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Seong MJ, Yoon YR, Kwon KK, Kim H, Lee SG, Shin J, Lee DH. Automated Construction of a Yeast-Based Multigene Library via Homologous Recombination in a Biofoundry Workflow. ACS Synth Biol 2025; 14:1549-1556. [PMID: 40331904 DOI: 10.1021/acssynbio.4c00812] [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] [Indexed: 05/08/2025]
Abstract
Efficiently building metabolic pathways via multigene assembly has long been constrained by the limitations of traditional cloning techniques, necessitating a breakthrough in gene assembly methods. Notably, various in vitro gene assembly methods have been developed to simplify the construction of an expression-tunable library. However, in vitro gene assembly requires a tedious multistep construction process, making it time-consuming and labor-intensive. Therefore, in this study, we developed an automated one-step multigene assembly method for constructing an expression-tunable library based on in vivo homologous recombination. We optimized the shuttle vector for in vivo homologous recombination to improve the assembly efficiency. We also scaled down the whole assembly method for a high-throughput gene assembly. Finally, the developed method demonstrated the construction of the expression-tunable multigene library in the biofoundry. Therefore, this study offers a versatile strategy for parallel and high-throughput genetic engineering in synthetic biology.
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Affiliation(s)
- Min-Jun Seong
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Ye Rin Yoon
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jonghyeok Shin
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center and the K-Biofoundry, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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2
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Ruan H, Wu Y, Zhang N, Tao Y, Wang K, Yan B, Zhao J, Zhang H, Gänzle MG, Chen W, Fan D. Serratia marcescens Causes the Brown Discoloration of Frozen Steamed Stuffed Buns during Resteaming. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4991-5002. [PMID: 38346801 DOI: 10.1021/acs.jafc.3c08467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Brown discoloration was observed in the crust of commercial frozen steamed stuffed buns (FSSBs) during resteaming. Culture-dependent and culture-independent analyses demonstrated that Serratia marcescens, a prodigiosin-producing species, was more abundant in spoiled samples than in unspoiled samples. Inoculation of experimental FSSBs with S. marcescens isolated from spoiled FSSBs confirmed that this species causes brown discoloration of FSSBs during resteaming. S. marcescens formed prodigiosin only between 15 and 28 °C but brown discoloration appeared only upon resteaming after storage at 4 °C. High-performance liquid chromatography analyses revealed that prodigiosin was absent from yellow-brown FSSBs. The pigmentation observed during resteaming is thus likely attributable to the intermediate 2-methyl-3-amylpyrrole. These findings provide valuable insights into the microbial contamination of FSSBs and will facilitate the prevention of spoilage of FSSBs.
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Affiliation(s)
- Huan Ruan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yejun Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuan Tao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kai Wang
- Wuxi Huashun Minsheng Food Co. Ltd., Wuxi 214218, China
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, AB T6G 2P5, Canada
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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3
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Bacterial Pigments and Their Multifaceted Roles in Contemporary Biotechnology and Pharmacological Applications. Microorganisms 2023; 11:microorganisms11030614. [PMID: 36985186 PMCID: PMC10053885 DOI: 10.3390/microorganisms11030614] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/05/2023] Open
Abstract
Synthetic dyes and colourants have been the mainstay of the pigment industry for decades. Researchers are eager to find a more environment friendly and non-toxic substitute because these synthetic dyes have a negative impact on the environment and people’s health. Microbial pigments might be an alternative to synthetic pigments. Microbial pigments are categorized as secondary metabolites and are mainly produced due to impaired metabolism under stressful conditions. These pigments have vibrant shades and possess nutritional and therapeutic properties compared to synthetic pigment. Microbial pigments are now widely used within the pharmaceuticals, food, paints, and textile industries. The pharmaceutical industries currently use bacterial pigments as a medicine alternative for cancer and many other bacterial infections. Their growing popularity is a result of their low cost, biodegradable, non-carcinogenic, and environmentally beneficial attributes. This audit article has made an effort to take an in-depth look into the existing uses of bacterial pigments in the food and pharmaceutical industries and project their potential future applications.
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Metibemu DS, Ogungbe IV. Carotenoids in Drug Discovery and Medicine: Pathways and Molecular Targets Implicated in Human Diseases. Molecules 2022; 27:6005. [PMID: 36144741 PMCID: PMC9503763 DOI: 10.3390/molecules27186005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Carotenoids are isoprenoid-derived natural products produced in plants, algae, fungi, and photosynthetic bacteria. Most animals cannot synthesize carotenoids because the biosynthetic machinery to create carotenoids de novo is absent in animals, except arthropods. Carotenoids are biosynthesized from two C20 geranylgeranyl pyrophosphate (GGPP) molecules made from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) via the methylerythritol 4-phosphate (MEP) route. Carotenoids can be extracted by a variety of methods, including maceration, Soxhlet extraction, supercritical fluid extraction (SFE), microwave-assisted extraction (MAE), accelerated solvent extraction (ASE), ultrasound-assisted extraction (UAE), pulsed electric field (PEF)-assisted extraction, and enzyme-assisted extraction (EAE). Carotenoids have been reported to exert various biochemical actions, including the inhibition of the Akt/mTOR, Bcl-2, SAPK/JNK, JAK/STAT, MAPK, Nrf2/Keap1, and NF-κB signaling pathways and the ability to increase cholesterol efflux to HDL. Carotenoids are absorbed in the intestine. A handful of carotenoids and carotenoid-based compounds are in clinical trials, while some are currently used as medicines. The application of metabolic engineering techniques for carotenoid production, whole-genome sequencing, and the use of plants as cell factories to produce specialty carotenoids presents a promising future for carotenoid research. In this review, we discussed the biosynthesis and extraction of carotenoids, the roles of carotenoids in human health, the metabolism of carotenoids, and carotenoids as a source of drugs and supplements.
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Affiliation(s)
| | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS 39217-0095, USA
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Cheng T, Wang L, Sun C, Xie C. Optimizing the downstream MVA pathway using a combination optimization strategy to increase lycopene yield in Escherichia coli. Microb Cell Fact 2022; 21:121. [PMID: 35718767 PMCID: PMC9208136 DOI: 10.1186/s12934-022-01843-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
Background Lycopene is increasing in demand due to its widespread use in the pharmaceutical and food industries. Metabolic engineering and synthetic biology technologies have been widely used to overexpress the heterologous mevalonate pathway and lycopene pathway in Escherichia coli to produce lycopene. However, due to the tedious metabolic pathways and complicated metabolic background, optimizing the lycopene synthetic pathway using reasonable design approaches becomes difficult. Results In this study, the heterologous lycopene metabolic pathway was introduced into E. coli and divided into three modules, with mevalonate and DMAPP serving as connecting nodes. The module containing the genes (MVK, PMK, MVD, IDI) of downstream MVA pathway was adjusted by altering the expression strength of the four genes using the ribosome binding sites (RBSs) library with specified strength to improve the inter-module balance. Three RBS libraries containing variably regulated MVK, PMK, MVD, and IDI were constructed based on different plasmid backbones with the variable promoter and replication origin. The RBS library was then transformed into engineered E. coli BL21(DE3) containing pCLES and pTrc-lyc to obtain a lycopene producer library and employed high-throughput screening based on lycopene color to obtain the required metabolic pathway. The shake flask culture of the selected high-yield strain resulted in a lycopene yield of 219.7 mg/g DCW, which was 4.6 times that of the reference strain. Conclusion A strain capable of producing 219.7 mg/g DCW with high lycopene metabolic flux was obtained by fine-tuning the expression of the four MVA pathway enzymes and visual selection. These results show that the strategy of optimizing the downstream MVA pathway through RBS library design can be effective, which can improve the metabolic flux and provide a reference for the synthesis of other terpenoids. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01843-z.
