymatic Bottlenecks for the Aerobic Production of Malate from Glycerol by the Systematic Gene Overexpression of Anaplerotic Enzymes in Escherichia coli. Int J Mol Sci 2021; 22:ijms22052266. [PMID: 33668723 PMCID: PMC7956688 DOI: 10.3390/ijms22052266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
The biotechnological production of dicarboxylic acids (C4) from renewable carbon sources represents an attractive approach for the provision of these valuable compounds by green chemistry means. Glycerol has become a waste product of the biodiesel industry that serves as a highly reduced carbon source for some microorganisms. Escherichia coli is capable of consuming glycerol to produce succinate under anaerobic fermentation, but with the deletion of some tricarboxylic acid (TCA) cycle genes, it is also able to produce succinate and malate in aerobiosis. In this study, we investigate possible rate-limiting enzymes by overexpressing the C-feeding anaplerotic enzymes Ppc, MaeA, MaeB, and Pck in a mutant that lacks the succinate dehydrogenase (Sdh) enzyme. The overexpression of the TCA enzyme Mdh and the activation of the glyoxylate shunt was also examined. Using this unbiased approach, we found that phosphoenol pyruvate carboxylase (Ppc) overexpression enhances an oxidative pathway that leads to increasing succinate, while phosphoenol pyruvate carboxykinase (Pck) favors a more efficient reductive branch that produces mainly malate, at 57.5% of the theoretical maximum molar yield. The optimization of the culture medium revealed the importance of bicarbonate and pH in the production of malate. An additional mutation of the ppc gene highlights its central role in growth and C4 production.
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Affiliation(s)
- Zamira E. Soto-Varela
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (Z.E.S.-V.); (A.R.)
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (G.C.); (D.C.)
- Faculty of Basic and Biomedical Sciences, Universidad Simón Bolívar, 080020 Barranquilla, Colombia
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (G.C.); (D.C.)
- Institute of Viticulture and Agri-Food Research (IVAGRO)—International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Spain
| | - Agustin Romero
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (Z.E.S.-V.); (A.R.)
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (G.C.); (D.C.)
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (G.C.); (D.C.)
- Institute of Viticulture and Agri-Food Research (IVAGRO)—International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Spain
| | - Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (Z.E.S.-V.); (A.R.)
- Institute of Viticulture and Agri-Food Research (IVAGRO)—International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Spain
- Correspondence: (A.V.); (J.B.); Tel.: +34-956-012820 (A.V.); +34-956-012791 (J.B.)
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain; (Z.E.S.-V.); (A.R.)
- Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
- Correspondence: (A.V.); (J.B.); Tel.: +34-956-012820 (A.V.); +34-956-012791 (J.B.)
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17
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da Silva VZ, Ourique LJ, de David C, Ayub MAZ. Construction of Recombinant Klebsiella pneumoniae to Increase Ethanol Production on Residual Glycerol Fed-Batch Cultivations. Appl Biochem Biotechnol 2020; 192:1147-1162. [PMID: 32700204 DOI: 10.1007/s12010-020-03397-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
K. pneumoniae BLh-1 strain was genetically modified aiming at obtaining high ethanol productivity in cultivations using residual glycerol from biodiesel synthesis as substrate. The recombinant strain K. pneumoniae Kp17 was obtained by inserting the multicopy plasmid pTOPOBL17 containing the AdhE gene, and its own promoter, from K. pneumoniae BLh-1. Influence of Fe2+ supplementation and initial glycerol concentration on culture conditions were analyzed, both in rotatory shaker and in batch bioreactors. In the bioreactor cultures, K. pneumoniae Kp17 strain produced 4.5 g L-1 of ethanol (productivity of 0.50 g L-1 h-1 and yields of 0.15 g g-1) after 24-h cultivation, corresponding to an increase of approximately 40% in ethanol concentration compared to wild strain, K. pneumoniae BLh-1. Best conditions were then applied in exponential fed-batch bioreactors, with final ethanol concentration of 17.30 g L-1 (productivity of 0.59 g L-1 h-1 and yields of 0.16 g g-1) after 30 h of feeding, representing 11.5% of increment in titer of ethanol compared to the wild strain. Mutant cells kept 92.5% of the plasmids under batch in 24 h, and 71.9% under fed-batch after 27 h of exponential feeding. The findings in this work show the possibility of using a simple approach to genetically modify K. pneumoniae to be employed this versatile bacterium for the bioconversion of residual glycerol into ethanol.
