1
|
Chen Y, Huang L, Yu T, Yao Y, Zhao M, Pang A, Zhou J, Zhang B, Liu Z, Zheng Y. Balancing the AspC and AspA Pathways of Escherichia coli by Systematic Metabolic Engineering Strategy for High-Efficient l-Homoserine Production. ACS Synth Biol 2024; 13:2457-2469. [PMID: 39042380 DOI: 10.1021/acssynbio.4c00208] [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: 07/24/2024]
Abstract
l-Homoserine is a promising C4 platform compound used in the agricultural, cosmetic, and pharmaceutical industries. Numerous works have been conducted to engineer Escherichia coli to be an excellent l-homoserine producer, but it is still unable to meet the industrial-scale demand. Herein, we successfully engineered a plasmid-free and noninducible E. coli strain with highly efficient l-homoserine production through balancing AspC and AspA synthesis pathways. First, an initial strain was constructed by increasing the accumulation of the precursor oxaloacetate and attenuating the organic acid synthesis pathway. To remodel the carbon flux toward l-aspartate, a balanced route prone to high yield based on TCA intensity regulation was designed. Subsequently, the main synthetic pathway and the cofactor system were strengthened to reinforce the l-homoserine synthesis. Ultimately, under two-stage DO control, strain HSY43 showed 125.07 g/L l-homoserine production in a 5 L fermenter in 60 h, with a yield of 0.62 g/g glucose and a productivity of 2.08 g/L/h. The titer, yield, and productivity surpassed the highest reported levels for plasmid-free strains in the literature. The strategies adopted in this study can be applied to the production of other l-aspartate family amino acids.
Collapse
Affiliation(s)
- Yuanyuan Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Lianggang Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Tao Yu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yuan Yao
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Mingming Zhao
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Aiping Pang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Junping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhiqiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| |
Collapse
|
2
|
Ye DY, Moon JH, Jung GY. Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:10916-10931. [PMID: 37458388 DOI: 10.1021/acs.jafc.3c02156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.
Collapse
Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| |
Collapse
|
3
|
Jiang Z, Jiang Y, Wu H, Zhang W, Xin F, Ma J, Jiang M. Cofactor Metabolic Engineering of Escherichia coli for Aerobic L-Malate Production with Lower CO 2 Emissions. Bioengineering (Basel) 2023; 10:881. [PMID: 37627766 PMCID: PMC10451681 DOI: 10.3390/bioengineering10080881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/27/2023] Open
Abstract
Escherichia coli has been engineered for L-malate production via aerobic cultivation. However, the maximum yield obtained through this mode is inferior to that of anaerobic fermentation due to massive amounts of CO2 emissions. Here, we aim to address this issue by reducing CO2 emissions of recombinant E. coli during aerobic L-malate production. Our findings indicated that NADH oxidation and ATP-synthesis-related genes were down-regulated with 2 g/L of YE during aerobic cultivations of E. coli E23, as compared to 5 g/L of YE. Then, E23 was engineered via the knockout of nuoA and the introduction of the nonoxidative glycolysis (NOG) pathway, resulting in a reduction of NAD+ and ATP supplies. The results demonstrate that E23 (ΔnuoA, NOG) exhibited decreased CO2 emissions, and it produced 21.3 g/L of L-malate from glucose aerobically with the improved yield of 0.43 g/g. This study suggests that a restricted NAD+ and ATP supply can prompt E. coli to engage in incomplete oxidization of glucose, leading to the accumulation of metabolites instead of utilizing them in cellular respiration.
