1
|
Regmi P, Knesebeck M, Boles E, Weuster-Botz D, Oreb M. A comparative analysis of NADPH supply strategies in Saccharomyces cerevisiae: Production of d-xylitol from d-xylose as a case study. Metab Eng Commun 2024; 19:e00245. [PMID: 39072283 PMCID: PMC11283233 DOI: 10.1016/j.mec.2024.e00245] [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: 05/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024] Open
Abstract
Enhancing the supply of the redox cofactor NADPH in metabolically engineered cells is a critical target for optimizing the synthesis of many product classes, such as fatty acids or terpenoids. In S. cerevisiae, several successful approaches have been developed in different experimental contexts. However, their systematic comparison has not been reported. Here, we established the reduction of xylose to xylitol by an NADPH-dependent xylose reductase as a model reaction to compare the efficacy of different NADPH supply strategies in the course of a batch fermentation, in which glucose and ethanol are sequentially used as carbon sources and redox donors. We show that strains overexpressing the glucose-6-phosphate dehydrogenase Zwf1 perform best, producing up to 16.9 g L-1 xylitol from 20 g L-1 xylose in stirred tank bioreactors. The beneficial effect of increased Zwf1 activity is especially pronounced during the ethanol consumption phase. The same notion applies to the deletion of the aldehyde dehydrogenase ALD6 gene, albeit at a quantitatively lower level. Reduced expression of the phosphoglucose isomerase Pgi1 and heterologous expression of the NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase Gdp1 from Kluyveromyces lactis acted synergistically with ZWF1 overexpression in the presence of glucose, but had a detrimental effect after the diauxic shift. Expression of the mitochondrial NADH kinase Pos5 in the cytosol likewise improved the production of xylitol only on glucose, but not in combination with enhanced Zwf1 activity. To demonstrate the generalizability of our observations, we show that the most promising strategies - ZWF1 overexpression and deletion of ALD6 - also improve the production of l-galactonate from d-galacturonic acid. Therefore, we expect that these findings will provide valuable guidelines for engineering not only the production of xylitol but also of diverse other pathways that require NADPH.
Collapse
Affiliation(s)
- Priti Regmi
- Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Molecular Biosciences, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Melanie Knesebeck
- Technical University of Munich, Chair of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
| | - Eckhard Boles
- Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Molecular Biosciences, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Chair of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
| | - Mislav Oreb
- Goethe University Frankfurt, Faculty of Biological Sciences, Institute of Molecular Biosciences, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| |
Collapse
|
2
|
Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
Collapse
Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
| |
Collapse
|
3
|
Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
Collapse
Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
4
|
Liu X, Li K, Yu J, Ma C, Che Q, Zhu T, Li D, Pfeifer BA, Zhang G. Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering. Metab Eng 2024; 82:147-156. [PMID: 38382797 DOI: 10.1016/j.ymben.2024.02.009] [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: 11/28/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust cFF production system which entailed stepwise engineering of the filamentous fungal strain Aspergillus nidulans A1145 as a heterologous expression host. We first established a preliminary cFF producing strain by introducing the heterologous nonribosomal peptide synthetase (NRPS) gene penP1 to A. nidulans A1145. Key metabolic pathways involving shikimate and aromatic amino acid biosynthetic support were then engineered through a combination of gene deletions of competitive pathway steps, over-expressing feedback-insensitive enzymes in phenylalanine biosynthesis, and introducing a phosphoketolase-based pathway, which diverted glycolytic flux toward the formation of erythrose 4-phosphate (E4P). Through the stepwise engineering of A. nidulans A1145 outlined above, involving both heterologous pathway addition and native pathway metabolic engineering, we were able to produce cFF with titers reaching 611 mg/L in shake flask culture and 2.5 g/L in bench-scale fed-batch bioreactor culture. Our study establishes a production platform for cFF biosynthesis and successfully demonstrates engineering of phenylalanine derived diketopiperazines in a filamentous fungal host.
Collapse
Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Kang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, 14260, United States.
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Department for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao, 266237, China; Lab of Marine Medicinal Resources Discovery, Marine Biomedical Research Institute of Qingdao, Qingdao, 266075, China.
| |
Collapse
|
5
|
Gong Y, Wang R, Ma L, Wang S, Li C, Xu Q. Optimization of trans-4-hydroxyproline synthesis pathway by rearrangement center carbon metabolism in Escherichia coli. Microb Cell Fact 2023; 22:240. [PMID: 37986164 PMCID: PMC10659092 DOI: 10.1186/s12934-023-02236-6] [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: 08/08/2023] [Accepted: 10/22/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND trans-4-Hydroxyproline (T-4-HYP) is a promising intermediate in the synthesis of antibiotic drugs. However, its industrial production remains challenging due to the low production efficiency of T-4-HYP. This study focused on designing the key nodes of anabolic pathway to enhance carbon flux and minimize carbon loss, thereby maximizing the production potential of microbial cell factories. RESULTS First, a basic strain, HYP-1, was developed by releasing feedback inhibitors and expressing heterologous genes for the production of trans-4-hydroxyproline. Subsequently, the biosynthetic pathway was strengthened while branching pathways were disrupted, resulting in increased metabolic flow of α-ketoglutarate in the Tricarboxylic acid cycle. The introduction of the NOG (non-oxidative glycolysis) pathway rearranged the central carbon metabolism, redirecting glucose towards acetyl-CoA. Furthermore, the supply of NADPH was enhanced to improve the acid production capacity of the strain. Finally, the fermentation process of T-4-HYP was optimized using a continuous feeding method. The rate of sugar supplementation controlled the dissolved oxygen concentrations during fermentation, and Fe2+ was continuously fed to supplement the reduced iron for hydroxylation. These modifications ensured an effective supply of proline hydroxylase cofactors (O2 and Fe2+), enabling efficient production of T-4-HYP in the microbial cell factory system. The strain HYP-10 produced 89.4 g/L of T-4-HYP in a 5 L fermenter, with a total yield of 0.34 g/g, the highest values reported by microbial fermentation, the yield increased by 63.1% compared with the highest existing reported yield. CONCLUSION This study presents a strategy for establishing a microbial cell factory capable of producing T-4-HYP at high levels, making it suitable for large-scale industrial production. Additionally, this study provides valuable insights into regulating synthesis of other compounds with α-ketoglutaric acid as precursor.
Collapse
Affiliation(s)
- Yu Gong
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Ruiqi Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Ling Ma
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Shuo Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Changgeng Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.
| |
Collapse
|
6
|
Kusmayadi A, Huang CY, Kit Leong Y, Yen HW, Lee DJ, Chang JS. Utilizing microalgal hydrolysate from dairy wastewater-grown Chlorella sorokiniana SU-1 as sustainable feedstock for polyhydroxybutyrate and β-carotene production by engineered Rhodotorula glutinis #100-29. BIORESOURCE TECHNOLOGY 2023:129277. [PMID: 37290703 DOI: 10.1016/j.biortech.2023.129277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
The objective of this study was to explore the potential of utilizing Chlorella sorokiniana SU-1 biomass grown on dairy wastewater-amended medium as sustainable feedstock for the biosynthesis of β-carotene and polyhydroxybutyrate (PHB) by Rhodotorula glutinis #100-29. To break down the rigid cell wall, 100 g/L of microalgal biomass was treated with 3% sulfuric acid, followed by detoxification using 5% activated carbon to remove the hydroxymethylfurfural inhibitor. The detoxified microalgal hydrolysate (DMH) was used for flask-scale fermentation, which yielded a maximum biomass production of 9.22 g/L, with PHB and β-carotene concentration of 897 mg/L and 93.62 mg/L, respectively. Upon scaling up to a 5-L fermenter, the biomass concentration increased to 11.2 g/L, while the PHB and β-carotene concentrations rose to 1830 mg/L and 134.2 mg/L. These outcomes indicate that DMH holds promise as sustainable feedstock for the production of PHB and β-carotene by yeast.
