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Liang Q, Tu B, Cui L. Recombinant T7 RNA polymerase production using ClearColi BL21(DE3) and animal-free media for in vitro transcription. Appl Microbiol Biotechnol 2024; 108:41. [PMID: 38180552 DOI: 10.1007/s00253-023-12939-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
In vitro transcription (IVT) using T7 RNA polymerase (RNAP) is integral to RNA research, yet producing this enzyme in E. coli presents challenges regarding endotoxins and animal-sourced toxins. This study demonstrates the viable production and characterization of T7 RNAP using ClearColi BL21(DE3) (an endotoxin-free E. coli strain) and animal-free media. Compared to BL21(DE3) with animal-free medium, soluble T7 RNAP expression is ~50% lower in ClearColi BL21(DE3). Optimal soluble T7 RNAP expression in flask fermentation is achieved through the design of experiments (DoE). Specification and functional testing showed that the endotoxin-free T7 RNAP has comparable activity to conventional T7 RNAP. After Ni-NTA purification, endotoxin levels were approximately 109-fold lower than T7 RNAP from BL21(DE3) with animal-free medium. Furthermore, a full factorial DoE created an optimal IVT system that maximized mRNA yield from the endotoxin-free and animal-free T7 RNAP. This work addresses critical challenges in recombinant T7 RNAP production through innovative host and medium combinations, avoided endotoxin risks and animal-derived toxins. Together with an optimized IVT reaction system, this study represents a significant advance for safe and reliable reagent manufacturing and RNA therapeutics. KEY POINTS: • Optimized IVT system maximizes mRNA yields, enabling the synthesis of long RNAs. • Novel production method yields endotoxin-free and animal-free T7 RNAP. • The T7 RNAP has equivalent specifications and function to conventional T7 RNAP.
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Affiliation(s)
- Qianying Liang
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou, 213164, Jiangsu Province, China
| | - Bowen Tu
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu Province, China
| | - Lun Cui
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou, 213164, Jiangsu Province, China.
- CCZU-JITRI Joint Bio-X Lab, Changzhou AiRiBio Healthcare CO., LTD, Changzhou, 213164, Jiangsu Province, China.
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2
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Phosriran C, Jantama K. Systematic reengineering of Klebsiella oxytoca KC004-TF160 for enhancing metabolic carbon flux towards succinate production pathway. BIORESOURCE TECHNOLOGY 2024; 407:131137. [PMID: 39043278 DOI: 10.1016/j.biortech.2024.131137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/01/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Klebsiella oxytoca KP001-TF60 (ΔadhEΔpta-ackAΔldhAΔbudABΔpflBΔtdcDΔpmd) was re-engineered to direct more carbon flux towards succinate production with less acetate. Glucose uptake, cell growth, and carbon distribution were restricted by alterations in relative expressions and nucleotide sequences of genes associated with PEP and pyruvate metabolisms. Transcripts of pck, ppc, and frd genes were up-regulated for enhancing NADH reoxidation during succinate production while increased pyk and tdcE transcripts were observed due to maintenance of acetyl-CoA through the oxidative branch of TCA cycle. Based on whole-genome sequencing, several genes in sugars-specific PTS (ptsG, bglF, chbR, fruA, mtlR, and treY), ABC transporters (alsK, and rbsK), Major Facilitator Superfamily (uhpB and setB), and catabolite repression (cyaA and csrB) were found to be mutated. The strain produced succinate yield up to 0.89 g/g (∼80 % theoretical maximum) with acetate < 1 g/L, and may be one of the succinate producers applied in an industrial-production scale with simplified purification processes.
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Affiliation(s)
- Chutchawan Phosriran
- Metabolic Engineering Research Unit, School of Biotechnology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Suranaree University of Technology, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000, Thailand.
