1
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Li Z, Deng Y, Yang GY. Growth-coupled high throughput selection for directed enzyme evolution. Biotechnol Adv 2023; 68:108238. [PMID: 37619825 DOI: 10.1016/j.biotechadv.2023.108238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.
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Affiliation(s)
- Zhengqun Li
- 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
| | - Yuting Deng
- 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
| | - Guang-Yu Yang
- 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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2
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Liu L, Li J, Gai Y, Tian Z, Wang Y, Wang T, Liu P, Yuan Q, Ma H, Lee SY, Zhang D. Protein engineering and iterative multimodule optimization for vitamin B 6 production in Escherichia coli. Nat Commun 2023; 14:5304. [PMID: 37652926 PMCID: PMC10471632 DOI: 10.1038/s41467-023-40928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.
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Affiliation(s)
- Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jinlong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanming Gai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhizhong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tenghe Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Fan J, Xu W, Xu X, Wang Y. Production of Coenzyme Q 10 by microbes: an update. World J Microbiol Biotechnol 2022; 38:194. [PMID: 35984526 DOI: 10.1007/s11274-022-03326-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
Coenzyme Q10 (CoQ10) is the main CoQ species in human and is used extensively in food, cosmetic and medicine industries because of its antioxidant properties and its benefit in prophylactic medicine and therapy for a variety of diseases. Among various approaches to increase the production of CoQ10, microbial fermentation is the most effective. As knowledge of the biosynthetic enzymes and regulatory mechanisms modulating CoQ10 production increases, opportunities arise for metabolic engineering of CoQ10 in microbial hosts. In this review, we present various strategies used up to date to improve CoQ10 production and focus on metabolic engineering of CoQ10 overproduction in microbes. General strategies of metabolic engineering include providing sufficient precursors for CoQ10, increasing metabolic fluxes, and expanding storage capacity for CoQ10. Based on these strategies, CoQ10 production has been significantly improved in natural CoQ10 producers, as well as in heterologous hosts.
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Affiliation(s)
- Jinbo Fan
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Wen Xu
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Xi Xu
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China.
| | - Yang Wang
- Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an, China.
- School of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China.
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4
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Zhang L, Li YL, Hu JH, Liu ZY. Overexpression of enzymes in glycolysis and energy metabolic pathways to enhance coenzyme Q10 production in Rhodobacter sphaeroides VK-2-3. Front Microbiol 2022; 13:931470. [PMID: 36033867 PMCID: PMC9412181 DOI: 10.3389/fmicb.2022.931470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
We subjected the components of the glycolysis and energy metabolism pathways of Rhodobacter sphaeroides (R. sphaeroides) to metabolic engineering to improve the titer and yield of coenzyme Q10 (CoQ10). Phosphofructokinase (PFK), cyclic adenylate-dependent protein kinase (PKAC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and adenosine triphosphate hydrolase (KdpC) were overexpressed in R. sphaeroides VK-2-3 (VK-2-3). The strains were labeled R. sphaeroides PFK (RS.PFK), RS.PKAC, RS.PFK–PKAC, RS.KdpC, RS.GAPDH, and RS.KdpC–GAPDH. Results showed that the CoQ10 titers of RS.PFK, RS.PKAC, and RS.PFK–PKAC were 300.96 ± 0.87, 405.94 ± 4.77, and 379.94 ± 0.42 mg/l, respectively. The CoQ10 titers of RS.PFK and VK-2-3 were not significantly different; however, those for RS.PKAC and RS.PFK–PKAC were 13 and 6% higher than that of VK-2-3, respectively. Further, the titers of RS.KdpC, RS.GAPDH, and RS.KdpC–GAPDH were 360.17 ± 0.39, 409.79 ± 0.76, and 359.87 ± 1.14 mg/l, respectively. The titers of RS.KdpC and RS.KdpC–GAPDH were not significantly different from that for VK-2-3, whereas that for RS.GAPDH was 14% higher than that of VK-2-3. Finally, when the cultures of RS.GAPDH and VK-2-3 were scaled up in 5-L fermenters, the CoQ10 titers and RS.GAPDH yields increased by 44.3 and 37.8%, respectively, compared with VK-2-3.To the best of our knowledge, the glycolysis pathway of R. sphaeroides was studied for the first time in this study. We genetically modified the components of the energy metabolism pathway to obtain the strain with high yield of CoQ10 mutant RS.GAPDH. The findings of this study can serve as a basis for future studies involving metabolic engineering of CoQ10-producing strains.
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Affiliation(s)
- Long Zhang
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Yong-li Li
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Jian-hua Hu
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
| | - Zhan-ying Liu
- Inner Mongolia Energy Conservation and Emission Reduction Engineering Technology Research Center for Fermentation Industry, Hohhot, Inner Mongolia, China
- Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, Hohhot, Inner Mongolia, China
- College of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, Inner Mongolia, China
- *Correspondence: Zhan-ying Liu,
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5
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Yu J, Moon SK, Kim YH, Min J. Isoprene production by Rhodobacter sphaeroides and its antimicrobial activity. Res Microbiol 2022; 173:103938. [DOI: 10.1016/j.resmic.2022.103938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 11/25/2022]
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6
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Zhu Y, Pan M, Wang C, Ye L, Xia C, Yu H. Enhanced CoQ10 production by genome modification of Rhodobacter sphaeroides via Tn7 transposition. FEMS Microbiol Lett 2022; 369:6537402. [PMID: 35218188 DOI: 10.1093/femsle/fnab160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/31/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
As a native CoQ10 producer, Rhodobacter sphaeroides has been extensively engineered to enhance CoQ10 production. However, the genetic manipulations using plasmids suffer from risk of plasmid loss during propagation process, biomass impairment due to cellular burden and bio-safety concerns. In this paper, genomic manipulations via Tn7 transposition was conducted to boost the CoQ10 biosynthesis in R. sphaeroides. The titer production and content of CoQ10 were improved by 18.44% and 18.87% respectively compared to the wild type, when an additional copy of dxs and dxr were integrated into the genome. Further overexpression of idi and ispD by genomic integration created strain RSPCDDII with CoQ10 production and content of 81.23 mg/L and 5.93 mg/g, which were 54.28% and 55.97% higher than those of the wild type. The gene segments were successfully inserted into the attTn7 site of the R. sphaeroides genome. Meanwhile, the biomass was not affected. Compared to overexpression of genes on plasmids, this strategy could enhance protein expression to a proper level without affecting cell growth, and in a more stable manner.