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Affiliation(s)
- Vanessa Zimmer da Silva
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Laura Jensen Ourique
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cíntia de David
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Marco Antonio Zachia Ayub
- Biotechnology & Biochemical Engineering Laboratory (BiotecLab), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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18
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Cardoso VM, Campani G, Santos MP, Silva GG, Pires MC, Gonçalves VM, de C. Giordano R, Sargo CR, Horta AC, Zangirolami TC. Cost analysis based on bioreactor cultivation conditions: Production of a soluble recombinant protein using Escherichia coli BL21(DE3). BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00441. [PMID: 32140446 PMCID: PMC7049567 DOI: 10.1016/j.btre.2020.e00441] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 12/20/2022]
Abstract
The impact of cultivation strategy on the cost of recombinant protein production is crucial for defining cost-effective bioreactor operation conditions. This paper presents a methodology to estimate and compare cost impacts related to utilities as well as medium composition, using simple design equations and accessible data. Data from batch bioreactor cultures were used as case study involving the production of pneumococcal surface protein A, a soluble recombinant protein, employing E. coli BL21(DE3). Cultivation strategies and corresponding process costs covered a wide range of operational conditions, including different media, inducers, and temperatures. The core expenses were related to the medium and cooling. When the price of peptone was above the threshold value of US$ 30/kg, defined medium became the best choice. IPTG and temperatures around 32 °C led to shorter cultures and lower PspA4Pro production costs. The procedure offers a simple, accessible theoretical tool to identify cost-effective production strategies using bioreactors.
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Affiliation(s)
- Valdemir M. Cardoso
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Gilson Campani
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
- Department of Engineering, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Maurício P. Santos
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Gabriel G. Silva
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Manuella C. Pires
- Laboratory of Vaccine Development, Butantan Institute, Av. Vital Brasil 1500, 05508-900, São Paulo, SP, Brazil
| | - Viviane M. Gonçalves
- Laboratory of Vaccine Development, Butantan Institute, Av. Vital Brasil 1500, 05508-900, São Paulo, SP, Brazil
| | - Roberto de C. Giordano
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Cíntia R. Sargo
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, SP, Brazil
| | - Antônio C.L. Horta
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Teresa C. Zangirolami
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
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19
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Lee MK, Mohamad MS, Choon YW, Mohd Daud K, Nasarudin NA, Ismail MA, Ibrahim Z, Napis S, Sinnott RO. Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli. J Integr Bioinform 2020; 17:jib-2019-0073. [PMID: 32374287 PMCID: PMC7734505 DOI: 10.1515/jib-2019-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/18/2020] [Indexed: 11/15/2022] Open
Abstract
The metabolic network is the reconstruction of the metabolic pathway of an organism that is used to represent the interaction between enzymes and metabolites in genome level. Meanwhile, metabolic engineering is a process that modifies the metabolic network of a cell to increase the production of metabolites. However, the metabolic networks are too complex that cause problem in identifying near-optimal knockout genes/reactions for maximizing the metabolite’s production. Therefore, through constraint-based modelling, various metaheuristic algorithms have been improvised to optimize the desired phenotypes. In this paper, PSOMOMA was compared with CSMOMA and ABCMOMA for maximizing the production of succinic acid in E. coli. Furthermore, the results obtained from PSOMOMA were validated with results from the wet lab experiment.
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Affiliation(s)
- Mee K Lee
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor, Malaysia
| | - Mohd Saberi Mohamad
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, 16100 Kota Bharu Kelantan, Malaysia.,Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Jeli Campus, Lock Bag 100, 17600 Jeli Kelantan, Malaysia
| | - Yee Wen Choon
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor, Malaysia
| | - Kauthar Mohd Daud
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor, Malaysia
| | - Nurul Athirah Nasarudin
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor, Malaysia
| | - Mohd Arfian Ismail
- Soft Computing and Intelligent System Research Group, Faculty of Computer Systems and Software Engineering, Universiti Malaysia Pahang, 26300 Kuantan, Pahang, Malaysia
| | - Zuwairie Ibrahim
- Faculty of Manufacturing Engineering, Universiti Malaysia Pahang, Pekan, Pahang, Malaysia
| | - Suhaimi Napis
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Richard O Sinnott
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC 3052 Australia
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20
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Construction of an energy-conserving glycerol utilization pathways for improving anaerobic succinate production in Escherichia coli. Metab Eng 2019; 56:181-189. [DOI: 10.1016/j.ymben.2019.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023]
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21
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Lin WR, Tan SI, Hsiang CC, Sung PK, Ng IS. Challenges and opportunity of recent genome editing and multi-omics in cyanobacteria and microalgae for biorefinery. BIORESOURCE TECHNOLOGY 2019; 291:121932. [PMID: 31387837 DOI: 10.1016/j.biortech.2019.121932] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Microalgae and cyanobacteria are easy to culture, with higher growth rates and photosynthetic efficiencies compared to terrestrial plants, and thus generating higher productivity. The concept of microalgal biorefinery is to assimilate carbon dioxide and convert it to chemical energy/value-added products, such as vitamins, carotenoids, fatty acids, proteins and nucleic acids, to be applied in bioenergy, health foods, aquaculture feed, pharmaceutical and medical fields. Therefore, microalgae are annotated as the third generation feedstock in bioenergy and biorefinery. In past decades, many studies thrived to improve the carbon sequestration efficiency as well as enhance value-added compounds from different algae, especially via genetic engineering, synthetic biology, metabolic design and regulation. From the traditional Agrobacterium-mediated transformation DNA to novel CRISPR (clustered regularly interspaced short palindromic repeats) technology applied in microalgae and cyanobacteria, this review has highlighted the genome editing technology for biorefinery that is a highly environmental friendly trend to sustainable and renewable development.