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3
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Chen L, Wei G, Zhang Y, Wang K, Wang C, Deng X, Li Y, Xie X, Chen J, Huang F, Chen H, Zhang B, Wei C, Qiu G. Candidatus Accumulibacter use fermentation products for enhanced biological phosphorus removal. WATER RESEARCH 2023; 246:120713. [PMID: 37839225 DOI: 10.1016/j.watres.2023.120713] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 10/17/2023]
Abstract
Previous research suggested that two major groups of polyphosphate-accumulating organisms (PAOs), i.e., Ca. Accumulibacter and Tetrasphaera, play cooperative roles in enhanced biological phosphorus removal (EBPR). The fermentation of complex organic compounds by Tetrasphaera provides carbon sources for Ca. Accumulibacter. However, the viability of the fermentation products (e.g., lactate, succinate, alanine) as carbon sources for Ca. Accumulibacter and their potential effects on the metabolism of Ca. Accumulibacter were largely unknown. This work for the first time investigated the capability and metabolic details of Ca. Accumulibacter cognatus clade IIC strain SCUT-2 (enriched in a lab-scale reactor with a relative abundance of 42.8%) in using these fermentation products for EBPR. The enrichment culture was able to assimilate lactate and succinate with the anaerobic P release to carbon uptake ratios of 0.28 and 0.36 P mol/C mol, respectively. In the co-presence of acetate, the uptake of lactate was strongly inhibited, since two substrates shared the same transporter as suggested by the carbon uptake bioenergetic analysis. When acetate and succinate were fed at the same time, Ca. Accumulibacter assimilated two carbon sources simultaneously. Proton motive force (PMF) was the key driving force (up to 90%) for the uptake of lactate and succinate by Ca. Accumulibacter. Apart from the efflux of proton in symport with phosphate via the inorganic phosphate transport system, translocation of proton via the activity of fumarate reductase contributed to the generation of PMF, which agreed with the fact that PHV was a major component of PHA when lactate and succinate were used as carbon sources, involving the succinate-propionate pathway. Metabolic models for the usage of lactate and succinate by Ca. Accumulibacter for EBPR were built based on the combined physiological, biochemical, metagenomic, and metatranscriptomic analyses. Alanine was shown as an invalid carbon source for Ca. Accumulibacter. Instead, it significantly and adversely affected Ca. Accumulibacter-mediated EBPR. Phosphate release was observed without alanine uptake. Significant inhibitions on the aerobic phosphate uptake was also evident. Overall, this study suggested that there might not be a simply synergic relationship between Ca. Accumulibacter and Tetrasphaera. Their interactions would largely be determined by the kind of fermentation products released by the latter.
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Affiliation(s)
- Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Gengrui Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Yushen Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Kaiying Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Cenchao Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Yaqian Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Jinling Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Fu Huang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Bin Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, PR China.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China; Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, Guangzhou 510006, PR China.
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4
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Engineered Microbial Cell Factories for Sustainable Production of L-Lactic Acid: A Critical Review. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
With the increasing demand for the biodegradable polymer material polylactic acid and its advantage of being metabolized by the human body, L-lactic acid (L-LA) is becoming increasingly attractive in environmental protection and food industry applications. However, the supply of L-LA is not satisfied, and the price is still high. Compared to enzymatic and chemical synthesis methods, L-LA production by microbial fermentation has the advantages of low cost, large yield, simple operation, and environmental protection. This review summarizes the advances in engineering microbial cell factories to produce L-LA. First, the synthetic pathways and microorganisms for L-LA production are outlined. Then, the metabolic engineering strategies for constructing cell factories to overproduce L-LA are summarized and fermentation modes for L-LA production are also given. Finally, the challenges and prospects of the microbial production of L-LA are discussed. This review provides theoretical guidance for researchers engaged in L-LA production.
