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Wang J, Li C, Jiang T, Yan Y. Biosensor-assisted titratable CRISPRi high-throughput (BATCH) screening for over-production phenotypes. Metab Eng 2023; 75:58-67. [PMID: 36375746 PMCID: PMC9845192 DOI: 10.1016/j.ymben.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
With rapid advances in the development of metabolic pathways and synthetic biology toolkits, a persisting challenge in microbial bioproduction is how to optimally rewire metabolic fluxes and accelerate the concomitant high-throughput phenotype screening. Here we developed a biosensor-assisted titratable CRISPRi high-throughput (BATCH) screening approach that combines a titratable mismatch CRISPR interference and a biosensor mediated screening for high-production phenotypes in Escherichia coli. We first developed a programmable mismatch CRISPRi that could afford multiple levels of interference efficacy with a one-pot sgRNA pool (a total of 16 variants for each target gene) harboring two consecutive random mismatches in the seed region of sgRNA spacers. The mismatch CRISPRi was demonstrated to enable almost a full range of gene knockdown when targeting different positions on genes. As a proof-of-principle demonstration of the BATCH screening system, we designed doubly mismatched sgRNA pools targeting 20 relevant genes in E. coli and optimized a PadR-based p-coumaric acid biosensor with broad dynamic range for the eGFP fluorescence guided high-production screening. Using sgRNA variants for the combinatorial knockdown of pfkA and ptsI, the p-coumaric acid titer was increased by 40.6% to o 1308.6 mg/l from glycerol in shake flasks. To further demonstrate the general applicability of the BATCH screening system, we recruited a HpdR-based butyrate biosensor that facilitated the screening of E. coli strains achieving 19.0% and 25.2% increase of butyrate titer in shake flasks with sgRNA variants targeting sucA and ldhA, respectively. This work reported the establishment of a plug-and-play approach that enables multilevel modulation of metabolic fluxes and high-throughput screening of high-production phenotypes.
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Affiliation(s)
- Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.
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Kim S, Kim KJ. Crystal Structure and Molecular Mechanism of Phosphotransbutyrylase from Clostridium acetobutylicum. J Microbiol Biotechnol 2021; 31:1393-1400. [PMID: 34584034 PMCID: PMC9706017 DOI: 10.4014/jmb.2109.09036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.
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Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioSesearch Group, Kyungpook National University, Daegu 41566, Republic of Korea,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioSesearch Group, Kyungpook National University, Daegu 41566, Republic of Korea,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-950-5377 Fax: +82-53-955-5522 E-mail:
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3
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Kim K, Choe D, Song Y, Kang M, Lee SG, Lee DH, Cho BK. Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design. Metab Eng 2021; 68:174-186. [PMID: 34655791 DOI: 10.1016/j.ymben.2021.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 12/29/2022]
Abstract
Bacteroides thetaiotaomicron represents a major symbiont of the human gut microbiome that is increasingly viewed as a promising candidate strain for microbial therapeutics. Here, we engineer B. thetaiotaomicron for heterologous production of non-native butyrate as a proof-of-concept biochemical at therapeutically relevant concentrations. Since B. thetaiotaomicron is not a natural producer of butyrate, we heterologously expressed a butyrate biosynthetic pathway in the strain, which led to the production of butyrate at the final concentration of 12 mg/L in a rich medium. Further optimization of butyrate production was achieved by a round of metabolic engineering guided by an expanded genome-scale metabolic model (GEM) of B. thetaiotaomicron. The in silico knock-out simulation of the expanded model showed that pta and ldhD were the potent knock-out targets to enhance butyrate production. The maximum titer and specific productivity of butyrate in the pta-ldhD double knockout mutant increased by nearly 3.4 and 4.8 folds, respectively. To our knowledge, this is the first engineering attempt that enabled butyrate production from a non-butyrate producing commensal B. thetaiotaomicron. The study also highlights that B. thetaiotaomicron can serve as an effective strain for live microbial therapeutics in human.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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4
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Chiang CJ, Hong YH. In situ delivery of biobutyrate by probiotic Escherichia coli for cancer therapy. Sci Rep 2021; 11:18172. [PMID: 34518590 PMCID: PMC8438071 DOI: 10.1038/s41598-021-97457-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Butyrate has a bioactive function to reduce carcinogenesis. To achieve targeted cancer therapy, this study developed bacterial cancer therapy (BCT) with butyrate as a payload. By metabolic engineering, Escherichia coli Nissle 1917 (EcN) was reprogrammed to synthesize butyrate (referred to as biobutyrate) and designated EcN-BUT. The adopted strategy includes construction of a synthetic pathway for biobutyrate and the rational design of central metabolism to increase the production of biobutyrate at the expense of acetate. With glucose, EcN-BUT produced primarily biobutyrate under the hypoxic condition. Furthermore, human colorectal cancer cell was administrated with the produced biobutyrate. It caused the cell cycle arrest at the G1 phase and induced the mitochondrial apoptosis pathway independent of p53. In the tumor-bearing mice, the injected EcN-BUT exhibited tumor-specific colonization and significantly reduced the tumor volume by 70%. Overall, this study opens a new avenue for BCT based on biobutyrate.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, Taiwan, 40402.