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Affiliation(s)
- Tao Cheng
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Road, Qingdao, 266042, China. .,CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China.
| | - Lili Wang
- Department of Pathology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, China
| | - Chao Sun
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Road, Qingdao, 266042, China.,CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Laoshan District, Qingdao, 266101, China
| | - Congxia Xie
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Road, Qingdao, 266042, China.
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Shin KC, Seo MJ, Kim YS, Yeom SJ. Molecular Properties of β-Carotene Oxygenases and Their Potential in Industrial Production of Vitamin A and Its Derivatives. Antioxidants (Basel) 2022; 11:1180. [PMID: 35740077 PMCID: PMC9227343 DOI: 10.3390/antiox11061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
β-Carotene 15,15'-oxygenase (BCO1) and β-carotene 9',10'-oxygenase (BCO2) are potential producers of vitamin A derivatives, since they can catalyze the oxidative cleavage of dietary provitamin A carotenoids to retinoids and derivative such as apocarotenal. Retinoids are a class of chemical compounds that are vitamers of vitamin A or are chemically related to it, and are essential nutrients for humans and highly valuable in the food and cosmetics industries. β-carotene oxygenases (BCOs) from various organisms have been overexpressed in heterogeneous bacteria, such as Escherichia coli, and their biochemical properties have been studied. For the industrial production of retinal, there is a need for increased production of a retinal producer and biosynthesis of retinal using biocatalyst systems improved by enzyme engineering. The current review aims to discuss BCOs from animal, plants, and bacteria, and to elaborate on the recent progress in our understanding of their functions, biochemical properties, substrate specificity, and enzyme activities with respect to the production of retinoids in whole-cell conditions. Moreover, we specifically propose ways to integrate BCOs into retinal biosynthetic bacterial systems to improve the performance of retinal production.
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Affiliation(s)
- Kyung-Chul Shin
- Department of Integrative Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Yeong-Su Kim
- Wild Plants Industrialization Research Division, Baekdudaegan National Arboretum, Bonghwa 36209, Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
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7
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Prasanna D, Runthala A. Computationally Decoding NudF Residues To Enhance the Yield of the DXP Pathway. ACS OMEGA 2022; 7:19898-19912. [PMID: 35721994 PMCID: PMC9202048 DOI: 10.1021/acsomega.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Terpenoids form a large pool of highly diverse organic compounds possessing several economically important properties, including nutritional, aromatic, and pharmacological properties. The 1-deoxy-d-xylulose 5-phosphate (DXP) pathway's end enzyme, nuclear distribution protein (NudF), interacting with isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), is critical for the synthesis of isoprenol/prenol/downstream compounds. The enzyme is yet to be thoroughly investigated to increase the overall yield of terpenoids in the Bacillus subtilis, which is widely used in industry and is generally regarded as a safe (GRAS) bacterium. The study aims to analyze the evolutionary conservation across the active site for mapping the key residues for mutagenesis studies. The 37-sequence data set, extracted from 103 Bacillus subtilis entries, shows a high phylogenetic divergence, and only six one-motif sequences ASB92783.1, ASB69297.1, ASB56714.1, AOR97677.1, AOL97023.1, and OAZ71765.1 show a monophyly relationship, unlike a complete polyphyly relationship between the other 31 three-motif sequences. Furthermore, only 47 of 179 residues of the representative sequence CUB50584.1 are observed to be significantly conserved. Docking analysis suggests a preferential bias of adenosine diphosphate (ADP)-ribose pyrophosphatase toward IPP, and a nearly threefold energetic difference is observed between IPP and DMAPP. The loops are hereby shown to play a regulatory role in guiding the promiscuity of NudF toward a specific ligand. Computational saturation mutagenesis of the seven hotspot residues identifies two key positions LYS78 and PHE116, orderly encoded within loop1 and loop7, majorly interacting with the ligands DMAPP and IPP, and their mutants K78I/K78L and PHE116D/PHE116E are found to stabilize the overall conformation. Molecular dynamics analysis shows that the IPP complex is significantly more stable than the DMAPP complex, and the NudF structure is very unstable. Besides showing a promiscuous binding of NudF with ligands, the analysis suggests its rate-limiting nature. The study would allow us to customize the metabolic load toward the synthesis of any of the downstream molecules. The findings would pave the way for the development of catalytically improved NudF mutants for the large-scale production of specific terpenoids with significant nutraceutical or commercial value.
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Usuda Y, Nishio Y, Nonaka G, Hara Y. Microbial Production Potential of Pantoea ananatis: From Amino Acids to Secondary Metabolites. Microorganisms 2022; 10:microorganisms10061133. [PMID: 35744651 PMCID: PMC9231021 DOI: 10.3390/microorganisms10061133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Pantoea ananatis, a gram-negative bacterium belonging to the Erwiniaceae family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also provides us with various beneficial characteristics, such as the growth promotion of their host plants and increased crop yield. Some isolated non-pathogenic strains are promising for the microbial production of useful substances. P. ananatis AJ13355 was isolated as an acidophilic bacterium and was used as an excellent host to produce L-glutamic acid under acidic conditions. The genome sequence of P. ananatis AJ13355 was determined, and specific genome-engineering technologies were developed. As a result, P. ananatis was successfully used to construct a bacterial strain that produces cysteine, a sulfur-containing amino acid that has been difficult to produce through fermentation because of complex regulation. Furthermore, by heterologous expression including plant-derived genes, construction of a strain that produces isoprenoids such as isoprene and linalool as secondary metabolites was achieved. P. ananatis is shown to be a useful host for the production of secondary metabolites, as well as amino acids, and is expected to be used as a platform for microbial production of bioactive substances, aromatic substances, and other high-value-added substances of plant origin in the future.
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Affiliation(s)
- Yoshihiro Usuda
- Research and Business Planning Department, Ajinomoto Co., Inc., Tokyo 104-8315, Japan
- Correspondence: ; Tel.: +81-70-4361-3762; Fax: +81-3-5250-8352
| | - Yousuke Nishio
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
| | - Gen Nonaka
- Ajinomoto-Genetika Research Institute, Moscow 117545, Russia;
| | - Yoshihiko Hara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
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Patel AK, Albarico FPJB, Perumal PK, Vadrale AP, Nian CT, Chau HTB, Anwar C, Wani HMUD, Pal A, Saini R, Ha LH, Senthilkumar B, Tsang YS, Chen CW, Dong CD, Singhania RR. Algae as an emerging source of bioactive pigments. BIORESOURCE TECHNOLOGY 2022; 351:126910. [PMID: 35231601 DOI: 10.1016/j.biortech.2022.126910] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Algae have been identified as natural producer of bioactive commercial pigments. To perform photosynthesis, algae use pigments to harvest sunlight energy. The pigments found in algae are categorized in chlorophylls, phycobilins, and carotenoids. Popular carotenoids include astaxanthin, lutein,fucoxanthin, canthaxanthin, zeaxanthin, β-cryptoxanthin and finds application as antioxidant, anti-inflammatory, immunoprophylactic, antitumor activities among others. Due to double-bonds in their structure, they exhibit broad health applications while protecting other molecules from oxidative stress induced by active radicals using various mechanisms. These carotenoids are synthesized by certain species as major products however they also present as byproducts in several species based on the pathway and genetic capability. Haematococcus pluvialis and Chlorella zofingiensis are ideal strains for commercial astaxanthin production. This review provides recent updates on microalgal pigment production, extraction, and purification processes to standardize and analyze for commercial production. Also, discussed the factors affecting its production, application, market potential, bottlenecks, and future prospects.