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5
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Temperature shift and feeding strategies for improving l-lactic acid production by Lactiplantibacillus plantarum in batch and fed-batch cultures. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. Impact of the Expression System on Recombinant Protein Production in Escherichia coli BL21. Front Microbiol 2021; 12:682001. [PMID: 34234760 PMCID: PMC8257044 DOI: 10.3389/fmicb.2021.682001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production for medical, academic, or industrial applications is essential for our current life. Recombinant proteins are obtained mainly through microbial fermentation, with Escherichia coli being the host most used. In spite of that, some problems are associated with the production of recombinant proteins in E. coli, such as the formation of inclusion bodies, the metabolic burden, or the inefficient translocation/transport system of expressed proteins. Optimizing transcription of heterologous genes is essential to avoid these drawbacks and develop competitive biotechnological processes. Here, expression of YFP reporter protein is evaluated under the control of four promoters of different strength (PT7lac, Ptrc, Ptac, and PBAD) and two different replication origins (high copy number pMB1′ and low copy number p15A). In addition, the study has been carried out with the E. coli BL21 wt and the ackA mutant strain growing in a rich medium with glucose or glycerol as carbon sources. Results showed that metabolic burden associated with transcription and translation of foreign genes involves a decrease in recombinant protein expression. It is necessary to find a balance between plasmid copy number and promoter strength to maximize soluble recombinant protein expression. The results obtained represent an important advance on the most suitable expression system to improve both the quantity and quality of recombinant proteins in bioproduction engineering.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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7
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Sierra-Ibarra E, Leal-Reyes LJ, Huerta-Beristain G, Hernández-Orihuela AL, Gosset G, Martínez-Antonio A, Martinez A. Limited oxygen conditions as an approach to scale-up and improve D and L-lactic acid production in mineral media and avocado seed hydrolysates with metabolically engineered Escherichia coli. Bioprocess Biosyst Eng 2020; 44:379-389. [PMID: 33029675 DOI: 10.1007/s00449-020-02450-1] [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: 05/30/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
The effectiveness of micro-aeration on lactate (LA) production by metabolically engineered Escherichia coli was evaluated in 1 L bioreactors containing mineral media and glucose (70 g/L). Volumetric oxygen transfer coefficients (kLa) between 12.6 and 28.7 h-1 increased the specific growth rate (µ) and volumetric productivity (QLA) by 300 and 400%, respectively, without a significant decrease in lactate yield (YLA), when compared with non-aerated fermentations. A kLa of 12.6 h-1 was successfully used as a criterion to scale-up the production of L and D-lactate from 1 to 11 and 130 L. Approximately constant QLA and YLA values were obtained throughout the fermentation scale-up process. Furthermore, a D-lactogenic fermentation was carried out in 1 L bioreactors using avocado seed hydrolysate as a culture medium under the same kLa value, displaying high QLA and YLA.
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Affiliation(s)
- Estefanía Sierra-Ibarra
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Laura J Leal-Reyes
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Gerardo Huerta-Beristain
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México.,Facultad de Ciencias Quıímico Biológicas, Universidad Autónoma de Guerrero, Av. Lazaro Cardenas S/N. Cd. Universitaria, 39070, Chilpancingo, Guerrero, Mexico
| | - Ana L Hernández-Orihuela
- Departamento de Ingeniería Genética. Centro de Investigación Y de Estudios Avanzados del, Instituto Politécnico Nacional. Unidad Irapuato. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, C.P. 36821, Guanajuato, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Agustino Martínez-Antonio
- Departamento de Ingeniería Genética. Centro de Investigación Y de Estudios Avanzados del, Instituto Politécnico Nacional. Unidad Irapuato. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, C.P. 36821, Guanajuato, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México.
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8
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High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
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9
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Garcia S, Trinh CT. Harnessing Natural Modularity of Metabolism with Goal Attainment Optimization to Design a Modular Chassis Cell for Production of Diverse Chemicals. ACS Synth Biol 2020; 9:1665-1681. [PMID: 32470305 DOI: 10.1021/acssynbio.9b00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Modular design is key to achieve efficient and robust systems across engineering disciplines. Modular design potentially offers advantages to engineer microbial systems for biocatalysis, bioremediation, and biosensing, overcoming the slow and costly design-build-test-learn cycles in the conventional cell engineering approach. These systems consist of a modular (chassis) cell compatible with exchangeable modules that enable programmed functions such as overproduction of a desirable chemical. We previously proposed a multiobjective optimization framework coupled with metabolic flux models to design modular cells and solved it using multiobjective evolutionary algorithms. However, such approach might not achieve solution optimality and hence limits design options for experimental implementation. In this study, we developed the goal attainment formulation compatible with optimization algorithms that guarantee solution optimality. We applied goal attainment to design an Escherichia coli modular cell capable of synthesizing all molecules in a biochemically diverse library at high yields and rates with only a few genetic manipulations. To elucidate modular organization of the designed cells, we developed a flux variance clustering (FVC) method by identifying reactions with high flux variance and clustering them to identify metabolic modules. Using FVC, we identified reaction usage patterns for different modules in the modular cell, revealing that its broad pathway compatibility is enabled by the natural modularity and flexible flux capacity of endogenous core metabolism. Overall, this study not only sheds light on modularity in metabolic networks from their topology and metabolic functions but also presents a useful synthetic biology toolbox to design modular cells with broad applications.
