1
|
Yang Y, Zou Y, Chen X, Sun H, Hua X, Johnston L, Zeng X, Qiao S, Ye C. Metabolic engineering of Escherichia coli for the production of 5-aminolevulinic acid based on combined metabolic pathway modification and reporter-guided mutant selection (RGMS). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:82. [PMID: 38886801 PMCID: PMC11184883 DOI: 10.1186/s13068-024-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields such as medicine, nutrition and agriculture. Metabolic engineering is an efficient strategy to improve microbial production of 5-ALA. RESULTS In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement. A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via both C4 and C5 pathways was applied herein. The expression of a modified hemARS gene and rational metabolic engineering by gene knockouts significantly improved ALA production from 765.9 to 2056.1 mg/L. Next, we tried to improve ALA production by RGMS-directed evolution of eamA gene. After RGMS, the ALA yield of strain A2-ASK reached 2471.3 mg/L in flask. Then, we aimed to improve the oxidation resistance of cells by overexpressing sodB and katE genes and ALA yield reached 2703.8 mg/L. A final attempt is to replace original promoter of hemB gene in genome with a weaker one to decrease its expression. After 24 h cultivation, a high ALA yield of 19.02 g/L was achieved by 108-ASK in a 5 L fermenter. CONCLUSIONS These results suggested that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification and optimization of gene expression.
Collapse
Affiliation(s)
- Yuting Yang
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Yuhong Zou
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Haidong Sun
- National Feed Engineering Technology Research Centre, Beijing, 100193, China
| | - Xia Hua
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Lee Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, 56267, USA
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Changchuan Ye
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.
- Department of Animal Science, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
2
|
Wu T, Jiang J, Zhang H, Liu J, Ruan H. Transcending membrane barriers: advances in membrane engineering to enhance the production capacity of microbial cell factories. Microb Cell Fact 2024; 23:154. [PMID: 38796463 PMCID: PMC11128114 DOI: 10.1186/s12934-024-02436-8] [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: 03/15/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.
Collapse
Affiliation(s)
- Tao Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| | - Jingjing Jiang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Hongyang Zhang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Jiazhi Liu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| |
Collapse
|
3
|
Raghavan I, Juman R, Wang ZQ. The non-mevalonate pathway requires a delicate balance of intermediates to maximize terpene production. Appl Microbiol Biotechnol 2024; 108:245. [PMID: 38421431 PMCID: PMC10904526 DOI: 10.1007/s00253-024-13077-7] [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: 05/31/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Terpenes are valuable industrial chemicals whose demands are increasingly being met by bioengineering microbes such as E. coli. Although the bioengineering efforts commonly involve installing the mevalonate (MVA) pathway in E. coli for terpene production, the less studied methylerythritol phosphate (MEP) pathway is a more attractive target due to its higher energy efficiency and theoretical yield, despite its tight regulation. In this study, we integrated an additional copy of the entire MEP pathway into the E. coli genome for stable, marker-free terpene production. The genomically integrated strain produced more monoterpene geraniol than a plasmid-based system. The pathway genes' transcription was modulated using different promoters to produce geraniol as the reporter of the pathway flux. Pathway genes, including dxs, idi, and ispDF, expressed from a medium-strength promoter, led to the highest geraniol production. Quantifying the MEP pathway intermediates revealed that the highest geraniol producers had high levels of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), but moderate levels of the pathway intermediates upstream of these two building blocks. A principal component analysis demonstrated that 1-deoxy-D-xylulose 5-phosphate (DXP), the product of the first enzyme of the pathway, was critical for determining the geraniol titer, whereas MEP, the product of DXP reductoisomerase (Dxr or IspC), was the least essential. This work shows that an intricate balance of the MEP pathway intermediates determines the terpene yield in engineered E. coli. The genetically stable and intermediate-balanced strains created in this study will serve as a chassis for producing various terpenes. KEY POINTS: • Genome-integrated MEP pathway afforded higher strain stability • Genome-integrated MEP pathway produced more terpene than the plasmid-based system • High monoterpene production requires a fine balance of MEP pathway intermediates.
Collapse
Affiliation(s)
- Indu Raghavan
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Rosheena Juman
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA.
| |
Collapse
|
4
|
Yang H, Zhang K, Shen W, Chen L, Xia Y, Zou W, Cao Y, Chen X. Efficient production of cembratriene-ol in Escherichia coli via systematic optimization. Microb Cell Fact 2023; 22:17. [PMID: 36694175 PMCID: PMC9872381 DOI: 10.1186/s12934-023-02022-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The tobacco leaf-derived cembratriene-ol exhibits anti-insect effects, but its content in plants is scarce. Cembratriene-ol is difficult and inefficiently chemically synthesised due to its complex structure. Moreover, the titer of reported recombinant hosts producing cembratriene-ol was low and cannot be applied to industrial production. RESULTS In this study, Pantoea ananatis geranylgeranyl diphosphate synthase (CrtE) and Nicotiana tabacum cembratriene-ol synthase (CBTS) were heterologously expressed to synthsize the cembratriene-ol in Escherichia coli. Overexpression of cbts*, the 1-deoxy-D-xylulose 5-phosphate synthase gene dxs, and isopentenyl diphosphate isomerase gene idi promoted the production of cembratriene-ol. The cembratriene-ol titer was 1.53-folds higher than that of E. coli Z17 due to the systematic regulation of ggpps, cbts*, dxs, and idi expression. The production of cembratriene-ol was boosted via the overexpression of genes ispA, ispD, and ispF. The production level of cembratriene-ol in the optimal medium at 72 h was 8.55-folds higher than that before fermentation optimisation. The cembratriene-ol titer in the 15-L fermenter reached 371.2 mg L- 1, which was the highest titer reported. CONCLUSION In this study, the production of cembratriene-ol in E. coli was significantly enhanced via systematic optimization. It was suggested that the recombinant E. coli producing cembratriene-ol constructed in this study has potential for industrial production and applications.
Collapse
Affiliation(s)
- Haiquan Yang
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Kunjie Zhang
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Wei Shen
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Lei Chen
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Yuanyuan Xia
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Wei Zou
- grid.412605.40000 0004 1798 1351College of Bioengineering, Sichuan University of Science & Engineering, 644000 Yibin, Sichuan China
| | - Yu Cao
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Xianzhong Chen
- grid.258151.a0000 0001 0708 1323The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| |
Collapse
|
5
|
Huang S, Xue Y, Ma Y, Zhou C. Microbial (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate reductase (IspH) and its biotechnological potential: A mini review. Front Bioeng Biotechnol 2022; 10:1057938. [DOI: 10.3389/fbioe.2022.1057938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
(E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) reductase (IspH) is a [4Fe-4S] cluster-containing enzyme, involved in isoprenoid biosynthesis as the final enzyme of the methylerythritol phosphate (MEP) pathway found in many bacteria and malaria parasites. In recent years, many studies have revealed that isoprenoid compounds are an alternative to petroleum-derived fuels. Thus, ecofriendly methods harnessing the methylerythritol phosphate pathway in microbes to synthesize isoprenoid compounds and IspH itself have received notable attention from researchers. In addition to its applications in the field of biosynthesis, IspH is considered to be an attractive drug target for infectious diseases such as malaria and tuberculosis due to its survivability in most pathogenic bacterium and its absence in humans. In this mini-review, we summarize previous reports that have systematically illuminated the fundamental and structural properties, substrate binding and catalysis, proposed catalytic mechanism, and novel catalytic activities of IspH. Potential bioengineering and biotechnological applications of IspH are also discussed.