| | - Yan-Hong Hong
- Department of Chemical Engineering, Feng Chia University, Taichung, Taiwan, 40724
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Chiang CJ, Hu RC, Huang ZC, Chao YP. Production of Succinic Acid from Amino Acids in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8172-8178. [PMID: 34282894 DOI: 10.1021/acs.jafc.1c02958] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glutamate (Glu) and aspartate (Asp) are the most abundant amino acids in various sources of protein waste, recognized as a sustainable resource. In this study, Escherichia coli was engineered to produce succinic acid (SA) from Glu and Asp. Succinate dehydrogenase involved in the tricarboxylic acid was inactivated in the Glu-utilizing strain. To grow on Asp, this mutant strain was subjected to metabolic evolution. One resulting strain capable of metabolizing Asp was further evolved to improve the growth of Glu and Asp. After the deletion of arcA, the resulting strain was employed for the aerobic production of SA. The shake-flask culture was conducted with the minimal medium containing 10 g/L Glu and 10 g/L Asp. Finally, it resulted in the SA production, with a titer, the molar yield, and productivity reaching 72.8 mM (i.e., 8.6 g/L), 0.54 (ca. 75.4% of the theoretical yield), and 0.66 g/L/h, respectively. Overall, this study opens up a new avenue of the biorefinery platform based on renewable amino acids.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Ruo-Ciao Hu
- Department of Chemical Engineering, Feng Chia University 100 Wenhwa Road, Taichung 40724, Taiwan
| | - Zih-Ci Huang
- Department of Chemical Engineering, Feng Chia University 100 Wenhwa Road, Taichung 40724, Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University 100 Wenhwa Road, Taichung 40724, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung 41354, Taiwan
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7
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Fu H, Lin M, Tang IC, Wang J, Yang ST. Effects of benzyl viologen on increasing NADH availability, acetate assimilation, and butyric acid production by Clostridium tyrobutyricum. Biotechnol Bioeng 2020; 118:770-783. [PMID: 33058166 DOI: 10.1002/bit.27602] [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] [Received: 09/18/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022]
Abstract
Clostridium tyrobutyricum produces butyric and acetic acids from glucose. The butyric acid yield and selectivity in the fermentation depend on NADH available for acetate reassimilation to butyric acid. In this study, benzyl viologen (BV), an artificial electron carrier that inhibits hydrogen production, was used to increase NADH availability and butyric acid production while eliminating acetic acid accumulation by facilitating its reassimilation. To better understand the mechanism of and find the optimum condition for BV effect on enhancing acetate assimilation and butyric acid production, BV at various concentrations and addition times during the fermentation were studied. Compared with the control without BV, the addition of 1 μM BV increased butyric acid production from glucose by ∼50% in yield and ∼29% in productivity while acetate production was completely inhibited. Furthermore, BV also increased the coutilization of glucose and exogenous acetate for butyric acid production. At a concentration ratio of acetate (g/L) to BV (mM) of 4, both acetate assimilation and butyrate biosynthesis increased with increasing the concentrations of BV (0-6.25 μM) and exogenous acetate (0-25 g/L). In a fed-batch fermentation with glucose and ∼15 g/L acetate and 3.75 μM BV, butyrate production reached 55.9 g/L with productivity 0.93 g/L/h, yield 0.48 g/g, and 97.4% purity, which would facilitate product purification and reduce production cost. Manipulating metabolic flux and redox balance via BV and acetate addition provided a simple to implement metabolic process engineering approach for butyric acid production from sugars and biomass hydrolysates.
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Affiliation(s)
- Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Meng Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - I-Ching Tang
- Bioprocessing Innovative Company, Dublin, Ohio, USA
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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Shahab RL, Brethauer S, Davey MP, Smith AG, Vignolini S, Luterbacher JS, Studer MH. A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose. Science 2020; 369:369/6507/eabb1214. [DOI: 10.1126/science.abb1214] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
Microbial consortia are a promising alternative to monocultures of genetically modified microorganisms for complex biotransformations. We developed a versatile consortium-based strategy for the direct conversion of lignocellulose to short-chain fatty acids, which included the funneling of the lignocellulosic carbohydrates to lactate as a central intermediate in engineered food chains. A spatial niche enabled in situ cellulolytic enzyme production by an aerobic fungus next to facultative anaerobic lactic acid bacteria and the product-forming anaerobes. Clostridium tyrobutyricum, Veillonella criceti, or Megasphaera elsdenii were integrated into the lactate platform to produce 196 kilograms of butyric acid per metric ton of beechwood. The lactate platform demonstrates the benefits of mixed cultures, such as their modularity and their ability to convert complex substrates into valuable biochemicals.