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Affiliation(s)
- Anil Kumar Patel
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Frank Paolo Jay B Albarico
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Fisheries and Marine Research Station (FaMaRS), Fisheries and Marine Sciences Department, College of Fisheries and Allied Sciences, Northern Negros State College of Science and Technology, Sagay City 6122, Philippines
| | - Pitchurajan Krishna Perumal
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Akash Pralhad Vadrale
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Cherry T Nian
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Aquaculture Department, College of Fisheries, Mindanao State University-Tawi-Tawi College of Technology and Oceanography, Philippines
| | - Ho Thi Bao Chau
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Choirul Anwar
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Henna Mohi Ud Din Wani
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Anugunj Pal
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Reetu Saini
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Le Hai Ha
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Balamurugan Senthilkumar
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Yi-Sheng Tsang
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Chiu-Wen Chen
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Cheng-Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan.
| | - Reeta Rani Singhania
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
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Casas A, Bultelle M, Motraghi C, Kitney R. PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies. ACS Synth Biol 2022; 11:1272-1291. [PMID: 35261238 PMCID: PMC8938949 DOI: 10.1021/acssynbio.1c00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present here a
newly developed workflow—which we have
called PASIV—designed to provide a solution to a practical
problem with design of experiments (DoE) methodology: i.e., what can
be done if the scoping phase of the DoE cycle is severely hampered
by burden and toxicity issues (caused by either the metabolite or
an intermediary), making it unreliable or impossible to proceed to
the screening phase? PASIV—standing for pooled approach, screening,
identification, and visualization—was designed so the (viable)
region of interest can be made to appear through an interplay between
biology and software. This was achieved by combining multiplex construction
in a pooled approach (one-pot reaction) with a viability assay and
with a range of bioinformatics tools (including a novel construct
matching tool). PASIV was tested on the exemplar of the lycopene pathway—under
stressful constitutive expression—yielding a region of interest
with comparatively stronger producers.
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Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
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11
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Seo SO, Jin YS. Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annu Rev Food Sci Technol 2022; 13:463-488. [DOI: 10.1146/annurev-food-052720-012228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Nutrition, Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Bu X, Lin JY, Duan CQ, Koffas MAG, Yan GL. Dual regulation of lipid droplet-triacylglycerol metabolism and ERG9 expression for improved β-carotene production in Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:3. [PMID: 34983533 PMCID: PMC8725481 DOI: 10.1186/s12934-021-01723-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 12/05/2022] Open
Abstract
Background The limitation of storage space, product cytotoxicity and the competition for precursor are the major challenges for efficiently overproducing carotenoid in engineered non-carotenogenic microorganisms. In this work, to improve β-carotene accumulation in Saccharomyces cerevisiae, a strategy that simultaneous increases cell storage capability and strengthens metabolic flux to carotenoid pathway was developed using exogenous oleic acid (OA) combined with metabolic engineering approaches. Results The direct separation of lipid droplets (LDs), quantitative analysis and genes disruption trial indicated that LDs are major storage locations of β-carotene in S. cerevisiae. However, due to the competition for precursor between β-carotene and LDs-triacylglycerol biosynthesis, enlarging storage space by engineering LDs related genes has minor promotion on β-carotene accumulation. Adding 2 mM OA significantly improved LDs-triacylglycerol metabolism and resulted in 36.4% increase in β-carotene content. The transcriptome analysis was adopted to mine OA-repressible promoters and IZH1 promoter was used to replace native ERG9 promoter to dynamically down-regulate ERG9 expression, which diverted the metabolic flux to β-carotene pathway and achieved additional 31.7% increase in β-carotene content without adversely affecting cell growth. By inducing an extra constitutive β-carotene synthesis pathway for further conversion precursor farnesol to β-carotene, the final strain produced 11.4 mg/g DCW and 142 mg/L of β-carotene, which is 107.3% and 49.5% increase respectively over the parent strain. Conclusions This strategy can be applied in the overproduction of other heterogeneous FPP-derived hydrophobic compounds with similar synthesis and storage mechanisms in S. cerevisiae. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01723-y.
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Affiliation(s)
- Xiao Bu
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China.,Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, People's Republic of China
| | - Jing-Yuan Lin
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Chang-Qing Duan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Guo-Liang Yan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China. .,Innovation Research Center of Future Foods, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Key Laboratory of Food Bioengineering (China National Light Industry), China Agricultural University, Beijing, 100083, China.
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13
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Takemura M, Kubo A, Watanabe A, Sakuno H, Minobe Y, Sahara T, Murata M, Araki M, Harada H, Terada Y, Yaoi K, Ohdan K, Misawa N. Pathway engineering for high-yield production of lutein in Escherichia coli. Synth Biol (Oxf) 2021; 6:ysab012. [PMID: 34712837 PMCID: PMC8546607 DOI: 10.1093/synbio/ysab012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/15/2021] [Indexed: 11/15/2022] Open
Abstract
Lutein is an industrially important carotenoid pigment, which is essential for photoprotection and photosynthesis in plants. Lutein is crucial for maintaining human health due to its protective ability from ocular diseases. However, its pathway engineering research has scarcely been performed for microbial production using heterologous hosts, such as Escherichia coli, since the engineering of multiple genes is required. These genes, which include tricky key carotenoid biosynthesis genes typically derived from plants, encode two sorts of cyclases (lycopene ε- and β-cyclase) and cytochrome P450 CYP97C. In this study, upstream genes effective for the increase in carotenoid amounts, such as isopentenyl diphosphate isomerase (IDI) gene, were integrated into the E. coli JM101 (DE3) genome. The most efficient set of the key genes (MpLCYe, MpLCYb and MpCYP97C) was selected from among the corresponding genes derived from various plant (or bacterial) species using E. coli that had accumulated carotenoid substrates. Furthermore, to optimize the production of lutein in E. coli, we introduced several sorts of plasmids that contained some of the multiple genes into the genome-inserted strain and compared lutein productivity. Finally, we achieved 11 mg/l as lutein yield using a mini jar. Here, the high-yield production of lutein was successfully performed using E. coli through approaches of pathway engineering. The findings obtained here should be a base reference for substantial lutein production with microorganisms in the future.
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Akiko Kubo
- Applied Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Asuka Watanabe
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Hanayo Sakuno
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yuka Minobe
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Takehiko Sahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | | | - Hisashi Harada
- Faculty of Engineering, Tottori University, Tottori, Japan
| | - Yoshinobu Terada
- Mechanism-Based Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kohji Ohdan
- Applied Research Laboratory, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
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14
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Takemura M, Sahara T, Misawa N. Violaxanthin: natural function and occurrence, biosynthesis, and heterologous production. Appl Microbiol Biotechnol 2021; 105:6133-6142. [PMID: 34338805 DOI: 10.1007/s00253-021-11452-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Violaxanthin is biosynthesized from zeaxanthin with zeaxanthin epoxidase (ZEP) by way of antheraxanthin only in photosynthetic eukaryotes including higher plants and involved in the xanthophyll cycle to eliminate excessive light energy. Violaxanthin and antheraxanthin have commercially been unavailable, in contrast to commercial production of other carotenoids contained in higher plants, e.g., lycopene, β-carotene, lutein, zeaxanthin, β-cryptoxanthin, and capsanthin. One of the reasons is considered that resource plants or other resource organisms do not exist for enabling efficient supply of the epoxy-carotenoids, which are expected to be produced through (metabolic) pathway engineering with heterologous microbial hosts such as Escherichia coli and Saccharomyces cerevisiae. In this Mini-Review, we show heterologous production of violaxanthin with the two microorganisms that have exhibited significant advances these days. We further describe natural function and occurrence, and biosynthesis involving violaxanthin, antheraxanthin, and their derivatives that include auroxanthin and mutatoxanthin. KEY POINTS: • A comprehensive review on epoxy-carotenoids violaxanthin and antheraxanthin. • Pathway engineering for the epoxy-carotenoids in heterologous microbes. • Our new findings on violaxanthin production with the budding yeast.