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Affiliation(s)
- Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory Oak Ridge, Tennessee 37830, United States
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory Oak Ridge, Tennessee 37830, United States
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10
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Uchikura H, Ninomiya K, Takahashi K, Tsuge Y. Requirement of de novo synthesis of pyruvate carboxylase in long-term succinic acid production in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2020; 104:4313-4320. [PMID: 32232530 DOI: 10.1007/s00253-020-10556-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 11/28/2022]
Abstract
Protein turnover through de novo synthesis is critical for sustainable cellular functions. We previously found that glucose consumption rate in Corynebacterium glutamicum under anaerobic conditions increased at temperature higher than the upper limit of growth temperature. Here, we showed that production of lactic and succinic acids increased at higher temperature for long-term (48 h) anaerobic reaction in metabolically engineered strains. At 42 °C, beyond the upper limit of growth temperature range, biomass-specific lactic acid production rate was 8% higher than that at 30 °C, the optimal growth temperature. In contrast, biomass-specific succinic acid production rate was highest at 36 °C, 28% higher than that at 30 °C, although the production at 42 °C was still 23% higher than that at 30 °C. As enzymes are usually unstable at high temperatures, we investigated whether protein turnover of metabolic enzymes is required for the production of lactic and succinic acids under these conditions. Interestingly, when de novo protein synthesis was inhibited by addition of chloramphenicol, after 6 h, only succinic acid production was inhibited. Because glycolytic enzymes are involved in both lactic and succinic acids synthesis, enzymes in the anaplerotic pathway and the tricarboxylic acid (TCA) cycle leading to succinic acid synthesis were likely to be responsible for its decreased production. Among the five enzymes examined, the specific activity of only pyruvate carboxylase was drastically decreased after 48 h at 42 °C. Thus, the de novo synthesis of pyruvate carboxylase is required for long-term production of succinic acid. Graphical abstract KEY POINTS: • Long-term reaction for organic acids can be improved at temperature beyond ideal growth conditions. • De novo synthesis of pyruvate carboxylase is required for long-term succinic acid production.
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Affiliation(s)
- Hiroto Uchikura
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kazuaki Ninomiya
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kenji Takahashi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yota Tsuge
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan. .,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
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11
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Lee JW, Trinh CT. Microbial biosynthesis of lactate esters. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:226. [PMID: 31548868 PMCID: PMC6753613 DOI: 10.1186/s13068-019-1563-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/07/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated. RESULTS In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase (ldhA) to convert pyruvate to lactate, a propionate CoA-transferase (pct) to convert lactate to lactyl-CoA, and an alcohol acyltransferase (AAT) to condense lactyl-CoA and alcohol(s) to make lactate ester(s). By generating a library of five pyruvate-to-lactate ester modules with divergent AATs, we screened for the best module(s) capable of producing a wide range of linear, branched, and aromatic lactate esters with an external alcohol supply. By co-introducing a pyruvate-to-lactate ester module and an alcohol (i.e., ethanol, isobutanol) module into a modular Escherichia coli (chassis) cell, we demonstrated for the first time the microbial biosynthesis of ethyl and isobutyl lactate esters directly from glucose. In an attempt to enhance ethyl lactate production as a proof-of-study, we re-modularized the pathway into (1) the upstream module to generate the ethanol and lactate precursors and (2) the downstream module to generate lactyl-CoA and condense it with ethanol to produce the target ethyl lactate. By manipulating the metabolic fluxes of the upstream and downstream modules through plasmid copy numbers, promoters, ribosome binding sites, and environmental perturbation, we were able to probe and alleviate the metabolic bottlenecks by improving ethyl lactate production by 4.96-fold. We found that AAT is the most rate-limiting step in biosynthesis of lactate esters likely due to its low activity and specificity toward the non-natural substrate lactyl-CoA and alcohols. CONCLUSIONS We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an E. coli modular cell. This study defines a cornerstone for the microbial production of lactate esters as green solvents from renewable resources with novel industrial applications.