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Affiliation(s)
- Yongqiang Zhu
- Institute of Materials Engineering, Suqian University, Suqian 223800, PR China.,Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China.,Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Mengyao Pan
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Chenfei Wang
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Lidan Ye
- Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Chunmiao Xia
- Anhui Laboratory of Clean Energy Materials and Chemistry for Sustainable Conversion of Natural Resources, School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu 241000, PR China
| | - Hongwei Yu
- Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
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7
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Screening and engineering of high-activity promoter elements through transcriptomics and red fluorescent protein visualization in Rhodobacter sphaeroides. Synth Syst Biotechnol 2021; 6:335-342. [PMID: 34738044 PMCID: PMC8531756 DOI: 10.1016/j.synbio.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
The versatile photosynthetic α-proteobacterium Rhodobacter sphaeroides, has recently been extensively engineered as a novel microbial cell factory (MCF) to produce pharmaceuticals, nutraceuticals, commodity chemicals and even hydrogen. However, there are no well-characterized high-activity promoters to modulate gene transcription during the engineering of R. sphaeroides. In this study, several native promoters from R. sphaeroides JDW-710 (JDW-710), an industrial strain producing high levels of co-enzyme Q10 (Q10) were selected on the basis of transcriptomic analysis. These candidate promoters were then characterized by using gusA as a reporter gene. Two native promoters, Prsp_7571 and Prsp_6124, showed 620% and 800% higher activity, respectively, than the tac promoter, which has previously been used for gene overexpression in R. sphaeroides. In addition, a Prsp_7571-derived synthetic promoter library with strengths ranging from 54% to 3200% of that of the tac promoter, was created on the basis of visualization of red fluorescent protein (RFP) expression in R. sphaeroides. Finally, as a demonstration, the synthetic pathway of Q10 was modulated by the selected promoter T334* in JDW-710; the Q10 yield in shake-flasks increased 28% and the production reached 226 mg/L. These well-characterized promoters should be highly useful in current synthetic biology platforms for refactoring the biosynthetic pathway in R. sphaeroides-derived MCFs.
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8
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Wu X, Ma G, Liu C, Qiu XY, Min L, Kuang J, Zhu L. Biosynthesis of pinene in purple non-sulfur photosynthetic bacteria. Microb Cell Fact 2021; 20:101. [PMID: 34001115 PMCID: PMC8130110 DOI: 10.1186/s12934-021-01591-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Background Pinene is a monoterpene, that is used in the manufacture of fragrances, insecticide, fine chemicals, and renewable fuels. Production of pinene by metabolic-engineered microorganisms is a sustainable method. Purple non-sulfur photosynthetic bacteria belong to photosynthetic chassis that are widely used to synthesize natural chemicals. To date, researches on the synthesis of pinene by purple non-sulfur photosynthetic bacteria has not been reported, leaving the potential of purple non-sulfur photosynthetic bacteria synthesizing pinene unexplored. Results Rhodobacter sphaeroides strain was applied as a model and engineered to express the fusion protein of heterologous geranyl diphosphate synthase (GPPS) and pinene synthase (PS), hence achieving pinene production. The reaction condition of pinene production was optimized and 97.51 μg/L of pinene was yielded. Then, genes of 1-deoxy-d-xylulose 5-phosphate synthase, 1-deoxy-d-xylulose 5-phosphate reductoisomerase and isopentenyl diphosphate isomerase were overexpressed, and the ribosome binding site of GPPS-PS mRNA was optimized, improving pinene titer to 539.84 μg/L. Conclusions In this paper, through heterologous expression of GPPS-PS, pinene was successfully produced in R. sphaeroides, and pinene production was greatly improved by optimizing the expression of key enzymes. This is the first report on pinene produce by purple non-sulfur photosynthetic bacteria, which expands the availability of photosynthetic chassis for pinene production. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01591-6.
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Affiliation(s)
- Xiaomin Wu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
| | - Guang Ma
- China Astronaut Research and Training Center, Beijing, 100094, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Xin-Yuan Qiu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Lu Min
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Jingyu Kuang
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
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9
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Xu W, Ma X, Yao J, Wang D, Li W, Liu L, Shao L, Wang Y. Increasing coenzyme Q 10 yield from Rhodopseudomonas palustris by expressing rate-limiting enzymes and blocking carotenoid and hopanoid pathways. Lett Appl Microbiol 2021; 73:88-95. [PMID: 33783839 DOI: 10.1111/lam.13479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
Coenzyme Q10 (CoQ10 ), a strong antioxidant, is used extensively in food, cosmetic and medicine industries. A natural producer, Rhodopseudomonas palustris, was engineered to overproduce CoQ10 . For increasing the CoQ10 content, crtB gene was deleted to block the carotenoid pathway. crtB gene deletion led to 33% improvement of CoQ10 content over the wild type strain. However, it was found that the yield of hopanoids was also increased by competing for the precursors from carotenoid pathway with CoQ10 pathway. To further increase the CoQ10 content, hopanoid pathway was blocked by deleting shc gene, resulting in R. palustris [Δshc, ΔcrtB] to produce 4·7 mg g-1 DCW CoQ10 , which was 1·2 times higher than the CoQ10 content in the wild type strain. The common strategy of co-expression of rate-limiting enzymes (DXS, DPS and UbiA) was combined with the pathway blocking method resulted in 8·2 mg g-1 DCW of CoQ10 , which was 2·9 times higher than that of wild type strain. The results suggested a synergistic effect among different metabolic engineering strategies. This study demonstrates the potential of R. palustris for CoQ10 production and provides viable strategies to increase CoQ10 titer.