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi-shi, 921-8836, Japan
| | - Takehiko Sahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba-shi, 305-8566, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi-shi, 921-8836, Japan.
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15
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One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE). mSystems 2021; 6:e0018121. [PMID: 34042466 PMCID: PMC8269212 DOI: 10.1128/msystems.00181-21] [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] [Indexed: 01/21/2023] Open
Abstract
Soil harbors arguably the most metabolically and genetically heterogeneous microbiomes on Earth, yet establishing the link between metabolic functions and genome at the precisely one-cell level has been difficult. Here, for mock microbial communities and then for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) platform, which identifies, sorts, and sequences precisely one bacterial cell via its anabolic (incorporating D from heavy water) and physiological (carotenoid-containing) functions. We showed that (i) metabolically active cells from numerically rare soil taxa, such as Corynebacterium spp., Clostridium spp., Moraxella spp., Pantoea spp., and Pseudomonas spp., can be readily identified and sorted based on D2O uptake, and their one-cell genome coverage can reach ∼93% to allow high-quality genome-wide metabolic reconstruction; (ii) similarly, carotenoid-containing cells such as Pantoea spp., Legionella spp., Massilia spp., Pseudomonas spp., and Pedobacter spp. were identified and one-cell genomes were generated for tracing the carotenoid-synthetic pathways; and (iii) carotenoid-producing cells can be either metabolically active or inert, suggesting culture-based approaches can miss many such cells. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at exactly one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems. IMPORTANCE Soil is home to an enormous and complex microbiome that features arguably the highest genomic diversity and metabolic heterogeneity of cells on Earth. Their in situ metabolic activities drive many natural processes of pivotal ecological significance or underlie industrial production of numerous valuable bioactivities. However, pinpointing “who is doing what” in a soil microbiome, which consists of mainly yet-to-be-cultured species, has remained a major challenge. Here, for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) method, which identifies, sorts, and sequences at the resolution of precisely one microbial cell via its catabolic and anabolic functions. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems.
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16
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Wang J, Zhu L, Li Y, Xu S, Jiang W, Liang C, Fang Y, Chu A, Zhang L, Ding Z, Shi G. Enhancing Geranylgeraniol Production by Metabolic Engineering and Utilization of Isoprenol as a Substrate in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4480-4489. [PMID: 33823596 DOI: 10.1021/acs.jafc.1c00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The amount of geranylgeranyl diphosphate (GGPP) is vital for microbial production of geranylgeraniol (GGOH) in Saccharomyces cerevisiae. In this study, a GGPP synthase with stronger catalytic ability was used to increase the supply of GGPP, and an engineered strain producing 374.02 mg/L GGOH at the shake flask level was constructed. Then, by increasing the metabolic flux of the mevalonate (MVA) pathway and the supply of isopentenyl pyrophosphate (IPP), the titer was further increased to 772.98 mg/L at the shake flask level, and we achieved the highest GGOH titer to date of 5.07 g/L in a 5 L bioreactor. This is the first report on the utilization of isoprenol for increasing the amount of IPP and enhancing GGOH production in S. cerevisiae. In the future, these strategies and engineered strains can be used to enhance the production of other terpenoids in S. cerevisiae.
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Affiliation(s)
- Junhua Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Linghuan Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wei Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, People's Republic of China
| | - Chaojuan Liang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yakun Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Alex Chu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, People's Republic of China
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17
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Kang CK, Yang JE, Park, HW, Choi YJ. Enhanced Lycopene Production by UV-C Irradiation in Radiation-Resistant Deinococcus radiodurans R1. J Microbiol Biotechnol 2020; 30:1937-1943. [PMID: 33046679 PMCID: PMC9728254 DOI: 10.4014/jmb.2009.09013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 12/15/2022]
Abstract
Although classical metabolic engineering strategies have succeeded in developing microbial strains capable of producing desired bioproducts, metabolic imbalance resulting from extensive genetic manipulation often leads to decreased productivity. Thus, abiotic strategies for improving microbial production performance can be an alternative to overcome drawbacks arising from intensive metabolic engineering. Herein, we report a promising abiotic method for enhancing lycopene production by UV-C irradiation using a radiation-resistant ΔcrtLm/crtB+dxs+ Deinococcus radiodurans R1 strain. First, the onset of UV irradiation was determined through analysis of the expression of 11 genes mainly involved in the carotenoid biosynthetic pathway in the ΔcrtLm/crtB+dxs+ D. radiodurans R1 strain. Second, the effects of different UV wavelengths (UV-A, UV-B, and UV-C) on lycopene production were investigated. UV-C irradiation induced the highest production, resulting in a 69.9% increase in lycopene content [64.2 ± 3.2 mg/g dry cell weight (DCW)]. Extended UV-C irradiation further enhanced lycopene content up to 73.9 ± 2.3 mg/g DCW, a 95.5% increase compared to production without UV-C irradiation (37.8 ± 0.7 mg/g DCW).
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Affiliation(s)
- Chang Keun Kang
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jung Eun Yang
- Department of Advanced Process Technology and Fermentation, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Hae Woong Park,
- Department of Advanced Process Technology and Fermentation, World Institute of Kimchi, Gwangju 61755, Republic of Korea,Corresponding authors H.W.Park Phone: +82-62-610-1728 Fax: +82-62-610-1850
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea,Y.J.Choi Phone: +82-2-6490-2873 Fax: +82-2-6490-2859
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18
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Li M, Xia Q, Zhang H, Zhang R, Yang J. Metabolic Engineering of Different Microbial Hosts for Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14104-14122. [PMID: 33207118 DOI: 10.1021/acs.jafc.0c06020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As a result of the extensive use of lycopene in a variety of fields, especially the dietary supplement and health food industries, the production of lycopene has attracted considerable interest. Lycopene can be obtained through extraction from vegetables and chemical synthesis. Alternatively, the microbial production of lycopene has been extensively researched in recent years. Various types of microbial hosts have been evaluated for their potential to accumulate a high level of lycopene. Metabolic engineering of the hosts and optimization of culture conditions are performed to enhance lycopene production. After years of research, great progress has been made in lycopene production. In this review, strategies used to improve lycopene production in different microbial hosts and the advantages and disadvantages of each microbial host are summarized. In addition, future perspectives of lycopene production in different microbial hosts are discussed.
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Affiliation(s)
- Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Qingqing Xia
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Rubing Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Jianming Yang
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
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19
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Tang RQ, Wagner JM, Alper HS, Zhao XQ, Bai FW. Design, Evolution, and Characterization of a Xylose Biosensor in Escherichia coli Using the XylR/ xylO System with an Expanded Operating Range. ACS Synth Biol 2020; 9:2714-2722. [PMID: 32886884 DOI: 10.1021/acssynbio.0c00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded biosensors are extensively utilized in synthetic biology and metabolic engineering. However, reported xylose biosensors are far too sensitive with a limited operating range to be useful for most sensing applications. In this study, we describe directed evolution of Escherichia coli XylR, and construction of biosensors based on XylR and the corresponding operator xylO. The operating range of biosensors containing the mutant XylR was increased by nearly 10-fold comparing with the control. Two individual amino acid mutations (either L73P or N220T) in XylR were sufficient to extend the linear response range to upward of 10 g/L xylose. The evolved biosensors described here are well suited for developing whole-cell biosensors for detecting varying xylose concentrations across an expanded range. As an alternative use of this system, we also demonstrate the utility of XylR and xylO as a xylose inducible system to enable graded gene expression through testing with β-galactosidase gene and the lycopene synthetic pathway. This evolution strategy identified a less-sensitive biosensor for real applications, thus providing new insights into strategies for expanding operating ranges of other biosensors for synthetic biology applications.