Collapse
Affiliation(s)
| | | | | | | | | | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | | |
Collapse
|
4
|
Khandelwal R, Srivastava P, Bisaria VS. Recent advances in the production of malic acid by native fungi and engineered microbes. World J Microbiol Biotechnol 2023; 39:217. [PMID: 37269376 DOI: 10.1007/s11274-023-03666-5] [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: 02/23/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO2 emissions and resulting global warming. Since malic acid is naturally synthesized, microorganisms offer an eco-friendly and cost-effective alternative for its production. An additional advantage of microbial production is the synthesis of pure L-form of malic acid. Due to its numerous applications, biotechnologically- produced L-malic acid is a much sought-after platform chemical. Malic acid can be produced by microbial fermentation via oxidative/reductive TCA and glyoxylate pathways. This article elaborates the potential and limitations of high malic acid producing native fungi belonging to Aspergillus, Penicillium, Ustilago and Aureobasidium spp. The utilization of industrial side streams and low value renewable substrates such as crude glycerol and lignocellulosic biomass is also discussed with a view to develop a competitive bio-based production process. The major impediments present in the form of toxic compounds from lignocellulosic residues or synthesized during fermentation along with their remedial measures are also described. The article also focuses on production of polymalic acid from renewable substrates which opens up a cost-cutting dimension in production of this biodegradable polymer. Finally, the recent strategies being employed for its production in recombinant organisms have also been covered.
Collapse
Affiliation(s)
- Rohit Khandelwal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
- Corporate Research & Development Centre, Bharat Petroleum Corporation Limited, Udyog Kendra, P. O. Surajpur, Greater Noida, 201306, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Virendra Swarup Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|
5
|
Zuo H, Ji L, Pan J, Chen X, Gao C, Liu J, Wei W, Wu J, Song W, Liu L. Engineering growth phenotypes of Aspergillus oryzae for L-malate production. BIORESOUR BIOPROCESS 2023; 10:25. [PMID: 38647943 PMCID: PMC10991988 DOI: 10.1186/s40643-023-00642-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/09/2023] [Indexed: 04/09/2023] Open
Abstract
Improving the growth status of Aspergillus oryzae is an efficient way to enhance L-malate production. However, the growth mechanism of filamentous fungi is relatively complex, which limits A. oryzae as a cell factory to produce L-malate industrially. This study determined the relationship between growth status and L-malate production. The optimal ranges of colony diameter, percentage of vegetative mycelia, and pellet number of A. oryzae were determined to be 26-30 mm, 35-40%, and 220-240/mL, respectively. To achieve this optimum range, adaptive evolution was used to obtain the evolved strain Z07 with 132.54 g/L L-malate and a productivity of 1.1 g/L/h. Finally, a combination of transcriptome analysis and morphological characterization was used to identify the relevant pathway genes that affect the growth mechanism of A. oryzae. The strategies used in this study and the growth mechanism provide a good basis for efficient L-malate production by filamentous fungi.
Collapse
Affiliation(s)
- Huiyun Zuo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Lihao Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jingyu Pan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
6
|
Ding Q, Ye C. Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application. Microb Biotechnol 2023; 16:709-725. [PMID: 36604311 PMCID: PMC10034640 DOI: 10.1111/1751-7915.14206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.
Collapse
Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| |
Collapse
|
7
|
Chen Y, Han A, Wang M, Wei D, Wang W. Metabolic Engineering of Trichoderma reesei for l-Malic Acid Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4043-4050. [PMID: 36812909 DOI: 10.1021/acs.jafc.2c09078] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
l-Malic acid has various applications in the chemical and food industries. The filamentous fungus Trichoderma reesei is known to be an efficient enzyme producer. Here, through metabolic engineering, T. reesei was constructed for the first time as an excellent cell factory for l-malic acid production. The heterologous overexpression of genes encoding the C4-dicarboxylate transporter from Aspergillus oryzae and Schizosaccharomyces pombe initiated l-malic acid production. The overexpression of pyruvate carboxylase from A. oryzae in the reductive tricarboxylic acid pathway further increased both the titer and yield of l-malic acid, resulting in the highest titer reported in a shake-flask culture. Furthermore, the deletion of malate thiokinase blocked l-malic acid degradation. Finally, the engineered T. reesei strain produced 220.5 g/L of l-malic acid in a 5 L fed-batch culture (productivity of 1.15 g/L/h). A T. reesei cell factory was created for the efficient production of l-malic acid.