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Affiliation(s)
- Way-Rong Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Chuan-Chieh Hsiang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Po-Kuei Sung
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC.
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22
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Sarma S, Ortega D, Minton NP, Dubey VK, Moholkar VS. Homologous overexpression of hydrogenase and glycerol dehydrogenase in Clostridium pasteurianum to enhance hydrogen production from crude glycerol. BIORESOURCE TECHNOLOGY 2019; 284:168-177. [PMID: 30933825 DOI: 10.1016/j.biortech.2019.03.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
This study reports engineering of a hypertransformable variant of C. pasteurianum for bioconversion of glycerol into hydrogen (H2). A functional glycerol-triggered hydrogen pathway was engineered based on two approaches: (1) increasing product yield by overexpression of immediate enzyme catalyzing H2 production, (2) increasing substrate uptake by overexpression of enzymes involved in glycerol utilization. The first strategy aimed at overexpression of hydA gene encoding hydrogenase, and the second one, through combination of overexpression of dhaD1 and dhaK genes encoding glycerol dehydrogenase and dihydroxyacetone kinase. These genetic manipulations resulted in two recombinant strains (hydA++/dhaD1K++) capable of producing 97% H2 (v/v), with yields of 1.1 mol H2/mol glycerol in hydA overexpressed strain, and 0.93 mol H2/mol glycerol in dhaD1K overexpressed strain, which was 1.5 fold higher than wild type. Among two strains, dhaD1K++ consumed more glycerol than hydA++ which proves that overexpression of glycerol enzymes has enhanced glycerol intake rate.
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Affiliation(s)
- Shyamali Sarma
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - David Ortega
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, Nottingham NG72RD, United Kingdom
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham, Nottingham NG72RD, United Kingdom
| | - Vikash Kumar Dubey
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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23
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Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP. Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 2019; 37:538-568. [DOI: 10.1016/j.biotechadv.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
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24
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Semkiv M, Kata I, Ternavska O, Sibirny W, Dmytruk K, Sibirny A. Overexpression of the genes of glycerol catabolism and glycerol facilitator improves glycerol conversion to ethanol in the methylotrophic thermotolerant yeastOgataea polymorpha. Yeast 2019; 36:329-339. [DOI: 10.1002/yea.3387] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/12/2019] [Accepted: 03/02/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Marta Semkiv
- Institute of Cell BiologyNational Academy of Science of Ukraine Lviv Ukraine
| | - Iwona Kata
- Department of Microbiology and BiotechnologyUniversity of Rzeszow Rzeszow Poland
| | - Orysya Ternavska
- Institute of Cell BiologyNational Academy of Science of Ukraine Lviv Ukraine
| | - Wladimir Sibirny
- Department of Microbiology and BiotechnologyUniversity of Rzeszow Rzeszow Poland
| | - Kostyantyn Dmytruk
- Institute of Cell BiologyNational Academy of Science of Ukraine Lviv Ukraine
| | - Andriy Sibirny
- Institute of Cell BiologyNational Academy of Science of Ukraine Lviv Ukraine
- Department of Microbiology and BiotechnologyUniversity of Rzeszow Rzeszow Poland
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25
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Complete genome sequence of acetate-producing Klebsiella pneumoniae L5-2 isolated from infant feces. 3 Biotech 2019; 9:84. [PMID: 30800595 DOI: 10.1007/s13205-019-1578-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/17/2019] [Indexed: 12/12/2022] Open
Abstract
Acetate is an important metabolite in infants as it can affect metabolism as well as immune and inflammatory responses. However, there have been no studies on acetate production by Klebsiella pneumoniae isolated from infant feces. In this study, we isolated a K. pneumoniae strain, L5-2, from infant feces, and we found it produces acetate. The genome of L5-2 consisted of a 5,237,123-bp single chromosome and a 139,211-bp single plasmid. The G + C content was 57.27%. By whole-genome analysis of K. pneumoniae L5-2, we identified seven genes related to acetate production (poxA, pta, eutD, ackA, eutP, eutQ, and adhE). We confirmed acetate production by K. pneumoniae L5-2 by ion chromatography. The aldehyde/alcohol dehydrogenase (adhE) activity of K. pneumoniae L5-2 was significantly higher than that of the K. pneumoniae subsp. ozaenae ATCC 11296. Thus, the acetate-producing ability of K. pneumoniae L5-2 was influenced by the adhE gene. In addition, K. pneumoniae L5-2 had significantly less virulence factor-encoding genes than other K. pneumoniae strains isolated from humans. In conclusion, K. pneumoniae L5-2 isolated from infant feces has less virulence factors and higher adhE activity than other K. pneumoniae strains.