Collapse
Affiliation(s)
- Adi Kusmayadi
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, Taiwan
| | - Chi-Yu Huang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, Taiwan; Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
| | - Yoong Kit Leong
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, Taiwan
| | - Hong-Wei Yen
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, Tunghai University, Taichung, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
| |
Collapse
|
7
|
Mussagy CU, Ribeiro HF, Pereira JFB. Rhodotorula sp. as a cell factory for production of valuable biomolecules. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:133-156. [PMID: 37400173 DOI: 10.1016/bs.aambs.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Rhodotorula sp. are well-known for their ability to biosynthesize a diverse range of valuable biomolecules, including carotenoids, lipids, enzymes, and polysaccharides. Despite the high number of studies conducted using Rhodotorula sp. at the laboratory scale, most of these do not address all processual aspects necessary for scaling up these processes for industrial applications. This chapter explores the potential of Rhodotorula sp. as a cell factory for the production of distinct biomolecules, with a particular emphasis on exploring their use from a biorefinery perspective. Through in-depth discussions of the latest research and insights into non-conventional applications, we aim to provide a comprehensive understanding of Rhodotorula sp.'s ability to produce biofuels, bioplastics, pharmaceuticals, and other valuable biochemicals. This book chapter also examines the fundamentals and challenges associated with the optimizing upstream and downstream processing of Rhodotorula sp-based processes. We believe that through this chapter, readers with different levels of expertise will gain insights into strategies for enhancing the sustainability, efficiency, and effectiveness of producing biomolecules using Rhodotorula sp.
Collapse
Affiliation(s)
- Cassamo U Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota, Chile.
| | - Helena F Ribeiro
- Department of Chemical Engineering, University of Coimbra, CIEPQPF, Coimbra, Portugal
| | - Jorge F B Pereira
- Department of Chemical Engineering, University of Coimbra, CIEPQPF, Coimbra, Portugal
| |
Collapse
|
8
|
Wu Z, Liang X, Li M, Ma M, Zheng Q, Li D, An T, Wang G. Advances in the optimization of central carbon metabolism in metabolic engineering. Microb Cell Fact 2023; 22:76. [PMID: 37085866 PMCID: PMC10122336 DOI: 10.1186/s12934-023-02090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.
Collapse
Affiliation(s)
- Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| |
Collapse
|
9
|
Tharasirivat V, Jantaro S. Increased Biomass and Polyhydroxybutyrate Production by Synechocystis sp. PCC 6803 Overexpressing RuBisCO Genes. Int J Mol Sci 2023; 24:ijms24076415. [PMID: 37047389 PMCID: PMC10094337 DOI: 10.3390/ijms24076415] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
The overexpression of the RuBisCO (rbc) gene has recently become an achievable strategy for increasing cyanobacterial biomass and overcoming the biocompound production restriction. We successfully constructed two rbc-overexpressing Synechocystis sp. PCC 6803 strains (OX), including a strain overexpressing a large subunit of RuBisCO (OXrbcL) and another strain overexpressing all large, chaperone, and small subunits of RuBisCO (OXrbcLXS), resulting in higher and faster growth than wild type under sodium bicarbonate supplementation. This increased biomass of OX strains significantly contributed to the higher polyhydroxybutyrate (PHB) production induced by nutrient-deprived conditions, in particular nitrogen (N) and phosphorus (P). As a result of higher PHB contents in OX strains occurring at days 7 and 9 of nutrient deprivation, this enhancement was apparently made possible by cells preferentially maintaining their internal lipids while accumulating less glycogen. The OXrbcLXS strain, with the highest level of PHB at about 39 %w/dry cell weight (DCW) during 7 days of BG11-NP treatment, contained a lower glycogen level (31.9 %w/DCW) than wild type control (40 %w/DCW). In contrast, the wild type control strain exposed to N- and NP-stresses tended to retain lipid levels and store more glycogen than PHB. In this model, we, for the first time, implemented a RuBisCO-overexpressing cyanobacterial factory for overproducing PHB, destined for biofuel and biomaterial biotechnology.
Collapse
|
10
|
Priyanka U, Lens PNL. Enhanced production of amylase, pyruvate and phenolic compounds from glucose by light-driven Aspergillus niger-CuS nanobiohybrids. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2023; 98:602-614. [PMID: 37066082 PMCID: PMC10087041 DOI: 10.1002/jctb.7153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/29/2022] [Accepted: 06/08/2022] [Indexed: 06/19/2023]
Abstract
BACKGROUND The demand for value-added compounds such as amylase, pyruvate and phenolic compounds produced by biological methods has prompted the rapid development of advanced technologies for their enhanced production. Nanobiohybrids (NBs) make use of both the microbial properties of whole-cell microorganisms and the light-harvesting efficiency of semiconductors. Photosynthetic NBs were constructed that link the biosynthetic pathways of Aspergillus niger with CuS nanoparticles. RESULTS In this work, NB formation was confirmed by negative values of the interaction energy, i.e., 2.31 × 108 to -5.52 × 108 kJ mol-1 for CuS-Che NBs, whereas for CuS-Bio NBs the values were -2.31 × 108 to -4.62 × 108 kJ mol-1 for CuS-Bio NBs with spherical nanoparticle interaction. For CuS-Bio NBs with nanorod interaction, it ranged from -2.3 × 107 to -3.47 × 107 kJ mol-1 . Further, the morphological changes observed by scanning electron microscopy showed the presence of the elements Cu and S in the energy-dispersive X-ray spectra and the presence of CuS bonds in Fourier transform infrared spectroscopy indicate NB formation. In addition, the quenching effect in photoluminescence studies confirmed NB formation. Production yields of amylase, phenolic compounds and pyruvate amounted to 11.2 μmol L-1, 52.5 μmol L-1 and 28 nmol μL-1, respectively, in A. niger-CuS Bio NBs on the third day of incubation in the bioreactor. Moreover, A niger cells-CuS Bio NBs had amino acids and lipid yields of 6.2 mg mL-1 and 26.5 mg L-1, respectively. Furthermore, probable mechanisms for the enhanced production of amylase, pyruvate and phenolic compounds are proposed. CONCLUSION Aspergillus niger-CuS NBs were used for the production of the amylase enzyme and value-added compounds such as pyruvate and phenolic compounds. Aspergillus niger-CuS Bio NBs showed a greater efficiency compared to A. niger-CuS Che NBs as the biologically produced CuS nanoparticles had a higher compatibility with A. niger cells. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).
Collapse
Affiliation(s)
- Uddandarao Priyanka
- Department of Microbiology and Ryan InstituteNational University of IrelandGalwayIreland
| | - Piet NL Lens
- Department of Microbiology and Ryan InstituteNational University of IrelandGalwayIreland
| |
Collapse
|
11
|
Janasch M, Crang N, Asplund-Samuelsson J, Sporre E, Bruch M, Gynnå A, Jahn M, Hudson EP. Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator. Metab Eng 2022; 73:256-269. [PMID: 35987434 DOI: 10.1016/j.ymben.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/10/2022] [Accepted: 08/06/2022] [Indexed: 11/30/2022]
Abstract
The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields from formate for different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were then verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified additional reactions associated with low and high PHB yield. Proteomics analysis of the engineered strains confirmed an increased abundance of aconitase and cofactor balancing. The findings of this study aid in understanding metabolic adaptation. Furthermore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria.
Collapse
Affiliation(s)
- Markus Janasch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Nick Crang
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Emil Sporre
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Manuel Bruch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Arvid Gynnå
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Michael Jahn
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Elton P Hudson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| |
Collapse
|
12
|
Zhang M, Wang Z, Chi Z, Liu GL, Chi ZM. Metabolic engineering of Aureobasidium melanogenum 9-1 for overproduction of liamocins by enhancing supply of acetyl-CoA and ATP. Microbiol Res 2022; 265:127172. [DOI: 10.1016/j.micres.2022.127172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/09/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022]
|
13
|
Ylinen A, de Ruijter JC, Jouhten P, Penttilä M. PHB production from cellobiose with Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:124. [PMID: 35729556 PMCID: PMC9210708 DOI: 10.1186/s12934-022-01845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Replacement of petrochemical-based materials with microbially produced biodegradable alternatives calls for industrially attractive fermentation processes. Lignocellulosic materials offer non-edible alternatives for cultivated sugars, but require often use of expensive sugar releasing enzymes, such as β-glucosidases. These cellulose treatment costs could be reduced if microbial production hosts could use short cellodextrins such as cellobiose directly as their substrates. In this study, we demonstrate production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Yeast strains expressing PHB pathway genes from Cupriavidus necator and cellodextrin transporter gene CDT-1 from Neurospora crassa were complemented either with β-glucosidase gene GH1-1 from N. crassa or with cellobiose phosphorylase gene cbp from Ruminococcus flavefaciens. These cellobiose utilization routes either with Gh1-1 or Cbp enzymes differ in energetics and dynamics. However, both routes enabled higher PHB production per consumed sugar and higher PHB accumulation % of cell dry weight (CDW) than use of glucose as a carbon source. As expected, the strains with Gh1-1 consumed cellobiose faster than the strains with Cbp, both in flask and bioreactor batch cultures. In shake flasks, higher final PHB accumulation % of CDW was reached with Cbp route (10.0 ± 0.3%) than with Gh1-1 route (8.1 ± 0.2%). However, a higher PHB accumulation was achieved in better aerated and pH-controlled bioreactors, in comparison to shake flasks, and the relative performance of strains switched. In bioreactors, notable PHB accumulation levels per CDW of 13.4 ± 0.9% and 18.5 ± 3.9% were achieved with Cbp and Gh1-1 routes, respectively. The average molecular weights of accumulated PHB were similar using both routes; approximately 500 kDa and 450 kDa for strains expressing either cbp or GH1-1 genes, respectively. The formation of PHB with high molecular weights, combined with efficient cellobiose conversion, demonstrates a highly potential solution for improving attractiveness of sustainable polymer production using microbial cells.