Collapse
|
6
|
Jing Y, Wang Y, Zhou D, Wang J, Li J, Sun J, Feng Y, Xin F, Zhang W. Advances in the synthesis of three typical tetraterpenoids including β-carotene, lycopene and astaxanthin. Biotechnol Adv 2022; 61:108033. [PMID: 36096404 DOI: 10.1016/j.biotechadv.2022.108033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022]
Abstract
Carotenoids are natural pigments that widely exist in nature. Due to their excellent antioxidant, anticancer and anti-inflammatory properties, carotenoids are commonly used in food, medicine, cosmetic and other fields. At present, natural carotenoids are mainly extracted from plants, algae and microorganisms. With the rapid development of metabolic engineering and molecular biology as well as the continuous in-depth study of carotenoids synthesis pathways, industrial microorganisms have showed promising applications in the synthesis of carotenoids. In this review, we introduced the properties of several carotenoids and their biosynthetic metabolism process. Then, the microorganisms synthesizing carotenoids through the natural and non-natural pathways and the extraction methods of carotenoids were summarized and compared. Meanwhile, the influence of substrates on the carotenoids production was also listed. The methods and strategies for achieving high carotenoid production are categorized to help with future research.
Collapse
Affiliation(s)
- Yiwen Jing
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yanxia Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, PR China
| | - Dawei Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jingnan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jiawen Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jingxiang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yifan Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| |
Collapse
|
7
|
Singh RV, Sambyal K. An overview of β-carotene production: Current status and future prospects. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
8
|
Lyu X, Lyu Y, Yu H, Chen W, Ye L, Yang R. Biotechnological advances for improving natural pigment production: a state-of-the-art review. BIORESOUR BIOPROCESS 2022; 9:8. [PMID: 38647847 PMCID: PMC10992905 DOI: 10.1186/s40643-022-00497-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.
Collapse
Affiliation(s)
- Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - WeiNing Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
| |
Collapse
|
9
|
Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
Collapse
Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
10
|
Carruthers DN, Lee TS. Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol 2021; 12:791089. [PMID: 34925299 PMCID: PMC8677530 DOI: 10.3389/fmicb.2021.791089] [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: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.
Collapse
Affiliation(s)
- David N Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
11
|
Klamrak A, Nabnueangsap J, Puthongking P, Nualkaew N. Synthesis of Ferulenol by Engineered Escherichia coli: Structural Elucidation by Using the In Silico Tools. Molecules 2021; 26:6264. [PMID: 34684845 PMCID: PMC8537342 DOI: 10.3390/molecules26206264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/26/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
4-Hydroxycoumarin (4HC) has been used as a lead compound for the chemical synthesis of various bioactive substances and drugs. Its prenylated derivatives exhibit potent antibacterial, antitubercular, anticoagulant, and anti-cancer activities. In doing this, E. coli BL21(DE3)pLysS strain was engineered as the in vivo prenylation system to produce the farnesyl derivatives of 4HC by coexpressing the genes encoding Aspergillus terreus aromatic prenyltransferase (AtaPT) and truncated 1-deoxy-D-xylose 5-phosphate synthase of Croton stellatopilosus (CstDXS), where 4HC was the fed precursor. Based on the high-resolution LC-ESI(±)-QTOF-MS/MS with the use of in silico tools (e.g., MetFrag, SIRIUS (version 4.8.2), CSI:FingerID, and CANOPUS), the first major prenylated product (named compound-1) was detected and ultimately elucidated as ferulenol, in which information concerning the correct molecular formula, chemical structure, substructures, and classifications were obtained. The prenylated product (named compound-2) was also detected as the minor product, where this structure proposed to be the isomeric structure of ferulenol formed via the tautomerization. Note that both products were secreted into the culture medium of the recombinant E. coli and could be produced without the external supply of prenyl precursors. The results suggested the potential use of this engineered pathway for synthesizing the farnesylated-4HC derivatives, especially ferulenol.
Collapse
Affiliation(s)
- Anuwatchakij Klamrak
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand; (A.K.); (P.P.)
| | - Jaran Nabnueangsap
- Salaya Central Instrument Facility RSPG, Research Management and Development Division, Office of the President, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Ploenthip Puthongking
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand; (A.K.); (P.P.)
| | - Natsajee Nualkaew
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand; (A.K.); (P.P.)
| |
Collapse
|
12
|
Zhu K, Kong J, Zhao B, Rong L, Liu S, Lu Z, Zhang C, Xiao D, Pushpanathan K, Foo JL, Wong A, Yu A. Metabolic engineering of microbes for monoterpenoid production. Biotechnol Adv 2021; 53:107837. [PMID: 34555428 DOI: 10.1016/j.biotechadv.2021.107837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022]
Abstract
Monoterpenoids are an important class of natural products that are derived from the condensation of two five‑carbon isoprene subunits. They are widely used for flavouring, fragrances, colourants, cosmetics, fuels, chemicals, and pharmaceuticals in various industries. They can also serve as precursors for the production of many industrially important products. Currently, monoterpenoids are produced predominantly through extraction from plant sources. However, the small quantity of monoterpenoids in nature renders this method of isolation non-economically viable. Similarly impractical is the chemical synthesis of these compounds as they suffer from high energy consumption and pollutant discharge. Microbial biosynthesis, however, exists as a potential solution to these hindrances, but the transformation of cells into efficient factories remains a major impediment. Here, we critically review the recent advances in engineering microbes for monoterpenoid production, with an emphasis on categorized strategies, and discuss the challenges and perspectives to offer guidance for future engineering.
Collapse
Affiliation(s)
- Kun Zhu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Jing Kong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| | - Krithi Pushpanathan
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Adison Wong
- Chemical Engineering and Food Technology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore.
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin 300457, PR China.
| |
Collapse
|
13
|
Wang J, Zhao D, Li J, Hu M, Xin X, Price MA, Li Q, Liu L, Li S, Rosser SJ, Zhang C, Bi C, Zhang X. Helicase-AID: A novel molecular device for base editing at random genomic loci. Metab Eng 2021; 67:396-402. [PMID: 34411701 DOI: 10.1016/j.ymben.2021.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/06/2021] [Accepted: 08/14/2021] [Indexed: 01/09/2023]
Abstract
CRISPR-enabled deaminase base editing has become a powerful tool for precisely editing nucleotides on the chromosome. In this study DNA helicases, such as Escherichia coli DnaB, were fused to activation-induced cytidine deaminase (AID) to form enzyme complexes which randomly introduces edited bases throughout the chromosome. DnaB-AID was found to increase 2.5 × 103 fold relative to the mutagenesis frequency of wildtype. 97.9% of these edits were observed on the leading strand during DNA replication suggesting deamination to be highly coordinated with DNA replication. Using DnaB-AID, a 371.4% increase in β-carotene production was obtained following four rounds of editing. In Saccharomyces cerevisiae Helicase-AID was constructed by fusing AID to one of the subunits of eukaryotic helicase Mcm2-7 complex, MCM5. Using MCM5-AID, the average editing efficiency of five strains was 2.1 ± 0.4 × 103 fold higher than the native genomic mutation rate. MCM5-AID was able to improve β-carotene production of S. cerevisiae 4742crt by 75.4% following eight rounds of editing. The S. cerevisiae MCM5-AID technique is the first biological tool for generating and accumulating single base mutations in eukaryotic chromosomes. Since the helicase complex is highly conservative in all eukaryotes, Helicase-AID could be adapted for various applications and research in all eukaryotic cells.