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Affiliation(s)
- W Xu
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - X Ma
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - J Yao
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - D Wang
- Department of Prosthodontics, School of Stomatology, Xi'an Medical University, Xi'an, Shaanxi, China
| | - W Li
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Li Liu
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - L Shao
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Y Wang
- The Xi'an key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi'an Medical University, Xi'an, Shaanxi, China
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10
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Burgardt A, Moustafa A, Persicke M, Sproß J, Patschkowski T, Risse JM, Peters-Wendisch P, Lee JH, Wendisch VF. Coenzyme Q 10 Biosynthesis Established in the Non-Ubiquinone Containing Corynebacterium glutamicum by Metabolic Engineering. Front Bioeng Biotechnol 2021; 9:650961. [PMID: 33859981 PMCID: PMC8042324 DOI: 10.3389/fbioe.2021.650961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Coenzyme Q10 (CoQ10) serves as an electron carrier in aerobic respiration and has become an interesting target for biotechnological production due to its antioxidative effect and benefits in supplementation to patients with various diseases. For the microbial production, so far only bacteria have been used that naturally synthesize CoQ10 or a related CoQ species. Since the whole pathway involves many enzymatic steps and has not been fully elucidated yet, the set of genes required for transfer of CoQ10 synthesis to a bacterium not naturally synthesizing CoQ species remained unknown. Here, we established CoQ10 biosynthesis in the non-ubiquinone-containing Gram-positive Corynebacterium glutamicum by metabolic engineering. CoQ10 biosynthesis involves prenylation and, thus, requires farnesyl diphosphate as precursor. A carotenoid-deficient strain was engineered to synthesize an increased supply of the precursor molecule farnesyl diphosphate. Increased farnesyl diphosphate supply was demonstrated indirectly by increased conversion to amorpha-4,11-diene. To provide the first CoQ10 precursor decaprenyl diphosphate (DPP) from farnesyl diphosphate, DPP synthase gene ddsA from Paracoccus denitrificans was expressed. Improved supply of the second CoQ10 precursor, para-hydroxybenzoate (pHBA), resulted from metabolic engineering of the shikimate pathway. Prenylation of pHBA with DPP and subsequent decarboxylation, hydroxylation, and methylation reactions to yield CoQ10 was achieved by expression of ubi genes from Escherichia coli. CoQ10 biosynthesis was demonstrated in shake-flask cultivation and verified by liquid chromatography mass spectrometry analysis. To the best of our knowledge, this is the first report of CoQ10 production in a non-ubiquinone-containing bacterium.
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Affiliation(s)
- Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ayham Moustafa
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Thomas Patschkowski
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Petra Peters-Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jin-Ho Lee
- Major in Food Science & Biotechnology, School of Food Biotechnology & Nutrition, Kyungsung University, Busan, South Korea
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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11
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Orsi E, Beekwilder J, Eggink G, Kengen SWM, Weusthuis RA. The transition of Rhodobacter sphaeroides into a microbial cell factory. Biotechnol Bioeng 2020; 118:531-541. [PMID: 33038009 PMCID: PMC7894463 DOI: 10.1002/bit.27593] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Wageningen Food and Biobased Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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12
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Oxygen Uptake Rate Controlling Strategy Balanced with Oxygen Supply for Improving Coenzyme Q10 Production by Rhodobacter sphaeroides. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0461-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Luo Y, Ge M, Wang B, Sun C, Wang J, Dong Y, Xi JJ. CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. Microb Cell Fact 2020; 19:93. [PMID: 32334589 PMCID: PMC7183636 DOI: 10.1186/s12934-020-01345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
Background CRISPR/Cas9 systems have been repurposed as canonical genome editing tools in a variety of species, but no application for the model strain Rhodobacter sphaeroides 2.4.1 was unveiled. Results Here we showed two kinds of programmable base editing systems, cytosine base editors (CBEs) and adenine base editors (ABEs), generated by fusing endonuclease Cas9 variant to cytosine deaminase PmCDA1 or heterodimer adenine deaminase TadA–TadA*, respectively. Using CBEs, we were able to obtain C-to-T mutation of single and double targets following the first induction step, with the efficiency of up to 97% and 43%; while the second induction step was needed in the case of triple target, with the screening rate of 47%. Using ABEs, we were only able to gain A-to-G mutation of single target after the second induction step, with the screening rate of 30%. Additionally, we performed a knockout analysis to identify the genes responsible for coenzyme Q10 biosynthesis and found that ubiF, ubiA, ubiG, and ubiX to be the most crucial ones. Conclusions Together, CBEs and ABEs serve as alternative methods for genetic manipulation in Rhodobacter sphaeroides and will shed light on the fundamental research of other bacteria that are hard to be directly edited by Cas9-sgRNA.
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Affiliation(s)
- Yufeng Luo
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bolun Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Changhong Sun
- Beijing Viewsolid Biotech Co. Ltd, Beijing, 100071, China
| | - Junyi Wang
- Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China
| | - Yuyang Dong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA, 30332, USA
| | - Jianzhong Jeff Xi
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Department of Biomedical Engineering, State Key Laboratory of Natural and Biomimetic Drugs, College of Engineering, Peking University, Beijing, 100871, China.
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14
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Zhang L, Liu L, Wang KF, Xu L, Zhou L, Wang W, Li C, Xu Z, Shi T, Chen H, Li Y, Xu H, Yang X, Zhu Z, Chen B, Li D, Zhan G, Zhang SL, Zhang LX, Tan GY. Phosphate limitation increases coenzyme Q 10 production in industrial Rhodobacter sphaeroides HY01. Synth Syst Biotechnol 2019; 4:212-219. [PMID: 31890925 PMCID: PMC6909082 DOI: 10.1016/j.synbio.2019.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is an important component of the respiratory chain in humans and some bacteria. As a high-value-added nutraceutical antioxidant, CoQ10 has excellent capacity to prevent cardiovascular disease. The content of CoQ10 in the industrial Rhodobacter sphaeroides HY01 is hundreds of folds higher than normal physiological levels. In this study, we found that overexpression or optimization of the synthetic pathway failed CoQ10 overproduction in the HY01 strain. Moreover, under phosphate- limited conditions (decreased phosphate or in the absence of inorganic phosphate addition), CoQ10 production increased significantly by 12% to220 mg/L, biomass decreased by 12%, and the CoQ10 productivity of unit cells increased by 27%. In subsequent fed-batch fermentation, CoQ10 production reached 272 mg/L in the shake-flask fermentation and 1.95 g/L in a 100-L bioreactor under phosphate limitation. Furthermore, to understand the mechanism associated with CoQ10 overproduction under phosphate- limited conditions, the comparatve transcriptome analysis was performed. These results indicated that phosphate limitation combined with glucose fed-batch fermentation represented an effective strategy for CoQ10 production in the HY01. Phosphate limitation induced a pleiotropic effect on cell metabolism, and that improved CoQ10 biosynthesis efficiency was possibly related to the disturbance of energy metabolism and redox potential.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Leshi Liu
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Ke-Feng Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Lan Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Liming Zhou
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Chuan Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Zheng Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Haihong Chen
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Yuanhang Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - XiuLiang Yang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd, No. 117 Qixing River Road, Zibo, 255130, China
| | - Zhichun Zhu
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Biqin Chen
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Dan Li
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Guanghuang Zhan
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Si-Liang Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Li-Xin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
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15
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Improving biosynthetic production of pinene through plasmid recombination elimination and pathway optimization. Plasmid 2019; 105:102431. [DOI: 10.1016/j.plasmid.2019.102431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 11/21/2022]
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16
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Wang Y, Chen S, Liu J, Lv P, Cai D, Zhao G. Efficient production of coenzyme Q 10 from acid hydrolysate of sweet sorghum juice by Rhodobacter sphaeroides. RSC Adv 2019; 9:22336-22342. [PMID: 35519485 PMCID: PMC9066795 DOI: 10.1039/c9ra03964c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/12/2019] [Indexed: 12/02/2022] Open
Abstract
In order to achieve efficient bioconversion of biomass-derived sugars, acid hydrolysate of sweet sorghum juice (SSJAH) containing abundant fermentable sugars was used for coenzyme Q10 (CoQ10) fermentation by Rhodobacter sphaeroides CQ-09-1. The synthesis of CoQ10 was facilitated when the initial concentration of total sugar was 80.00 g L-1. And the highest CoQ10 titer was obtained when the pH and temperature were maintained at 7.00 and 30.00 °C, respectively. Moreover, corn steep powder (CSP) was proved to be an efficient nitrogen & salt supplement to SSJAH. Under the optimized conditions, the titer of CoQ10 reached 141.95 mg L-1 in a fed-batch fermentation. The CoQ10 titer reported was about two times higher than that obtained in the previous study using wild strains. This process introduces a potential way to produce CoQ10 using the concept of biorefinery, while making full use of sweet sorghum juice (SSJ).