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Affiliation(s)
- Robert L. Shahab
- Laboratory of Sustainable and Catalytic Processing, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Laboratory of Biofuels and Biochemicals, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences (BFH), CH-3052 Zollikofen, Switzerland
| | - Simone Brethauer
- Laboratory of Biofuels and Biochemicals, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences (BFH), CH-3052 Zollikofen, Switzerland
| | - Matthew P. Davey
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Silvia Vignolini
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Jeremy S. Luterbacher
- Laboratory of Sustainable and Catalytic Processing, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael H. Studer
- Laboratory of Biofuels and Biochemicals, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences (BFH), CH-3052 Zollikofen, Switzerland
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9
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Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum. World J Microbiol Biotechnol 2020; 36:138. [PMID: 32794091 DOI: 10.1007/s11274-020-02914-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022]
Abstract
Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.
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Tanoh EA, Boué GB, Nea F, Genva M, Wognin EL, Ledoux A, Martin H, Tonzibo ZF, Frederich M, Fauconnier ML. Seasonal Effect on the Chemical Composition, Insecticidal Properties and Other Biological Activities of Zanthoxylum leprieurii Guill. & Perr. Essential oils. Foods 2020; 9:foods9050550. [PMID: 32369948 PMCID: PMC7278710 DOI: 10.3390/foods9050550] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 12/12/2022] Open
Abstract
This study focused, for the first time, on the evaluation of the seasonal effect on the chemical composition and biological activities of essential oils hydrodistillated from leaves, trunk bark and fruits of Zanthoxylum leprieurii (Z. leprieurii), a traditional medicinal wild plant growing in Côte d'Ivoire. The essential oils were obtained by hydrodistillation from fresh organs of Z. leprieurii growing on the same site over several months using a Clevenger-type apparatus and analyzed by gas chromatography-mass spectrometry (GC/MS). Leaf essential oils were dominated by tridecan-2-one (9.00 ± 0.02-36.80 ± 0.06%), (E)-β-ocimene (1.30 ± 0.50-23.57 ± 0.47%), β-caryophyllene (7.00 ± 1.02-19.85 ± 0.48%), dendrolasin (1.79 ± 0.08-16.40 ± 0.85%) and undecan-2-one (1.20 ± 0.03-8.51 ± 0.35%). Fruit essential oils were rich in β-myrcene (16.40 ± 0.91-48.27 ± 0.26%), citronellol (1.90 ± 0.02-28.24 ± 0.10%) and geranial (5.30 ± 0.53-12.50 ± 0.47%). Tridecan-2-one (45.26 ± 0.96-78.80 ± 0.55%), β-caryophyllene (1.80 ± 0.23-13.20 ± 0.33%), ?-humulene (4.30 ±1.09-12.73 ± 1.41%) and tridecan-2-ol (2.23 ± 0.17-10.10 ± 0.61%) were identified as major components of trunk bark oils. Statistical analyses of essential oil compositions showed that the variability mainly comes from the organs. Indeed, principal component analysis (PCA) and hierarchical cluster analysis (HCA) allowed us to cluster the samples into three groups, each one consisting of one different Z. leprieurii organ, showing that essential oils hydrodistillated from the different organs do not display the same chemical composition. However, significant differences in essential oil compositions for the same organ were highlighted during the studied period, showing the impact of the seasonal effect on essential oil compositions. Biological activities of the produced essential oils were also investigated. Essential oils exhibited high insecticidal activities against Sitophilus granarius, as well as antioxidant, anti-inflammatory and moderate anti-plasmodial properties.
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Affiliation(s)
- Evelyne Amenan Tanoh
- Laboratory of Biological Organic Chemistry, UFR-SSMT, University Felix Houphouet-Boigny, 01 BP 582 Abidjan 01, Ivory Coast; (G.B.B.); (F.N.); (Z.F.T.)
- Laboratory of Chemistry of Natural Molecules, University of Liège, Gembloux Agro-Bio Tech, 2, Passage des Déportés, 5030 Gembloux, Belgium; (M.G.); (H.M.); (M.-L.F.)
- Correspondence: ; Tel.: +32-(0)4-6566-3587
| | - Guy Blanchard Boué
- Laboratory of Biological Organic Chemistry, UFR-SSMT, University Felix Houphouet-Boigny, 01 BP 582 Abidjan 01, Ivory Coast; (G.B.B.); (F.N.); (Z.F.T.)
| | - Fatimata Nea
- Laboratory of Biological Organic Chemistry, UFR-SSMT, University Felix Houphouet-Boigny, 01 BP 582 Abidjan 01, Ivory Coast; (G.B.B.); (F.N.); (Z.F.T.)