Collapse
Affiliation(s)
- Jie Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Muzi Hu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiuqing Xin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Marcus A Price
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Li Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Susan J Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| |
Collapse
|
14
|
Harada H, Senda D, Shima T, Nakane C. Carboxylesterases for the hydrolysis of acetoacetate esters and their applications in terpenoid production using Escherichia coli. Appl Microbiol Biotechnol 2021; 105:5821-5832. [PMID: 34324009 DOI: 10.1007/s00253-021-11447-z] [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: 01/28/2021] [Revised: 06/14/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
Pathway engineering is a useful technology for producing desired compounds on a large scale by modifying the biosynthetic pathways of host organisms using genetic engineering. We focused on acetoacetate esters as novel low-cost substrates and established an efficient terpenoid production system using pathway-engineered recombinant Escherichia coli. Functional analysis using recombinant E. coli proteins of 18 carboxylesterases identified from the microbial esterases and lipases database showed that the p-nitrobenzyl esterase (PnbA) from Bacillus subtilis specifically hydrolyzed two acetoacetate esters: methyl acetoacetate (MAA) and ethyl acetoacetate (EAA). We generated a plasmid (pAC-Mev/Scidi/Aacl/PnbA) co-expressing PnbA and six enzymes of the mevalonate pathway gene cluster from Streptomyces, isopentenyl diphosphate isomerase type I from Saccharomyces cerevisiae, and acetoacetyl-coenzyme A ligase from Rattus norvegicus. The plasmid pAC-Mev/Scidi/Aacl/PnbA was introduced into E. coli along with plasmid expressing carotenoid (lycopene) or sesquiterpene (β-bisabolene) biosynthesis genes, and the terpenoid production was evaluated following the addition of acetoacetate esters as substrates. These recombinant E. coli strains used MAA and EAA as substrates for the biosynthesis of terpenoids and produced almost equivalent concentrations of target compounds compared with the previous production system that used mevalonolactone and lithium acetoacetate. The findings of this study will enable the production of useful terpenoids from low-cost substrates, which may facilitate their commercial production on an industrial scale in the future. KEY POINTS: • PnbA from Bacillus subtilis exhibits acetoacetate hydrolysis activity. • A plasmid enabling terpenoid synthesis from acetoacetate esters was constructed. • Acetoacetate esters as substrates enable a low-cost production of terpenoids.
Collapse
Affiliation(s)
- Hisashi Harada
- Department of Chemistry & Biotechnology, Faculty of Engineering, Tottori University, 4-101 Koyamacho-Minami, Tottori, 680-8552, Japan.
| | - Daiki Senda
- Department of Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-Minami, Tottori, 680-8552, Japan
| | - Takanori Shima
- Department of Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-Minami, Tottori, 680-8552, Japan
| | - Chika Nakane
- Department of Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyamacho-Minami, Tottori, 680-8552, Japan
| |
Collapse
|
15
|
Liao C, Ayansola H, Ma Y, Ito K, Guo Y, Zhang B. Advances in Enhanced Menaquinone-7 Production From Bacillus subtilis. Front Bioeng Biotechnol 2021; 9:695526. [PMID: 34354987 PMCID: PMC8330505 DOI: 10.3389/fbioe.2021.695526] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 12/02/2022] Open
Abstract
The production of nutraceutical compounds through biosynthetic approaches has received considerable attention in recent years. For example, Menaquinone-7 (MK-7), a sub-type of Vitamin K2, biosynthesized from Bacillus subtilis (B. subtilis), proved to be more efficiently produced than the conventional chemical synthesis techniques. This is possible due to the development of B. subtilis as a chassis cell during the biosynthesis stages. Hence, it is imperative to provide insights on the B. subtilis membrane permeability modifications, biofilm reactors, and fermentation optimization as advanced techniques relevant to MK-7 production. Although the traditional gene-editing method of homologous recombination improves the biosynthetic pathway, CRISPR-Cas9 could potentially resolve the drawbacks of traditional genome editing techniques. For these reasons, future studies should explore the applications of CRISPRi (CRISPR interference) and CRISPRa (CRISPR activation) system gene-editing tools in the MK-7 anabolism pathway.
Collapse
Affiliation(s)
- Chaoyong Liao
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hammed Ayansola
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Department of Animal Physiology, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Koichi Ito
- Department of Food and Physiological Models, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Ibaraki, Japan
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bingkun Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
16
|
Swapnil P, Meena M, Singh SK, Dhuldhaj UP, Harish, Marwal A. Vital roles of carotenoids in plants and humans to deteriorate stress with its structure, biosynthesis, metabolic engineering and functional aspects. CURRENT PLANT BIOLOGY 2021; 26:100203. [DOI: 10.1016/j.cpb.2021.100203] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
|
17
|
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: 6] [Impact Index Per Article: 2.0] [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.
Collapse
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.
| |
Collapse
|
18
|
|
19
|
Jing Y, Guo F, Zhang S, Dong W, Zhou J, Xin F, Zhang W, Jiang M. Recent Advances on Biological Synthesis of Lycopene by Using Industrial Yeast. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c05228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yiwen Jing
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, P. R. China
| |
Collapse
|
20
|
Pathway Engineering Using Escherichia coli to Produce Commercialized Carotenoids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1261:191-199. [PMID: 33783741 DOI: 10.1007/978-981-15-7360-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biosynthesis of commercialized carotenoids (e.g., lycopene, β-carotene, zeaxanthin, and astaxanthin) using recombinant microorganisms is one of the reasonable and cost-effective alternatives to extraction from natural sources and chemical synthesis. Among heterologous hosts, Escherichia coli is one of the most useful and manageable. To date, many approaches using recombinant E. coli are available to produce various carotenoids. Here we outline the latest carotenoid production research using recombinant E. coli produced through pathway engineering and its future prospects.
Collapse
|
21
|
Zhao W, Ruan J, Wang Q, Du G, Zhou J, Liu S. Metabolic pathway optimization through fusion with self-assembling amphipathic peptides. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
22
|
Liu H, Wang Y, Hou Y, Li Z. Fitness of Chassis Cells and Metabolic Pathways for l-Cysteine Overproduction in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14928-14937. [PMID: 33264003 DOI: 10.1021/acs.jafc.0c06134] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
l-Cysteine is a ubiquitous and unique sulfur-containing amino acid with numerous applications in agricultural and food industries. The efficient production of l-cysteine via microbial fermentation has received a great deal of attention. In this study, the fitness of different Escherichia coli K-12 strains harboring plasmid pLH03 was investigated. The enhancement of the precursor synthetic pathway and thiosulfate assimilation pathway resulted in the good performance of the E. coli BW25113 strain. The expression levels of synthetic pathway genes were optimized by two constitutive promoters to assess their effects on cysteine production. In conjunction, the main degradation pathway genes were also deleted for more efficient production of cysteine. l-Cysteine production was further increased through the manipulation of the sulfur transcription regulator cysB and sulfur supplementation. After process optimization in a 1.5 L bioreactor, LH2A1M0BΔYTS-pLH03 [BW25113 Ptrc2-serA Ptrc1-cysMPtrc-cysBΔyhaMΔtnaAΔsdaA-(pLH03)] accumulated 8.34 g/L cysteine, laying a foundation for application in the cysteine fermentation industry.
Collapse
Affiliation(s)
- Han Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yu Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yehua Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
23
|
Microbial production of limonene and its derivatives: Achievements and perspectives. Biotechnol Adv 2020; 44:107628. [DOI: 10.1016/j.biotechadv.2020.107628] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
|
24
|
Transcriptomic analysis of gene expression of menaquinone-7 in Bacillus subtilis natto toward different oxygen supply. Food Res Int 2020; 137:109700. [PMID: 33233274 DOI: 10.1016/j.foodres.2020.109700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/11/2020] [Accepted: 09/06/2020] [Indexed: 02/08/2023]
Abstract
Menaquinone-7 (MK-7) is an important kind of vitamin K2 which plays significant roles in the treatment of coagulation and osteoporosis, and prevention of cardiovascular disease. This work was purposed to study the differences of gene expression at different oxygen supply conditions in Bacillus natto. The differences of fermentation characteristics, gene expression related to MK-7 biosynthesis, spore and biofilm formation were analyzed. The yield of MK-7 increased by two fold under high oxygen supply condition of 200 rpm. Further transcriptome analysis indicated that most of the enzymes in MK-7 biosynthesis pathway were also up-regulated. Moreover, glycerol kinase, fructose-bisphosphate aldolase and phosphofructokinase in glycolysis pathway were all up-regulated indicating that high oxygen supply can increase the consumption of substrate glycerol. Meanwhile, menD, encoded the rate-limiting enzyme in the MK pathway, was obviously up-regulated by 3.49-fold while most of the enzymes related to spore formation were down regulated at 200 rpm. Besides, superoxide dismutase (SOD2), catalase (CAT), hydroperoxide reductase (AhpF) and DNA-binding protein MrgA in the antioxidant defense system were up-regulated, while superoxide dismutase (SOD1) and glutathione peroxidase (GSH-Px) were down-regulated. These results could contribute to a better understanding for the effect of oxygen on the MK-7 production in Bacillus natto, and further analyze the molecular regulation mechanism of MK-7 biosynthesis.