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Affiliation(s)
- Y Wang
- Fermentation Engineering Technology Research Center of Heibei Province, College of Bioscience & Bioengineering, Hebei University of Science and Technology No. 26 Yuxiang Road, Yuhua District Shijiazhuang 050018 PR China
| | - S Chen
- Fermentation Engineering Technology Research Center of Heibei Province, College of Bioscience & Bioengineering, Hebei University of Science and Technology No. 26 Yuxiang Road, Yuhua District Shijiazhuang 050018 PR China
| | - J Liu
- Fermentation Engineering Technology Research Center of Heibei Province, College of Bioscience & Bioengineering, Hebei University of Science and Technology No. 26 Yuxiang Road, Yuhua District Shijiazhuang 050018 PR China
| | - P Lv
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Hebei Branch of National Sorghum Improvement Center Shijiazhuang 050035 PR China
| | - D Cai
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology Beijing 100029 People's Republic of China
| | - G Zhao
- Fermentation Engineering Technology Research Center of Heibei Province, College of Bioscience & Bioengineering, Hebei University of Science and Technology No. 26 Yuxiang Road, Yuhua District Shijiazhuang 050018 PR China
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17
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Orsi E, Folch PL, Monje-López VT, Fernhout BM, Turcato A, Kengen SWM, Eggink G, Weusthuis RA. Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium. J Ind Microbiol Biotechnol 2019; 46:1179-1190. [PMID: 31187318 PMCID: PMC6697705 DOI: 10.1007/s10295-019-02201-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
Abstract
Rhodobacter sphaeroides is a metabolically versatile bacterium capable of producing terpenes natively. Surprisingly, terpene biosynthesis in this species has always been investigated in complex media, with unknown compounds possibly acting as carbon and nitrogen sources. Here, a defined medium was adapted for R. sphaeroides dark heterotrophic growth, and was used to investigate the conversion of different organic substrates into the reporter terpene amorphadiene. The amorphadiene synthase was cloned in R. sphaeroides, allowing its biosynthesis via the native 2-methyl-d-erythritol-4-phosphate (MEP) pathway and, additionally, via a heterologous mevalonate one. The latter condition increased titers up to eightfold. Consequently, better yields and productivities to previously reported complex media cultivations were achieved. Productivity was further investigated under different cultivation conditions, including nitrogen and oxygen availability. This novel cultivation setup provided useful insight into the understanding of terpene biosynthesis in R. sphaeroides, allowing to better comprehend its dynamics and regulation during chemoheterotrophic cultivation.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Pauline L Folch
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Vicente T Monje-López
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas M Fernhout
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Alessandro Turcato
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands
| | - Gerrit Eggink
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.,Biobased Products Food and Biobased Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Department of Agrotechnology and Food, Wageningen University and Research, Wageningen, The Netherlands.
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18
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19
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Chen X, Jiang X, Xu M, Zhang M, Huang R, Huang J, Qi F. Co-production of farnesol and coenzyme Q 10 from metabolically engineered Rhodobacter sphaeroides. Microb Cell Fact 2019; 18:98. [PMID: 31151455 PMCID: PMC6544981 DOI: 10.1186/s12934-019-1145-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Farnesol is an acyclic sesquiterpene alcohol present in the essential oils of various plants in nature. It has been reported to be valuable in medical applications, such as alleviation of allergic asthma, gliosis, and edema as well as anti-cancerous and anti-inflammatory effects. Coenzyme Q10 (CoQ10), an essential cofactor in the aerobic respiratory electron transport chain, has attracted growing interest owing to its clinical benefits and important applications in the pharmaceutical, food, and health industries. In this work, co-production of (E,E)-farnesol (FOH) and CoQ10 was achieved by combining 3 different exogenous terpenes or sesquiterpene synthase with the RNA interference of psy (responsible for phytoene synthesis in Rhodobacter sphaeroides GY-2). RESULTS FOH production was significantly increased by overexpressing exogenous terpene synthase (TPS), phosphatidylglycerophosphatase B (PgpB), and sesquiterpene synthase (ATPS), as well as RNAi-mediated silencing of psy coding phytoene synthase (PSY) in R. sphaeroides strains. Rs-TPS, Rs-ATPS, and Rs-PgpB respectively produced 68.2%, 43.4%, and 21.9% higher FOH titers than that of the control strain. Interestingly, the CoQ10 production of these 3 recombinant R. sphaeroides strains was exactly opposite to that of FOH. However, CoQ10 production was almost unaffected in R. sphaeroides strains modified by psy RNA interference. The highest FOH production of 40.45 mg/L, which was twice as high as that of the control, was obtained from the TPS-PSYi strain, where the exogenous TPS was combined with the weakening of the phytoene synthesis pathway via psy RNA interference. CoQ10 production in TPS-PSYi, ATPS-PSYi, and PgpB-PSYi was decreased and lower than that of the control strain. CONCLUSIONS The original flux that contributed to phytoene synthesis was effectively redirected to provide precursors toward FOH or CoQ10 synthesis via psy RNA interference, which led to weakened carotenoid synthesis. The improved flux that was originally involved in CoQ10 production and phytoene synthesis was redirected toward FOH synthesis via metabolic modification. This is the first reported instance of FOH and CoQ10 co-production in R. sphaeroides using a metabolic engineering strategy.