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Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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12
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Capnophilic Lactic Fermentation from Thermotoga neapolitana: A Resourceful Pathway to Obtain Almost Enantiopure L-lactic Acid. FERMENTATION-BASEL 2019. [DOI: 10.3390/fermentation5020034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The industrial production of lactic acid (LA) is mainly based on bacterial fermentation. This process can result in enantiopure or racemic mixture according to the producing organism. Between the enantiomers, L-lactic acid shows superior market value. Recently, we reported a novel anaplerotic pathway called capnophilic lactic fermentation (CLF) that produces a high concentration of LA by fermentation of sugar in the anaerobic thermophilic bacterium Thermotoga neapolitana. The aim of this work was the identification of the enantiomeric characterization of the LA produced by T. neapolitana and identification of the lactate dehydrogenase in T. neapolitana (TnLDH) and related bacteria of the order Thermotogales. Chemical derivatization and GC/MS analysis were applied to define the stereochemistry of LA from T. neapolitana. A bioinformatics study on TnLDH was carried out for the characterization of the enzyme. Chemical analysis showed a 95.2% enantiomeric excess of L-LA produced by T. neapolitana. A phylogenetic approach clearly clustered the TnLDH together with the L-LDH from lactic acid bacteria. We report for the first time that T. neapolitana is able to produce almost enantiopure L-lactic acid. The result was confirmed by bioinformatics analysis on TnLDH, which is a member of the L-LDH sub-family.
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13
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Tsuge Y, Kato N, Yamamoto S, Suda M, Jojima T, Inui M. Metabolic engineering of Corynebacterium glutamicum for hyperproduction of polymer-grade L- and D-lactic acid. Appl Microbiol Biotechnol 2019; 103:3381-3391. [PMID: 30877357 DOI: 10.1007/s00253-019-09737-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 01/22/2023]
Abstract
Strain development is critical for microbial production of bio-based chemicals. The stereo-complex form of polylactic acid, a complex of poly-L- and poly-D-lactic acid, is a promising polymer candidate due to its high thermotolerance. Here, we developed Corynebacterium glutamicum strains producing high amounts of L- and D-lactic acid through intensive metabolic engineering. Chromosomal overexpression of genes encoding the glycolytic enzymes, glucokinase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, triosephosphate isomerase, and enolase, increased L- and D-lactic acid concentration by 146% and 56%, respectively. Chromosomal integration of two genes involved in the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-dehydro-3-deoxyphosphogluconate aldolase), together with a gene encoding glucose-6-phosphate dehydrogenase from Zymomonas mobilis, to bypass the carbon flow from glucose, further increased L- and D-lactic acid concentration by 11% and 44%, respectively. Finally, additional chromosomal overexpression of a gene encoding NADH dehydrogenase to modulate the redox balance resulted in the production of 212 g/L L-lactic acid with a 97.9% yield and 264 g/L D-lactic acid with a 95.0% yield. The optical purity of both L- and D-lactic acid was 99.9%. Because the constructed metabolically engineered strains were devoid of plasmids and antibiotic resistance genes and were cultivated in mineral salts medium, these strains could contribute to the cost-effective production of the stereo-complex form of polylactic acid in practical scale.
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Affiliation(s)
- Yota Tsuge
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Naoto Kato
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Shogo Yamamoto
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Toru Jojima
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan. .,Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0101, Japan.
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14
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Wang B, Zhang X, Yu X, Cui Z, Wang Z, Chen T, Zhao X. Evolutionary engineering of Escherichia coli for improved anaerobic growth in minimal medium accelerated lactate production. Appl Microbiol Biotechnol 2019; 103:2155-2170. [PMID: 30623201 DOI: 10.1007/s00253-018-09588-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/24/2018] [Accepted: 12/16/2018] [Indexed: 01/28/2023]
Abstract
Anaerobic fermentation is a favorable process for microbial production of bulk chemicals like ethanol and organic acids. Low productivity is the bottleneck of several anaerobic processes which has significant impact on the technique competitiveness of production strain. Improving growth rate of production strain can speed up the total production cycle and may finally increase productivity of anaerobic processes. In this work, evolutionary engineering of wild-type strain Escherichia coli W3110 was adopted to improve anaerobic growth in mineral medium. Significant increases in exponential growth rate and stationary cell density were achieved in evolved strain WE269, and a 96.5% increase in lactate productivity has also been observed in batch fermentation of this strain with M9 minimal medium. Then, an engineered strain for lactate production (BW100) was constructed by using WE269 as a platform and 98.3 g/L lactate (with an optical purity of D-lactate above 95%) was produced in a 5-L bioreactor after 48 h with a productivity of 2.05 g/(L·h). Finally, preliminary investigation demonstrated that mutation in sucD (sucD M245I) (encoding succinyl-CoA synthetase); ilvG (ilvG Δ1bp) (encoding acetolactate synthase 2 catalytic subunit), and rpoB (rpoB T1037P) (encoding RNA polymerase β subunit) significantly improved anaerobic growth of E. coli. Double-gene mutation in ilvG and sucD resumed most of the growth potential of evolved strain WE269. This work suggested that improving anaerobic growth of production host can increase productivity of organic acids like lactate, and specific mutation-enabled improved growth may also be applied to metabolic engineering for production of other bulk chemicals.