Collapse
|
25
|
Sun L, Atkinson CA, Lee YG, Jin YS. High-level β-carotene production from xylose by engineered Saccharomyces cerevisiae without overexpression of a truncated HMG1 (tHMG1). Biotechnol Bioeng 2020; 117:3522-3532. [PMID: 33616900 DOI: 10.1002/bit.27508] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 01/18/2023]
Abstract
β-Carotene is a natural pigment and health-promoting metabolite, and has been widely used in the nutraceutical, feed, and cosmetic industries. Here, we engineered a GRAS yeast Saccharomyces cerevisiae to produce β-carotene from xylose, the second most abundant and inedible sugar component of lignocellulose biomass. Specifically, a β-carotene biosynthetic pathway containing crtYB, crtI, and crtE from Xanthophyllomyces dendrorhous was introduced into a xylose-fermenting S. cerevisiae. The resulting strain produced β-carotene from xylose at a titer threefold higher than from glucose. Interestingly, overexpression of tHMG1, which has been reported as a critical genetic perturbation to enhance metabolic fluxes in the mevalonate pathway and β-carotene production in yeast when glucose is used, did not further improve the production of β-carotene from xylose. Through fermentation profiling, metabolites analysis, and transcriptional studies, we found the advantages of using xylose as a carbon source, instead of glucose, for β-carotene production to be a more respiratory feature of xylose consumption, a larger cytosolic acetyl-CoA pool, and an upregulated expression level of rate-limiting genes in the β-carotene-producing pathway, including ACS1 and HMG1. As a result, 772.8 mg/L of β-carotene was obtained in a fed-batch bioreactor culture with xylose feeding. Considering the inevitable large scale production of xylose when cellulosic biomass-based bioeconomy is implemented, our results suggest xylose utilization is a promising strategy for overproduction of carotenoids and other isoprenoids in engineered S. cerevisiae.
Collapse
Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Christine A Atkinson
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ye-Gi Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| |
Collapse
|
26
|
Cheng MH, Sun L, Jin YS, Dien B, Singh V. Production of xylose enriched hydrolysate from bioenergy sorghum and its conversion to β-carotene using an engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2020; 308:123275. [PMID: 32272391 DOI: 10.1016/j.biortech.2020.123275] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
A new bioprocess has been developed that allows for producing β-carotene from the xylose portion of bioenergy sorghum. Bioenergy sorghum was pretreated in a pilot-scale continuous hydrothermal reactor followed by disc refining. Xylose was extracted using low-severity dilute acid hydrolysis. A xylose yield of 64.9% (17.4 g/L) was obtained by hydrolyzing at 120 °C for 5 min with 2% sulfuric acid. The xylose-enriched syrup was separated and concentrated to either 32 g xylose/L (medium-concentrated hydrolysate, MCB) or 66 g xylose/L (high-concentrated hydrolysate, HCB). The non- (NCB), medium-, and high-concentrated xylose syrup were neutralized and fermented to β-carotene using Saccharomyces cerevisiae strain SR8B, which had been engineered for xylose utilization and β-carotene production. In HCB, MCB, and NCB cultures, the yeast produced β-carotene titers of 114.50 mg/L, 93.56 mg/L, and 82.50 mg/L, which corresponds to specific yeast biomass productions of 7.32 mg/g DCW, 8.10 mg/g DCW, and 8.29 mg/g DCW, respectively.
Collapse
Affiliation(s)
- Ming-Hsun Cheng
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bruce Dien
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604, USA
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
27
|
Wu Y, Yan P, Li Y, Liu X, Wang Z, Chen T, Zhao X. Enhancing β-Carotene Production in Escherichia coli by Perturbing Central Carbon Metabolism and Improving the NADPH Supply. Front Bioeng Biotechnol 2020; 8:585. [PMID: 32582683 PMCID: PMC7296177 DOI: 10.3389/fbioe.2020.00585] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/13/2020] [Indexed: 01/12/2023] Open
Abstract
Beta (β)-carotene (C40H56; a provitamin) is a particularly important carotenoid for human health. Many studies have focused on engineering Escherichia coli as an efficient heterologous producer of β-carotene. Moreover, several strains with potential for use in the industrial production of this provitamin have already been constructed via different metabolic engineering strategies. In this study, we aimed to improve the β-carotene-producing capacity of our previously engineered E. coli strain ZF43ΔgdhA through further gene deletion and metabolic pathway manipulations. Deletion of the zwf gene increased the resultant strain's β-carotene production and content by 5.1 and 32.5%, respectively, relative to the values of strain ZF43ΔgdhA, but decreased the biomass by 26.2%. Deletion of the ptsHIcrr operon further increased the β-carotene production titer from 122.0 to 197.4 mg/L, but the provitamin content was decreased. Subsequently, comparative transcriptomic analysis was used to explore the dynamic transcriptional responses of the strains to the blockade of the pentose phosphate pathway and inactivation of the phosphotransferase system. Lastly, based on the analyses of comparative transcriptome and reduction cofactor, several strategies to increase the NADPH supply were evaluated for enhancement of the β-carotene content. The combination of yjgB gene deletion and nadK overexpression led to increased β-carotene production and content. The best strain, ECW4/p5C-nadK, produced 266.4 mg/L of β-carotene in flask culture and 2,579.1 mg/L in a 5-L bioreactor. The latter value is the highest reported from production via the methylerythritol phosphate pathway in E. coli. Although the strategies applied is routine in this study, the combinations reported were first implemented, are simple but efficient and will be helpful for the production of many other natural products, especially isoprenoids. Importantly, we demonstrated that the use of the methylerythritol phosphate pathway alone for efficient β-carotene biosynthesis could be achieved via appropriate modifications of the cell metabolic functions.