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Affiliation(s)
- Xueduan Chen
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Xianzhang Jiang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Man Xu
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Mingliang Zhang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Runye Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China. .,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, Fujian Normal University, Fuzhou, 350117, Fujian, China.
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20
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Mutagenesis of Rhodobacter sphaeroides using atmospheric and room temperature plasma treatment for efficient production of coenzyme Q10. J Biosci Bioeng 2019; 127:698-702. [PMID: 30709705 DOI: 10.1016/j.jbiosc.2018.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/03/2018] [Accepted: 12/13/2018] [Indexed: 11/20/2022]
Abstract
Coenzyme Q10 (CoQ10) plays an important role in the human respiratory chain and is widely used as medicine and dietary supplement. To improve the fermentation efficiency of CoQ10, a modified version of atmospheric and room temperature plasma (ARTP) treatment was used to mutate Rhodobacter sphaeroides. Meanwhile, Vitamin K3, a structural analog of CoQ10, was used as an inhibitor for mutant selection. In the first round of screening in 24-well plates, three mutants were obtained, with the production of CoQ10 at 311 mg/L, 307 mg/L, and 309 mg/L, which were increased from the parent's production at 265 mg/L. Furthermore, a second round of mutation and screening was performed based on the mutant strain with the highest production in the first round, leading to the identification of a mutant AR01 with the production of CoQ10 at ∼330 mg/L. Finally, 590 mg/L CoQ10 was obtained for AR01 after 100 h fermentation, which was ∼25.5% higher than that of the original parent strain. It is the first report of ARTP treatment usage for the selection of CoQ10 producing bacteria and the results show that plasma jet, driven by helium-based ARTP, can be a feasible strategy for mutation feeding.
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Zhang J, Gao D, Cai J, Liu H, Qi Z. Improving coenzyme Q10 yield of Rhodobacter sphaeroides via modifying redox respiration chain. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Weaver JB, Boxer SG. Genetic Code Expansion in Rhodobacter sphaeroides to Incorporate Noncanonical Amino Acids into Photosynthetic Reaction Centers. ACS Synth Biol 2018; 7:1618-1628. [PMID: 29763307 DOI: 10.1021/acssynbio.8b00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosynthetic reaction centers (RCs) are the membrane proteins responsible for the initial charge separation steps central to photosynthesis. As a complex and spectroscopically complicated membrane protein, the RC (and other associated photosynthetic proteins) would benefit greatly from the insight offered by site-specifically encoded noncanonical amino acids in the form of probes and an increased chemical range in key amino acid analogues. Toward that goal, we developed a method to transfer amber codon suppression machinery developed for E. coli into the model bacterium needed to produce RCs, Rhodobacter sphaeroides. Plasmids were developed and optimized to incorporate 3-chlorotyrosine, 3-bromotyrosine, and 3-iodotyrosine into RCs. Multiple challenges involving yield and orthogonality were overcome to implement amber suppression in R. sphaeroides, providing insights into the hurdles that can be involved in host transfer of amber suppression systems from E. coli. In the process of verifying noncanonical amino acid incorporation, characterization of this membrane protein via mass spectrometry (which has been difficult previously) was substantially improved. Importantly, the ability to incorporate noncanonical amino acids in R. sphaeroides expands research capabilities in the photosynthetic field.
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Affiliation(s)
- Jared Bryce Weaver
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Su A, Chi S, Li Y, Tan S, Qiang S, Chen Z, Meng Y. Metabolic Redesign of Rhodobacter sphaeroides for Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5879-5885. [PMID: 29806774 DOI: 10.1021/acs.jafc.8b00855] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lycopene plays an important role as an antioxidative and anticancer agent, and is an increasingly valuable commodity in the global market. Rhodobacter sphaeroides, a carotenogenic and phototrophic bacterium, is an efficient and practical host for carotenoid production. Herein, we explored the potential of metabolically engineered Rb. sphaeroides as a novel platform to produce lycopene. The basal lycopene-producing strain was generated by introducing an exogenous crtI4 from Rhodospirillum rubrum to replace the native crtI3 and deleting crtC in Rb. sphaeroides. Furthermore, knocking out zwf blocked the competitive pentose phosphate pathway and improved the lycopene content by 88%. Finally, the methylerythritol phosphate pathway was reinforced by integration of dxs combined with zwf deletion, which further increased the lycopene content. The final engineered strain produced lycopene to 10.32 mg/g dry cell weight. This study describes a new lycopene producer and provides insight into a photosynthetic bacterium as a host for lycopene biosynthesis.