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26
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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27
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Fan M, Zhang S, Ye G, Zhang H, Xie J. Integrating sugarcane molasses into sequential cellulosic biofuel production based on SSF process of high solid loading. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:329. [PMID: 30568729 PMCID: PMC6297951 DOI: 10.1186/s13068-018-1328-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Sugarcane bagasse (SCB) is one of the most promising lignocellulosic biomasses for use in the production of biofuels. However, bioethanol production from pure SCB fermentation is still limited by its high process cost and low fermentation efficiency. Sugarcane molasses, as a carbohydrate-rich biomass, can provide fermentable sugars for ethanol production. Herein, to reduce high processing costs, molasses was integrated into lignocellulosic ethanol production in batch modes to improve the fermentation system and to boost the final ethanol concentration and yield. RESULTS The co-fermentation of pretreated SCB and molasses at ratios of 3:1 (mixture A) and 1:1 (mixture B) were conducted at solid loadings of 12% to 32%, and the fermentation of pretreated SCB alone at the same solid loading was also compared. At a solid loading of 32%, the ethanol concentrations of 64.10 g/L, 74.69 g/L, and 75.64 g/L were obtained from pure SCB, mixture A, and mixture B, respectively. To further boost the ethanol concentration, the fermentation of mixture B (1:1), with higher solid loading from 36 to 48%, was also implemented. The highest ethanol concentration of 94.20 g/L was generated at a high solid loading of 44%, with an ethanol yield of 72.37%. In addition, after evaporation, the wastewater could be converted to biogas by anaerobic digestion. The final methane production of 312.14 mL/g volatile solids (VS) was obtained, and the final chemical oxygen demand removal and VS degradation efficiency was 85.9% and 95.9%, respectively. CONCLUSIONS Molasses could provide a good environment for the growth of yeast and inoculum. Integrating sugarcane molasses into sequential cellulosic biofuel production could improve the utilization of biomass resources.
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Affiliation(s)
- Meishan Fan
- College of Forestry and Landscape Architecture, Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Shuaishuai Zhang
- College of Forestry and Landscape Architecture, Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Guangying Ye
- College of Forestry and Landscape Architecture, Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Hongdan Zhang
- College of Forestry and Landscape Architecture, Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Jun Xie
- College of Forestry and Landscape Architecture, Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
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28
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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29
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Tack ILMM, Nimmegeers P, Akkermans S, Logist F, Van Impe JFM. A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli. PLoS One 2018; 13:e0202565. [PMID: 30157229 PMCID: PMC6114798 DOI: 10.1371/journal.pone.0202565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
Over the last decades, predictive microbiology has made significant advances in the mathematical description of microbial spoiler and pathogen dynamics in or on food products. Recently, the focus of predictive microbiology has shifted from a (semi-)empirical population-level approach towards mechanistic models including information about the intracellular metabolism in order to increase model accuracy and genericness. However, incorporation of this subpopulation-level information increases model complexity and, consequently, the required run time to simulate microbial cell and population dynamics. In this paper, results of metabolic flux balance analyses (FBA) with a genome-scale model are used to calibrate a low-complexity linear model describing the microbial growth and metabolite secretion rates of Escherichia coli as a function of the nutrient and oxygen uptake rate. Hence, the required information about the cellular metabolism (i.e., biomass growth and secretion of cell products) is selected and included in the linear model without incorporating the complete intracellular reaction network. However, the applied FBAs are only representative for microbial dynamics under specific extracellular conditions, viz., a neutral medium without weak acids at a temperature of 37℃. Deviations from these reference conditions lead to metabolic shifts and adjustments of the cellular nutrient uptake or maintenance requirements. This metabolic dependency on extracellular conditions has been taken into account in our low-complex metabolic model. In this way, a novel approach is developed to take the synergistic effects of temperature, pH, and undissociated acids on the cell metabolism into account. Consequently, the developed model is deployable as a tool to describe, predict and control E. coli dynamics in and on food products under various combinations of environmental conditions. To emphasize this point,three specific scenarios are elaborated: (i) aerobic respiration without production of weak acid extracellular metabolites, (ii) anaerobic fermentation with secretion of mixed acid fermentation products into the food environment, and (iii) respiro-fermentative metabolic regimes in between the behaviors at aerobic and anaerobic conditions.