Collapse
Affiliation(s)
- Yuanqing Wu
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Panpan Yan
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yang Li
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- College of Life Science, Shihezi University, Shihezi, China
| | - Xuewei Liu
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zhiwen Wang
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Tao Chen
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xueming Zhao
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| |
Collapse
|
28
|
Cruet-Burgos C, Cox S, Ioerger BP, Perumal R, Hu Z, Herald TJ, Bean SR, Rhodes DH. Advancing provitamin A biofortification in sorghum: Genome-wide association studies of grain carotenoids in global germplasm. THE PLANT GENOME 2020; 13:e20013. [PMID: 33016639 DOI: 10.1002/tpg2.20013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/19/2020] [Indexed: 06/11/2023]
Abstract
Vitamin A deficiency is one of the most prevalent nutritional deficiencies worldwide. Sorghum [Sorghum bicolor L. (Moench)] is a major cereal crop consumed by millions of people in regions with high vitamin A deficiency. We quantified carotenoid concentrations in a diverse sorghum panel using high-performance liquid chromatography and conducted a genome-wide association study (GWAS) of grain carotenoids to identify genes underlying carotenoid variation. There was moderate variation for β-carotene (00.8 μg g-1 ), lutein (0.3-9.4 μg g-1 ), and zeaxanthin (0.2-9.1 μg g-1 ), but β-cryptoxanthin and α-carotene were nearly undetectable. Genotype had the largest effect size, at 81% for zeaxanthin, 62% for β-carotene, and 53% for lutein. Using multiple models, GWAS identified several significant associations between carotenoids and single nucleotide polymorphisms (SNPs), some of which colocalized with known carotenoid genes that have not been previously implicated in carotenoid variation. Several of the candidate genes identified have also been identified in maize (Zea mays L.) and Arabidopsis (Arabidopsis thaliana) carotenoid GWAS studies. Notably, an SNP inside the putative ortholog of maize zeaxanthin epoxidase (ZEP) had the most significant association with zeaxanthin and with the ratio between lutein and zeaxanthin, suggesting that ZEP is a major gene controlling sorghum carotenoid variation. Overall findings suggest there is oligogenic inheritance for sorghum carotenoids and suitable variation for marker-assisted selection. The high carotenoid germplasm and significant associations identified in this study can be used in biofortification efforts to improve the nutritional quality of sorghum.
Collapse
Affiliation(s)
- Clara Cruet-Burgos
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sarah Cox
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Brian P Ioerger
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Thomas J Herald
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Scott R Bean
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Davina H Rhodes
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
29
|
Orsi E, Mougiakos I, Post W, Beekwilder J, Dompè M, Eggink G, van der Oost J, Kengen SWM, Weusthuis RA. Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:123. [PMID: 32684976 PMCID: PMC7359475 DOI: 10.1186/s13068-020-01765-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Microbial cell factories are usually engineered and employed for cultivations that combine product synthesis with growth. Such a strategy inevitably invests part of the substrate pool towards the generation of biomass and cellular maintenance. Hence, engineering strains for the formation of a specific product under non-growth conditions would allow to reach higher product yields. In this respect, isoprenoid biosynthesis represents an extensively studied example of growth-coupled synthesis with rather unexplored potential for growth-independent production. Rhodobacter sphaeroides is a model bacterium for isoprenoid biosynthesis, either via the native 2-methyl-d-erythritol 4-phosphate (MEP) pathway or the heterologous mevalonate (MVA) pathway, and for poly-β-hydroxybutyrate (PHB) biosynthesis. RESULTS This study investigates the use of this bacterium for growth-independent production of isoprenoids, with amorpha-4,11-diene as reporter molecule. For this purpose, we employed the recently developed Cas9-based genome editing tool for R. sphaeroides to rapidly construct single and double deletion mutant strains of the MEP and PHB pathways, and we subsequently transformed the strains with the amorphadiene producing plasmid. Furthermore, we employed 13C-metabolic flux ratio analysis to monitor the changes in the isoprenoid metabolic fluxes under different cultivation conditions. We demonstrated that active flux via both isoprenoid pathways while inactivating PHB synthesis maximizes growth-coupled isoprenoid synthesis. On the other hand, the strain that showed the highest growth-independent isoprenoid yield and productivity, combined the plasmid-based heterologous expression of the orthogonal MVA pathway with the inactivation of the native MEP and PHB production pathways. CONCLUSIONS Apart from proposing a microbial cell factory for growth-independent isoprenoid synthesis, this work provides novel insights about the interaction of MEP and MVA pathways under different growth conditions.
Collapse
Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present Address: Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present Address: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Wilbert Post
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Marco Dompè
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Food & Biobased Research, 6708WG Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
30
|
Enhanced Lycopene Production in Escherichia coli by Expression of Two MEP Pathway Enzymes from Vibrio sp. Dhg. Catalysts 2019. [DOI: 10.3390/catal9121003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbial production is a promising method that can overcome major limitations in conventional methods of lycopene production, such as low yields and variations in product quality. Significant efforts have been made to improve lycopene production by engineering either the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway or mevalonate (MVA) pathway in microorganisms. To further improve lycopene production, it is critical to utilize metabolic enzymes with high specific activities. Two enzymes, 1-deoxy-d-xylulose-5-phosphate synthase (Dxs) and farnesyl diphosphate synthase (IspA), are required in lycopene production using MEP pathway. Here, we evaluated the activities of Dxs and IspA of Vibrio sp. dhg, a newly isolated and fast-growing microorganism. Considering that the MEP pathway is closely related to the cell membrane and electron transport chain, the activities of the two enzymes of Vibrio sp. dhg were expected to be higher than the enzymes of Escherichia coli. We found that Dxs and IspA in Vibrio sp. dhg exhibited 1.08-fold and 1.38-fold higher catalytic efficiencies, respectively. Consequently, the heterologous overexpression improved the specific lycopene production by 1.88-fold. Our findings could be widely utilized to enhance production of lycopene and other carotenoids.
Collapse
|
31
|
Liu M, Sandmann G, Chen F, Huang J. Enhanced Coproduction of Cell-Bound Zeaxanthin and Secreted Exopolysaccharides by Sphingobium sp. via Metabolic Engineering and Optimized Fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12228-12236. [PMID: 31638826 DOI: 10.1021/acs.jafc.9b05342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zeaxanthin is a value-added carotenoid with wide applications. This study aims to manipulate a generally recognized as safe and carotenoid-producing bacterium, Sphingobium sp., for enhanced production of zeaxanthin and exopolysaccharides. First, whole-genome sequencing and analysis of pathway genes were applied to define the carotenoid pathway in Sphingobium sp. Second, a Sphingobium transformation system was established to engineer metabolite flux into zeaxanthin. By a combination of chemical mutagenesis and removal of bottlenecks of carotenoid biosynthesis via overexpression of three rate-limiting enzymes, the genetically modified Sphingobium DIZ strain produced 21.26 mg/g dry cell weight of zeaxanthin, which was about 4-fold higher than the wild type. Upon optimization of culture conditions, the DIZ strain produced 479.5 mg/L of zeaxanthin with the productivity of 4.99 mg/L/h and 21.9 g/L of exopolysaccharides using a fed-batch fermentation strategy. This study represents the first genetic manipulation of Sphingobium sp., a biotechnologically important bacterium, for high-yield production of value-added metabolites.
Collapse
Affiliation(s)
- Mengmeng Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany , Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Gerhard Sandmann
- Institute of Molecular Bioscience , J.W. Goethe Universitat , Max von Laue Str. 9 , Frankfurt 60438 , Germany
| | - Feng Chen
- Institute for Advanced Study , Shenzhen University , Shenzhen 518060 , People's Republic of China
| | - Junchao Huang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany , Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
| |
Collapse
|
32
|
Sun L, Kwak S, Jin YS. Vitamin A Production by Engineered Saccharomyces cerevisiae from Xylose via Two-Phase in Situ Extraction. ACS Synth Biol 2019; 8:2131-2140. [PMID: 31374167 DOI: 10.1021/acssynbio.9b00217] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vitamin A is an essential human micronutrient and plays critical roles in vision, reproduction, immune system, and skin health. Current industrial methods for the production of vitamin A rely on chemical synthesis from petroleum-derived substrates, such as acetone and acetylene. Here, we developed a biotechnological method for production of vitamin A from an abundant and nonedible sugar. Specifically, we engineered Saccharomyces cerevisiae to produce vitamin A from xylose-the second most abundant sugar in plant cell wall hydrolysates-by introducing a β-carotene biosynthetic pathway, and a gene coding for β-carotene 15,15'-dioxygenase (BCMO) into a xylose-fermenting S. cerevisiae. The resulting yeast strain produced vitamin A from xylose at a titer 4-fold higher than from glucose. When a two-phase in situ extraction strategy with dodecane or olive oil as an extractive agent was employed, vitamin A production improved additional 2-fold. Furthermore, a xylose fed-batch fermentation with dodecane in situ extraction achieved a final titer of 3350 mg/L vitamin A, which consisted of retinal (2094 mg/L) and retinol (1256 mg/L). These results suggest that potential limiting factors of vitamin A production in yeast, such as insufficient supply of isoprenoid precursors, and limited intracellular storage capacity, can be effectively addressed by using xylose as a carbon source, and two-phase in situ extraction. The engineered S. cerevisiae and fermentation strategies described in this study might contribute to sustainable and economic production of vitamin A, and vitamin A-enriched bioproducts from renewable biomass.