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Affiliation(s)
- Anping Su
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shuang Chi
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Siyuan Tan
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
| | - Shan Qiang
- Xi'an Healthful Biotechnology Co., Ltd., HangTuo Road , Chang'an, Xi'an 710100 , P.R. China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District , Beijing 100193 , P.R. China
| | - Yonghong Meng
- Shaanxi Engineering Lab for Food Green Processing and Security Control, College of Food Engineering and Nutritional Science , Shaanxi Normal University , 620 West Chang'an Avenue , Chang'an, Xi'an 710119 , P.R. China
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Liu Y, Yang ZM, Xue ZL, Qian SH, Wang Z, Hu LX, Wang J, Zhu H, Ding XM, Yu F. Influence of site-directed mutagenesis of UbiA, overexpression of dxr, menA and ubiE, and supplementation with precursors on menaquinone production in Elizabethkingia meningoseptica. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Loeschcke A, Dienst D, Wewer V, Hage-Hülsmann J, Dietsch M, Kranz-Finger S, Hüren V, Metzger S, Urlacher VB, Gigolashvili T, Kopriva S, Axmann IM, Drepper T, Jaeger KE. The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis. PLoS One 2017; 12:e0189816. [PMID: 29281679 PMCID: PMC5744966 DOI: 10.1371/journal.pone.0189816] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
Cyclic triterpenes constitute one of the most diverse groups of plant natural products. Besides the intriguing biochemistry of their biosynthetic pathways, plant triterpenes exhibit versatile bioactivities, including antimicrobial effects against plant and human pathogens. While prokaryotes have been extensively used for the heterologous production of other classes of terpenes, the synthesis of cyclic triterpenes, which inherently includes the two-step catalytic formation of the universal linear precursor 2,3-oxidosqualene, is still a major challenge. We thus explored the suitability of the metabolically versatile photosynthetic α-proteobacterium Rhodobacter capsulatus SB1003 and cyanobacterium Synechocystis sp. PCC 6803 as alternative hosts for biosynthesis of cyclic plant triterpenes. Therefore, 2,3-oxidosqualene production was implemented and subsequently combined with different cyclization reactions catalyzed by the representative oxidosqualene cyclases CAS1 (cycloartenol synthase), LUP1 (lupeol synthase), THAS1 (thalianol synthase) and MRN1 (marneral synthase) derived from model plant Arabidopsis thaliana. While successful accumulation of 2,3-oxidosqualene could be detected by LC-MS analysis in both hosts, cyclase expression resulted in differential production profiles. CAS1 catalyzed conversion to only cycloartenol, but expression of LUP1 yielded lupeol and a triterpenoid matching an oxidation product of lupeol, in both hosts. In contrast, THAS1 expression did not lead to cyclic product formation in either host, whereas MRN1-dependent production of marnerol and hydroxymarnerol was observed in Synechocystis but not in R. capsulatus. Our findings thus indicate that 2,3-oxidosqualene cyclization in heterologous phototrophic bacteria is basically feasible but efficient conversion depends on both the respective cyclase enzyme and individual host properties. Therefore, photosynthetic α-proteo- and cyanobacteria are promising alternative candidates for providing new bacterial access to the broad class of triterpenes for biotechnological applications.
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Affiliation(s)
- Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Dennis Dienst
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vera Wewer
- Cluster of Excellence on Plant Sciences (CEPLAS)
- MS Platform, Department of Biology, University of Cologne, Cologne, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Maximilian Dietsch
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sarah Kranz-Finger
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Biochemistry II, Department of Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vanessa Hüren
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sabine Metzger
- Cluster of Excellence on Plant Sciences (CEPLAS)
- MS Platform, Department of Biology, University of Cologne, Cologne, Germany
| | - Vlada B. Urlacher
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Biochemistry II, Department of Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tamara Gigolashvili
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Botanical Institute, University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Botanical Institute, University of Cologne, Cologne, Germany
| | - Ilka M. Axmann
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail: (IMA); (TD)
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
- * E-mail: (IMA); (TD)
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
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Bioconversion of farnesol and 1,4-dihydroxy-2-naphthoate to menaquinone by an immobilized whole-cell biocatalyst using engineered Elizabethkingia meningoseptica. World J Microbiol Biotechnol 2017; 33:215. [PMID: 29181599 DOI: 10.1007/s11274-017-2382-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
Menaquinone (MK) has important applications in the pharmaceutical and food industries. To increase the production rate (QP) of MK-4, we developed a straightforward biotransformation method for MK-4 synthesis directly from its precursors 1,4-dihydroxy-2-naphthoate (DHNA) and farnesol using whole cells of genetically engineered Elizabethkingia meningoseptica. Results showed that MK-4 can be produced directly from farnesol and DHNA using both free and immobilized FM-D198 cells. MK-4 yield peaked at 29.85 ± 0.36 mg/L in the organic phase and 24.08 ± 0.33 mg/g DCW after 12 h of bioconversion using free cells in a two-phase conversion system. MK-4 yield reached 26.34 ± 1.35 mg/L and 17.44 ± 1.05 mg/g DCW after 8 h using immobilized cells. Although this yield was lower than that using free cells, immobilized cells can be re-used for MK-4 production via repeated-batch culture. After ten batch cultures, efficient MK-4 production was maintained at a yield of more than 20 mg/L. After optimizing the catalysis system, the MK-4 yield reached 26.91 ± 1.27 mg/L using the immobilized cells and had molar conversion rates of 58.56 and 76.90% for DHNA and farnesol, respectively.
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From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution. Appl Microbiol Biotechnol 2017; 102:559-567. [PMID: 29181567 DOI: 10.1007/s00253-017-8568-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 01/17/2023]
Abstract
With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.
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Zhu Y, Lu W, Ye L, Chen Z, Hu W, Wang C, Chen J, Yu H. Enhanced synthesis of Coenzyme Q 10 by reducing the competitive production of carotenoids in Rhodobacter sphaeroides. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Qi Z, Dong D, Yang H, Xia X. Improving fermented quality of cider vinegar via rational nutrient feeding strategy. Food Chem 2017; 224:312-319. [DOI: 10.1016/j.foodchem.2016.12.078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/28/2022]
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30
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Zhu Y, Ye L, Chen Z, Hu W, Shi Y, Chen J, Wang C, Li Y, Li W, Yu H. Synergic regulation of redox potential and oxygen uptake to enhance production of coenzyme Q 10 in Rhodobacter sphaeroides. Enzyme Microb Technol 2017; 101:36-43. [PMID: 28433189 DOI: 10.1016/j.enzmictec.2017.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/10/2017] [Accepted: 03/12/2017] [Indexed: 11/24/2022]
Abstract
The physiological role of Coenzyme Q10 (CoQ10) as an electron carrier suggests its association with redox potential. Overexpression of glyceraldehyde-3-phosphate dehydrogenase type I (gapA-1) in Rhodobacter sphaeroides elevated the NADH/NAD+ ratio and meanwhile enhanced the CoQ10 content by 58%, but at the sacrifice of biomass. On the other hand, Vitreoscilla hemoglobin was heterologously expressed to enhance the oxygen uptake ability of the cells, leading to 127% improvement of biomass. Subsequent coexpression of gapA-1 and vgb resulted in a CoQ10 titer of 83.24mg/L, representing 71% improvement as compared to the control strain RspMCS. When gapA-1 and vgb genes were co-expressed in a previously created strain RspMQd [1], 163.5mg/L of CoQ10 was produced. Finally, 600mg/L of CoQ10 production was achieved in fed-batch fermentation. These results demonstrated the synergic effect of redox potential regulation and oxygen uptake improvement on enhancing CoQ10 production in R. sphaeroides.