Collapse
Affiliation(s)
- Yumeng Chen
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ao Han
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
8
|
Engineering Escherichia coli for Efficient Aerobic Conversion of Glucose to Malic Acid through the Modified Oxidative TCA Cycle. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Malic acid is a versatile building-block chemical that can serve as a precursor of numerous valuable products, including food additives, pharmaceuticals, and biodegradable plastics. Despite the present petrochemical synthesis, malic acid, being an intermediate of the TCA cycle of a variety of living organisms, can also be produced from renewable carbon sources using wild-type and engineered microbial strains. In the current study, Escherichia coli was engineered for efficient aerobic conversion of glucose to malic acid through the modified oxidative TCA cycle resembling that of myco- and cyanobacteria and implying channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation. The formation of succinate semialdehyde was enabled in the core strain MAL 0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP, ∆aceBAK, ∆glcB) by the expression of Mycobacterium tuberculosis kgd gene. The secretion of malic acid by the strain was ensured, resulting from the deletion of the mdh, maeA, maeB, and mqo genes. The Bacillus subtilis pycA gene was expressed in the strain to allow pyruvate to oxaloacetate conversion. The corresponding recombinant was able to synthesise malic acid from glucose aerobically with a yield of 0.65 mol/mol. The yield was improved by the derepression in the strain of the electron transfer chain and succinate dehydrogenase due to the enforcement of ATP hydrolysis and reached 0.94 mol/mol, amounting to 94% of the theoretical maximum. The implemented strategy offers the potential for the development of highly efficient strains and processes of bio-based malic acid production.
Collapse
|
9
|
Qiao W, Xu S, Liu Z, Fu X, Zhao H, Shi S. Challenges and opportunities in C1-based biomanufacturing. BIORESOURCE TECHNOLOGY 2022; 364:128095. [PMID: 36220528 DOI: 10.1016/j.biortech.2022.128095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The intensifying impact of green-house gas (GHG) emission on environment and climate change has attracted increasing attention, and biorefinery represents one of the most effective routes for reducing GHG emissions from human activities. However, this requires a shift for microbial fermentation from the current use of sugars to the use of biomass, and even better to the primary fixation of single carbon (C1) compounds. Here how microorganisms can be engineered for fixation and conversion of C1 compounds into metabolites that can serve as fuels and platform chemicals are reviewed. Meanwhile, key factors for utilization of these different pathways are discussed, followed by challenges and barriers for the development of C1-based biorefinery.
Collapse
Affiliation(s)
- Weibo Qiao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shijie Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoying Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
10
|
Engineering microbial cell viability for enhancing chemical production by second codon engineering. Metab Eng 2022; 73:235-246. [PMID: 35987432 DOI: 10.1016/j.ymben.2022.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 06/29/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022]
Abstract
Microbial cell factories offer a promising strategy for the sustainable production of industrial chemicals from renewable biomass feedstock. However, their performance is often limited by poor microbial cell viability (MCV). Here, MCV was engineered to enhance chemical production by optimizing the regulation of lifespan-specific genes to reduce the accumulation of reactive oxygen species (ROS). In Escherichia coli, MCV was improved by reducing ROS accumulation using second codon engineering to regulate hypoxia-inducible transcription factor (arcA), resulting in lysine production up to 213 g L-1 with its productivity 5.90 g L-1·h-1. In Saccharomyces cerevisiae, MCV was increased by decreasing ROS accumulation using second codon engineering to fine-tune ceramide synthase (lag1), leading to glucaric acid production up to 9.50 g L-1 with its productivity 0.057 g L-1·h-1. These results demonstrate that engineering MCV is a potential strategy to boost the performance of microbial cell factories in industrial processes.
Collapse
|
11
|
Liu J, Liu J, Guo L, Liu J, Chen X, Liu L, Gao C. Advances in microbial synthesis of bioplastic monomers. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:35-81. [DOI: 10.1016/bs.aambs.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
12
|
Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
13
|
Guo L, Ding S, Liu Y, Gao C, Hu G, Song W, Liu J, Chen X, Liu L. