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Hao S, Xu M, Li L, Wang L, Su Z. Enhancing isoprene production by supplementing mevalonate pathway expressed in E. coli with immobilized enzymes. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03093-2. [PMID: 39333406 DOI: 10.1007/s00449-024-03093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024]
Abstract
Isoprene is an important component in rubber production, which can be produced using the E. coli mevalonic acid (MVA) pathway, and this method has the advantage of green environmental protection and sustainable. However, due to the excessive accumulation of intermediates, the growth of cells was inhibited and the enzyme activity decreased gradually, so it was difficult to increase the yield of isoprene. The immobilized enzyme has the characteristics of high stability and strong reusability, so in this study, the immobilized enzyme was added to the fermentation process of isoprene production by mevalonate metabolizing bacteria (PT-P), to explore the effect on isoprene synthesis. Under the optimum conditions, compared with PT-P fermentation alone, the enzyme catalyzes the conversion of MVA with an efficiency of up to 50.86%, and the yield of isoprene increased by about 30%, reaching 234.47 mg/L.
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Affiliation(s)
- Shenghu Hao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, Shandong, People's Republic of China
| | - Mei Xu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, Shandong, People's Republic of China
| | - Lu Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, Shandong, People's Republic of China
| | - Luyao Wang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, Shandong, People's Republic of China
| | - Zhongliang Su
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, Shandong, People's Republic of China.
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2
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Wu X, Yang Y, Wang M, Shao C, Morillas JIV, Yuan F, Liu J, Zhang H. Improving coriander yield and quality with a beneficial bacterium. MOLECULAR HORTICULTURE 2024; 4:8. [PMID: 38419111 PMCID: PMC10903023 DOI: 10.1186/s43897-024-00087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Xiaoxuan Wu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Miao Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuyang Shao
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Juan I V Morillas
- Instituto de Tecnologia Química e Biológica (ITQB), Oeiras, Lisbon, Portugal
| | - Fengtong Yuan
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang, 330224, China
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang, 330200, China
| | - Jie Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
- Nanchang Institute of Industrial Innovation, Chinese Academy of Sciences, Nanchang, 330224, China.
- Jiangxi Center for Innovation and Incubation of Industrial Technologies, Chinese Academy of Sciences, Nanchang, 330200, China.
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3
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Bhat S, Banerjee A, Alagesan S. AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS OMEGA 2023; 8:26806-26815. [PMID: 37546622 PMCID: PMC10399174 DOI: 10.1021/acsomega.3c01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Isoprene is a valuable platform chemical, which is produced by engineered microorganisms, albeit in low quantities. The amount of isoprene produced is usually measured by gas chromatography, which can be time-consuming and expensive. Alternatively, biosensors have evolved as a powerful tool for real-time high-throughput screening and monitoring of product synthesis. The AraC-pBAD-inducible system has been widely studied, evolved, and engineered to develop biosensors for small molecules. In our preliminary studies, the AraC-pBAD system was mildly induced at higher isoprene concentrations when arabinose was also available. Hence, in the present study, we designed and constructed a synthetic biosensor based on the AraC-pBAD system, wherein the ligand-binding domain of AraC was replaced with IsoA. On introducing this chimeric AraC-IsoA (AcIa) transcription factor with the native PBAD promoter system regulating rfp gene expression, fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were further enhanced by removing operator sequences and by substituting the native promoter (PAraC) with the strong tac promoter (Ptac). The chimeric sensor did not work in AraC knockout strains; however, functionality was restored by reintroducing AraC. Hence, AraC is essential for the functioning of our biosensor, while AcIa provides enhanced sensitivity and specificity for isoprene. However, insights into how AraC-AcIa interacts and the possible working mechanism remain to be explored. This study provides a prototype for developing chimeric AraC-based biosensors with proteins devoid of known dimerizing domains and opens a new avenue for further study and exploration.