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Affiliation(s)
- Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - James M. Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Wang Z, Sun J, Yang Q, Yang J. Metabolic Engineering Escherichia coli for the Production of Lycopene. Molecules 2020; 25:molecules25143136. [PMID: 32659911 PMCID: PMC7397254 DOI: 10.3390/molecules25143136] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/25/2022] Open
Abstract
Lycopene, a potent antioxidant, has been widely used in the fields of pharmaceuticals, nutraceuticals, and cosmetics. However, the production of lycopene extracted from natural sources is far from meeting the demand. Consequently, synthetic biology and metabolic engineering have been employed to develop microbial cell factories for lycopene production. Due to the advantages of rapid growth, complete genetic background, and a reliable genetic operation technique, Escherichia coli has become the preferred host cell for microbial biochemicals production. In this review, the recent advances in biological lycopene production using engineered E. coli strains are summarized: First, modification of the endogenous MEP pathway and introduction of the heterogeneous MVA pathway for lycopene production are outlined. Second, the common challenges and strategies for lycopene biosynthesis are also presented, such as the optimization of other metabolic pathways, modulation of regulatory networks, and optimization of auxiliary carbon sources and the fermentation process. Finally, the future prospects for the improvement of lycopene biosynthesis are also discussed.
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Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
| | - JingXin Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
| | - Qun Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
- Correspondence: (Q.Y.); (J.Y.); Tel.: +86-131-4543-1413 (Q.Y.); +86-135-8938-5827 (J.Y.); Fax: +86-532-589-57640 (J.Y.)
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China;
- Correspondence: (Q.Y.); (J.Y.); Tel.: +86-131-4543-1413 (Q.Y.); +86-135-8938-5827 (J.Y.); Fax: +86-532-589-57640 (J.Y.)
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Li C, Swofford CA, Sinskey AJ. Modular engineering for microbial production of carotenoids. Metab Eng Commun 2020; 10:e00118. [PMID: 31908924 PMCID: PMC6938962 DOI: 10.1016/j.mec.2019.e00118] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/02/2019] [Accepted: 12/08/2019] [Indexed: 12/12/2022] Open
Abstract
There is an increasing demand for carotenoids due to their applications in the food, flavor, pharmaceutical and feed industries, however, the extraction and synthesis of these compounds can be expensive and technically challenging. Microbial production of carotenoids provides an attractive alternative to the negative environmental impacts and cost of chemical synthesis or direct extraction from plants. Metabolic engineering and synthetic biology approaches have been widely utilized to reconstruct and optimize pathways for carotenoid overproduction in microorganisms. This review summarizes the current advances in microbial engineering for carotenoid production and divides the carotenoid biosynthesis building blocks into four distinct metabolic modules: 1) central carbon metabolism, 2) cofactor metabolism, 3) isoprene supplement metabolism and 4) carotenoid biosynthesis. These four modules focus on redirecting carbon flux and optimizing cofactor supplements for isoprene precursors needed for carotenoid synthesis. Future perspectives are also discussed to provide insights into microbial engineering principles for overproduction of carotenoids.
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Affiliation(s)
- Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Charles A. Swofford
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
| | - Anthony J. Sinskey
- Department of Biology, Massachusetts Institute of Technology, Boston, MA, 02139, USA
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore
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Kang CK, Jeong SW, Yang JE, Choi YJ. High-Yield Production of Lycopene from Corn Steep Liquor and Glycerol Using the Metabolically Engineered Deinococcus radiodurans R1 Strain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5147-5153. [PMID: 32275417 DOI: 10.1021/acs.jafc.0c01024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Developing a highly efficient and ecofriendly system to produce desired products from waste can be considered important to a sustainable society. Here, we report for the first time high-yield production of lycopene through metabolically engineering an extremophilic microorganism, Deinococcus radiodurans R1, from corn steep liquor (CSL) and glycerol. First, the crtLm gene-encoding lycopene cyclase was deleted to prevent the conversion of lycopene to γ-carotene. Then, the crtB gene-encoding phytoene synthase and the dxs gene-encoding 1-deoxy-d-xylulose 5-phosphate synthase were overexpressed to increase carbon flux toward lycopene. The engineered ΔcrtLm/crtB+dxs+ D. radiodurans R1 could produce 273.8 mg/L [80.7 mg/g dry cell weight (DCW)] and 373.5 mg/L (108.0 mg/g DCW) of lycopene from 10 g/L of glucose with 5 g/L of yeast extract and 9.9 g/L of glucose with 20 g/L of CSL, respectively. Moreover, the lycopene titer and content were increased by 26% (470.6 mg/L) and 28% (138.2 mg/g DCW), respectively, when the carbon source was changed to glycerol. Finally, fed-batch fermentation of the final engineered strain allowed the production of 722.2 mg/L (203.5 mg/g DCW) of lycopene with a yield and productivity of 20.3 mg/g glycerol and 6.0 mg/L/h, respectively, from 25 g/L of CSL and 35.7 g/L of glycerol.
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Affiliation(s)
- Chang Keun Kang
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Sun-Wook Jeong
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jung Eun Yang
- World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
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23
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Metabolic engineering for the production of fat-soluble vitamins: advances and perspectives. Appl Microbiol Biotechnol 2019; 104:935-951. [DOI: 10.1007/s00253-019-10157-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 01/02/2023]
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Takemura M, Kubo A, Higuchi Y, Maoka T, Sahara T, Yaoi K, Ohdan K, Umeno D, Misawa N. Pathway engineering for efficient biosynthesis of violaxanthin in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:9393-9399. [PMID: 31673744 DOI: 10.1007/s00253-019-10182-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 11/27/2022]
Abstract
Carotenoids are naturally synthesized in some species of bacteria, archaea, and fungi (including yeasts) as well as all photosynthetic organisms. Escherichia coli has been the most popular bacterial host for the heterologous production of a variety of carotenoids, including even xanthophylls unique to photosynthetic eukaryotes such as lutein, antheraxanthin, and violaxanthin. However, conversion efficiency of these epoxy-xanthophylls (antheraxanthin and violaxanthin) from zeaxanthin remained substantially low. We here examined several factors affecting their productivity in E. coli. Two sorts of plasmids were introduced into the bacterial host, i.e., a plasmid to produce zeaxanthin due to the presence of the Pantoea ananatis crtE, crtB, crtI, crtY, and crtZ genes in addition to the Haematococcus pluvialis IDI gene, and one containing each of zeaxanthin epoxidase (ZEP) genes originated from nine photosynthetic eukaryotes. It was consequently found that paprika (Capsicum annuum) ZEP (CaZEP) showed the highest conversion activity. Next, using the CaZEP gene, we performed optimization experiments in relation to E. coli strains as the production hosts, expression vectors, and ribosome-binding site (RBS) sequences. As a result, the highest productivity of violaxanthin (231 μg/g dry weight) was observed, when the pUC18 vector was used with CaZEP preceded by a RBS sequence of score 5000 in strain JM101(DE3).