Collapse
|
33
|
Ward VCA, Chatzivasileiou AO, Stephanopoulos G. Metabolic engineering of Escherichia coli for the production of isoprenoids. FEMS Microbiol Lett 2019; 365:4953741. [PMID: 29718190 DOI: 10.1093/femsle/fny079] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/25/2018] [Indexed: 12/22/2022] Open
Abstract
Metabolic engineering is the practice of using directed genetic manipulations to rewire cellular metabolism primarily with the aim to transform the organism into a single-celled chemical factory. Using biological processes, we can produce more complex chemicals in a more sustainable way. This is particularly important for chemicals which are hard to synthesize using traditional chemistry. However, cells have evolved for growth and must be engineered to produce a single chemical at commercially viable levels. This review focuses on the strategies used to rewire cellular metabolism to produce chemicals using isoprenoid production in Escherichia coli as an example that illustrates many of the challenges faced in metabolic engineering.
Collapse
Affiliation(s)
- Valerie C A Ward
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | | | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
34
|
Qiang S, Su AP, Li Y, Chen Z, Hu CY, Meng YH. Elevated β-Carotene Synthesis by the Engineered Rhodobacter sphaeroides with Enhanced CrtY Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9560-9568. [PMID: 31368704 DOI: 10.1021/acs.jafc.9b02597] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Carotene is a precursor of vitamin A and a dietary supplement for its antioxidant property. Producing β-carotene by microbial fermentation has attracted much attention owing to consumers' preference for the natural product. In this study, an engineered photosynthetic Rhodobacter sphaeroides producing β-carotene was constructed by the following strategies: (1) five promoters of different strengths were used to investigate the effect of the expression level of crtY on β-carotene content. It was found that PrrnB increased the β-carotene content by 109%. (2) blocking of the branched pentose phosphate pathway by zwf deletion, and (3) overexpressing dxs could restore the transcriptional levels of crtE and crtB. Finally, the engineered RS-C3 has the highest β-carotene content of 14.93 mg/g dry cell weight (DCW) among all of the reported photosynthetic bacteria and the β-carotene content reached 3.34 mg/g DCW under light conditions. Our results will be available for industrial use to supply a large quantity of natural β-carotene.
Collapse
Affiliation(s)
- Shan Qiang
- 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
- Xi'an Healthful Biotechnology Co., Ltd. , HangTuo Road , Chang'an, Xi'an 710100 , P. R. China
| | - An Ping 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
| | - Ying Li
- State Key Laboratory of Agrobiotechnology , China Agricultural University , No. 2 Yuanmingyuan West Road , Haidian District, Beijing 100193 , 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
| | - Ching Yuan Hu
- Human Nutrition, Food, and Animal Science , University of Hawai'i at Manoa , 1955 East-West Road, AgSci. 415J , Honolulu , Hawaii 96822-2217 , United States
| | - Yong Hong 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
| |
Collapse
|
35
|
Ma Y, McClure DD, Somerville MV, Proschogo NW, Dehghani F, Kavanagh JM, Coleman NV. Metabolic Engineering of the MEP Pathway in Bacillus subtilis for Increased Biosynthesis of Menaquinone-7. ACS Synth Biol 2019; 8:1620-1630. [PMID: 31250633 DOI: 10.1021/acssynbio.9b00077] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vitamin K is essential for blood coagulation and plays important roles in bone and cardiovascular health. Menaquinone-7 (MK-7) is one form of vitamin K that is especially useful due to its long half-life in the circulation. MK-7 is difficult to make via organic synthesis, and is thus commonly produced by fermentation. This study aimed to genetically modify Bacillus subtilis cultures to increase their MK-7 yield and reduce production costs. We constructed 12 different strains of B. subtilis 168 by overexpressing different combinations of the rate-limiting enzymes Dxs, Dxr, Idi, and MenA. We observed an 11-fold enhancement of production in the best-performing strain, resulting in 50 mg/L MK-7. Metabolite analysis revealed new bottlenecks in the pathway at IspG and IspH, which suggest avenues for further optimization. This work highlights the usefulness of Bacillus subtilis for industrial production of high value compounds.
Collapse
Affiliation(s)
- Yanwei Ma
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark V. Somerville
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - John M. Kavanagh
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
36
|
Wu T, Li S, Ye L, Zhao D, Fan F, Li Q, Zhang B, Bi C, Zhang X. Engineering an Artificial Membrane Vesicle Trafficking System (AMVTS) for the Excretion of β-Carotene in Escherichia coli. ACS Synth Biol 2019; 8:1037-1046. [PMID: 30990999 DOI: 10.1021/acssynbio.8b00472] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Large hydrophobic molecules, such as carotenoids, cannot be effectively excreted from cells by natural transportation systems. These products accumulate inside the cells and affect normal cellular physiological functions, which hinders further improvement of carotenoid production by microbial cell factories. In this study, we proposed to construct a novel artificial transport system utilizing membrane lipids to carry and transport hydrophobic molecules. Membrane lipids allow the physiological mechanism of membrane dispersion to be reconstructed and amplified to establish a novel artificial membrane vesicle transport system (AMVTS). Specifically, a few proteins in E. coli were reported or proposed to be related to the formation mechanism of outer membrane vesicles, and were individually knocked out or overexpressed to test their physiological functions. The effects on tolR and nlpI were the most significant. Knocking out both tolR and nlpI resulted in a 13.7% increase of secreted β-carotene with a 35.6% increase of specific production. To supplement the loss of membrane components of the cells due to the increased membrane vesicle dispersion, the synthesis pathway of phosphatidylethanolamine was engineered. While overexpression of AccABCD and PlsBC in TW-013 led to 15% and 17% increases of secreted β-carotene, respectively, the overexpression of both had a synergistic effect and caused a 53-fold increase of secreted β-carotene, from 0.2 to 10.7 mg/g dry cell weight (DCW). At the same time, the specific production of β-carotene increased from 6.9 to 21.9 mg/g DCW, a 3.2-fold increase. The AMVTS was also applied to a β-carotene hyperproducing strain, CAR025, which led to a 24-fold increase of secreted β-carotene, from 0.5 to 12.7 mg/g DCW, and a 61% increase of the specific production, from 27.7 to 44.8 mg/g DCW in shake flask fermentation. The AMVTS built in this study establishes a novel artificial transport mechanism different from natural protein-based cellular transport systems, which has great potential to be applied to various cell factories for the excretion of a wide range of hydrophobic compounds.