Collapse
Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 00076, Espoo, Finland
| |
Collapse
|
14
|
Su B, Lai P, Yang F, Li A, Deng MR, Zhu H. Engineering a Balanced Acetyl Coenzyme A Metabolism in Saccharomyces cerevisiae for Lycopene Production through Rational and Evolutionary Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4019-4029. [PMID: 35319878 DOI: 10.1021/acs.jafc.2c00531] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Saccharomyces cerevisiae is increasingly being used for the production of chemicals derived from acetyl coenzyme A (acetyl-CoA). However, the inadequate supply of cytosolic acetyl-CoA often leads to low yields. Here, we developed a novel strategy for balancing acetyl-CoA metabolism and increasing the amount of the downstream product. First, the combination of acetaldehyde dehydrogenase (eutE) and acetoacetyl-CoA thiolase (AtoB) was optimized to redirect the acetyl-CoA flux toward the target pathway, with a 21-fold improvement in mevalonic acid production. Second, pathway engineering and evolutionary engineering were conducted to attenuate the growth deficiency, and a 10-fold improvement of the maximum productivity was achieved. Third, acetyl-CoA carboxylase (ACC1) was dynamically downregulated as the complementary acetyl-CoA pathway, and the yield was improved more than twofold. Fourth, the most efficient and complementary acetyl-CoA pathways were combined, and the final strain produced 68 mg/g CDW lycopene, which was among the highest yields reported in S. cerevisiae. This study demonstrates a new method of producing lycopene products by regulating acetyl-CoA metabolism.
Collapse
Affiliation(s)
- Buli Su
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Peixuan Lai
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Fan Yang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Anzhang Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| |
Collapse
|
15
|
Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system. Metab Eng Commun 2022; 14:e00199. [PMID: 35571351 PMCID: PMC9095885 DOI: 10.1016/j.mec.2022.e00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022] Open
Abstract
The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation in vivo at gene expression level, independent of cultivation conditions. We used the modified doxycycline-based Tet-On approach to adjust the expression of the stereospecific D-lactate dehydrogenase gene (ldhA) from Leuconostoc mesenteroides to control D-lactic acid formation in yeast Saccharomyces cerevisiae. The synthetic Tet-On transcription factor with a VP16 activation domain was continuously expressed and its binding to a synthetic promoter with eight transcription factor specific binding sites upstream of the ldhA gene was controlled with the doxycycline concentration in the media. The increase in doxycycline concentration correlated positively with ldhA expression, D-lactic acid production, poly(D-lactic acid) (PDLA) accumulation in vivo, and D-lactic acid content in the poly(D-lactate-co-3-hydroxybutyrate) P(LA-3HB) copolymer. We demonstrated that the D-lactic acid content of the P(LA-3HB) copolymer can be adjusted linearly from 6 mol% to 93 mol% in vivo in S. cerevisiae. These results highlight the power of controlling gene expression and monomer formation in the tuning of the polymer composition. In addition, we obtained 5.6% PDLA and 19% P(LA-3HB) of the cell dry weight (CDW), which are over two- and five-fold higher accumulation levels, respectively, than reported in the previous studies with yeast. We also compared two engineered PHA synthases and discovered that in S. cerevisiae the PHA synthase PhaC1437Ps6-19 produced P(LA-3HB) copolymers with lower D-lactic acid content, but with higher molecular weight, in comparison to the PHA synthase PhaC1Pre. P(LA-3HB) monomer structure was adjusted with controlled gene expression. Expression of D-lactate dehydrogenase (ldhA) was controlled with Tet-On approach. Lactic acid content in copolymer P(LA-3HB) was adjusted from 6 mol% up to 93 mol%. 5.6% PDLA and 19% P(LA-3HB) of cell dry weight (CDW) were obtained in S. cerevisiae. PhaC1437Ps6-19 P(LA-3HB) had lower D-lactic acid % than PhaC1Pre P(LA-3HB).
Collapse
|
16
|
Zhang Q, Zeng W, Xu S, Zhou J. Metabolism and strategies for enhanced supply of acetyl-CoA in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2021; 342:125978. [PMID: 34598073 DOI: 10.1016/j.biortech.2021.125978] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Acetyl-CoA is a kind of important cofactor that is involved in many metabolic pathways. It serves as the precursor for many interesting commercial products, such as terpenes, flavonoids and anthraquinones. However, the insufficient supply of acetyl-CoA limits biosynthesis of its derived compounds in the intracellular. In this review, we outlined metabolic pathways involved in the catabolism and anabolism of acetyl-CoA, as well as some important derived products. We examined several strategies for the enhanced supply of acetyl-CoA, and provided insight into pathways that generate acetyl-CoA to balance metabolism, which can be harnessed to improve the titer, yield and productivities of interesting products in Saccharomyces cerevisiae and other eukaryotic microorganisms. We believe that peroxisomal fatty acid β-oxidation could be an attractive strategy for enhancing the supply of acetyl-CoA.
Collapse
Affiliation(s)
- Qian Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| |
Collapse
|
17
|
Kim J, Hwang S, Lee SM. Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass. Metab Eng 2021; 71:2-12. [PMID: 34626808 DOI: 10.1016/j.ymben.2021.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/16/2021] [Accepted: 10/03/2021] [Indexed: 01/01/2023]
Abstract
The petrochemical industry has grown to meet the need for massive production of energy and commodities along with an explosive population growth; however, serious side effects such as greenhouse gas emissions and global warming have negatively impacted the environment. Lignocellulosic biomass with myriad quantities on Earth is an attractive resource for the production of carbon-neutral fuels and chemicals through environmentally friendly processes of microbial fermentation. This review discusses metabolic engineering efforts to achieve economically feasible industrial production of fuels and chemicals from microbial cell factories using the carbohydrate portion of lignocellulosic biomass as substrates. The combined knowledge of systems biology and metabolic engineering has been applied to construct robust platform microorganisms with maximum conversion of monomeric sugars, such as glucose and xylose, derived from lignocellulosic biomass. By comprehensively revisiting carbon conversion pathways, we provide a rationale for engineering strategies, as well as their features, feasibility, and recent representative studies. In addition, we briefly discuss how tools in systems biology can be applied in the field of metabolic engineering to accelerate the development of microbial cell factories that convert lignocellulosic biomass into carbon-neutral fuels and chemicals with economic feasibility.
Collapse
Affiliation(s)
- Jiwon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sungmin Hwang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Clean Energy and Chemical Engineering, University of Science and Technology, Daejeon, 34113, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, Seoul, 02841, Republic of Korea.
| |
Collapse
|
18
|
Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
Collapse
Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
19
|
Wegner SA, Chen JM, Ip SS, Zhang Y, Dugar D, Avalos JL. Engineering acetyl-CoA supply and ERG9 repression to enhance mevalonate production in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2021; 48:6342157. [PMID: 34351398 PMCID: PMC8788843 DOI: 10.1093/jimb/kuab050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Mevalonate is a key precursor in isoprenoid biosynthesis and a promising commodity chemical. Although mevalonate is a native metabolite in Saccharomyces cerevisiae, its production is challenged by the relatively low flux toward acetyl-CoA in this yeast. In this study we explore different approaches to increase acetyl-CoA supply in S. cerevisiae to boost mevalonate production. Stable integration of a feedback-insensitive acetyl-CoA synthetase (Se-acsL641P) from Salmonella enterica and the mevalonate pathway from Enterococcus faecalis results in the production of 1,390 ± 10 mg/l of mevalonate from glucose. While bifid shunt enzymes failed to improve titers in high-producing strains, inhibition of squalene synthase (ERG9) results in a significant enhancement. Finally, increasing coenzyme A (CoA) biosynthesis by overexpression of pantothenate kinase (CAB1) and pantothenate supplementation further increased production to 3,830 ± 120 mg/l. Using strains that combine these strategies in lab-scale bioreactors results in the production of 13.3 ± 0.5 g/l, which is ∼360-fold higher than previously reported mevalonate titers in yeast. This study demonstrates the feasibility of engineering S. cerevisiae for high-level mevalonate production.