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Akiko Kubo
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka, 555-8502, Japan
| | - Yuki Higuchi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Takashi Maoka
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
- Division of Food Function and Chemistry, Research Institute for Production Development, Kyoto, 606-0805, Japan
| | - Takehiko Sahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kohji Ohdan
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka, 555-8502, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, 263-8522, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
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Abdallah II, Pramastya H, van Merkerk R, Sukrasno, Quax WJ. Metabolic Engineering of Bacillus subtilis Toward Taxadiene Biosynthesis as the First Committed Step for Taxol Production. Front Microbiol 2019; 10:218. [PMID: 30842758 PMCID: PMC6391936 DOI: 10.3389/fmicb.2019.00218] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
Terpenoids are natural products known for their medicinal and commercial applications. Metabolic engineering of microbial hosts for the production of valuable compounds, such as artemisinin and Taxol, has gained vast interest in the last few decades. The Generally Regarded As Safe (GRAS) Bacillus subtilis 168 with its broad metabolic potential is considered one of these interesting microbial hosts. In the effort toward engineering B. subtilis as a cell factory for the production of the chemotherapeutic Taxol, we expressed the plant-derived taxadiene synthase (TXS) enzyme. TXS is responsible for the conversion of the precursor geranylgeranyl pyrophosphate (GGPP) to taxa-4,11-diene, which is the first committed intermediate in Taxol biosynthesis. Furthermore, overexpression of eight enzymes in the biosynthesis pathway was performed to increase the flux of the GGPP precursor. This was achieved by creating a synthetic operon harboring the B. subtilis genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway (dxs, ispD, ispF, ispH, ispC, ispE, ispG) together with ispA (encoding geranyl and farnesyl pyrophosphate synthases) responsible for providing farnesyl pyrophosphate (FPP). In addition, a vector harboring the crtE gene (encoding geranylgeranyl pyrophosphate synthase, GGPPS, of Pantoea ananatis) to increase the supply of GGPP was introduced. The overexpression of the MEP pathway enzymes along with IspA and GGPPS caused an 83-fold increase in the amount of taxadiene produced compared to the strain only expressing TXS and relying on the innate pathway of B. subtilis. The total amount of taxadiene produced by that strain was 17.8 mg/l. This is the first account of the successful expression of taxadiene synthase in B. subtilis. We determined that the expression of GGPPS through the crtE gene is essential for the formation of sufficient precursor, GGPP, in B. subtilis as its innate metabolism is not efficient in producing it. Finally, the extracellular localization of taxadiene production by overexpressing the complete MEP pathway along with IspA and GGPPS presents the prospect for further engineering aiming for semisynthesis of Taxol.
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Affiliation(s)
- Ingy I Abdallah
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Hegar Pramastya
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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Ye J, Liu M, He M, Ye Y, Huang J. Illustrating and Enhancing the Biosynthesis of Astaxanthin and Docosahexaenoic Acid in Aurantiochytrium sp. SK4. Mar Drugs 2019; 17:md17010045. [PMID: 30634667 PMCID: PMC6357005 DOI: 10.3390/md17010045] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
The marine thraustochytrids are a promising source of docosahexaenoic acid (DHA) and the ketocarotenoid astaxanthin. In this study, the biosynthetic pathways of these two important metabolites in Aurantiochytrium sp. SK4 was illustrated by the analyses of the genome, transcriptome, key enzymes, and pathway products. Two sets of genes were involved in two pathways for the biosynthesis of fatty acids. The absence of Δ-15 desaturase genes and the presence of docosapentaenoic acid (DPA), up to 12% of total fatty acids suggest that Aurantiochytrium sp. SK4 may synthesize DHA mainly via a polyketide synthase (PKS) pathway. Three enzymes, namely geranyl diphosphate synthase (GPPS), farnysyl diphosphate synthase (FPPS), and geranylgeranyle diphosphate synthase (GGPPS) were found to be involved in the formation of GGPP that was subsequently catalyzed to β-carotene by a trifunctional CrtIBY enzyme. β-Carotene might be ketolated and then hydroxylated into astaxanthin based on the carotenoid profiles. The formation of GGPP was proposed to be the limiting steps for carotenoid production. Overexpression of the Archaeoglobus GPS together with the Escherichia coli isopentenyl pyrophosphate isomerase, and Vitreoscilla hemoglobin resulted in not only 1.85- and 5.02-fold increases of total carotenoids and astaxanthin, but also 2.40- and 2.74-fold increases of total fatty acids and DHA. This study provides insights into the biosynthesis of carotenoids and fatty acids in Aurantiochytrium.
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Affiliation(s)
- Jingrun Ye
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Mengmeng Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Mingxia He
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Ying Ye
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junchao Huang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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28
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Improving lycopene production in Saccharomyces cerevisiae through optimizing pathway and chassis metabolism. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2018.09.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- Kai‐Xiong Ye
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Ting‐Ting Fan
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Lawrence Jordan Keen
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Bing‐Nan Han
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
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30
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Meyer AJ, Segall-Shapiro TH, Glassey E, Zhang J, Voigt CA. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat Chem Biol 2018; 15:196-204. [DOI: 10.1038/s41589-018-0168-3] [Citation(s) in RCA: 298] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/05/2018] [Indexed: 11/09/2022]
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31
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Adadi P, Barakova NV, Krivoshapkina EF. Selected Methods of Extracting Carotenoids, Characterization, and Health Concerns: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5925-5947. [PMID: 29851485 DOI: 10.1021/acs.jafc.8b01407] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Carotenoids are the most powerful nutrients (medicine) on earth due to their potent antioxidant properties. The ability of these tetraterpenoids in obviating human chronic ailments like cancer, cardiovascular disease, osteoporosis, and diabetes has drawn public attention toward these novel compounds. Conventionally, carotenoids have been extracted from plant materials and agro-industrial byproduct using different solvents, but these procedures result in contaminating the target compound (carotenoids) with extraction solvents. Furthermore, some utilized solvents are not safe and hence are harmful to the environment. This has attracted criticism from consumers, ecologists, environmentalists, and public health workers. However, there is clear consumer preference for carotenoids from natural origin without traces of extracting solvent. Therefore, this review seeks to discuss methods for higher recovery of pure carotenoids without contamination from a solvent. Methods such as enzyme-based extraction, supercritical fluid extraction, microwave-assisted extraction, Soxhlet extraction, ultrasonic extraction, and postextraction treatment (saponification) are discussed. Merits and demerits of these methods along with health concerns during intake of carotenoids were also considered.
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Affiliation(s)
- Parise Adadi
- ITMO University , Lomonosova Street 9 , 191002 , St. Petersburg , Russia Federation
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32
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Xu X, Tian L, Xu J, Xie C, Jiang L, Huang H. Analysis and expression of the carotenoid biosynthesis genes from Deinococcus wulumuqiensis R12 in engineered Escherichia coli. AMB Express 2018; 8:94. [PMID: 29860613 PMCID: PMC5984946 DOI: 10.1186/s13568-018-0624-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/28/2018] [Indexed: 01/07/2023] Open
Abstract
Deinococcus wulumuqiensis R12 is a red-pigmented extremophilic microorganism with powerful antioxidant properties that was isolated from radiation-contaminated soil in Xinjiang Uyghur Autonomous Region of China. The key carotenoid biosynthesis genes, crtE, crtB and crtI, which are related to the cells’ antioxidant defense, were identified in the sequenced genome of R12 and analyzed. In order to improve the carotenoid yield in engineered Escherichia coli, the origin of carotenoid biosynthesis genes was discussed, and a strain containing the R12 carotenoid biosynthesis genes was constructed to produce lycopene, an important intermediate in carotenoid metabolism. The gene order and fermentation conditions, including the culture medium, temperature, and light, were optimized to obtain a genetically engineered strain with a high lycopene production capacity. The highest lycopene content was 688 mg L−1 in strain IEB, which corresponds to a 2.2-fold improvement over the original recombinant strain EBI.