Collapse
Affiliation(s)
- Tao Wu
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300314, PR China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Qinyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Bolin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| |
Collapse
|
37
|
Chou YL, Ko CY, Yen CC, Chen LFO, Shaw JF. Multiple promoters driving the expression of astaxanthin biosynthesis genes can enhance free-form astaxanthin production. J Microbiol Methods 2019; 160:20-28. [DOI: 10.1016/j.mimet.2019.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 01/15/2023]
|
38
|
Jiang R, Chen X, Lian J, Huang L, Cai J, Xu Z. Efficient production of Pseudoionone with multipathway engineering in
Escherichia coli. J Appl Microbiol 2019; 126:1751-1760. [DOI: 10.1111/jam.14245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/21/2019] [Accepted: 03/02/2019] [Indexed: 12/18/2022]
Affiliation(s)
- R. Jiang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry) College of Chemical and Biological Engineering Zhejiang University Hangzhou China
- Institute of Biological Engineering College of Chemical and Biological Engineering Zhejiang University Hangzhou China
| | - X. Chen
- Hangzhou Tongjuntang Biotechnology Corporation, Ltd Hangzhou China
| | - J. Lian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry) College of Chemical and Biological Engineering Zhejiang University Hangzhou China
- Institute of Biological Engineering College of Chemical and Biological Engineering Zhejiang University Hangzhou China
| | - L. Huang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry) College of Chemical and Biological Engineering Zhejiang University Hangzhou China
- Institute of Biological Engineering College of Chemical and Biological Engineering Zhejiang University Hangzhou China
| | - J. Cai
- Institute of Biological Engineering College of Chemical and Biological Engineering Zhejiang University Hangzhou China
| | - Z. Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry) College of Chemical and Biological Engineering Zhejiang University Hangzhou China
- Institute of Biological Engineering College of Chemical and Biological Engineering Zhejiang University Hangzhou China
| |
Collapse
|
39
|
Lee Y, Cho IJ, Choi SY, Lee SY. Systems Metabolic Engineering Strategies for Non-Natural Microbial Polyester Production. Biotechnol J 2019; 14:e1800426. [PMID: 30851138 DOI: 10.1002/biot.201800426] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/04/2019] [Indexed: 11/07/2022]
Abstract
Plastics, used everyday, are mostly synthetic polymers derived from fossil resources, and their accumulation is becoming a serious concern worldwide. Polyhydroxyalkanoates (PHAs) are naturally produced polyesters synthesized and intracellularly accumulated by many different microorganisms. PHAs are good alternatives to petroleum-based plastics because they possess a wide range of material properties depending on monomer types and molecular weights. In addition, PHAs are biodegradable and can be produced from renewable biomass. Thus, producing PHAs through the development of high-performance engineered microorganisms and efficient bioprocesses gained much interest. In addition, non-natural polyesters comprising 2-hydroxycarboxylic acids as monomers have been produced by fermentation of metabolically engineered bacteria. For example, poly(lactic acid) and poly(lactic acid-co-glycolic acid), which have been chemically synthesized using the corresponding monomers either fermentatively or chemically produced, can be produced by metabolically engineered bacteria by one-step fermentation. Recently, PHAs containing aromatic monomers could be produced by fermentation of metabolically engineered bacteria. Here, metabolic engineering strategies applied in developing microbial strains capable of producing non-natural polyesters in a stepwise manner are reviewed. It is hoped that the detailed strategies described will be helpful for designing metabolic engineering strategies for developing diverse microbial strains capable of producing various polymers that can replace petroleum-derived polymers.
Collapse
Affiliation(s)
- Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - In J Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - So Y Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Applied Science Research Institute, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang Y Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Applied Science Research Institute, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| |
Collapse
|
40
|
Xu N, Wei L, Liu J. Recent advances in the applications of promoter engineering for the optimization of metabolite biosynthesis. World J Microbiol Biotechnol 2019; 35:33. [DOI: 10.1007/s11274-019-2606-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/23/2019] [Indexed: 01/24/2023]
|
41
|
Li M, Chen H, Liu C, Guo J, Xu X, Zhang H, Nian R, Xian M. Improvement of isoprene production in Escherichia coli by rational optimization of RBSs and key enzymes screening. Microb Cell Fact 2019; 18:4. [PMID: 30626394 PMCID: PMC6327615 DOI: 10.1186/s12934-018-1051-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/26/2018] [Indexed: 01/13/2023] Open
Abstract
Background As an essential platform chemical mostly used for rubber synthesis, isoprene is produced in industry through chemical methods, derived from petroleum. As an alternative, bio-production of isoprene has attracted much attention in recent years. Previous researches were mostly focused on key enzymes to improve isoprene production. In this research, besides screening of key enzymes, we also paid attention to expression intensity of non-key enzymes. Results Firstly, screening of key enzymes, IDI, MK and IspS, from other organisms and then RBS optimization of the key enzymes were carried out. The strain utilized IDIsa was firstly detected to produce more isoprene than other IDIs. IDIsa expression was improved after RBS modification, leading to 1610-fold increase of isoprene production. Secondly, RBS sequence optimization was performed to reduce translation initiation rate value of non-key enzymes, ERG19 and MvaE. Decreased ERG19 and MvaE expression and increased isoprene production were detected. The final strain showed 2.6-fold increase in isoprene production relative to the original strain. Furthermore, for the first time, increased key enzyme expression and decreased non-key enzyme expression after RBS sequence optimization were obviously detected through SDS-PAGE analysis. Conclusions This study prove that desired enzyme expression and increased isoprene production were obtained after RBS sequence optimization. RBS optimization of genes could be a powerful strategy for metabolic engineering of strain. Moreover, to increase the production of engineered strain, attention should not only be focused on the key enzymes, but also on the non-key enzymes. Electronic supplementary material The online version of this article (10.1186/s12934-018-1051-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hailin Chen
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Changqing Liu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Jing Guo
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Xin Xu
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.135 Songlin Road, Qingdao, 266101, People's Republic of China.
| |
Collapse
|
42
|
Pandiarajan R, Grover A. In vivo promoter engineering in plants: Are we ready? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:132-138. [PMID: 30466578 DOI: 10.1016/j.plantsci.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 05/27/2023]
Abstract
Engineering plant promoter sequence for optimal expression of a gene has been a long standing goal for plant scientists. In recent times, Sequence Specific Nucleases (SSNs) like CRISPR/Cas9 are enabling researchers to achieve this goal, in vivo in the genome. It is well known that SSNs have met with unprecedented success in rapid transgene free crop improvement largely by targeting the coding sequence. Here, we discuss the strategies being employed by plant scientists in targeting SSNs to non-coding promoter regions/Cis Regulatory Elements (CRE). We collectively refer all such endeavors as in vivo promoter engineering (IPE). We further classify the IPE efforts into CRE addition, CRE deletion/disruption, promoter swap/insertion and targeted promoter polymorphism. Till date, IPE has proven useful in altering plant architecture in tomato, developing resistance against Xanthomonas sp in rice and citrus, and engineering drought tolerance in maize. However it is quite challenging to achieve predictable changes in gene expression using IPE at this point. In future years, data generated from high throughput techniques to investigate non coding genome may immensely augment the efforts in this direction. As IPE does not involve addition of the transgene for modifying crop traits, it will be relatively more conducive to public acceptance in crop improvement programs.
Collapse
Affiliation(s)
- Ramakrishnan Pandiarajan
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India.
| |
Collapse
|
43
|
Wang T, Guo J, Liu Y, Xue Z, Zhang C, Xing XH. Genome-wide screening identifies promiscuous phosphatases impairing terpenoid biosynthesis in Escherichia coli. Appl Microbiol Biotechnol 2018; 102:9771-9780. [DOI: 10.1007/s00253-018-9330-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/12/2018] [Indexed: 01/11/2023]
|
44
|
Park SY, Binkley RM, Kim WJ, Lee MH, Lee SY. Metabolic engineering of Escherichia coli for high-level astaxanthin production with high productivity. Metab Eng 2018; 49:105-115. [DOI: 10.1016/j.ymben.2018.08.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
|
45
|
Ou B, Garcia C, Wang Y, Zhang W, Zhu G. Techniques for chromosomal integration and expression optimization in Escherichia coli. Biotechnol Bioeng 2018; 115:2467-2478. [PMID: 29981268 DOI: 10.1002/bit.26790] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 12/31/2022]
Abstract
Due to the inherent expression stability and low metabolic burden to the host cell, the expression of heterologous proteins in the bacterial chromosome in a precise and efficient manner is highly desirable for metabolic engineering and live bacterial applications. However, obtaining suitable chromosome expression levels is particularly challenging. In this minireview, we briefly present the technologies available for the integration of heterologous genes into Escherichia coli chromosomes and strategies to optimize the expression levels of heterologous proteins.