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Nirati Y, Purushotham N, Alagesan S. Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady state 13C-MFA. PHOTOSYNTHESIS RESEARCH 2022; 154:195-206. [PMID: 36070060 DOI: 10.1007/s11120-022-00957-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria are photosynthetic bacteria, widely studied for the conversion of atmospheric carbon dioxide to useful platform chemicals. Isoprene is one such industrially important chemical, primarily used for production of synthetic rubber and biofuels. Synechocystis sp. PCC 6803, a genetically amenable cyanobacterium, produces isoprene on heterologous expression of isoprene synthase gene, albeit in very low quantities. Rationalized metabolic engineering to re-route the carbon flux for enhanced isoprene production requires in-dept knowledge of the metabolic flux distribution in the cell. Hence, in the present study, we undertook steady state 13C-metabolic flux analysis of glucose-tolerant wild-type (GTN) and isoprene-producing recombinant (ISP) Synechocystis sp. to understand and compare the carbon flux distribution in the two strains. The R-values for amino acids, flux analysis predictions and gene expression profiles emphasized predominance of Calvin cycle and glycogen metabolism in GTN. Alternatively, flux analysis predicted higher activity of the anaplerotic pathway through phosphoenolpyruvate carboxylase and malic enzyme in ISP. The striking difference in the Calvin cycle, glycogen metabolism and anaplerotic pathway activity in GTN and ISP suggested a possible role of energy molecules (ATP and NADPH) in regulating the carbon flux distribution in GTN and ISP. This claim was further supported by the transcript level of selected genes of the electron transport chain. This study provides the first quantitative insight into the carbon flux distribution of isoprene-producing cyanobacterium, information critical for developing Synechocystis sp. as a single cell factory for isoprenoid/terpenoid production.
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Affiliation(s)
- Yasha Nirati
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
| | - Nidhish Purushotham
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India
- Dayananda Sagar University, Bengaluru, India
| | - Swathi Alagesan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560100, India.
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5
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Rinaldi MA, Tait S, Toogood HS, Scrutton NS. Bioproduction of Linalool From Paper Mill Waste. Front Bioeng Biotechnol 2022; 10:892896. [PMID: 35711639 PMCID: PMC9195575 DOI: 10.3389/fbioe.2022.892896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
A key challenge in chemicals biomanufacturing is the maintenance of stable, highly productive microbial strains to enable cost-effective fermentation at scale. A “cookie-cutter” approach to microbial engineering is often used to optimize host stability and productivity. This can involve identifying potential limitations in strain characteristics followed by attempts to systematically optimize production strains by targeted engineering. Such targeted approaches however do not always lead to the desired traits. Here, we demonstrate both ‘hit and miss’ outcomes of targeted approaches in attempts to generate a stable Escherichia coli strain for the bioproduction of the monoterpenoid linalool, a fragrance molecule of industrial interest. First, we stabilized linalool production strains by eliminating repetitive sequences responsible for excision of pathway components in plasmid constructs that encode the pathway for linalool production. These optimized pathway constructs were then integrated within the genome of E. coli in three parts to eliminate a need for antibiotics to maintain linalool production. Additional strategies were also employed including: reduction in cytotoxicity of linalool by adaptive laboratory evolution and modification or homologous gene replacement of key bottleneck enzymes GPPS/LinS. Our study highlights that a major factor influencing linalool titres in E. coli is the stability of the genetic construct against excision or similar recombination events. Other factors, such as decreasing linalool cytotoxicity and changing pathway genes, did not lead to improvements in the stability or titres obtained. With the objective of reducing fermentation costs at scale, the use of minimal base medium containing paper mill wastewater secondary paper fiber as sole carbon source was also investigated. This involved simultaneous saccharification and fermentation using either supplemental cellulase blends or by co-expressing secretable cellulases in E. coli containing the stabilized linalool production pathway. Combined, this study has demonstrated a stable method for linalool production using an abundant and low-cost feedstock and improved production strains, providing an important proof-of-concept for chemicals production from paper mill waste streams. For scaled production, optimization will be required, using more holistic approaches that involve further rounds of microbial engineering and fermentation process development.