- Laboratory of Chemistry of Natural Molecules, University of Liège, Gembloux Agro-Bio Tech, 2, Passage des Déportés, 5030 Gembloux, Belgium; (M.G.); (H.M.); (M.-L.F.)
| | - Manon Genva
- Laboratory of Chemistry of Natural Molecules, University of Liège, Gembloux Agro-Bio Tech, 2, Passage des Déportés, 5030 Gembloux, Belgium; (M.G.); (H.M.); (M.-L.F.)
| | - Esse Leon Wognin
- Laboratory of Instrumentation Image and Spectroscopy, National Polytechnic Institute Felix Houphouët-Boigny, BP 1093 Yamoussoukro, Ivory Coast;
| | - Allison Ledoux
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium; (A.L.); (M.F.)
| | - Henri Martin
- Laboratory of Chemistry of Natural Molecules, University of Liège, Gembloux Agro-Bio Tech, 2, Passage des Déportés, 5030 Gembloux, Belgium; (M.G.); (H.M.); (M.-L.F.)
| | - Zanahi Felix Tonzibo
- Laboratory of Biological Organic Chemistry, UFR-SSMT, University Felix Houphouet-Boigny, 01 BP 582 Abidjan 01, Ivory Coast; (G.B.B.); (F.N.); (Z.F.T.)
| | - Michel Frederich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium; (A.L.); (M.F.)
| | - Marie-Laure Fauconnier
- Laboratory of Chemistry of Natural Molecules, University of Liège, Gembloux Agro-Bio Tech, 2, Passage des Déportés, 5030 Gembloux, Belgium; (M.G.); (H.M.); (M.-L.F.)
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Satowa D, Fujiwara R, Uchio S, Nakano M, Otomo C, Hirata Y, Matsumoto T, Noda S, Tanaka T, Kondo A. Metabolic engineering of E. coli for improving mevalonate production to promote NADPH regeneration and enhance acetyl-CoA supply. Biotechnol Bioeng 2020; 117:2153-2164. [PMID: 32255505 DOI: 10.1002/bit.27350] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/17/2020] [Accepted: 04/05/2020] [Indexed: 12/17/2022]
Abstract
Microbial production of mevalonate from renewable feedstock is a promising and sustainable approach for the production of value-added chemicals. We describe the metabolic engineering of Escherichia coli to enhance mevalonate production from glucose and cellobiose. First, the mevalonate-producing pathway was introduced into E. coli and the expression of the gene atoB, which encodes the gene for acetoacetyl-CoA synthetase, was increased. Then, the deletion of the pgi gene, which encodes phosphoglucose isomerase, increased the NADPH/NADP+ ratio in the cells but did not improve mevalonate production. Alternatively, to reduce flux toward the tricarboxylic acid cycle, gltA, which encodes citrate synthetase, was disrupted. The resultant strain, MGΔgltA-MV, increased levels of intracellular acetyl-CoA up to sevenfold higher than the wild-type strain. This strain produced 8.0 g/L of mevalonate from 20 g/L of glucose. We also engineered the sugar supply by displaying β-glucosidase (BGL) on the cell surface. When cellobiose was used as carbon source, the strain lacking gnd displaying BGL efficiently consumed cellobiose and produced mevalonate at 5.7 g/L. The yield of mevalonate was 0.25 g/g glucose (1 g of cellobiose corresponds to 1.1 g of glucose). These results demonstrate the feasibility of producing mevalonate from cellobiose or cellooligosaccharides using an engineered E. coli strain.
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Affiliation(s)
- Daichi Satowa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Ryosuke Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Shogo Uchio
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Mariko Nakano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Chisako Otomo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Prefecture University, Osaka, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
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12
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Wainaina S, Lukitawesa, Kumar Awasthi M, Taherzadeh MJ. Bioengineering of anaerobic digestion for volatile fatty acids, hydrogen or methane production: A critical review. Bioengineered 2020; 10:437-458. [PMID: 31570035 PMCID: PMC6802927 DOI: 10.1080/21655979.2019.1673937] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Anaerobic digestion (AD) is a well-established technology used for producing biogas or biomethane alongside the slurry used as biofertilizer. However, using a variety of wastes and residuals as substrate and mixed cultures in the bioreactor makes AD as one of the most complicated biochemical processes employing hydrolytic, acidogenic, hydrogen-producing, acetate-forming bacteria as well as acetoclastic and hydrogenoclastic methanogens. Hydrogen and volatile fatty acids (VFAs) including acetic, propionic, isobutyric, butyric, isovaleric, valeric and caproic acid and other carboxylic acids such as succinic and lactic acids are formed as intermediate products. As these acids are important precursors for various industries as mixed or purified chemicals, the AD process can be bioengineered to produce VFAs alongside hydrogen and therefore biogas plants can become biorefineries. The current review paper provides the theory and means to produce and accumulate VFAs and hydrogen, inhibit their conversion to methane and to extract them as the final products. The effects of pretreatment, pH, temperature, hydraulic retention time (HRT), organic loading rate (OLR), chemical methane inhibitions, and heat shocking of the inoculum on VFAs accumulation, hydrogen production, VFAs composition, and the microbial community were discussed. Furthermore, this paper highlights the possible techniques for recovery of VFAs from the fermentation media in order to minimize product inhibition as well as to supply the carboxylates for downstream procedures.