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Srivastava SK, Piwek P, Ayakar SR, Bonakdarpour A, Wilkinson DP, Yadav VG. A Biogenic Photovoltaic Material. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800729. [PMID: 29855136 DOI: 10.1002/smll.201800729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/05/2018] [Indexed: 06/08/2023]
Abstract
A proof-of-concept for the fabrication of genetically customizable biogenic materials for photovoltaic applications is presented. E. coli is first genetically engineered to heterologously express the carotenoid biosynthetic pathway from plants. This modification yields a strain that overproduces the photoactive pigment lycopene. The pigment-producing cells are then coated with TiO2 nanoparticles via a tryptophan-mediated supramolecular interface, and subsequent incorporation of the resulting biogenic material (cells@TiO2 ) as an anode in an I- /I3- -based dye-sensitized solar cell yields an excellent photovoltaic (PV) response. This work lays strong foundations for the development of bio-PV materials and next-generation organic optoelectronics that are green, inexpensive, and easy to manufacture.
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Affiliation(s)
- Sarvesh Kumar Srivastava
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Przemyslaw Piwek
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Sonal R Ayakar
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Arman Bonakdarpour
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
- Clean Energy Research Centre, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - David P Wilkinson
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
- Clean Energy Research Centre, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
- School of Biomedical Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
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Efficient production of lycopene by engineered E. coli strains harboring different types of plasmids. Bioprocess Biosyst Eng 2018; 41:489-499. [DOI: 10.1007/s00449-017-1883-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023]
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Chen H, Liu C, Li M, Zhang H, Xian M, Liu H. Directed evolution of mevalonate kinase in Escherichia coli by random mutagenesis for improved lycopene. RSC Adv 2018; 8:15021-15028. [PMID: 35541305 PMCID: PMC9080002 DOI: 10.1039/c8ra01783b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/18/2019] [Accepted: 04/12/2018] [Indexed: 11/21/2022] Open
Abstract
Lycopene is a terpenoid pigment that has diverse applications in the fields of food and medicine.
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Affiliation(s)
- Hailin Chen
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
| | - Changqing Liu
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
| | - Meijie Li
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
| | - Haibo Zhang
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
| | - Huizhou Liu
- CAS Key Laboratory of Bio-based Materials
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- People's Republic of China
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36
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Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
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37
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Yu P, Chen X, Li P. Enhancing microbial production of biofuels by expanding microbial metabolic pathways. Biotechnol Appl Biochem 2017; 64:606-619. [PMID: 27507087 DOI: 10.1002/bab.1529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/31/2016] [Indexed: 12/29/2022]
Abstract
Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected.
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Affiliation(s)
- Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xingge Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Peng Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
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38
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Fermentative Production of Cysteine by Pantoea ananatis. Appl Environ Microbiol 2017; 83:AEM.02502-16. [PMID: 28003193 DOI: 10.1128/aem.02502-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/15/2016] [Indexed: 11/20/2022] Open
Abstract
Cysteine is a commercially important amino acid; however, it lacks an efficient fermentative production method. Due to its cytotoxicity, intracellular cysteine levels are stringently controlled via several regulatory modes. Managing its toxic effects as well as understanding and deregulating the complexities of regulation are crucial for establishing the fermentative production of cysteine. The regulatory modes include feedback inhibition of key metabolic enzymes, degradation, efflux pumps, and the transcriptional regulation of biosynthetic genes by a master cysteine regulator, CysB. These processes have been extensively studied using Escherichia coli for overproducing cysteine by fermentation. In this study, we genetically engineered Pantoea ananatis, an emerging host for the fermentative production of bio-based materials, to identify key factors required for cysteine production. According to this and our previous studies, we identified a major cysteine desulfhydrase gene, ccdA (formerly PAJ_0331), involved in cysteine degradation, and the cysteine efflux pump genes cefA and cefB (formerly PAJ_3026 and PAJ_p0018, respectively), which may be responsible for downregulating the intracellular cysteine level. Our findings revealed that ccdA deletion and cefA and cefB overexpression are crucial factors for establishing fermentative cysteine production in P. ananatis and for obtaining a higher cysteine yield when combined with genes in the cysteine biosynthetic pathway. To our knowledge, this is the first demonstration of cysteine production in P. ananatis, which has fundamental implications for establishing overproduction in this microbe.IMPORTANCE The efficient production of cysteine is a major challenge in the amino acid fermentation industry. In this study, we identified cysteine efflux pumps and degradation pathways as essential elements and genetically engineered Pantoea ananatis, an emerging host for the fermentative production of bio-based materials, to establish the fermentative production of cysteine. This study provides crucial insights into the design and construction of cysteine-producing strains, which may play central roles in realizing commercial basis production.
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Saeki K, Tominaga M, Kawai-Noma S, Saito K, Umeno D. Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits. ACS Synth Biol 2016; 5:1201-1210. [PMID: 26991155 DOI: 10.1021/acssynbio.5b00230] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic biologists are in need of genetic switches, or inducible sensor/promoter systems, that can be reliably integrated in multiple contexts. Using a liquid-based selection method, we systematically engineered the choline-inducible transcription factor BetI, yielding various choline-inducible and choline-repressive promoter systems with various input-output characteristics. In addition to having high stringency and a high maximum induction level, they underwent a graded and single-peaked response to choline. Taking advantage of these features, we demonstrated the utility of these systems for controlling the carotenoid biosynthetic pathway and for constructing two-input logic gates. Additionally, we demonstrated the rapidity, throughput, robustness, and cost-effectiveness of our selection method, which facilitates the conversion of natural genetic controlling systems into systems that are designed for various synthetic biology applications.
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Affiliation(s)
- Kazuya Saeki
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Tominaga
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research
for Embryonic Science and Technology (PRESTO), Japan Science and Technology
Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Li Y, Wang G. Strategies of isoprenoids production in engineered bacteria. J Appl Microbiol 2016; 121:932-40. [DOI: 10.1111/jam.13237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/24/2016] [Accepted: 07/14/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Y. Li
- College of Pharmaceutical and Biological Engineering; Shenyang University of Chemical Technology; Shenyang China
| | - G. Wang
- Key Laboratory of Environmental and Applied Microbiology; Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
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Xu X, Jin W, Jiang L, Xu Q, Li S, Zhang Z, Huang H. A high-throughput screening method for identifying lycopene-overproducing E. coli strain based on an antioxidant capacity assay. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Du W, Song Y, Liu M, Yang H, Zhang Y, Fan Y, Luo X, Li Z, Wang N, He H, Zhou H, Ma W, Zhang T. Gene expression pattern analysis of a recombinant Escherichia coli strain possessing high growth and lycopene production capability when using fructose as carbon source. Biotechnol Lett 2016; 38:1571-7. [PMID: 27379652 DOI: 10.1007/s10529-016-2133-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/25/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Escherichia coli K12f-pACLYC has a high capability for growth and lycopene production when using fructose as carbon source and the transcription of genes involved was compared in glucose-grown and fructose-grown cells. RESULTS Escherichia coli K12f-pACLYC was grown on 10 g fructose l(-1) and reached 4.6 g DCW l(-1) with lycopene at 192 mg g DCW(-1), values that are 3-fold and 7-fold higher than when growing on glucose. Gene transcription profiles of fructose-grown and glucose-grown cells were compared. 384 differentially expressed genes (DEGs) with fold changes ≥4 were identified, and the transcription of genes involved in fructose uptake and metabolism, pyruvate catabolism, tricarboxylic acid cycle and oxidative phosphorylation varied significantly. These changes enhanced the metabolic flux into the Embden-Meyerhof-Parnas pathway and the tricarboxylic acid cylcle and coupled to oxidative phosphorylation. These enhanced activities provide more precursors, cofactors and energy needed for growth lycopene production. CONCLUSION The high capability of E. coli K12f-pACLYC for growth and lycopene production when growing on fructose is due to transcriptional regulation, and the relevant genes were identified.