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Affiliation(s)
- Yongqiang Zhu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Zhaofeng Chen
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Weijiang Hu
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Yanghui Shi
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Jianbo Chen
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Chenfei Wang
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Yong Li
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Weifeng Li
- Group of Bioengineering, ZheJiang NHU Company Limited, Shaoxing 312521, PR China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China.
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31
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Lee SQE, Tan TS, Kawamukai M, Chen ES. Cellular factories for coenzyme Q 10 production. Microb Cell Fact 2017; 16:39. [PMID: 28253886 PMCID: PMC5335738 DOI: 10.1186/s12934-017-0646-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/10/2017] [Indexed: 04/20/2023] Open
Abstract
Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role in the electron-transport chain, and its deficiency is associated with various neuropathies and muscular disorders. CoQ10 is the only lipid-soluble antioxidant found in humans, and for this, it is gaining popularity in the cosmetic and healthcare industries. To meet the growing demand for CoQ10, there has been considerable interest in ways to enhance its production, the most effective of which remains microbial fermentation. Previous attempts to increase CoQ10 production to an industrial scale have thus far conformed to the strategies used in typical metabolic engineering endeavors. However, the emergence of new tools in the expanding field of synthetic biology has provided a suite of possibilities that extend beyond the traditional modes of metabolic engineering. In this review, we cover the various strategies currently undertaken to upscale CoQ10 production, and discuss some of the potential novel areas for future research.
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Affiliation(s)
- Sean Qiu En Lee
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tsu Soo Tan
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, 690-8504, Japan
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
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32
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Chen H, Huang R, Zhang YHP. Systematic comparison of co-expression of multiple recombinant thermophilic enzymes in Escherichia coli BL21(DE3). Appl Microbiol Biotechnol 2017; 101:4481-4493. [PMID: 28251267 DOI: 10.1007/s00253-017-8206-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 01/08/2023]
Abstract
The precise control of multiple heterologous enzyme expression levels in one Escherichia coli strain is important for cascade biocatalysis, metabolic engineering, synthetic biology, natural product synthesis, and studies of complexed proteins. We systematically investigated the co-expression of up to four thermophilic enzymes (i.e., α-glucan phosphorylase (αGP), phosphoglucomutase (PGM), glucose 6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH)) in E. coli BL21(DE3) by adding T7 promoter or T7 terminator of each gene for multiple genes in tandem, changing gene alignment, and comparing one or two plasmid systems. It was found that the addition of T7 terminator after each gene was useful to decrease the influence of the upstream gene. The co-expression of the four enzymes in E. coli BL21(DE3) was demonstrated to generate two NADPH molecules from one glucose unit of maltodextrin, where NADPH was oxidized to convert xylose to xylitol. The best four-gene co-expression system was based on two plasmids (pET and pACYC) which harbored two genes. As a result, apparent enzymatic activities of the four enzymes were regulated to be at similar levels and the overall four-enzyme activity was the highest based on the formation of xylitol. This study provides useful information for the precise control of multi-enzyme-coordinated expression in E. coli BL21(DE3).
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Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
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33
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Qi F, Zou L, Jiang X, Cai S, Zhang M, Zhao X, Huang J. Integration of heterologous 4-hydroxybenzoic acid transport proteins in Rhodobacter sphaeroides for enhancement of coenzyme Q10production. RSC Adv 2017. [DOI: 10.1039/c7ra02346d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work provides a novel genetic engineering strategy that improves uptake of extracellular 4-hydroxybenzoic acid by heterologously expressing the membrane transport protein PcaK inR. sphaeroidesfor enhancement of CoQ10production.
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Affiliation(s)
- Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education
- College of Life Sciences
- Fujian Normal University
- Fuzhou 350117
- China
| | - Limei Zou
- Engineering Research Center of Industrial Microbiology of Ministry of Education
- College of Life Sciences
- Fujian Normal University
- Fuzhou 350117
- China
| | - Xianzhang Jiang
- Engineering Research Center of Industrial Microbiology of Ministry of Education
- College of Life Sciences
- Fujian Normal University
- Fuzhou 350117
- China
| | - Shaoli Cai
- Biomedical Research Center of South China
- Fujian Normal University
- Fuzhou 350117
- China
| | - Mingliang Zhang
- Engineering Research Center of Industrial Microbiology of Ministry of Education
- College of Life Sciences
- Fujian Normal University
- Fuzhou 350117
- China
| | - Xuebing Zhao
- Institute of Applied Chemistry
- Department of Chemical Engineering
- Tsinghua University
- Beijing 100084
- China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education
- College of Life Sciences
- Fujian Normal University
- Fuzhou 350117
- China
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34
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Wang F, Lv X, Xie W, Zhou P, Zhu Y, Yao Z, Yang C, Yang X, Ye L, Yu H. Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae. Metab Eng 2017; 39:257-266. [DOI: 10.1016/j.ymben.2016.12.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 12/14/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022]
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35
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Xu W, Yuan J, Yang S, Ching CB, Liu J. Programming Saposin-Mediated Compensatory Metabolic Sinks for Enhanced Ubiquinone Production. ACS Synth Biol 2016; 5:1404-1411. [PMID: 27389347 DOI: 10.1021/acssynbio.6b00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Microbial synthesis of ubiquinone by fermentation processes has been emerging in recent years. However, as ubiquinone is a primary metabolite that is tightly regulated by the host central metabolism, tweaking the individual pathway components could only result in a marginal improvement on the ubiquinone production. Given that ubiquinone is stored in the lipid bilayer, we hypothesized that introducing additional metabolic sink for storing ubiquinone might improve the CoQ10 production. As human lipid binding/transfer protein saposin B (hSapB) was reported to extract ubiquinone from the lipid bilayer and form the water-soluble complex, hSapB was chosen to build a compensatory metabolic sink for the ubiquinone storage. As a proof-of-concept, hSapB-mediated metabolic sink systems were devised and systematically investigated in the model organism of Escherichia coli. The hSapB-mediated periplasmic sink resulted in more than 200% improvement of CoQ8 over the wild type strain. Further investigation revealed that hSapB-mediated sink systems could also improve the CoQ10 production in a CoQ10-hyperproducing E. coli strain obtained by a modular pathway rewiring approach. As the design principles and the engineering strategies reported here are generalizable to other microbes, compensatory sink systems will be a method of significant interest to the synthetic biology community.