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Affiliation(s)
- Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås , Borås , Sweden
| | - Lukitawesa
- Swedish Centre for Resource Recovery, University of Borås , Borås , Sweden
| | - Mukesh Kumar Awasthi
- Swedish Centre for Resource Recovery, University of Borås , Borås , Sweden.,College of Natural Resources and Environment, Northwest A&F University , Yangling , Shaanxi Province , PR China
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13
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Guo L, Diao W, Gao C, Hu G, Ding Q, Ye C, Chen X, Liu J, Liu L. Engineering Escherichia coli lifespan for enhancing chemical production. Nat Catal 2020. [DOI: 10.1038/s41929-019-0411-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Clostridium sp. as Bio-Catalyst for Fuels and Chemicals Production in a Biorefinery Context. Catalysts 2019. [DOI: 10.3390/catal9110962] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Clostridium sp. is a genus of anaerobic bacteria capable of metabolizing several substrates (monoglycerides, diglycerides, glycerol, carbon monoxide, cellulose, and more), into valuable products. Biofuels, such as ethanol and butanol, and several chemicals, such as acetone, 1,3-propanediol, and butyric acid, can be produced by these organisms through fermentation processes. Among the most well-known species, Clostridium carboxidivorans, C. ragsdalei, and C. ljungdahlii can be highlighted for their ability to use gaseous feedstocks (as syngas), obtained from the gasification or pyrolysis of waste material, to produce ethanol and butanol. C. beijerinckii is an important species for the production of isopropanol and butanol, with the advantage of using hydrolysate lignocellulosic material, which is produced in large amounts by first-generation ethanol industries. High yields of 1,3 propanediol by C. butyricum are reported with the use of another by-product from fuel industries, glycerol. In this context, several Clostridium wild species are good candidates to be used as biocatalysts in biochemical or hybrid processes. In this review, literature data showing the technical viability of these processes are presented, evidencing the opportunity to investigate them in a biorefinery context.
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15
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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16
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Antioxidant and Lipoxygenase Inhibitory Activities of Essential Oils from Endemic Plants of Côte d'Ivoire: Zanthoxylum mezoneurispinosum Ake Assi and Zanthoxylum psammophilum Ake Assi. Molecules 2019; 24:molecules24132445. [PMID: 31277326 PMCID: PMC6651734 DOI: 10.3390/molecules24132445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/19/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Zanthoxylum mezoneurispinosum Ake Assi and Zanthoxylum psammophilum Ake Assi are species endemic to Côte d’Ivoire. In this study, we determined, for the first time, the composition and biological activities of essential oils obtained from each of these plants. Essential oils were obtained by hydrodistillation from different organs of each plant with a Clevenger-type apparatus and analyzed by gas chromatography–mass spectrometry (GC-MS). Thirty-four components, accounting for more than 99.9% of the overall composition, were identified in the oils. The Z. psammophilum leaf and trunk bark oils exhibited two unusual methylketones, undecan-2-one and tridecan-2-one, whereas the root oil was rich in thymol and sesquiterpenoids. The Z. mezoneurispinosum leaf and trunk bark oils were rich in monoterpenoids, whereas sesquiterpenoids were predominant in the root oil. These samples produced, for the first time, some new chemical profiles of essential oils. The oils’ antioxidant activities were determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity and ferric reducing antioxidant power (FRAP) assays. The results showed that the essential oil isolated from roots of Z. mezoneurispinosum had the highest antioxidant activity, which is in accordance with the high thymol content of that oil. We also determined the lipoxygenase inhibitory activities of the essential oils. The results showed that all of the tested oils displayed high and close lipoxygenase inhibitory activities.
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17
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Wang L, Chauliac D, Moritz BE, Zhang G, Ingram LO, Shanmugam KT. Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:62. [PMID: 30949238 PMCID: PMC6429758 DOI: 10.1186/s13068-019-1408-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Several anaerobic bacteria produce butyric acid, a commodity chemical with use in chemical, pharmaceutical, food and feed industries, using complex media with acetate as a co-product. Butyrate titer of various recombinant Escherichia coli did not exceed 10 g l-1 in batch fermentations in any of the media tested. RESULTS A recombinant E. coli (strain LW393) that produced butyrate as the major fermentation product was constructed with genes from E. coli, Clostridium acetobutylicum and Treponema denticola. Strain LW393 produced 323 ± 6 mM (28.4 ± 0.4 g l-1) butyric acid in batch fermentations in mineral salt medium with glucose as C source at a yield of 0.37 ± 0.01 g (g glucose consumed)-1. Butyrate accounted for 90% of the total products produced by the culture. Supplementing this medium with yeast extract further increased butyric acid titer to 375 ± 4 mM. Average volumetric productivity of butyrate with xylose as C source was 0.89 ± 0.07 g l-1 h-1. CONCLUSIONS The butyrate titer reported in this study is about 2.5-3-times higher than the values reported for other recombinant E. coli and this is achieved in mineral salt medium with an expectation of lower purification and production cost of butyrate.