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Affiliation(s)
- Baowei Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Xiaoxia Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Xinlei Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China.
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
| | - Xueming Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
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15
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Multiobjective strain design: A framework for modular cell engineering. Metab Eng 2019; 51:110-120. [DOI: 10.1016/j.ymben.2018.09.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/28/2023]
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16
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Conversion of d-glucose to l-lactate via pyruvate by an optimized cell-free enzymatic biosystem containing minimized reactions. Synth Syst Biotechnol 2018; 3:204-210. [PMID: 30345406 PMCID: PMC6190511 DOI: 10.1016/j.synbio.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 11/22/2022] Open
Abstract
Cell-free synthetic enzymatic biosystem is emerging to expand the traditional biotechnological mode by utilizing a number of purified/partially purified enzymes and coenzymes in a single reaction vessel for the production of desired products from low-cost substrates. Here, a cell-free synthetic biosystem containing minimized number of reactions was designed for the conversion of d-glucose to l-lactate via pyruvate. This NADH-balanced biosystem was comprised of only 5 thermophilic enzymes without ATP supplementation. After optimization of enzyme loading amounts, buffer concentration and cofactor concentration, d-glucose was converted to l-lactate with a product yield of ∼90%. Our study has provided an emerging platform with potentials in producing pyruvate-derived chemicals, and may promote the development of cell-free synthetic enzymatic biosystems for biomanufacturing.
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17
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Couto MR, Rodrigues JL, Rodrigues LR. Optimization of fermentation conditions for the production of curcumin by engineered Escherichia coli. J R Soc Interface 2018; 14:rsif.2017.0470. [PMID: 28835544 DOI: 10.1098/rsif.2017.0470] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
Curcumin is a plant secondary metabolite with outstanding therapeutic effects. Therefore, there is a great interest in developing new strategies to produce this high-value compound in a cheaper and environmentally friendly way. Curcumin heterologous production in Escherichia coli using artificial biosynthetic pathways was previously demonstrated using synthetic biology approaches. However, the culturing conditions to produce this compound were not optimized and so far only a two-step fermentation process involving the exchange of culture medium allowed high concentrations of curcumin to be obtained, which limits its production at an industrial scale. In this study, the culturing conditions to produce curcumin were evaluated and optimized. In addition, it was concluded that E. coli BL21 allows higher concentrations of curcumin to be produced than E. coli K-12 strains. Different isopropyl β-d-thiogalactopyranoside concentrations, time of protein expression induction and substrate type and concentration were also evaluated. The highest curcumin production obtained was 959.3 µM (95.93% of per cent yield), which was 3.1-fold higher than the highest concentration previously reported. This concentration was obtained using a two-stage fermentation with lysogeny broth (LB) and M9. Moreover, terrific broth was also demonstrated to be a very interesting alternative medium to produce curcumin because it also led to high concentrations (817.7 µM). The use of this single fermentation medium represents an advantage at industrial scale and, although the final production is lower than that obtained with the LB-M9 combination, it leads to a significantly higher production of curcumin in the first 24 h of fermentation. This study allowed obtaining the highest concentrations of curcumin reported so far in a heterologous organism and is of interest for all of those working with the heterologous production of curcuminoids, other complex polyphenolic compounds or plant secondary metabolites.