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Affiliation(s)
- Wen Xu
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
| | - Jifeng Yuan
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585 Singapore
- Temasek
Laboratories, National University of Singapore, T-Lab Building 5A, 117411 Singapore
| | - Shuiyun Yang
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
| | - Chi-Bun Ching
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585 Singapore
| | - Jiankang Liu
- School
of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
- Key
Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, Shannxi, China
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36
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Jung J, Lim JH, Kim SY, Im DK, Seok JY, Lee SJV, Oh MK, Jung GY. Precise precursor rebalancing for isoprenoids production by fine control of gapA expression in Escherichia coli. Metab Eng 2016; 38:401-408. [DOI: 10.1016/j.ymben.2016.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 01/10/2023]
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37
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Guan Z, Xue D, Abdallah II, Dijkshoorn L, Setroikromo R, Lv G, Quax WJ. Metabolic engineering of Bacillus subtilis for terpenoid production. Appl Microbiol Biotechnol 2015; 99:9395-406. [PMID: 26373726 PMCID: PMC4628092 DOI: 10.1007/s00253-015-6950-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 11/04/2022]
Abstract
Terpenoids are the largest group of small-molecule natural products, with more than 60,000 compounds made from isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). As the most diverse group of small-molecule natural products, terpenoids play an important role in the pharmaceutical, food, and cosmetic industries. For decades, Escherichia coli (E. coli) and Saccharomyces cerevisiae (S. cerevisiae) were extensively studied to biosynthesize terpenoids, because they are both fully amenable to genetic modifications and have vast molecular resources. On the other hand, our literature survey (20 years) revealed that terpenoids are naturally more widespread in Bacillales. In the mid-1990s, an inherent methylerythritol phosphate (MEP) pathway was discovered in Bacillus subtilis (B. subtilis). Since B. subtilis is a generally recognized as safe (GRAS) organism and has long been used for the industrial production of proteins, attempts to biosynthesize terpenoids in this bacterium have aroused much interest in the scientific community. This review discusses metabolic engineering of B. subtilis for terpenoid production, and encountered challenges will be discussed. We will summarize some major advances and outline future directions for exploiting the potential of B. subtilis as a desired "cell factory" to produce terpenoids.
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Affiliation(s)
- Zheng Guan
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dan Xue
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Ingy I Abdallah
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Linda Dijkshoorn
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Rita Setroikromo
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands
| | - Guiyuan Lv
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Wim J Quax
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Building 3215, room 917, 9713 AV, Groningen, The Netherlands.
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38
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Quantitative characterization of gene regulation by Rho dependent transcription termination. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:940-54. [DOI: 10.1016/j.bbagrm.2015.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/03/2015] [Accepted: 05/07/2015] [Indexed: 11/23/2022]
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39
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Affiliation(s)
| | - Hal S. Alper
- McKetta Department of Chemical Engineering and
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712;
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40
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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: 15.2] [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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41
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Moriyama D, Hosono K, Fujii M, Washida M, Nanba H, Kaino T, Kawamukai M. Production of CoQ10 in fission yeast by expression of genes responsible for CoQ10 biosynthesis. Biosci Biotechnol Biochem 2015; 79:1026-33. [DOI: 10.1080/09168451.2015.1006573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Coenzyme Q10 (CoQ10) is essential for energy production and has become a popular supplement in recent years. In this study, CoQ10 productivity was improved in the fission yeast Schizosaccharomyces pombe. Ten CoQ biosynthetic genes were cloned and overexpressed in S. pombe. Strains expressing individual CoQ biosynthetic genes did not produce higher than a 10% increase in CoQ10 production. In addition, simultaneous expression of all ten coq genes did not result in yield improvements. Genes responsible for the biosynthesis of p-hydroxybenzoate and decaprenyl diphosphate, both of which are CoQ biosynthesis precursors, were also overexpressed. CoQ10 production was increased by overexpression of Eco_ubiC (encoding chorismate lyase), Eco_aroFFBR (encoding 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase), or Sce_thmgr1 (encoding truncated HMG-CoA reductase). Furthermore, simultaneous expression of these precursor genes resulted in two fold increases in CoQ10 production.
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Affiliation(s)
- Daisuke Moriyama
- QOL division, Kaneka Corporation, Takasago, Japan
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, Matsue, Japan
| | - Kouji Hosono
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, Matsue, Japan
| | - Makoto Fujii
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, Matsue, Japan
| | | | | | - Tomohiro Kaino
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, Matsue, Japan
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Department of Life Science and Biotechnology, Shimane University, Matsue, Japan
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Lu W, Ye L, Lv X, Xie W, Gu J, Chen Z, Zhu Y, Li A, Yu H. Identification and elimination of metabolic bottlenecks in the quinone modification pathway for enhanced coenzyme Q10 production in Rhodobacter sphaeroides. Metab Eng 2015; 29:208-216. [DOI: 10.1016/j.ymben.2015.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/09/2015] [Accepted: 03/18/2015] [Indexed: 01/09/2023]
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43
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Cheng D, Wang R, Prather KJ, Chow KL, Hsing IM. Tackling codon usage bias for heterologous expression in Rhodobacter sphaeroides by supplementation of rare tRNAs. Enzyme Microb Technol 2015; 72:25-34. [DOI: 10.1016/j.enzmictec.2015.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/05/2015] [Accepted: 02/07/2015] [Indexed: 10/24/2022]
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44
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Ye L, Xie W, Zhou P, Yu H. Biotechnological Production of Astaxanthin through Metabolic Engineering of Yeasts. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Wang G, Li Q, Xu D, Cui M, Sun X, Xu Y, Wang W. Construction of a host-independent T7 expression system with small RNA regulation. J Biotechnol 2014; 189:72-5. [DOI: 10.1016/j.jbiotec.2014.08.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/22/2014] [Accepted: 08/26/2014] [Indexed: 01/15/2023]
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46
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de Dieu Ndikubwimana J, Lee BH. Enhanced production techniques, properties and uses of coenzyme Q10. Biotechnol Lett 2014; 36:1917-26. [DOI: 10.1007/s10529-014-1587-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/11/2014] [Indexed: 12/22/2022]
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