Collapse
Affiliation(s)
- Scott A Wegner
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jhong-Min Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Samantha S Ip
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yanfei Zhang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Deepak Dugar
- Visolis, Inc., 1488 Zephyr Ave. Hayward, CA 94544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA.,High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
20
|
Ylinen A, Maaheimo H, Anghelescu-Hakala A, Penttilä M, Salusjärvi L, Toivari M. Production of D-lactic acid containing polyhydroxyalkanoate polymers in yeast Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2021; 48:6253250. [PMID: 33899921 PMCID: PMC9113173 DOI: 10.1093/jimb/kuab028] [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: 01/26/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022]
Abstract
Polyhydroxyalkanoates (PHAs) provide biodegradable and bio-based alternatives to conventional plastics. Incorporation of 2-hydroxy acid monomers into polymer, in addition to 3-hydroxy acids, offers possibility to tailor the polymer properties. In this study, poly(D-lactic acid) (PDLA) and copolymer P(LA-3HB) were produced and characterized for the first time in the yeast Saccharomyces cerevisiae. Expression of engineered PHA synthase PhaC1437Ps6–19, propionyl-CoA transferase Pct540Cp, acetyl-CoA acetyltransferase PhaA, and acetoacetyl-CoA reductase PhaB1 resulted in accumulation of 3.6% P(LA-3HB) and expression of engineered enzymes PhaC1Pre and PctMe resulted in accumulation of 0.73% PDLA of the cell dry weight (CDW). According to NMR, P(LA-3HB) contained D-lactic acid repeating sequences. For reference, expression of PhaA, PhaB1, and PHA synthase PhaC1 resulted in accumulation 11% poly(hydroxybutyrate) (PHB) of the CDW. Weight average molecular weights of these polymers were comparable to similar polymers produced by bacterial strains, 24.6, 6.3, and 1 130 kDa for P(LA-3HB), PDLA, and PHB, respectively. The results suggest that yeast, as a robust and acid tolerant industrial production organism, could be suitable for production of 2-hydroxy acid containing PHAs from sugars or from 2-hydroxy acid containing raw materials. Moreover, the wide substrate specificity of PHA synthase enzymes employed increases the possibilities for modifying copolymer properties in yeast in the future.
Collapse
Affiliation(s)
- Anna Ylinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
| | - Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| |
Collapse
|
21
|
Kamineni A, Consiglio AL, MacEwen K, Chen S, Chifamba G, Shaw AJ, Tsakraklides V. Increasing lipid yield in Yarrowia lipolytica through phosphoketolase and phosphotransacetylase expression in a phosphofructokinase deletion strain. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:113. [PMID: 33947437 PMCID: PMC8094482 DOI: 10.1186/s13068-021-01962-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/21/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lipids are important precursors in the biofuel and oleochemical industries. Yarrowia lipolytica is among the most extensively studied oleaginous microorganisms and has been a focus of metabolic engineering to improve lipid production. Yield improvement, through rewiring of the central carbon metabolism of Y. lipolytica from glucose to the lipid precursor acetyl-CoA, is a key strategy for achieving commercial success in this organism. RESULTS Building on YB-392, a Y. lipolytica isolate known for stable non-hyphal growth and low citrate production with demonstrated potential for high lipid accumulation, we assembled a heterologous pathway that redirects carbon flux from glucose through the pentose phosphate pathway (PPP) to acetyl-CoA. We used phosphofructokinase (Pfk) deletion to block glycolysis and expressed two non-native enzymes, phosphoketolase (Xpk) and phosphotransacetylase (Pta), to convert PPP-produced xylulose-5-P to acetyl-CoA. Introduction of the pathway in a pfk deletion strain that is unable to grow and accumulate lipid from glucose in defined media ensured maximal redirection of carbon flux through Xpk/Pta. Expression of Xpk and Pta restored growth and lipid production from glucose. In 1-L bioreactors, the engineered strains recorded improved lipid yield and cell-specific productivity by up to 19 and 78%, respectively. CONCLUSIONS Yields and cell-specific productivities are important bioprocess parameters for large-scale lipid fermentations. Improving these parameters by engineering the Xpk/Pta pathway is an important step towards developing Y. lipolytica as an industrially preferred microbial biocatalyst for lipid production.
Collapse
Affiliation(s)
| | | | - Kyle MacEwen
- Ginkgo Bioworks, 27 Drydock Ave, Boston, Massachusetts, United States
| | - Shuyan Chen
- Ginkgo Bioworks, 27 Drydock Ave, Boston, Massachusetts, United States
| | | | | | | |
Collapse
|
22
|
Hellgren J, Godina A, Nielsen J, Siewers V. Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metab Eng 2020; 62:150-160. [DOI: 10.1016/j.ymben.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 01/31/2023]
|
23
|
Su B, Song D, Zhu H. Metabolic Engineering of Saccharomyces cerevisiae for Enhanced Carotenoid Production From Xylose-Glucose Mixtures. Front Bioeng Biotechnol 2020; 8:435. [PMID: 32478054 PMCID: PMC7240070 DOI: 10.3389/fbioe.2020.00435] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 01/31/2023] Open
Abstract
Co-utilization of xylose and glucose from lignocellulosic biomass is an economically feasible bioprocess for chemical production. Many strategies have been implemented for efficiently assimilating xylose which is one of the predominant sugars of lignocellulosic biomass. However, there were few reports about engineering Saccharomyces cerevisiae for carotenoid production from xylose-glucose mixtures. Herein, we developed a platform for facilitating carotenoid production in S. cerevisiae by fermentation of xylose-glucose mixtures. Firstly, a xylose assimilation pathway with mutant xylose reductase (XYL1m), xylitol dehydrogenase (XYL2), and xylulokinase (XK) was constructed for utilizing xylose. Then, introduction of phosphoketolase (PK) pathway, deletion of Pho13 and engineering yeast hexose transporter Gal2 were conducted to improve carotenoid yields. The final strain SC105 produced a 1.6-fold higher production from mixed sugars than that from glucose in flask culture. In fed-batch fermentation with continuous feeding of mixed sugars, carotenoid production represented a 2.6-fold higher. To the best of our knowledge, this is the first report that S. cerevisiae was engineered to utilize xylose-glucose mixtures for carotenoid production with a considerable high yield. The present study exhibits a promising advantage of xylose-glucose mixtures assimilating strain as an industrial carotenoid producer from lignocellulosic biomass.
Collapse
Affiliation(s)
- Buli Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dandan Song
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
24
|
Donzella S, Cucchetti D, Capusoni C, Rizzi A, Galafassi S, Chiara G, Compagno C. Engineering cytoplasmic acetyl-CoA synthesis decouples lipid production from nitrogen starvation in the oleaginous yeast Rhodosporidium azoricum. Microb Cell Fact 2019; 18:199. [PMID: 31727065 PMCID: PMC6854766 DOI: 10.1186/s12934-019-1250-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/04/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Oleaginous yeasts are able to accumulate very high levels of neutral lipids especially under condition of excess of carbon and nitrogen limitation (medium with high C/N ratio). This makes necessary the use of two-steps processes in order to achieve high level of biomass and lipid. To simplify the process, the decoupling of lipid synthesis from nitrogen starvation, by establishing a cytosolic acetyl-CoA formation pathway alternative to the one catalysed by ATP-citrate lyase, can be useful. RESULTS In this work, we introduced a new cytoplasmic route for acetyl-CoA (AcCoA) formation in Rhodosporidium azoricum by overexpressing genes encoding for homologous phosphoketolase (Xfpk) and heterologous phosphotransacetylase (Pta). The engineered strain PTAPK4 exhibits higher lipid content and produces higher lipid concentration than the wild type strain when it was cultivated in media containing different C/N ratios. In a bioreactor process performed on glucose/xylose mixture, to simulate an industrial process for lipid production from lignocellulosic materials, we obtained an increase of 89% in final lipid concentration by the engineered strain in comparison to the wild type. This indicates that the transformed strain can produce higher cellular biomass with a high lipid content than the wild type. The transformed strain furthermore evidenced the advantage over the wild type in performing this process, being the lipid yields 0.13 and 0.05, respectively. CONCLUSION Our results show that the overexpression of homologous Xfpk and heterologous Pta activities in R. azoricum creates a new cytosolic AcCoA supply that decouples lipid production from nitrogen starvation. This metabolic modification allows improving lipid production in cultural conditions that can be suitable for the development of industrial bioprocesses using lignocellulosic hydrolysates.