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Affiliation(s)
- Márcia R Couto
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Joana L Rodrigues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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18
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Okano K, Uematsu G, Hama S, Tanaka T, Noda H, Kondo A, Honda K. Metabolic Engineering of Lactobacillus plantarum for Direct l-Lactic Acid Production From Raw Corn Starch. Biotechnol J 2018; 13:e1700517. [PMID: 29393585 DOI: 10.1002/biot.201700517] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/29/2018] [Indexed: 11/09/2022]
Abstract
Fermentative production of optically pure lactic acid (LA) has attracted great interest because of the increased demand for plant-based plastics. For cost-effective LA production, an engineered Lactobacillus plantarum NCIMB 8826 strain, which enables the production of optically pure l-LA from raw starch, is constructed. The wild-type strain produces a racemic mixture of d- and l-LA from pyruvate by the action of the respective lactate dehydrogenases (LDHs). Therefore, the gene encoding D-LDH (ldhD) is deleted. Although no decrease in d-LA formation is observed in the ΔldhD mutant, additional disruption of the operon encoding lactate racemase (larA-E), which catalyzes the interconversion between d- and l-LA, completely abolished d-LA production. From 100 g L-1 glucose, the ΔldhD ΔlarA-E mutant produces 87.0 g L-1 of l-LA with an optical purity of 99.4%. Subsequently, a plasmid is introduced into the ΔldhD ΔlarA-E mutant for the secretion of α-amylase from Streptococcus bovis 148. The resulting strain could produce 50.3 g L-1 of l-LA from raw corn starch with a yield of 0.91 (g per g of consumed sugar) and an optical purity of 98.6%. The engineered L. plantarum strain would be useful in the production of l-LA from starchy materials.
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Affiliation(s)
- Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Osaka, Japan
| | - Gentaro Uematsu
- Division of Applied Science, School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871 Osaka, Japan
| | - Shinji Hama
- Bio-energy Corporation, Research & Development Laboratory, 2-9-7 Minaminanamatsu, Amagasaki 660-0053, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Hideo Noda
- Bio-energy Corporation, Research & Development Laboratory, 2-9-7 Minaminanamatsu, Amagasaki 660-0053, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Osaka, Japan
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19
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Kashiwagi FM, Ojima Y, Taya M. Metabolic Engineering of Escherichia coli KO11 with the NADH Regeneration System for Enhancing Ethanol Production. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2018. [DOI: 10.1252/jcej.17we108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Yoshihiro Ojima
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University
| | - Masahito Taya
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
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20
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Li SY, Ng IS, Chen PT, Chiang CJ, Chao YP. Biorefining of protein waste for production of sustainable fuels and chemicals. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:256. [PMID: 30250508 PMCID: PMC6146663 DOI: 10.1186/s13068-018-1234-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 05/21/2023]
Abstract
To mitigate the climate change caused by CO2 emission, the global incentive to the low-carbon alternatives as replacement of fossil fuel-derived products continuously expands the need for renewable feedstock. There will be accompanied by the generation of enormous protein waste as a result. The economical viability of the biorefinery platform can be realized once the surplus protein waste is recycled in a circular economy scenario. In this context, the present review focuses on the current development of biotechnology with the emphasis on biotransformation and metabolic engineering to refine protein-derived amino acids for production of fuels and chemicals. Its scope starts with the explosion of potential feedstock sources rich in protein waste. The availability of techniques is applied for purification and hydrolysis of various feedstock proteins to amino acids. Useful lessons are leaned from the microbial catabolism of amino acids and lay a foundation for the development of the protein-based biotechnology. At last, the future perspective of the biorefinery scheme based on protein waste is discussed associated with remarks on possible solutions to overcome the technical bottlenecks.
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Affiliation(s)
- Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Po Ting Chen
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, 710 Taiwan
| | - Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
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21
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Bae JH, Kim HJ, Kim MJ, Sung BH, Jeon JH, Kim HS, Jin YS, Kweon DH, Sohn JH. Direct fermentation of Jerusalem artichoke tuber powder for production of l -lactic acid and d -lactic acid by metabolically engineered Kluyveromyces marxianus. J Biotechnol 2018; 266:27-33. [DOI: 10.1016/j.jbiotec.2017.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/22/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022]
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22
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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23
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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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24
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Doi H, Tokura Y, Mori Y, Mori K, Asakura Y, Usuda Y, Fukuda H, Chinen A. Identification of enzymes responsible for extracellular alginate depolymerization and alginate metabolism in Vibrio algivorus. Appl Microbiol Biotechnol 2017; 101:1581-1592. [PMID: 27915375 PMCID: PMC5266763 DOI: 10.1007/s00253-016-8021-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 12/15/2022]
Abstract
Alginate is a marine non-food-competing polysaccharide that has potential applications in biorefinery. Owing to its large size (molecular weight >300,000 Da), alginate cannot pass through the bacterial cell membrane. Therefore, bacteria that utilize alginate are presumed to have an enzyme that degrades extracellular alginate. Recently, Vibrio algivorus sp. SA2T was identified as a novel alginate-decomposing and alginate-utilizing species. However, little is known about the mechanism of alginate degradation and metabolism in this species. To address this issue, we screened the V. algivorus genomic DNA library for genes encoding polysaccharide-decomposing enzymes using a novel double-layer plate screening method and identified alyB as a candidate. Most identified alginate-decomposing enzymes (i.e., alginate lyases) must be concentrated and purified before extracellular alginate depolymerization. AlyB of V. algivorus heterologously expressed in Escherichia coli depolymerized extracellular alginate without requiring concentration or purification. We found seven homologues in the V. algivorus genome (alyB, alyD, oalA, oalB, oalC, dehR, and toaA) that are thought to encode enzymes responsible for alginate transport and metabolism. Introducing these genes into E. coli enabled the cells to assimilate soluble alginate depolymerized by V. algivorus AlyB as the sole carbon source. The alginate was bioconverted into L-lysine (43.3 mg/l) in E. coli strain AJIK01. These findings demonstrate a simple and novel screening method for identifying polysaccharide-degrading enzymes in bacteria and provide a simple alginate biocatalyst and fermentation system with potential applications in industrial biorefinery.