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Affiliation(s)
- Mauro A Rinaldi
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Shirley Tait
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Helen S Toogood
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester, United Kingdom.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,C3 Biotechnologies (Maritime and Aerospace) Ltd, Lancaster, United Kingdom
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Ezediokpu MN, Krause K, Kunert M, Hoffmeister D, Boland W, Kothe E. Ectomycorrhizal Influence on the Dynamics of Sesquiterpene Release by Tricholoma vaccinum. J Fungi (Basel) 2022; 8:555. [PMID: 35736037 PMCID: PMC9224709 DOI: 10.3390/jof8060555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Tricholoma vaccinum is an ectomycorrhizal basidiomycete with high host specificity. The slow-growing fungus is able to produce twenty sesquiterpenes, including α-barbatene, sativene, isocaryophyllene, α-cuprenene, β-cedrene, ß-copaene, 4-epi-α-acoradiene, and chamigrene in axenic culture. For the three major compounds, Δ6-protoilludene, β-barbatene, and an unidentified oxygenated sesquiterpene (m/z 218.18), changed production during co-cultivation with the ectomycorrhizal partner tree, Picea abies, could be shown with distinct dynamics. During the mycorrhizal growth of T. vaccinum-P. abies, Δ6-protoilludene and the oxygenated sesquiterpene appeared at similar times, which warranted further studies of potential biosynthesis genes. In silico analyses identified a putative protoilludene synthesis gene, pie1, as being up-regulated in the mycorrhizal stage, in addition to the previously identified, co-regulated geosmin synthase, ges1. We therefore hypothesize that the sesquiterpene synthase pie1 has an important role during mycorrhization, through Δ6-protoilludene and/or its accompanied oxygenated sesquiterpene production.
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Affiliation(s)
- Marycolette Ndidi Ezediokpu
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Katrin Krause
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
| | - Maritta Kunert
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Hans Knöll Institute, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany;
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany; (M.K.); (W.B.)
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; (M.N.E.); (K.K.)
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Ábrego-Gacía A, Poggi-Varaldo HM, Robles-González V, Ponce-Noyola T, Calva-Calva G, Ríos-Leal E, Estrada-Bárcenas D, Mendoza-Vargas A. Lovastatin as a supplement to mitigate rumen methanogenesis: an overview. J Anim Sci Biotechnol 2021; 12:123. [PMID: 34911584 PMCID: PMC8675506 DOI: 10.1186/s40104-021-00641-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/03/2021] [Indexed: 11/23/2022] Open
Abstract
Methane from enteric fermentation is the gas with the greatest environmental impact emitted by ruminants. Lovastatin (Lv) addition to feedstocks could be a strategy to mitigate rumen methane emissions via decreasing the population of methanogenic archaea (MA). Thus, this paper provides the first overview of the effects of Lv supplementation, focusing on the inhibition of methane production, rumen microbiota, and ruminal fermentation. Results indicated that Lv treatment had a strong anti-methanogenic effect on pure strains of MA. However, there are uncertainties from in vitro rumen fermentation trials with complex substrates and rumen inoculum. Solid-state fermentation (SSF) has emerged as a cost-effective option to produce Lv. In this way, SSF of agricultural residues as an Lv-carrier supplement in sheep and goats demonstrated a consistent decrease in ruminal methane emissions. The experimental evidence for in vitro conditions showed that Lv did not affect the volatile fatty acids (VFA). However, in vivo experiments demonstrated that the production of VFA was decreased. Lv did not negatively affect the digestibility of dry matter during in vitro and in vivo methods, and there is even evidence that it can induce an increase in digestibility. Regarding the rumen microbiota, populations of MA were reduced, and no differences were detected in alpha and beta diversity associated with Lv treatment. However, some changes in the relative abundance of the microbiota were induced. Further studies are recommended on: (i) Lv biodegradation products and stability, as well as its adsorption onto the solid matter in the rumen, to gain more insight on the “available” or effective Lv concentration; and (ii) to determine whether the effect of Lv on ruminal fermentation also depends on the feed composition and different ruminants.
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Affiliation(s)
- Amaury Ábrego-Gacía
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Héctor M Poggi-Varaldo
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico. .,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.
| | - Vania Robles-González
- Instituto de Hidrología, Universidad Tecnológica de la Mixteca, Oaxaca, 69000, Huajuapan de León, Mexico
| | - Teresa Ponce-Noyola
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Graciano Calva-Calva
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Elvira Ríos-Leal
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Daniel Estrada-Bárcenas
- National Collection of Microbial and Cellular Cultures, CINVESTAV-IPN, P.O.Box17-740, 07000, Mexico City, Mexico
| | - Alfredo Mendoza-Vargas
- Unidad de Secuenciación e Identificación de Polimorfismos, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
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8
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Lin J, Yao Z, Lyu X, Ye L, Yu H. Development of a dual temperature control system for isoprene biosynthesis in Saccharomyces cerevisiae. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Cui S, Lv X, Xu X, Chen T, Zhang H, Liu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Multilayer Genetic Circuits for Dynamic Regulation of Metabolic Pathways. ACS Synth Biol 2021; 10:1587-1597. [PMID: 34213900 DOI: 10.1021/acssynbio.1c00073] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The dynamic regulation of metabolic pathways is based on changes in external signals and endogenous changes in gene expression levels and has extensive applications in the field of synthetic biology and metabolic engineering. However, achieving dynamic control is not trivial, and dynamic control is difficult to obtain using simple, single-level, control strategies because they are often affected by native regulatory networks. Therefore, synthetic biologists usually apply the concept of logic gates to build more complex and multilayer genetic circuits that can process various signals and direct the metabolic flux toward the synthesis of the molecules of interest. In this review, we first summarize the applications of dynamic regulatory systems and genetic circuits and then discuss how to design multilayer genetic circuits to achieve the optimal control of metabolic fluxes in living cells.