Collapse
Affiliation(s)
- Silvia Donzella
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | | | - Claudia Capusoni
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Aurora Rizzi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Silvia Galafassi
- Water Research Institute, National Research Council, Verbania, Italy
| | - Gambaro Chiara
- Eni S.p.A.-Renewable Energy and Environmental R&D Center-Istituto Eni Donegani, Novara, Italy
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy.
| |
Collapse
|
25
|
Growth-coupled evolution of phosphoketolase to improve l-glutamate production by Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:8413-8425. [DOI: 10.1007/s00253-019-10043-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
|
26
|
Liu H, Fan J, Wang C, Li C, Zhou X. Enhanced β-Amyrin Synthesis in Saccharomyces cerevisiae by Coupling An Optimal Acetyl-CoA Supply Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3723-3732. [PMID: 30808164 DOI: 10.1021/acs.jafc.9b00653] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
β-Amyrin is a plant-derived triterpenoid skeleton with wide applications in food and medical industry. β-Amyrin biosynthesis in Saccharomyces cerevisiae is derived from the mevalonate pathway with cytosolic acetyl-CoA as a precursor. In this work, endogenous and several heterologous acetyl-CoA synthesis pathways were coupled to β-amyrin production and a combinational acetyl-CoA supply route was demonstrated to be optimal due to more balanced redox cofactors, much lower energy consumption, and glucose utilization as well as significantly enhanced β-amyrin production (a 200% increase compared to the original β-amyrin-producing strain). Further disruption of an acetyl-CoA competing pathway led to a 330% increase in β-amyrin production as compared to the original strain. Finally, the engineered strain harboring the optimal pathway configuration achieved a final β-amyrin production of 279.0 ± 13.0 mg/L in glucose fed-batch fermentation, which is the highest as ever reported. This work provides an efficient platform for triterpenoid biosynthesis in Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Jingjing Fan
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Chen Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300072 , China
| | - Xiaohong Zhou
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| |
Collapse
|
27
|
Bergman A, Hellgren J, Moritz T, Siewers V, Nielsen J, Chen Y. Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae. Microb Cell Fact 2019; 18:25. [PMID: 30709397 PMCID: PMC6359841 DOI: 10.1186/s12934-019-1072-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/23/2019] [Indexed: 12/05/2022] Open
Abstract
Introduction Phosphoketolases (Xfpk) are a non-native group of enzymes in yeast, which can be expressed in combination with other metabolic enzymes to positively influence the yield of acetyl-CoA derived products by reducing carbon losses in the form of CO2. In this study, a yeast strain expressing Xfpk from Bifidobacterium breve, which was previously found to have a growth defect and to increase acetate production, was characterized. Results Xfpk-expression was found to increase respiration and reduce biomass yield during glucose consumption in batch and chemostat cultivations. By cultivating yeast with or without Xfpk in bioreactors at different pHs, we show that certain aspects of the negative growth effects coupled with Xfpk-expression are likely to be explained by proton decoupling. At low pH, this manifests as a reduction in biomass yield and growth rate in the ethanol phase. Secondly, we show that intracellular sugar phosphate pools are significantly altered in the Xfpk-expressing strain. In particular a decrease of the substrates xylulose-5-phosphate and fructose-6-phosphate was detected (26% and 74% of control levels) together with an increase of the products glyceraldehyde-3-phosphate and erythrose-4-phosphate (208% and 542% of control levels), clearly verifying in vivo Xfpk enzymatic activity. Lastly, RNAseq analysis shows that Xfpk expression increases transcription of genes related to the glyoxylate cycle, the TCA cycle and respiration, while expression of genes related to ethanol and acetate formation is reduced. The physiological and transcriptional changes clearly demonstrate that a heterologous phosphoketolase flux in combination with endogenous hydrolysis of acetyl-phosphate to acetate increases the cellular demand for acetate assimilation and respiratory ATP-generation, leading to carbon losses. Conclusion Our study shows that expression of Xfpk in yeast diverts a relatively small part of its glycolytic flux towards acetate formation, which has a significant impact on intracellular sugar phosphate levels and on cell energetics. The elevated acetate flux increases the ATP-requirement for ion homeostasis and need for respiratory assimilation, which leads to an increased production of CO2. A majority of the negative growth effects coupled to Xfpk expression could likely be counteracted by preventing acetate accumulation via direct channeling of acetyl-phosphate towards acetyl-CoA. Electronic supplementary material The online version of this article (10.1186/s12934-019-1072-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexandra Bergman
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Hellgren
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Center (UPSC), 901 83, Umeå, Sweden.,Swedish Metabolomics Centre, Umeå Plant Science Center (UPSC), 901 83, Umeå, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296, Gothenburg, Sweden.
| |
Collapse
|
28
|
Production of biofuels and chemicals from xylose using native and engineered yeast strains. Biotechnol Adv 2018; 37:271-283. [PMID: 30553928 DOI: 10.1016/j.biotechadv.2018.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/13/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022]
Abstract
Numerous metabolic engineering strategies have allowed yeasts to efficiently assimilate xylose, the second most abundant sugar component of lignocellulosic biomass. During the investigation of xylose utilization by yeasts, a global rewiring of metabolic networks upon xylose cultivation has been captured, as opposed to a pattern of glucose repression. A clear understanding of the xylose-induced metabolic reprogramming in yeast would shed light on the optimization of yeast-based bioprocesses to produce biofuels and chemicals using xylose. In this review, we delved into the characteristics of yeast xylose metabolism, and potential benefits of using xylose as a carbon source to produce various biochemicals with examples. Transcriptomic and metabolomic patterns of xylose-grown yeast cells were distinct from those on glucose-a conventional sugar of industrial biotechnology-and the gap might lead to opportunities to produce biochemicals efficiently. Indeed, limited glycolytic metabolic fluxes during xylose utilization could result in enhanced production of metabolites whose biosynthetic pathways compete for precursors with ethanol fermentation. Also, alleviation of glucose repression on cytosolic acetyl coenzyme A (acetyl-CoA) synthesis, and respiratory energy metabolism during xylose utilization enhanced production of acetyl-CoA derivatives. Consideration of singular properties of xylose metabolism, such as redox cofactor imbalance between xylose reductase and xylitol dehydrogenase, is necessary to maximize these positive xylose effects. This review argues the importance and benefits of xylose utilization as not only a way of expanding a substrate range, but also an effective environmental perturbation for the efficient production of advanced biofuels and chemicals in yeasts.
Collapse
|
29
|
Hu G, Li Y, Ye C, Liu L, Chen X. Engineering Microorganisms for Enhanced CO 2 Sequestration. Trends Biotechnol 2018; 37:532-547. [PMID: 30447878 DOI: 10.1016/j.tibtech.2018.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Abstract
Microbial CO2 sequestration not only provides a green and sustainable approach for ameliorating global warming but also simultaneously produces biofuels and chemicals. However, the efficiency of microbial CO2 fixation is still very low. In addition, concomitant microbial CO2 emission decreases the carbon yield of desired chemicals. To address these issues, strategies including engineering CO2-fixing pathways and energy-harvesting systems have been developed to improve the efficiency of CO2 fixation in autotrophic and heterotrophic microorganisms. Furthermore, metabolic pathways and energy metabolism can be rewired to reduce microbial CO2 emissions and increase the carbon yield of value-added products. This review highlights the potential of biotechnology to promote microbial CO2 sequestration and provides guidance for the broader use of microorganisms as attractive carbon sinks.
Collapse
Affiliation(s)
- Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; http://www.fmme.cn/
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; http://www.fmme.cn/
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; http://www.fmme.cn/
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; http://www.fmme.cn/.
| |
Collapse
|
30
|
Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
|
31
|
Goldbeck O, Eck AW, Seibold GM. Real Time Monitoring of NADPH Concentrations in Corynebacterium glutamicum and Escherichia coli via the Genetically Encoded Sensor mBFP. Front Microbiol 2018; 9:2564. [PMID: 30405597 PMCID: PMC6207642 DOI: 10.3389/fmicb.2018.02564] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
Analyses of intracellular NADPH concentrations are prerequisites for the design of microbial production strains and process optimization. mBFP was described as metagenomics derived, blue fluorescent protein showing NADPH-dependent fluorescence. Characterization of mBFP showed a high specificity for binding of NADPH (KD 0.64 mM) and no binding of NADH, the protein exclusively amplified fluorescence of NADPH. mBFP catalyzed the NADPH-dependent reduction of benzaldehyde and further aldehydes, which fits to its classification as short chain dehydrogenase. For in vivo NADPH analyses a codon-optimized gene for mBFP was introduced into Corynebacterium glutamicum WT and the phosphoglucoisomerase-deficient strain C. glutamicum Δpgi, which accumulates high levels of NADPH. For determination of intracellular NADPH concentrations by mBFP a calibration method with permeabilized cells was developed. By this means an increase of intracellular NADPH concentrations within seconds after the addition of glucose to nutrient-starved cells of both C. glutamicum WT and C. glutamicum Δpgi was observed; as expected the internal NADPH concentration was significantly higher for C. glutamicum Δpgi (0.31 mM) when compared to C. glutamicum WT (0.19 mM). Addition of paraquat to E. coli cells carrying mBFP led as expected to an immediate decrease of intracellular NADPH concentrations, showing the versatile use of mBFP as intracellular sensor.