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Affiliation(s)
| | | | - Simen Akkermans
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Filip Logist
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
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30
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A synthetic pathway for the production of 2-hydroxyisovaleric acid in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:579-588. [DOI: 10.1007/s10295-018-2005-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/02/2018] [Indexed: 11/25/2022]
Abstract
Abstract
Synthetic biology, encompassing the design and construction of novel artificial biological pathways and organisms and the redesign of existing natural biological systems, is rapidly expanding the number of applications for which biological systems can play an integral role. In the context of chemical production, the combination of synthetic biology and metabolic engineering approaches continues to unlock the ability to biologically produce novel and complex molecules from a variety of feedstocks. Here, we utilize a synthetic approach to design and build a pathway to produce 2-hydroxyisovaleric acid in Escherichia coli and demonstrate how pathway design can be supplemented with metabolic engineering approaches to improve pathway performance from various carbon sources. Drawing inspiration from the native pathway for the synthesis of the 5-carbon amino acid l-valine, we exploit the decarboxylative condensation of two molecules of pyruvate, with subsequent reduction and dehydration reactions enabling the synthesis of 2-hydroxyisovaleric acid. Key to our approach was the utilization of an acetolactate synthase which minimized kinetic and regulatory constraints to ensure sufficient flux entering the pathway. Critical host modifications enabling maximum product synthesis from either glycerol or glucose were then examined, with the varying degree of reduction of these carbons sources playing a major role in the required host background. Through these engineering efforts, the designed pathway produced 6.2 g/L 2-hydroxyisovaleric acid from glycerol at 58% of maximum theoretical yield and 7.8 g/L 2-hydroxyisovaleric acid from glucose at 73% of maximum theoretical yield. These results demonstrate how the combination of synthetic biology and metabolic engineering approaches can facilitate bio-based chemical production.
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31
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Bioconversion of methane to C-4 carboxylic acids using carbon flux through acetyl-CoA in engineered Methylomicrobium buryatense 5GB1C. Metab Eng 2018; 48:175-183. [PMID: 29883803 DOI: 10.1016/j.ymben.2018.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/24/2022]
Abstract
Methane, the primary component of natural gas, is the second most abundant greenhouse gas (GHG) and contributes significantly to climate change. The conversion of methane to industrial platform chemicals provides an attractive opportunity to decrease GHG emissions and utilize this inexpensive and abundantly available gas as a carbon feedstock. While technologies exist for chemical conversion of methane to liquid fuels, the technical complexity of these processes mandate high capital expenditure, large-scale commercial facilities to leverage economies of scale that cannot be efficiently scaled down. Alternatively, bioconversion technologies capable of efficient small-scale operation with high carbon and energy efficiency can enable deployment at remote methane resources inaccessible to current chemical technologies. Aerobic obligate methanotrophs, specifically Methylomicrobium buryatense 5GB1, have recently garnered increased research interest for development of such bio-technologies. In this study, we demonstrate production of C-4 carboxylic acids non-native to the host, specifically crotonic and butyric acids, from methane in an engineered M. buryatense 5GB1C by diversion of carbon flux through the acetyl-CoA node of central 'sugar' linked metabolic pathways using reverse β-oxidation pathway genes. The synthesis of short chain carboxylic acids through the acetyl-CoA node demonstrates the potential for engineering M. buryatense 5GB1 as a platform for bioconversion of methane to a number of value added industrial chemicals, and presents new opportunities for further diversifying the products obtainable from methane as the feedstock.
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32
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Fatma Z, Hartman H, Poolman MG, Fell DA, Srivastava S, Shakeel T, Yazdani SS. Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production. Metab Eng 2018; 46:1-12. [DOI: 10.1016/j.ymben.2018.01.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/13/2017] [Accepted: 01/29/2018] [Indexed: 12/19/2022]
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33
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Parate R, Mane R, Dharne M, Rode C. Mixed bacterial culture mediated direct conversion of bio-glycerol to diols. BIORESOURCE TECHNOLOGY 2018; 250:86-93. [PMID: 29156369 DOI: 10.1016/j.biortech.2017.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Direct and economic transformation of biodiesel derived crude glycerol is gaining more significance. During screening of bacterial cultures Klebsiella pneumoniae and Enterobacter aerogenes were able to convert crude bio-glycerol to 2,3-butanediol (2,3-BDO) and 1,3-propanediol (1,3-PDO), as major compounds, ethanol and acetoin as minor compounds, with a conversion of 69% and 79% respectively. Process optimization could achieve maximum conversion at pH 7.0, 37 °C, 30-40 g/L glycerol and 1.5 g of inoculum until 120 h. Mixed cultures led to complete glycerol conversion with optimal yield and productivity. An innovative approach of using crude glycerol for sustained growth and tolerance of bacteria as source of carbon and energy makes this study more significant. In addition to this, a mixed culture concept introduced here is expected to make impact in process economics for industrial scale synthesis for direct transformation of glycerol into C3 and specifically, C4 diols.