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Affiliation(s)
- Shixiu Cui
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Taichi Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai’an 271000, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Wang Z, Zhang R, Yang Q, Zhang J, Zhao Y, Zheng Y, Yang J. Recent advances in the biosynthesis of isoprenoids in engineered Saccharomyces cerevisiae. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:1-35. [PMID: 33934850 DOI: 10.1016/bs.aambs.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Isoprenoids, as the largest group of chemicals in the domains of life, constitute more than 50,000 members. These compounds consist of different numbers of isoprene units (C5H8), by which they are typically classified into hemiterpenoids (C5), monoterpenoids (C10), sesquiterpenoids (C15), diterpenoids (C20), triterpenoids (C30), and tetraterpenoids (C40). In recent years, isoprenoids have been employed as food additives, in the pharmaceutical industry, as advanced biofuels, and so on. To realize the sufficient and efficient production of valuable isoprenoids on an industrial scale, fermentation using engineered microorganisms is a promising strategy compared to traditional plant extraction and chemical synthesis. Due to the advantages of mature genetic manipulation, robustness and applicability to industrial bioprocesses, Saccharomyces cerevisiae has become an attractive microbial host for biochemical production, including that of various isoprenoids. In this review, we summarized the advances in the biosynthesis of isoprenoids in engineered S. cerevisiae over several decades, including synthetic pathway engineering, microbial host engineering, and central carbon pathway engineering. Furthermore, the challenges and corresponding strategies towards improving isoprenoid production in engineered S. cerevisiae were also summarized. Finally, suggestions and directions for isoprenoid production in engineered S. cerevisiae in the future are discussed.
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Affiliation(s)
- Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qun Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jintian Zhang
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Youxi Zhao
- College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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11
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Xue L, He Z, Bi X, Xu W, Wei T, Wu S, Hu S. Transcriptomic profiling reveals MEP pathway contributing to ginsenoside biosynthesis in Panax ginseng. BMC Genomics 2019; 20:383. [PMID: 31101014 PMCID: PMC6524269 DOI: 10.1186/s12864-019-5718-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 04/18/2019] [Indexed: 11/10/2022] Open
Abstract
Background Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently. But their gene expression characteristics are still under reveal in P. ginseng. With the development of the high-throughput next generation sequencing (NGS) technologies, we have opportunities to discover more about the complex ginsenoside biosynthesis pathways in P. ginseng. Results We carried out deep RNA sequencing and comprehensive analyses on the ginseng root samples of 1–5 years old and five different tissues of 5 years old ginseng plants. The de novo assembly totally generated 48,165 unigenes, including 380 genes related to ginsenoside biosynthesis and all the genes encoding the enzymes of the MEP pathway and the MVA pathway. We further illustrated the gene expression profiles related to ginsenoside biosynthesis among 1–5 year-old roots and different tissues of 5 year-old ginseng plants. Particularly for the first time, we revealed that the gene transcript abundances of the MEP pathway were similar to those of the MVA pathway in ginseng roots but higher in ginseng leaves. The IspD was predicated to be the rate-limiting enzyme in the MEP pathway through both co-expression network and gene expression profile analyses. Conclusions At the transcriptional level, the MEP pathway has similar contribution to ginsenoside biosynthesis in ginseng roots, but much higher in ginseng leaves, compared with the MVA pathway. The IspD might be the key enzyme for ginsenoside generation through the MEP pathway. These results provide new information for further synthetic biology study on ginsenoside metabolic regulation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5718-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Xue
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xiaochun Bi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wei Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Ting Wei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Shuangxiu Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China.