Collapse
Affiliation(s)
- Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Alexander W Eck
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Gerd M Seibold
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany.,Institute for Biochemistry, University of Cologne, Cologne, Germany
| |
Collapse
|
32
|
Wang Q, Xu J, Sun Z, Luan Y, Li Y, Wang J, Liang Q, Qi Q. Engineering an in vivo EP-bifido pathway in Escherichia coli for high-yield acetyl-CoA generation with low CO 2 emission. Metab Eng 2018; 51:79-87. [PMID: 30102971 DOI: 10.1016/j.ymben.2018.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/25/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022]
Abstract
The low carbon yield from native metabolic machinery produces unfavorable process economics during the biological conversion of substrates to desirable bioproducts. To obtain higher carbon yields, we constructed a carbon conservation pathway named EP-bifido pathway in Escherichia coli by combining Embden-Meyerhof-Parnas Pathway, Pentose Phosphate Pathway and "bifid shunt", to generate high yield acetyl-CoA from glucose. 13C-Metabolic flux analysis confirmed the successful and appropriate employment of the EP-bifido pathway. The CO2 release during fermentation significantly reduced compared with the control strains. Then we demonstrated the in vivo effectiveness of the EP-bifido pathway using poly-β-hydroxybutyrate (PHB), mevalonate and fatty acids as example products. The engineered EP-bifido strains showed greatly improved PHB yield (from 26.0 mol% to 63.7 mol%), fatty acid yield (from 9.17% to 14.36%), and the highest mevalonate yield yet reported (64.3 mol% without considering the substrates used for cell mass formation). The synthetic pathway can be employed in the production of chemicals that use acetyl-CoA as a precursor and can be extended to other microorganisms.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Jiasheng Xu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Zhijie Sun
- Marine Biology Institute, Shantou University, Shantou 515063, PR China
| | - Yaqi Luan
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Ying Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Junshu Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China; CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China.
| |
Collapse
|
33
|
Huang YY, Jian XX, Lv YB, Nian KQ, Gao Q, Chen J, Wei LJ, Hua Q. Enhanced squalene biosynthesis in Yarrowia lipolytica based on metabolically engineered acetyl-CoA metabolism. J Biotechnol 2018; 281:106-114. [PMID: 29986837 DOI: 10.1016/j.jbiotec.2018.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
As a bioactive triterpenoid, squalene is widely used in the food industry, cosmetics, and pharmacology. Squalene's major commercial sources are the liver oil of deep-sea sharks and plant oils. In this study, we focused on the enhancement of squalene biosynthesis in Yarrowia lipolytica, with particular attention to the engineering of acetyl-CoA metabolism based on genome-scale metabolic reaction network analysis. Although the overexpression of the rate-limiting endogenous ylHMG1 (3-hydroxy-3-methylglutaryl-CoA reductase gene) could improve squalene synthesis by 3.2-fold over that by the control strain, the availability of the key intracellular precursor, acetyl-CoA, was found to play a more significant role in elevating squalene production. Analysis of metabolic networks with the newly constructed genome-scale metabolic model of Y. lipolytica iYL_2.0 showed that the acetyl-CoA pool size could be increased by redirecting carbon flux of pyruvate dehydrogenation towards the ligation of acetate and CoA or the cleavage of citrate to form oxaloacetate and acetyl-CoA. The overexpression of either acetyl-CoA synthetase gene from Salmonella enterica (acs*) or the endogenous ATP citrate lyase gene (ylACL1) resulted in a more than 50% increase in the cytosolic acetyl-CoA level. Moreover, iterative chromosomal integration of the ylHMG1, asc*, and ylACL1 genes resulted in a significant improvement in squalene production (16.4-fold increase in squalene content over that in the control strain). We also found that supplementation with 10 mM citrate in a flask culture further enhanced squalene production to 10 mg/g DCW. The information obtained in this study demonstrates that rationally engineering acetyl-CoA metabolism to ensure the supply of this key metabolic precursor is an efficient strategy for the enhancement of squalene biosynthesis.
Collapse
Affiliation(s)
- Yu-Ying Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Xing-Xing Jian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Yu-Bei Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Ke-Qing Nian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Qi Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, PR China
| |
Collapse
|
34
|
Wang CY, Li Y, Gao ZW, Liu LC, Zhang MY, Zhang TY, Wu CF, Zhang YX. Establishing an innovative carbohydrate metabolic pathway for efficient production of 2-keto-L-gulonic acid in Ketogulonicigenium robustum initiated by intronic promoters. Microb Cell Fact 2018; 17:81. [PMID: 29778095 PMCID: PMC5960096 DOI: 10.1186/s12934-018-0932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background 2-Keto-l-gulonic acid (2-KGA), the precursor of vitamin C, is currently produced by two-step fermentation. In the second step, l-sorbose is transformed into 2-KGA by the symbiosis system composed of Ketogulonicigenium vulgare and Bacillus megaterium. Due to the different nutrient requirements and the uncertain ratio of the two strains, the symbiosis system significantly limits strain improvement and fermentation optimization. Results In this study, Ketogulonicigenium robustum SPU_B003 was reported for its capability to grow well independently and to produce more 2-KGA than that of K. vulgare in a mono-culture system. The complete genome of K. robustum SPU_B003 was sequenced, and the metabolic characteristics were analyzed. Compared to the four reported K. vulgare genomes, K. robustum SPU_B003 contained more tRNAs, rRNAs, NAD and NADP biosynthetic genes, as well as regulation- and cell signaling-related genes. Moreover, the amino acid biosynthesis pathways were more complete. Two species-specific internal promoters, P1 (orf_01408 promoter) and P2 (orf_02221 promoter), were predicted and validated by detecting their initiation activity. To efficiently produce 2-KGA with decreased CO2 release, an innovative acetyl-CoA biosynthetic pathway (XFP-PTA pathway) was introduced into K. robustum SPU_B003 by expressing heterologous phosphoketolase (xfp) and phosphotransacetylase (pta) initiated by internal promoters. After gene optimization, the recombinant strain K. robustum/pBBR-P1_xfp2502-P2_pta2145 enhanced acetyl-CoA approximately 2.4-fold and increased 2-KGA production by 22.27% compared to the control strain K. robustum/pBBR1MCS-2. Accordingly, the transcriptional level of the 6-phosphogluconate dehydrogenase (pgd) and pyruvate dehydrogenase genes (pdh) decreased by 24.33 ± 6.67 and 8.67 ± 5.51%, respectively. The key genes responsible for 2-KGA biosynthesis, sorbose dehydrogenase gene (sdh) and sorbosone dehydrogenase gene (sndh), were up-regulated to different degrees in the recombinant strain. Conclusions The genome-based functional analysis of K. robustum SPU_B003 provided a new understanding of the specific metabolic characteristics. The new XFP-PTA pathway was an efficient route to enhance acetyl-CoA levels and to therefore promote 2-KGA production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0932-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Ye Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.,Northeast Pharmaceutical Group Co., Ltd, Shenyang, 110026, People's Republic of China
| | - Zi-Wei Gao
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Tian-Yuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Chun-Fu Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.
| |
Collapse
|
35
|
Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism. Proc Natl Acad Sci U S A 2018; 115:3538-3546. [PMID: 29555759 PMCID: PMC5889684 DOI: 10.1073/pnas.1802191115] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We constructed an Escherichia coli strain that does not use glycolysis for sugar catabolism. Instead, it uses the synthetic nonoxidative glycolysis cycle to directly synthesize stoichiometric amounts of the two-carbon building block (acetyl-CoA), which is then converted to three-carbon metabolites to support growth. The resulting strain grows aerobically in glucose minimal medium and can achieve near-complete carbon conservation in the production of acetyl-CoA–derived products during anaerobic fermentation. This strain improves the theoretical carbon yield from 66.7% to 100% in acetyl-CoA–derived product formation. The Embden–Meyerhoff–Parnas (EMP) pathway, commonly known as glycolysis, represents the fundamental biochemical infrastructure for sugar catabolism in almost all organisms, as it provides key components for biosynthesis, energy metabolism, and global regulation. EMP-based metabolism synthesizes three-carbon (C3) metabolites before two-carbon (C2) metabolites and must emit one CO2 in the synthesis of the C2 building block, acetyl-CoA, a precursor for many industrially important products. Using rational design, genome editing, and evolution, here we replaced the native glycolytic pathways in Escherichia coli with the previously designed nonoxidative glycolysis (NOG), which bypasses initial C3 formation and directly generates stoichiometric amounts of C2 metabolites. The resulting strain, which contains 11 gene overexpressions, 10 gene deletions by design, and more than 50 genomic mutations (including 3 global regulators) through evolution, grows aerobically in glucose minimal medium but can ferment anaerobically to products with nearly complete carbon conservation. We confirmed that the strain metabolizes glucose through NOG by 13C tracer experiments. This redesigned E. coli strain represents a different approach for carbon catabolism and may serve as a useful platform for bioproduction.