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Affiliation(s)
- Roopa Parate
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India; National Collection of Industrial Microorganisms, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Rasika Mane
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Chandrashekhar Rode
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.
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34
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Current state and perspectives in hydrogen production by Escherichia coli: roles of hydrogenases in glucose or glycerol metabolism. Appl Microbiol Biotechnol 2018; 102:2041-2050. [DOI: 10.1007/s00253-018-8752-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 01/07/2023]
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35
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Qi C, Zhao H, Li W, Li X, Xiang H, Zhang G, Liu H, Wang Q, Wang Y, Xian M, Zhang H. Production of γ-terpinene by metabolically engineered Escherichia coli using glycerol as feedstock. RSC Adv 2018; 8:30851-30859. [PMID: 35548758 PMCID: PMC9085526 DOI: 10.1039/c8ra02076k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/16/2018] [Indexed: 11/21/2022] Open
Abstract
A sustainable technology for gamma (γ)-terpinene was constructed in an engineered Escherichia coli. In-depth analysis at translation level for the engineered strain and intermediate metabolites were analyzed. The fed-batch fermentation of γ-terpinene was 275.41 mg L−1.
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36
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Soo CS, Yap WS, Hon WM, Ramli N, Md Shah UK, Phang LY. Co-production of hydrogen and ethanol by Escherichia coli SS1 and its recombinant. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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37
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A modular metabolic engineering approach for the production of 1,2-propanediol from glycerol by Saccharomyces cerevisiae. Metab Eng 2017; 44:223-235. [DOI: 10.1016/j.ymben.2017.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/06/2017] [Accepted: 10/04/2017] [Indexed: 01/20/2023]
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38
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Gargalo CL, Carvalho A, Gernaey KV, Sin G. Supply Chain Optimization of Integrated Glycerol Biorefinery: GlyThink Model Development and Application. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b00908] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carina L. Gargalo
- Process
and Systems Engineering Center (PROSYS), Department of Chemical and
Biochemical Engineering, Technical University of Denmark, Building
229, Lyngby 2800, Denmark
| | - Ana Carvalho
- CEG-IST,
Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco
Pais, 1, Lisboa 1049-001, Portugal
| | - Krist V. Gernaey
- Process
and Systems Engineering Center (PROSYS), Department of Chemical and
Biochemical Engineering, Technical University of Denmark, Building
229, Lyngby 2800, Denmark
| | - Gürkan Sin
- Process
and Systems Engineering Center (PROSYS), Department of Chemical and
Biochemical Engineering, Technical University of Denmark, Building
229, Lyngby 2800, Denmark
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39
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Metabolomics-driven approach to solving a CoA imbalance for improved 1-butanol production in Escherichia coli. Metab Eng 2017; 41:135-143. [PMID: 28400330 DOI: 10.1016/j.ymben.2017.04.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 11/23/2022]
Abstract
High titer 1-butanol production in Escherichia coli has previously been achieved by overexpression of a modified clostridial 1-butanol production pathway and subsequent deletion of native fermentation pathways. This strategy couples growth with production as 1-butanol pathway offers the only available terminal electron acceptors required for growth in anaerobic conditions. With further inclusion of other well-established metabolic engineering principles, a titer of 15g/L has been obtained. In achieving this titer, many currently existing strategies have been exhausted, and 1-butanol toxicity level has been surpassed. Therefore, continued engineering of the host strain for increased production requires implementation of alternative strategies that seek to identify non-obvious targets for improvement. In this study, a metabolomics-driven approach was used to reveal a CoA imbalance resulting from a pta deletion that caused undesirable accumulation of pyruvate, butanoate, and other CoA-derived compounds. Using metabolomics, the reduction of butanoyl-CoA to butanal catalyzed by alcohol dehydrogenase AdhE2 was determined as a rate-limiting step. Fine-tuning of this activity and subsequent release of free CoA restored the CoA balance that resulted in a titer of 18.3g/L upon improvement of total free CoA levels using cysteine supplementation. By enhancing AdhE2 activity, carbon flux was directed towards 1-butanol production and undesirable accumulation of pyruvate and butanoate was diminished. This study represents the initial report describing the improvement of 1-butanol production in E. coli by resolving CoA imbalance, which was based on metabolome analysis and rational metabolic engineering strategies.