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Functional Genetic Elements for Controlling Gene Expression in Cupriavidus necator H16. Appl Environ Microbiol 2018; 84:AEM.00878-18. [PMID: 30030234 PMCID: PMC6146998 DOI: 10.1128/aem.00878-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
A robust and predictable control of gene expression plays an important role in synthetic biology and biotechnology applications. Development and quantitative evaluation of functional genetic elements, such as constitutive and inducible promoters as well as ribosome binding sites (RBSs), are required. In this study, we designed, built, and tested promoters and RBSs for controlling gene expression in the model lithoautotroph Cupriavidus necator H16. A series of variable-strength, insulated, constitutive promoters exhibiting predictable activity within a >700-fold dynamic range was compared to the native P phaC , with the majority of promoters displaying up to a 9-fold higher activity. Positively (AraC/P araBAD -l-arabinose and RhaRS/P rhaBAD -l-rhamnose) and negatively (AcuR/P acuRI -acrylate and CymR/P cmt -cumate) regulated inducible systems were evaluated. By supplying different concentrations of inducers, a >1,000-fold range of gene expression levels was achieved. Application of inducible systems for controlling expression of the isoprene synthase gene ispS led to isoprene yields that exhibited a significant correlation to the reporter protein synthesis levels. The impact of designed RBSs and other genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was also evaluated. A second-order polynomial relationship was observed between the RBS activities and isoprene yields. This report presents quantitative data on regulatory genetic elements and expands the genetic toolbox of C. necatorIMPORTANCE This report provides tools for robust and predictable control of gene expression in the model lithoautotroph C. necator H16. To address a current need, we designed, built, and tested promoters and RBSs for controlling gene expression in C. necator H16. To answer a question on how existing and newly developed inducible systems compare, two positively (AraC/P araBAD -l-arabinose and RhaRS/P rhaBAD -l-rhamnose) and two negatively (AcuR/P acuRI -acrylate and CymR/P cmt -cumate) regulated inducible systems were quantitatively evaluated and their induction kinetics analyzed. To establish if gene expression can be further improved, the effect of genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was evaluated. Using isoprene production as an example, the study investigated if and to what extent chemical compound yield correlates to the level of gene expression of product-synthesizing enzyme.
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Schempp FM, Drummond L, Buchhaupt M, Schrader J. Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2247-2258. [PMID: 28418659 DOI: 10.1021/acs.jafc.7b00473] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.
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Affiliation(s)
- Florence M Schempp
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Laura Drummond
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
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Synthesis of Heterologous Mevalonic Acid Pathway Enzymes in Clostridium ljungdahlii for the Conversion of Fructose and of Syngas to Mevalonate and Isoprene. Appl Environ Microbiol 2017; 84:AEM.01723-17. [PMID: 29054870 PMCID: PMC5734045 DOI: 10.1128/aem.01723-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/15/2017] [Indexed: 11/30/2022] Open
Abstract
There is a growing interest in the use of microbial fermentation for the generation of high-demand, high-purity chemicals using cheap feedstocks in an environmentally friendly manner. One example explored here is the production of isoprene (C5H8), a hemiterpene, which is primarily polymerized to polyisoprene in synthetic rubber in tires but which can also be converted to C10 and C15 biofuels. The strictly anaerobic, acetogenic bacterium Clostridium ljungdahlii, used in all of the work described here, is capable of glycolysis using the Embden-Meyerhof-Parnas pathway and of carbon fixation using the Wood-Ljungdahl pathway. Clostridium-Escherichia coli shuttle plasmids, each bearing either 2 or 3 different heterologous genes of the eukaryotic mevalonic acid (MVA) pathway or eukaryotic isopentenyl pyrophosphate isomerase (Idi) and isoprene synthase (IspS), were constructed and electroporated into C. ljungdahlii. These plasmids, one or two of which were introduced into the host cells, enabled the synthesis of mevalonate and of isoprene from fructose and from syngas (H2, CO2, and CO) and the conversion of mevalonate to isoprene. All of the heterologous enzymes of the MVA pathway, as well as Idi and IspS, were shown to be synthesized at high levels in C. ljungdahlii, as demonstrated by Western blotting, and were enzymatically active, as demonstrated by in vivo product synthesis. The quantities of mevalonate and isoprene produced here are far below what would be required of a commercial production strain. However, proposals are made that could enable a substantial increase in the mass yield of product formation. IMPORTANCE This study demonstrates the ability to synthesize a heterologous metabolic pathway in C. ljungdahlii, an organism capable of metabolizing either simple sugars or syngas or both together (mixotrophy). Syngas, an inexpensive source of carbon and reducing equivalents, is produced as a major component of some industrial waste gas, and it can be generated by gasification of cellulosic biowaste and of municipal solid waste. Its conversion to useful products therefore offers potential cost and environmental benefits. The ability of C. ljungdahlii to grow mixotrophically also enables the recapture, should there be sufficient reducing equivalents available, of the CO2 released upon glycolysis, potentially increasing the mass yield of product formation. Isoprene is the simplest of the terpenoids, and so the demonstration of its production is a first step toward the synthesis of higher-value products of the terpenoid pathway.