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Affiliation(s)
- Hidetaka Doi
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Yuriko Tokura
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yukiko Mori
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kenichi Mori
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yoko Asakura
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yoshihiro Usuda
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
- Frontier Research Laboratories, Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akito Chinen
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
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25
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De Leon-Rodriguez A, Caño-Muñiz SL, Liu J, Summers DK. Indole modifies the central carbon flux in the anaerobic metabolism of Escherichia coli: application to the production of hydrogen and other metabolites. N Biotechnol 2016; 33:868-873. [DOI: 10.1016/j.nbt.2016.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/13/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
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26
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Bernal V, Castaño-Cerezo S, Cánovas M. Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond. Appl Microbiol Biotechnol 2016; 100:8985-9001. [DOI: 10.1007/s00253-016-7832-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022]
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27
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Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
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Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
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Tian K, Niu D, Liu X, Prior BA, Zhou L, Lu F, Singh S, Wang Z. Limitation of thiamine pyrophosphate supply to growingEscherichia coliswitches metabolism to efficientd-lactate formation. Biotechnol Bioeng 2015; 113:182-8. [DOI: 10.1002/bit.25699] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Kangming Tian
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457; P. R. China
| | - Dandan Niu
- College of Biological Science and Engineering; Fuzhou University; Fuzhou 350108 P. R. China
| | - Xiaoguang Liu
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457; P. R. China
| | - Bernard A. Prior
- Department of Microbiology; Stellenbosch University; Matieland, South Africa
| | - Li Zhou
- Center for Bioresource and Bioenergy; School of Biotechnology; Jiangnan University; Wuxi P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457; P. R. China
| | - Suren Singh
- Department of Biotechnology and Food Technology; Faculty of Applied Sciences; Durban University of Technology; Durban South Africa
| | - Zhengxiang Wang
- Key Laboratory of Industrial Fermentation Microbiology; Ministry of Education, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457; P. R. China
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Recent advances in the metabolic engineering of Corynebacterium glutamicum for the production of lactate and succinate from renewable resources. ACTA ACUST UNITED AC 2015; 42:375-89. [DOI: 10.1007/s10295-014-1538-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 02/02/2023]
Abstract
Abstract
Recent increasing attention to environmental issues and the shortage of oil resources have spurred political and industrial interest in the development of environmental friendly and cost-effective processes for the production of bio-based chemicals from renewable resources. Thus, microbial production of commercially important chemicals is viewed as a desirable way to replace current petrochemical production. Corynebacterium glutamicum, a Gram-positive soil bacterium, is one of the most important industrial microorganisms as a platform for the production of various amino acids. Recent research has explored the use of C. glutamicum as a potential cell factory for producing organic acids such as lactate and succinate, both of which are commercially important bulk chemicals. Here, we summarize current understanding in this field and recent metabolic engineering efforts to develop C. glutamicum strains that efficiently produce l- and d-lactate, and succinate from renewable resources.
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Ren Y, Yang S, Yuan Q, Sun X. Microbial production of phenol via salicylate decarboxylation. RSC Adv 2015. [DOI: 10.1039/c5ra20104g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel phenol biosynthetic pathway was designed and verified inE. coli.
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Affiliation(s)
- Yanxian Ren
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Sen Yang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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