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Affiliation(s)
- Liang Wang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
| | - Diane Chauliac
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
- Present Address: Galactic, Brussels, Belgium
| | - Brelan E. Moritz
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
| | - Guimin Zhang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, 430062 China
| | - Lonnie O. Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
| | - K. T. Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
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18
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Jiang L, Fu H, Yang HK, Xu W, Wang J, Yang ST. Butyric acid: Applications and recent advances in its bioproduction. Biotechnol Adv 2018; 36:2101-2117. [PMID: 30266343 DOI: 10.1016/j.biotechadv.2018.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Butyric acid is an important C4 organic acid with broad applications. It is currently produced by chemosynthesis from petroleum-based feedstocks. However, the fermentative production of butyric acid from renewable feedstocks has received growing attention because of consumer demand for green products and natural ingredients in foods, pharmaceuticals, animal feed supplements, and cosmetics. In this review, strategies for improving microbial butyric acid production, including strain engineering and novel fermentation process development are discussed and compared regarding product yield, titer, purity and productivity. Future perspectives on strain and process improvements for butyric acid production are also discussed.
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Affiliation(s)
- Ling Jiang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; College of Food Science and Light Industry, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Hongxin Fu
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hopen K Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; School of Chemical and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Jufang Wang
- School of Biology & Biological Engineering, South China University of Technology, Guangzhou 510006, China; Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
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19
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Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
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20
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Zhang J, Chen X, Liu P, Zhao J, Sun J, Guan W, Johnston LJ, Levesque CL, Fan P, He T, Zhang G, Ma X. Dietary Clostridium butyricum Induces a Phased Shift in Fecal Microbiota Structure and Increases the Acetic Acid-Producing Bacteria in a Weaned Piglet Model. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5157-5166. [PMID: 29683328 DOI: 10.1021/acs.jafc.8b01253] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Clostridium butyricum is known as a butyrate producer and a regulator of gut health, but whether it exerts a beneficial effect as a dietary supplement via modulating the intestinal microbiota remains elusive. This study investigated the impact of C. butyricum on the fecal microbiota composition and their metabolites 14 and 28 days after weaning with 10 g/kg dietary supplementation of C. butyricum. Dynamic changes of microbial compositions showed dramatically increasing Selenomonadales and decreasing Clostridiales on days 14 and 28. Within Selenomonadales, Megasphaera became the main responder by increasing from 3.79 to 11.31%. Following the prevalence of some acetate producers ( Magasphaera) and utilizers ( Eubacterium_hallii) at the genus level and even with a significant decrease in fecal acetate on day 28, the present data suggested that C. butyricum influenced microbial metabolism by optimizing the structure of microbiota and enhancing acetate production and utilization for butyrate production.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
- Department of Animal Husbandry and Veterinary , Beijing Vocational College of Agriculture , Beijing 102442 , People's Republic of China
| | - Xiyue Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Ping Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Jinbiao Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Jian Sun
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
- Department of Animal Husbandry and Veterinary , Beijing Vocational College of Agriculture , Beijing 102442 , People's Republic of China
| | - Wenyi Guan
- Department of Animal Husbandry and Veterinary , Beijing Vocational College of Agriculture , Beijing 102442 , People's Republic of China
| | - Lee J Johnston
- West Central Research & Outreach Center , University of Minnesota , Morris , Minnesota 56267 , United States
| | - Crystal L Levesque
- Department of Animal Science, College of Agriculture and Biological Sciences , South Dakota State University , Brookings , South Dakota 57007 , United States
| | - Peixin Fan
- Emerging Pathogens Institute , University of Florida , Gainesville , Florida 32608 , United States
- Department of Animal Sciences, Institute of Food and Agricultural Sciences , University of Florida , Gainesville , Florida 32608 , United States
| | - Ting He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Guolong Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
- Department of Animal Science , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology , China Agricultural University , Beijing 100193 , People's Republic of China
- College of Animal Science and Technology , Qingdao Agricultural University , Qingdao , 266109 , People's Republic of China
- Department of Internal Medicine, Department of Biochemistry , University of Texas Southwestern Medical Center , Dallas , Texas 75230 , United States
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21
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Yoon J, Woo HM. CRISPR interference-mediated metabolic engineering of Corynebacterium glutamicum for homo-butyrate production. Biotechnol Bioeng 2018; 115:2067-2074. [PMID: 29704438 DOI: 10.1002/bit.26720] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 02/02/2023]
Abstract
Combinatorial metabolic engineering enabled the development of efficient microbial cell factories for modulating gene expression to produce desired products. Here, we report the combinatorial metabolic engineering of Corynebacterium glutamicum to produce butyrate by introducing a synthetic butyrate pathway including phosphotransferase and butyrate kinase reactions and repressing the essential acn gene-encoding aconitase, which has been targeted for downregulation in a genome-scale model. An all-in-one clustered regularly interspaced short palindromic repeats interference system for C. glutamicum was used for tunable downregulation of acn in an engineered strain, where by-product-forming reactions were deleted and the synthetic butyrate pathway was inserted, resulting in butyrate production (0.52 ± 0.02 g/L). Subsequently, biotin limitation enabled the engineered strain to produce butyrate (0.58 ± 0.01 g/L) without acetate formation for the entire duration of the culture. These results demonstrate the potential homo-production of butyrate using engineered C. glutamicum. This method can also be applied to other industrial microorganisms.
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Affiliation(s)
- Jinkyung Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), Suwon, Republic of Korea
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22
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Zhao M, Huang D, Zhang X, Koffas MA, Zhou J, Deng Y. Metabolic engineering of Escherichia coli for producing adipic acid through the reverse adipate-degradation pathway. Metab Eng 2018; 47:254-262. [DOI: 10.1016/j.ymben.2018.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/19/2018] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
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23
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Suo Y, Ren M, Yang X, Liao Z, Fu H, Wang J. Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production with high butyrate/acetate ratio. Appl Microbiol Biotechnol 2018; 102:4511-4522. [DOI: 10.1007/s00253-018-8954-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 11/30/2022]
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24
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Luo H, Yang R, Zhao Y, Wang Z, Liu Z, Huang M, Zeng Q. Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation. BIORESOURCE TECHNOLOGY 2018; 253:343-354. [PMID: 29329775 DOI: 10.1016/j.biortech.2018.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 06/07/2023]
Abstract
Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mengyu Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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25
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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26
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Kataoka N, Vangnai AS, Pongtharangkul T, Yakushi T, Matsushita K. Butyrate production under aerobic growth conditions by engineered Escherichia coli. J Biosci Bioeng 2017; 123:562-568. [DOI: 10.1016/j.jbiosc.2016.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/26/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022]
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27
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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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28
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Engineered Production of Short Chain Fatty Acid in Escherichia coli Using Fatty Acid Synthesis Pathway. PLoS One 2016; 11:e0160035. [PMID: 27466817 PMCID: PMC4965127 DOI: 10.1371/journal.pone.0160035] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/12/2016] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids (SCFAs), such as butyric acid, have a broad range of applications in chemical and fuel industries. Worldwide demand of sustainable fuels and chemicals has encouraged researchers for microbial synthesis of SCFAs. In this study we compared three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron, for production of SCFAs in Escherichia coli utilizing native fatty acid synthesis (FASII) pathway and modulated the genetic and bioprocess parameters to improve its yield and productivity. E. coli strain expressing tesBT gene yielded maximum butyric acid titer at 1.46 g L-1, followed by tesBF at 0.85 g L-1 and tesAT at 0.12 g L-1. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. The modulation of genetic factors that are known to influence long chain fatty acid production, such as deletion of the fadD and fadE that initiates the fatty acid degradation cycle and overexpression of fadR that is a global transcriptional activator of fatty acid biosynthesis and repressor of degradation cycle, did not improve the butyric acid titer significantly. Use of chemical inhibitor cerulenin, which restricts the fatty acid elongation cycle, increased the butyric acid titer by 1.7-fold in case of TesBF, while it had adverse impact in case of TesBT. In vitro enzyme assay indicated that cerulenin also inhibited short chain specific thioesterase, though inhibitory concentration varied according to the type of thioesterase used. Further process optimization followed by fed-batch cultivation under phosphorous limited condition led to production of 14.3 g L-1 butyric acid and 17.5 g L-1 total free fatty acid at 28% of theoretical yield. This study expands our understanding of SCFAs production in E. coli through FASII pathway and highlights role of genetic and process optimization to enhance the desired product.