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Gomaa L, Loscar ME, Zein HS, Abdel-Ghaffar N, Abdelhadi AA, Abdelaal AS, Abdallah NA. Boosting isoprene production via heterologous expression of the Kudzu isoprene synthase gene (kIspS) into Bacillus spp. cell factory. AMB Express 2017; 7:161. [PMID: 28791618 PMCID: PMC5548705 DOI: 10.1186/s13568-017-0461-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/23/2017] [Indexed: 11/17/2022] Open
Abstract
Isoprene represents a key building block for the production of valuable materials such as latex, synthetic rubber or pharmaceutical precursors and serves as basis for advanced biofuel production. To enhance the production of the volatile natural hydrocarbon isoprene, released by plants, animals and bacteria, the Kudzu isoprene synthase (kIspS) gene has been heterologously expressed in Bacillus subtilis DSM 402 and Bacillus licheniformis DSM 13 using the pHT01 vector. As control, the heterologous expression of KIspS in E. coli BL21 (DE3) with the pET28b vector was used. Isoprene production was analyzed using Gas Chromatography Flame Ionization Detector. The highest isoprene production was observed by recombinant B. subtilis harboring the pHT01-kIspS plasmid which produced 1434.3 μg/L (1275 µg/L/OD) isoprene. This is threefold higher than the wild type which produced 388 μg/L (370 μg/L/OD) isoprene, when both incubated at 30 °C for 48 h and induced with 0.1 mM IPTG. Additionally, recombinant B. subtilis produced fivefold higher than the recombinant B. licheniformis, which produced 437.2 μg/L (249 μg/L/OD) isoprene when incubated at 37 °C for 48 h induced with 0.1 mM IPTG. This is the first report of optimized isoprene production in B. licheniformis. However, recombinant B. licheniformis showed less isoprene production. Therefore, recombinant B. subtilis is considered as a versatile host for heterologous production of isoprene.
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Junne S, Kabisch J. Fueling the future with biomass: Processes and pathways for a sustainable supply of hydrocarbon fuels and biogas. Eng Life Sci 2016; 17:14-26. [PMID: 32624725 DOI: 10.1002/elsc.201600112] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/08/2016] [Accepted: 08/23/2016] [Indexed: 12/11/2022] Open
Abstract
Global economic growth, wealth and security rely upon the availability of cheap, mostly fossil-derived energy and chemical compounds. The replacement by sustainable resources is widely discussed. However, the current state of biotechnological processes usually restricts them to be used as a true alternative in terms of economic feasibility and even sustainability. Among the rare examples of bioprocesses applied for the energetic use of biomass are biogas and bioethanol production. Usually, these processes lack in efficiency and they cannot be operated without the support of legislation. Although they represent a first step towards a greater share of bio-based processes for energy provision, there is no doubt that tremendous improvements in strain and process development, feedstock and process flexibility as well as in the integration of these processes into broader supply and production networks, in this review called smart bioproduction grids, are required to make them economically attractive, robust enough, and wider acceptance by society. All this requires an interdisciplinary approach, which includes the use of residues in closed carbon cycles and issues concerning the process safety. This short review aims to depict some of the promising strategies to achieve an improved process performance as a basis for future application.
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Affiliation(s)
- Stefan Junne
- Department of Biotechnology Chair of Bioprocess Engineering Technische Universität Berlin Berlin Germany
| | - Johannes Kabisch
- Institute of Biochemistry Ernst-Moritz-Arndt University Greifswald Greifswald Germany
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