Collapse
Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Carolina Garcia
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Weiping Zhang
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
46
|
Construction of an alternative glycerol-utilization pathway for improved β-carotene production in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:697-705. [DOI: 10.1007/s10295-018-2045-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/04/2018] [Indexed: 01/27/2023]
Abstract
Abstract
Glycerol, which is an inevitable by-product of biodiesel production, is an ideal carbon source for the production of carotenoids due to its low price, good availability and chemically reduced status, which results in a low requirement for additional reducing equivalents. In this study, an alternative carbon-utilization pathway was constructed in Escherichia coli to enable more efficient β-carotene production from glycerol. An aldehyde reductase gene (alrd) and an aldehyde dehydrogenase gene (aldH) from Ralstonia eutropha H16 were integrated into the E. coli chromosome to form a novel glycerol-utilization pathway. The β-carotene specific production value was increased by 50% after the introduction of alrd and aldH. It was found that the glycerol kinase gene (garK), alrd and aldH were the bottleneck of the alternative glycerol metabolic pathway, and modulation of garK gene with an mRS library further increased the β-carotene specific production value by 13%. Finally, co-modulation of genes in the introduced aldH–alrd operon led to 86% more of β-carotene specific production value than that of the strain without the alternative glycerol-utilization pathway and the glycerol-utilization rate was also increased. In this work, β-carotene production of E. coli was significantly improved by constructing and optimizing an alternative glycerol-utilization pathway. This strategy can potentially be used to improve the production of other isoprenoids using glycerol as a cheap and abundant substrate, and therefore has industrial relevance.
Collapse
|
47
|
Zou H, Zhang T, Li L, Huang J, Zhang N, Shi M, Hao H, Xian M. Systematic Engineering for Improved Carbon Economy in the Biosynthesis of Polyhydroxyalkanoates and Isoprenoids. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1271. [PMID: 30042344 PMCID: PMC6117667 DOI: 10.3390/ma11081271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/23/2022]
Abstract
With the rapid development of synthetic biology and metabolic engineering, a broad range of biochemicals can be biosynthesized, which include polyhydroxyalkanoates and isoprenoids. However, some of the bio-approaches in chemical synthesis have just started to be applied outside of laboratory settings, and many require considerable efforts to achieve economies of scale. One of the often-seen barriers is the low yield and productivity, which leads to higher unit cost and unit capital investment for the bioconversion process. In general, higher carbon economy (less carbon wastes during conversion process from biomass to objective bio-based chemicals) will result in higher bioconversion yield, which results in less waste being generated during the process. To achieve this goal, diversified strategies have been applied; matured strategies include pathway engineering to block competitive pathways, enzyme engineering to enhance the activities of enzymes, and process optimization to improve biomass/carbon yield. In this review, we analyze the impact of carbon sources from different types of biomass on the yield of bio-based chemicals (especially for polyhydroxyalkanoates and isoprenoids). Moreover, we summarize the traditional strategies for improving carbon economy during the bioconversion process and introduce the updated techniques in building up non-natural carbon pathways, which demonstrate higher carbon economies than their natural counterparts.
Collapse
Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Tongtong Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Lei Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Jingling Huang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Nan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - He Hao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| |
Collapse
|
48
|
Li M, Nian R, Xian M, Zhang H. Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli. Appl Microbiol Biotechnol 2018; 102:7725-7738. [PMID: 30006784 PMCID: PMC6132537 DOI: 10.1007/s00253-018-9200-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
The biotechnological production of isoprene and isopentenol has recently been studied. Isoprene, which is currently made mainly from petroleum, is an important platform chemical for synthesizing pesticides, medicines, oil additives, fragrances, and more and is especially important in the rubber production industry. Isopentenols, which have better combustion properties than well-known biofuels (ethanol), have recently received more attention. Supplies of petroleum, the conventional source of isoprene and isopentenols, are unsustainable, and chemical synthesis processes could cause serious environmental problems. As an alternative, the biosynthesis of isoprene and isopentenols in cell factories is more sustainable and environmentally friendly. With a number of advantages over other microorganisms, Escherichia coli is considered to be a powerful workhorse organism for producing these compounds. This review will highlight the recent advances in metabolic engineering for isoprene and isopentenol production, especially using E. coli cell factories.
Collapse
Affiliation(s)
- Meijie Li
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rui Nian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China
| | - Mo Xian
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 135 Songling Road, Qingdao, 266101, People's Republic of China.
| |
Collapse
|
49
|
Adadi P, Barakova NV, Krivoshapkina EF. Selected Methods of Extracting Carotenoids, Characterization, and Health Concerns: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5925-5947. [PMID: 29851485 DOI: 10.1021/acs.jafc.8b01407] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Carotenoids are the most powerful nutrients (medicine) on earth due to their potent antioxidant properties. The ability of these tetraterpenoids in obviating human chronic ailments like cancer, cardiovascular disease, osteoporosis, and diabetes has drawn public attention toward these novel compounds. Conventionally, carotenoids have been extracted from plant materials and agro-industrial byproduct using different solvents, but these procedures result in contaminating the target compound (carotenoids) with extraction solvents. Furthermore, some utilized solvents are not safe and hence are harmful to the environment. This has attracted criticism from consumers, ecologists, environmentalists, and public health workers. However, there is clear consumer preference for carotenoids from natural origin without traces of extracting solvent. Therefore, this review seeks to discuss methods for higher recovery of pure carotenoids without contamination from a solvent. Methods such as enzyme-based extraction, supercritical fluid extraction, microwave-assisted extraction, Soxhlet extraction, ultrasonic extraction, and postextraction treatment (saponification) are discussed. Merits and demerits of these methods along with health concerns during intake of carotenoids were also considered.
Collapse
Affiliation(s)
- Parise Adadi
- ITMO University , Lomonosova Street 9 , 191002 , St. Petersburg , Russia Federation
| | | | | |
Collapse
|
50
|
Wu T, Ye L, Zhao D, Li S, Li Q, Zhang B, Bi C. Engineering membrane morphology and manipulating synthesis for increased lycopene accumulation in Escherichia coli cell factories. 3 Biotech 2018; 8:269. [PMID: 29868307 DOI: 10.1007/s13205-018-1298-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/20/2018] [Indexed: 02/05/2023] Open
Abstract
The goal of this work was to improve the lycopene storage capacity of the E. coli membrane by engineering both morphological and biosynthetic aspects. First, Almgs, a protein from Acholeplasma laidlawii that is involved in membrane bending is overexpressed to expand the storage space for lycopene, which resulted in a 12% increase of specific lycopene production. Second, several genes related to the membrane-synthesis pathway in E. coli, including plsb, plsc, and dgka, were also overexpressed, which led to a further 13% increase. In addition, membrane separation and component analysis confirmed that the increased amount of lycopene was mainly accumulated within the cell membranes. Finally, by integrating both aforementioned modification strategies, a synergistic effect could be observed which caused a 1.32-fold increase of specific lycopene production, from the 27.5 mg/g of the parent to 36.4 mg/g DCW in the engineered strain. This work demonstrates that membrane engineering is a feasible strategy for increasing the production and accumulation of lycopene in E. coli.
Collapse
Affiliation(s)
- Tao Wu
- 1College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People's Republic of China
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Lijun Ye
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Dongdong Zhao
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Siwei Li
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Qingyan Li
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Bolin Zhang
- 1College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People's Republic of China
| | - Changhao Bi
- 2Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| |
Collapse
|