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Affiliation(s)
- Wen Du
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Yajian Song
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Mengya Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Haixu Yang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Yao Zhang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Yanli Fan
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Xuegang Luo
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Zhongyuan Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Nan Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Hongpeng He
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Hao Zhou
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Wenjian Ma
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, China.
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Chen Y, Xiao W, Wang Y, Liu H, Li X, Yuan Y. Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering. Microb Cell Fact 2016; 15:113. [PMID: 27329233 PMCID: PMC4915043 DOI: 10.1186/s12934-016-0509-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/06/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Microbial production of lycopene, a commercially and medically important compound, has received increasing concern in recent years. Saccharomyces cerevisiae is regarded as a safer host for lycopene production than Escherichia coli. However, to date, the lycopene yield (mg/g DCW) in S. cerevisiae was lower than that in E. coli and did not facilitate downstream extraction process, which might be attributed to the incompatibility between host cell and heterologous pathway. Therefore, to achieve lycopene overproduction in S. cerevisiae, both host cell and heterologous pathway should be delicately engineered. RESULTS In this study, lycopene biosynthesis pathway was constructed by integration of CrtE, CrtB and CrtI in S. cerevisiae CEN.PK2. When YPL062W, a distant genetic locus, was deleted, little acetate was accumulated and approximately 100 % increase in cytosolic acetyl-CoA pool was achieved relative to that in parental strain. Through screening CrtE, CrtB and CrtI from diverse species, an optimal carotenogenic enzyme combination was obtained, and CrtI from Blakeslea trispora (BtCrtI) was found to have excellent performance on lycopene production as well as lycopene proportion in carotenoid. Then, the expression level of BtCrtI was fine-tuned and the effect of cell mating types was also evaluated. Finally, potential distant genetic targets (YJL064W, ROX1, and DOS2) were deleted and a stress-responsive transcription factor INO2 was also up-regulated. Through the above modifications between host cell and carotenogenic pathway, lycopene yield was increased by approximately 22-fold (from 2.43 to 54.63 mg/g DCW). Eventually, in fed-batch fermentation, lycopene production reached 55.56 mg/g DCW, which is the highest reported yield in yeasts. CONCLUSIONS Saccharomyces cerevisiae was engineered to produce lycopene in this study. Through combining host engineering (distant genetic loci and cell mating types) with pathway engineering (enzyme screening and gene fine-tuning), lycopene yield was stepwise improved by 22-fold as compared to the starting strain. The highest lycopene yield (55.56 mg/g DCW) in yeasts was achieved in 5-L bioreactors. This study provides a good reference of combinatorial engineering of host cell and heterologous pathway for microbial overproduction of pharmaceutical and chemical products.
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Affiliation(s)
- Yan Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Wenhai Xiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Hong Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xia Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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Bacterial Cysteine-Inducible Cysteine Resistance Systems. J Bacteriol 2016; 198:1384-92. [PMID: 26883827 DOI: 10.1128/jb.01039-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 02/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cysteine donates sulfur to macromolecules and occurs naturally in many proteins. Because low concentrations of cysteine are cytotoxic, its intracellular concentration is stringently controlled. In bacteria, cysteine biosynthesis is regulated by feedback inhibition of the activities of serine acetyltransferase (SAT) and 3-phosphoglycerate dehydrogenase (3-PGDH) and is also regulated at the transcriptional level by inducing the cysteine regulon using the master regulator CysB. Here, we describe two novel cysteine-inducible systems that regulate the cysteine resistance of Pantoea ananatis, a member of the family Enterobacteriaceae that shows great potential for producing substances useful for biotechnological, medical, and industrial purposes. One locus, designated ccdA(formerly PAJ_0331), encodes a novel cysteine-inducible cysteine desulfhydrase (CD) that degrades cysteine, and its expression is controlled by the transcriptional regulator encoded byccdR(formerly PAJ_0332 orybaO), located just upstream of ccdA The other locus, designated cefA (formerly PAJ_3026), encodes a novel cysteine-inducible cysteine efflux pump that is controlled by the transcriptional regulator cefR(formerly PAJ_3027), located just upstream of cefA To our knowledge, this is the first example where the expression of CD and an efflux pump is regulated in response to cysteine and is directly involved in imparting resistance to excess levels of cysteine. We propose that ccdA and cefA function as safety valves that maintain homeostasis when the intra- or extracellular cysteine concentration fluctuates. Our findings contribute important insights into optimizing the production of cysteine and related biomaterials by P. ananatis IMPORTANCE Because of its toxicity, the bacterial intracellular cysteine level is stringently regulated at biosynthesis. This work describes the identification and characterization of two novel cysteine-inducible systems that regulate, through degradation and efflux, the cysteine resistance of Pantoea ananatis, a member of the family Enterobacteriaceae that shows great potential for producing substances useful for industrial purposes. We propose that this novel mechanism for sensing and regulating cysteine levels is a safety valve enabling adaptation to sudden changes in intra- or extracellular cysteine levels in bacteria. Our findings provide important insights into optimizing the production of cysteine and related biomaterials by P. ananatis and also a deep understanding of sulfur/cysteine metabolism and regulation in this plant pathogen and related bacteria.
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Putative carotenoid genes expressed under the regulation of Shine–Dalgarno regions in Escherichia coli for efficient lycopene production. Biotechnol Lett 2015; 37:2303-10. [DOI: 10.1007/s10529-015-1922-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/13/2015] [Indexed: 11/26/2022]
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Xie W, Lv X, Ye L, Zhou P, Yu H. Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering. Metab Eng 2015; 30:69-78. [DOI: 10.1016/j.ymben.2015.04.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 12/26/2022]
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Khan NE, Nybo SE, Chappell J, Curtis WR. Triterpene hydrocarbon production engineered into a metabolically versatile host--Rhodobacter capsulatus. Biotechnol Bioeng 2015; 112:1523-32. [PMID: 25728701 DOI: 10.1002/bit.25573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/14/2015] [Accepted: 02/11/2015] [Indexed: 11/08/2022]
Abstract
Triterpene hydrocarbon biosynthesis of the ancient algae Botryococcus braunii was installed into Rhodobacter capsulatus to explore the production of C30 hydrocarbon in a host capable of diverse growth habits-utilizing carbohydrate, sunlight or hydrogen (with CO2 fixation) as alternative energy feedstocks. Engineering an enhanced MEP pathway was also used to augment triterpene accumulation. Despite dramatically different sources of carbon and reducing power, nearly the same level of botryococcene or squalene (∼5 mg oil/g-dry-weight [gDW]) was achieved in small-scale aerobic heterotrophic, anaerobic photoheterotrophic, and aerobic chemoautotrophic growth conditions. A glucose fed-batch bioreactor reached 40 mg botryococcene/L (∼12 mg/gDW), while autotrophic bioreactor performance with CO2 , H2 , and O2 reached 110 mg/L (16.7 mg/gDW) during batch and 60 mg/L (23 mg/gDW) during continuous operation at a dilution rate corresponding to about 10% of μ(max). Batch and continuous autotrophic specific productivity was found to reach 0.5 and 0.32 mg triterpene/g DW/h, comparable to prior reports for terpene production driven by heterotrophic growth conditions. This demonstrates the feasibility of alternative feedstocks and trophic modes to provide comparable routes to biochemicals that do not rely on sugar.
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Affiliation(s)
- Nymul E Khan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802
| | - S Eric Nybo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, 40536
| | - Joe Chappell
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, 40536
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802.
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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: 22.3] [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: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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