Collapse
|
36
|
Kotopka BJ, Li Y, Smolke CD. Synthetic biology strategies toward heterologous phytochemical production. Nat Prod Rep 2018; 35:902-920. [DOI: 10.1039/c8np00028j] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
This review summarizes the recent progress in heterologous phytochemical biosynthetic pathway reconstitution in plant, bacteria, and yeast, with a focus on the synthetic biology strategies applied in these engineering efforts.
Collapse
Affiliation(s)
| | - Yanran Li
- Department of Chemical and Environmental Engineering
- Riverside
- USA
| | - Christina D. Smolke
- Department of Bioengineering
- Stanford University
- Stanford
- USA
- Chan Zuckerberg Biohub
| |
Collapse
|
37
|
Portugal-Nunes DJ, Pawar SS, Lidén G, Gorwa-Grauslund MF. Effect of nitrogen availability on the poly-3-D-hydroxybutyrate accumulation by engineered Saccharomyces cerevisiae. AMB Express 2017; 7:35. [PMID: 28176283 PMCID: PMC5296263 DOI: 10.1186/s13568-017-0335-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 12/04/2022] Open
Abstract
Poly-3-d-hydroxybutyrate (or PHB) is a polyester which can be used in the production of biodegradable plastics from renewable resources. It is naturally produced by several bacteria as a response to nutrient starvation in the excess of a carbon source. The yeast Saccharomyces cerevisiae could be an alternative production host as it offers good inhibitor tolerance towards weak acids and phenolic compounds and does not depolymerize the produced PHB. As nitrogen limitation is known to boost the accumulation of PHB in bacteria, the present study aimed at investigating the effect of nitrogen availability on PHB accumulation in two recombinant S. cerevisiae strains harboring different xylose consuming and PHB producing pathways: TMB4443 expressing an NADPH-dependent acetoacetyl-CoA reductase and a wild-type S. stipitis XR with preferential use of NADPH and TMB4425 which expresses an NADH-dependent acetoacetyl-CoA reductase and a mutated XR with a balanced affinity for NADPH/NADH. TMB4443 accumulated most PHB under aerobic conditions and with glucose as sole carbon source, whereas the highest PHB concentrations were obtained with TMB4425 under anaerobic conditions and xylose as carbon source. In both cases, the highest PHB contents were obtained with high availability of nitrogen. The major impact of nitrogen availability was observed in TMB4425, where a 2.7-fold increase in PHB content was obtained. In contrast to what was observed in natural PHB-producing bacteria, nitrogen deficiency did not improve PHB accumulation in S. cerevisiae. Instead the excess available carbon from xylose was shunted into glycogen, indicating a significant gluconeogenic activity on xylose.
Collapse
|
38
|
Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
39
|
Holistic bioengineering: rewiring central metabolism for enhanced bioproduction. Biochem J 2017; 474:3935-3950. [PMID: 29146872 PMCID: PMC5688466 DOI: 10.1042/bcj20170377] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/29/2022]
Abstract
What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH. In this review, we explore these strategies, focusing on key metabolic pathways and processes, such as glycolysis, anaplerosis, the TCA (tricarboxylic acid) cycle, and NADPH production. We show that only a holistic approach for bioengineering — considering the metabolic network of the host organism as a whole, rather than focusing on the production pathway alone — can truly mold microorganisms into efficient biofactories.
Collapse
|
40
|
Sacomboio ENM, Kim EYS, Ruchaud Correa HL, Bonato P, de Oliveira Pedrosa F, de Souza EM, Chubatsu LS, Müller-Santos M. The transcriptional regulator NtrC controls glucose-6-phosphate dehydrogenase expression and polyhydroxybutyrate synthesis through NADPH availability in Herbaspirillum seropedicae. Sci Rep 2017; 7:13546. [PMID: 29051509 PMCID: PMC5648810 DOI: 10.1038/s41598-017-12649-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/12/2017] [Indexed: 11/09/2022] Open
Abstract
The NTR system is the major regulator of nitrogen metabolism in Bacteria. Despite its broad and well-known role in the assimilation, biosynthesis and recycling of nitrogenous molecules, little is known about its role in carbon metabolism. In this work, we present a new facet of the NTR system in the control of NADPH concentration and the biosynthesis of molecules dependent on reduced coenzyme in Herbaspirillum seropedicae SmR1. We demonstrated that a ntrC mutant strain accumulated high levels of polyhydroxybutyrate (PHB), reaching levels up to 2-fold higher than the parental strain. In the absence of NtrC, the activity of glucose-6-phosphate dehydrogenase (encoded by zwf) increased by 2.8-fold, consequently leading to a 2.1-fold increase in the NADPH/NADP+ ratio. A GFP fusion showed that expression of zwf is likewise controlled by NtrC. The increase in NADPH availability stimulated the production of polyhydroxybutyrate regardless the C/N ratio in the medium. The mutant ntrC was more resistant to H2O2 exposure and controlled the propagation of ROS when facing the oxidative condition, a phenotype associated with the increase in PHB content.
Collapse
Affiliation(s)
- Euclides Nenga Manuel Sacomboio
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Edson Yu Sin Kim
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Henrique Leonardo Ruchaud Correa
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Paloma Bonato
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Leda Satie Chubatsu
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Laboratory of Nitrogen Fixation, Federal University of Paraná (UFPR), Curitiba, Brazil.
| |
Collapse
|
41
|
Raza ZA, Riaz S, Banat IM. Polyhydroxyalkanoates: Properties and chemical modification approaches for their functionalization. Biotechnol Prog 2017; 34:29-41. [PMID: 28960792 DOI: 10.1002/btpr.2565] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/23/2017] [Indexed: 01/08/2023]
Abstract
Polyhydroxyalkanoates (PHAs) have become an attractive biomaterial in research in the past few years due to their extensive potential industrial applications. Being long chain hydroxyl fatty acid molecules, the PHAs are hydrophobic in nature, and have less functional groups. These features limit their applications in various areas. To enhance their usage, these polymers may need to be modified including surface and chemical modifications. Such modifications may alter their mechanical properties, surface structure, amphiphilic character and rate of degradation to fulfil the requirements for their future applications. Chemical modifications allow incorporation of functional groups to PHAs that could not be introduced through biotechnological methods. These chemically reformed PHAs, with enhanced properties, could be used for broad range of applications. This review aims to introduce different chemical modification approaches including some recent methods that had not been explored or discussed so far for PHAs as possible technologies for widening the range of product and application potentials. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:29-41, 2018.
Collapse
Affiliation(s)
- Zulfiqar Ali Raza
- Dept. of Applied Sciences, National Textile University, Faisalabad, 37610, Pakistan
| | - Shahina Riaz
- Dept. of Applied Sciences, National Textile University, Faisalabad, 37610, Pakistan
| | - Ibrahim M Banat
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, U.K
| |
Collapse
|
42
|
Carpine R, Du W, Olivieri G, Pollio A, Hellingwerf KJ, Marzocchella A, Branco dos Santos F. Genetic engineering of Synechocystis sp. PCC6803 for poly-β-hydroxybutyrate overproduction. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.05.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
43
|
Kwak S, Jin YS. Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 2017; 16:82. [PMID: 28494761 PMCID: PMC5425999 DOI: 10.1186/s12934-017-0694-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD+-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.