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40
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Coordination of metabolic pathways: Enhanced carbon conservation in 1,3-propanediol production by coupling with optically pure lactate biosynthesis. Metab Eng 2017; 41:102-114. [PMID: 28396036 DOI: 10.1016/j.ymben.2017.03.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/09/2017] [Accepted: 03/31/2017] [Indexed: 11/23/2022]
Abstract
Metabolic engineering has emerged as a powerful tool for bioproduction of both fine and bulk chemicals. The natural coordination among different metabolic pathways contributes to the complexity of metabolic modification, which hampers the development of biorefineries. Herein, the coordination between the oxidative and reductive branches of glycerol metabolism was rearranged in Klebsiella oxytoca to improve the 1,3-propanediol production. After deliberating on the product value, carbon conservation, redox balance, biological compatibility and downstream processing, the lactate-producing pathway was chosen for coupling with the 1,3-propanediol-producing pathway. Then, the other pathways of 2,3-butanediol, ethanol, acetate, and succinate were blocked in sequence, leading to improved d-lactate biosynthesis, which as return drove the 1,3-propanediol production. Meanwhile, efficient co-production of 1,3-propanediol and l-lactate was also achieved by replacing ldhD with ldhL from Bacillus coagulans. The engineered strains PDL-5 and PLL co-produced over 70g/L 1,3-propanediol and over 100g/L optically pure d-lactate and l-lactate, respectively, with high conversion yields of over 0.95mol/mol from glycerol.
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41
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Soo CS, Yap WS, Hon WM, Ramli N, Md Shah UK, Phang LY. Improvement of hydrogen yield of ethanol-producing Escherichia coli recombinants in acidic conditions. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2016.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Menchavez RN, Morra MJ, He BB. Glycerol hydrogenolysis using a Ni/Ce-Mg catalyst for improved ethanol and 1,2-propanediol selectivities. CAN J CHEM ENG 2017. [DOI: 10.1002/cjce.22779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Russel N. Menchavez
- Department of Biological Engineering; University of Idaho; Moscow Idaho 83844 USA
| | - Matthew J. Morra
- Division of Soil & Land Resources; University of Idaho; Moscow Idaho 83844 USA
| | - B. Brian He
- Department of Biological Engineering; University of Idaho; Moscow Idaho 83844 USA
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Sundara Sekar B, Seol E, Park S. Co-production of hydrogen and ethanol from glucose in Escherichia coli by activation of pentose-phosphate pathway through deletion of phosphoglucose isomerase ( pgi) and overexpression of glucose-6-phosphate dehydrogenase ( zwf) and 6-phosphogluconate dehydrogenase ( gnd). BIOTECHNOLOGY FOR BIOFUELS 2017; 10:85. [PMID: 28360941 PMCID: PMC5372246 DOI: 10.1186/s13068-017-0768-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/22/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Biologically, hydrogen (H2) can be produced through dark fermentation and photofermentation. Dark fermentation is fast in rate and simple in reactor design, but H2 production yield is unsatisfactorily low as <4 mol H2/mol glucose. To address this challenge, simultaneous production of H2 and ethanol has been suggested. Co-production of ethanol and H2 requires enhanced formation of NAD(P)H during catabolism of glucose, which can be accomplished by diversion of glycolytic flux from the Embden-Meyerhof-Parnas (EMP) pathway to the pentose-phosphate (PP) pathway in Escherichia coli. However, the disruption of pgi (phosphoglucose isomerase) for complete diversion of carbon flux to the PP pathway made E. coli unable to grow on glucose under anaerobic condition. RESULTS Here, we demonstrate that, when glucose-6-phosphate dehydrogenase (Zwf) and 6-phosphogluconate dehydrogenase (Gnd), two major enzymes of the PP pathway, are homologously overexpressed, E. coli Δpgi can recover its anaerobic growth capability on glucose. Further, with additional deletions of ΔhycA, ΔhyaAB, ΔhybBC, ΔldhA, and ΔfrdAB, the recombinant Δpgi mutant could produce 1.69 mol H2 and 1.50 mol ethanol from 1 mol glucose. However, acetate was produced at 0.18 mol mol-1 glucose, indicating that some carbon is metabolized through the Entner-Doudoroff (ED) pathway. To further improve the flux via the PP pathway, heterologous zwf and gnd from Leuconostoc mesenteroides and Gluconobacter oxydans, respectively, which are less inhibited by NADPH, were overexpressed. The new recombinant produced more ethanol at 1.62 mol mol-1 glucose along with 1.74 mol H2 mol-1 glucose, which are close to the theoretically maximal yields, 1.67 mol mol-1 each for ethanol and H2. However, the attempt to delete the ED pathway in the Δpgi mutant to operate the PP pathway as the sole glycolytic route, was unsuccessful. CONCLUSIONS By deletion of pgi and overexpression of heterologous zwf and gnd in E. coli ΔhycA ΔhyaAB ΔhybBC ΔldhA ΔfrdAB, two important biofuels, ethanol and H2, could be successfully co-produced at high yields close to their theoretical maximums. The strains developed in this study should be applicable for the production of other biofuels and biochemicals, which requires supply of excessive reducing power under anaerobic conditions.
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Affiliation(s)
- Balaji Sundara Sekar
- Department of Chemical and Biomolecular Engineering, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan, 46241 Republic of Korea
| | - Eunhee Seol
- Department of Chemical and Biomolecular Engineering, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan, 46241 Republic of Korea
| | - Sunghoon Park
- Department of Chemical and Biomolecular Engineering, Pusan National University, 2, Busandaehak-ro 63 beon-gil, Geumjeong-gu, Busan, 46241 Republic of Korea
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Zhang Y, Liu D, Chen Z. Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:299. [PMID: 29255482 PMCID: PMC5727944 DOI: 10.1186/s13068-017-0992-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/17/2023]
Abstract
C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.
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Affiliation(s)
- Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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Switch of metabolic status: redirecting metabolic flux for acetoin production from glycerol by activating a silent glycerol catabolism pathway. Metab Eng 2017; 39:90-101. [DOI: 10.1016/j.ymben.2016.10.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 10/03/2016] [Accepted: 10/25/2016] [Indexed: 12/20/2022]
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46
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Vegetable Oil-Biorefinery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:69-98. [DOI: 10.1007/10_2016_65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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48
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Srirangan K, Liu X, Tran TT, Charles TC, Moo-Young M, Chou CP. Engineering of Escherichia coli for direct and modulated biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer using unrelated carbon sources. Sci Rep 2016; 6:36470. [PMID: 27819347 PMCID: PMC5098226 DOI: 10.1038/srep36470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022] Open
Abstract
While poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] is a biodegradable commodity plastic with broad applications, its microbial synthesis is hindered by high production costs primarily associated with the supplementation of related carbon substrates (e.g. propionate or valerate). Here we report construction of engineered Escherichia coli strains for direct synthesis of P(3HB-co-3HV) from an unrelated carbon source (e.g. glucose or glycerol). First, an E. coli strain with an activated sleeping beauty mutase (Sbm) operon was used to generate propionyl-CoA as a precursor. Next, two acetyl-CoA moieties or acetyl-CoA and propionyl-CoA were condensed to form acetoacetyl-CoA and 3-ketovaleryl-CoA, respectively, by functional expression of β-ketothiolases from Cupriavidus necator (i.e. PhaA and BktB). The resulting thioester intermediates were channeled into the polyhydroxyalkanoate (PHA) biosynthetic pathway through functional expression of acetoacetyl-CoA reductase (PhaB) for thioester reduction and PHA synthase (PhaC) for subsequent polymerization. Metabolic engineering of E. coli host strains was further conducted to enhance total PHA content and the 3-hydroxyvaleryl (3HV) monomer fraction in the copolymer. Using a selection of engineered E. coli strains for batch cultivation with an unrelated carbon source, we achieved high-level P(3HB-co-3HV) production with the 3HV monomer fraction ranging from 3 to 19 mol%, demonstrating the potential industrial applicability of these whole-cell biocatalysts.
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Affiliation(s)
- Kajan Srirangan
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - Xuejia Liu
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - Tam T Tran
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Murray Moo-Young
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
| | - C Perry Chou
- Department of Chemical Engineering , University of Waterloo, 200 University Avenue West Waterloo, Ontario N2L 3G1 Canada
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Valle A, Cabrera G, Cantero D, Bolivar J. Heterologous expression of the human Phosphoenol Pyruvate Carboxykinase (hPEPCK-M) improves hydrogen and ethanol synthesis in the Escherichia coli dcuD mutant when grown in a glycerol-based medium. N Biotechnol 2016; 35:1-12. [PMID: 27780757 DOI: 10.1016/j.nbt.2016.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 09/02/2016] [Accepted: 10/17/2016] [Indexed: 01/06/2023]
Abstract
The production of biodiesel has emerged as an alternative to fossil fuels. However, this industry generates glycerol as a by-product in such large quantities that it has become an environmental problem. The biotransformation of this excess glycerol into other renewable bio-energy sources, like H2 and ethanol, by microorganisms such as Escherichia coli is an interesting possibility that warrants investigation. In this work we hypothesized that the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) could be improved by a controlled expression of the human mitochondrial GTP-dependent PEP carboxykinase. This heterologous expression was tested in several E. coli mutant backgrounds with increased availability of C4 intermediates. It was found that this metabolic rewiring improved the synthesis of the target products in several mutants, with the dcuD mutant being the most suitable background for hydrogen and ethanol specific productions and glycerol consumption. These factors increased by 2.46, 1.73 and 1.95 times, respectively, when compared to those obtained for the wild-type strain.
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Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain.
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharaui s/n, 11510 Puerto Real, Cádiz, Spain
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharaui s/n, 11510 Puerto Real, Cádiz, Spain
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain.
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