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29
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Liao JC, Mi L, Pontrelli S, Luo S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 2016; 14:288-304. [DOI: 10.1038/nrmicro.2016.32] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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30
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Saini M, Li SY, Wang ZW, Chiang CJ, Chao YP. Systematic engineering of the central metabolism in Escherichia coli for effective production of n-butanol. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:69. [PMID: 26997975 PMCID: PMC4799531 DOI: 10.1186/s13068-016-0467-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/19/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Microbes have been extensively explored for production of environment-friendly fuels and chemicals. The microbial fermentation pathways leading to these commodities usually involve many redox reactions. This makes the fermentative production of highly reduced products challenging, because there is a limited NADH output from glucose catabolism. Microbial production of n-butanol apparently represents one typical example. RESULTS In this study, we addressed the issue by adjustment of the intracellular redox state in Escherichia coli. This was initiated with strain BuT-8 which carries the clostridial CoA-dependent synthetic pathway. Three metabolite nodes in the central metabolism of the strain were targeted for engineering. First, the pyruvate node was manipulated by enhancement of pyruvate decarboxylation in the oxidative pathway. Subsequently, the pentose phosphate (PP) pathway was amplified at the glucose-6-phosphate (G6P) node. The pathway for G6P isomerization was further blocked to force the glycolytic flux through the PP pathway. It resulted in a growth defect, and the cell growth was later recovered by limiting the tricarboxylic acid cycle at the acetyl-CoA node. Finally, the resulting strain exhibited a high NADH level and enabled production of 6.1 g/L n-butanol with a yield of 0.31 g/g-glucose and a productivity of 0.21 g/L/h. CONCLUSIONS The production efficiency of fermentative products in microbes strongly depends on the intracellular redox state. This work illustrates the flexibility of pyruvate, G6P, and acetyl-CoA nodes at the junction of the central metabolism for engineering. In principle, high production of reduced products of interest can be achieved by individual or coordinated modulation of these metabolite nodes.
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Affiliation(s)
- Mukesh Saini
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
| | - Si-Yu Li
- />Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan Republic of China
| | - Ze Win Wang
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
| | - Chung-Jen Chiang
- />Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan Republic of China
| | - Yun-Peng Chao
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
- />Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan Republic of China
- />Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan Republic of China
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Wang J, Lin M, Xu M, Yang ST. Anaerobic Fermentation for Production of Carboxylic Acids as Bulk Chemicals from Renewable Biomass. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:323-361. [DOI: 10.1007/10_2015_5009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wang ZW, Saini M, Lin LJ, Chiang CJ, Chao YP. Systematic Engineering of Escherichia coli for d-Lactate Production from Crude Glycerol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:9583-9. [PMID: 26477354 DOI: 10.1021/acs.jafc.5b04162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Crude glycerol resulting from biodiesel production is an abundant and renewable resource. However, the impurities in crude glycerol usually make microbial fermentation problematic. This issue was addressed by systematic engineering of Escherichia coli for the production of d-lactate from crude glycerol. First, mgsA and the synthetic pathways of undesired products were eliminated in E. coli, rendering the strain capable of homofermentative production of optically pure d-lactate. To direct carbon flux toward d-lactate, the resulting strain was endowed with an enhanced expression of glpD-glpK in the glycerol catabolism and of a heterologous gene encoding d-lactate dehydrogenase. Moreover, the strain was evolved to improve its utilization of cruder glycerol and subsequently equipped with the FocA channel to export intracellular d-lactate. Finally, the fed-batch fermentation with two-phase culturing was carried out with a bioreactor. As a result, the engineered strain enabled production of 105 g/L d-lactate (99.9% optical purity) from 121 g/L crude glycerol at 40 h. The result indicates the feasibility of our approach to engineering E. coli for the crude glycerol-based fermentation.
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Affiliation(s)
- Zei Wen Wang
- Department of Chemical Engineering, Feng Chia University , 100 Wenhwa Road, Taichung 40724, Taiwan
| | - Mukesh Saini
- Department of Chemical Engineering, Feng Chia University , 100 Wenhwa Road, Taichung 40724, Taiwan
| | - Li-Jen Lin
- School of Chinese Medicine, College of Chinese Medicine, China Medical University , Taichung 40402, 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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Becker J, Wittmann C. Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products. Angew Chem Int Ed Engl 2015; 54:3328-50. [DOI: 10.1002/anie.201409033] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 12/16/2022]
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Biotechnologie von Morgen: metabolisch optimierte Zellen für die bio-basierte Produktion von Chemikalien und Treibstoffen, Materialien und Gesundheitsprodukten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Saini M, Hong Chen M, Chiang CJ, Chao YP. Potential production platform of n-butanol in Escherichia coli. Metab Eng 2014; 27:76-82. [PMID: 25461833 DOI: 10.1016/j.ymben.2014.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 10/21/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
We proposed a potential production platform of n-butanol in Escherichia coli. First, a butyrate-conversion strain was developed by removal of undesired genes and recruiting endogenous atoDA and Clostridium adhE2. Consequently, this E. coli strain grown on the M9 mineral salt with yeast extract (M9Y) was shown to produce 6.2g/L n-butanol from supplemented butyrate at 36h. The molar conversion yield of n-butanol on butyrate reaches 92%. Moreover, the production platform was advanced by additional inclusion of a butyrate-producing strain. This strain was equipped with a pathway comprising atoDA and heterologous genes for the synthesis of butyrate. Without butyrate, the butyrate-conversion and the butyrate-producing strains were co-cultured in M9Y medium and produced 5.5g/L n-butanol from glucose at 24h. The production yield on glucose accounts for 69% of the theoretical yield. Overall, it indicates a promise of the developed platform for n-butanol production in E. coli.
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Affiliation(s)
- Mukesh Saini
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung 40724, Taiwan
| | - Min Hong Chen
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung 40724, 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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