Collapse
Affiliation(s)
- Suryang Kwak
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woose Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
44
|
Henard CA, Smith HK, Guarnieri MT. Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst. Metab Eng 2017; 41:152-158. [DOI: 10.1016/j.ymben.2017.03.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/17/2017] [Accepted: 03/31/2017] [Indexed: 12/20/2022]
|
45
|
Bergman A, Siewers V, Nielsen J, Chen Y. Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae. AMB Express 2016; 6:115. [PMID: 27848233 PMCID: PMC5110461 DOI: 10.1186/s13568-016-0290-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/08/2016] [Indexed: 01/20/2023] Open
Abstract
Phosphoketolases catalyze an energy- and redox-independent cleavage of certain sugar phosphates. Hereby, the two-carbon (C2) compound acetyl-phosphate is formed, which enzymatically can be converted into acetyl-CoA—a key precursor in central carbon metabolism. Saccharomyces cerevisiae does not demonstrate efficient phosphoketolase activity naturally. In this study, we aimed to compare and identify efficient heterologous phosphoketolase enzyme candidates that in yeast have the potential to reduce carbon loss compared to the native acetyl-CoA producing pathway by redirecting carbon flux directly from C5 and C6 sugars towards C2-synthesis. Nine phosphoketolase candidates were expressed in S. cerevisiae of which seven produced significant amounts of acetyl-phosphate after provision of sugar phosphate substrates in vitro. The candidates showed differing substrate specificities, and some demonstrated activity levels significantly exceeding those of candidates previously expressed in yeast. The conducted studies also revealed that S. cerevisiae contains endogenous enzymes capable of breaking down acetyl-phosphate, likely into acetate, and that removal of the phosphatases Gpp1 and Gpp2 could largely prevent this breakdown. An evaluation of in vivo function of a subset of phosphoketolases was conducted by monitoring acetate levels during growth, confirming that candidates showing high activity in vitro indeed showed increased acetate accumulation, but expression also decreased cellular fitness. The study shows that expression of several bacterial phosphoketolase candidates in S. cerevisiae can efficiently divert intracellular carbon flux toward C2-synthesis, thus showing potential to be used in metabolic engineering strategies aimed to increase yields of acetyl-CoA derived compounds.
Collapse
|
46
|
de Las Heras AM, Portugal-Nunes DJ, Rizza N, Sandström AG, Gorwa-Grauslund MF. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase. Microb Cell Fact 2016; 15:197. [PMID: 27863495 PMCID: PMC5116212 DOI: 10.1186/s12934-016-0598-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
Background Poly-3-d-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. Results In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. Conclusions This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0598-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Diogo J Portugal-Nunes
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden
| | - Nathasha Rizza
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Vattenhallen Science Center, John Ericssons väg 1, 223 63, Lund, Sweden
| | - Anders G Sandström
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, PO Box 124, 221 00, Lund, Sweden.
| |
Collapse
|
47
|
Li ZJ, Qiao K, Liu N, Stephanopoulos G. Engineering Yarrowia lipolytica for poly-3-hydroxybutyrate production. J Ind Microbiol Biotechnol 2016; 44:605-612. [PMID: 27826725 DOI: 10.1007/s10295-016-1864-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/30/2016] [Indexed: 01/12/2023]
Abstract
Strains of Yarrowia lipolytica were engineered to express the poly-3-hydroxybutyrate (PHB) biosynthetic pathway. The genes for β-ketothiolase, NADPH-dependent acetoacetyl-CoA reductase, and PHB synthase were cloned and inserted into the chromosome of Y. lipolytica. In shake flasks, the engineered strain accumulated PHB to 1.50 and 3.84% of cell dry weight in complex medium supplemented with glucose and acetate as carbon source, respectively. In fed-batch fermentation using acetate as sole carbon source, 7.35 g/l PHB (10.2% of cell dry weight) was produced. Selection of Y. lipolytica as host for PHB synthesis was motivated by the fact that this organism is a good lipids producer, which suggests robust acetyl-CoA supply also the precursor of the PHB pathway. Acetic acid could be supplied by gas fermentation, anaerobic digestion, and other low-cost supply route.
Collapse
Affiliation(s)
- Zheng-Jun Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.,Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| |
Collapse
|
48
|
Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 2016; 537:694-697. [PMID: 27654918 DOI: 10.1038/nature19769] [Citation(s) in RCA: 375] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 08/16/2016] [Indexed: 12/24/2022]
Abstract
A bio-based economy has the potential to provide sustainable substitutes for petroleum-based products and new chemical building blocks for advanced materials. We previously engineered Saccharomyces cerevisiae for industrial production of the isoprenoid artemisinic acid for use in antimalarial treatments. Adapting these strains for biosynthesis of other isoprenoids such as β-farnesene (C15H24), a plant sesquiterpene with versatile industrial applications, is straightforward. However, S. cerevisiae uses a chemically inefficient pathway for isoprenoid biosynthesis, resulting in yield and productivity limitations incompatible with commodity-scale production. Here we use four non-native metabolic reactions to rewire central carbon metabolism in S. cerevisiae, enabling biosynthesis of cytosolic acetyl coenzyme A (acetyl-CoA, the two-carbon isoprenoid precursor) with a reduced ATP requirement, reduced loss of carbon to CO2-emitting reactions, and improved pathway redox balance. We show that strains with rewired central metabolism can devote an identical quantity of sugar to farnesene production as control strains, yet produce 25% more farnesene with that sugar while requiring 75% less oxygen. These changes lower feedstock costs and dramatically increase productivity in industrial fermentations which are by necessity oxygen-constrained. Despite altering key regulatory nodes, engineered strains grow robustly under taxing industrial conditions, maintaining stable yield for two weeks in broth that reaches >15% farnesene by volume. This illustrates that rewiring yeast central metabolism is a viable strategy for cost-effective, large-scale production of acetyl-CoA-derived molecules.
Collapse
|
49
|
Engineered biosynthesis of biodegradable polymers. ACTA ACUST UNITED AC 2016; 43:1037-58. [DOI: 10.1007/s10295-016-1785-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
Abstract
Advances in science and technology have resulted in the rapid development of biobased plastics and the major drivers for this expansion are rising environmental concerns of plastic pollution and the depletion of fossil-fuels. This paper presents a broad view on the recent developments of three promising biobased plastics, polylactic acid (PLA), polyhydroxyalkanoate (PHA) and polybutylene succinate (PBS), well known for their biodegradability. The article discusses the natural and recombinant host organisms used for fermentative production of monomers, alternative carbon feedstocks that have been used to lower production cost, different metabolic engineering strategies used to improve product titers, various fermentation technologies employed to increase productivities and finally, the different downstream processes used for recovery and purification of the monomers and polymers.
Collapse
|
50
|
Chwa JW, Kim WJ, Sim SJ, Um Y, Woo HM. Engineering of a modular and synthetic phosphoketolase pathway for photosynthetic production of acetone from CO2 in Synechococcus elongatus PCC 7942 under light and aerobic condition. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1768-76. [PMID: 26879003 PMCID: PMC5021146 DOI: 10.1111/pbi.12536] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 11/23/2015] [Accepted: 01/04/2016] [Indexed: 05/12/2023]
Abstract
Capture and conversion of CO2 to valuable chemicals is intended to answer global challenges on environmental issues, climate change and energy security. Engineered cyanobacteria have been enabled to produce industry-relevant chemicals from CO2 . However, the final products from cyanobacteria have often been mixed with fermented metabolites during dark fermentation. In this study, our engineering of Synechococcus elongatus PCC 7942 enabled continuous conversion of CO2 to volatile acetone as sole product. This process occurred during lighted, aerobic culture via both ATP-driven malonyl-CoA synthesis pathway and heterologous phosphoketolase (PHK)-phosphotransacetylase (Pta) pathway. Because of strong correlations between the metabolic pathways of acetate and acetone, supplying the acetyl-CoA directly from CO2 in the engineered strain, led to sole production of acetone (22.48 mg/L ± 1.00) without changing nutritional constraints, and without an anaerobic shift. Our engineered S. elongatus strains, designed for acetone production, could be modified to create biosolar cell factories for sustainable photosynthetic production of acetyl-CoA-derived biochemicals.
Collapse
Affiliation(s)
- Jun-Won Chwa
- Clean Energy Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Green School (Graduate School of Energy and Environment), Korea University, Seongbuk-gu, Seoul, Korea
| | - Wook Jin Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Green School (Graduate School of Energy and Environment), Korea University, Seongbuk-gu, Seoul, Korea
| | - Sang Jun Sim
- Green School (Graduate School of Energy and Environment), Korea University, Seongbuk-gu, Seoul, Korea
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul, Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Department of Clean Energy and Chemical Engineering, Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| | - Han Min Woo
- Clean Energy Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Green School (Graduate School of Energy and Environment), Korea University, Seongbuk-gu, Seoul, Korea
- Department of Clean Energy and Chemical Engineering, Korea University of Science and Technology, Yuseong-gu, Daejeon, Korea
| |
Collapse
|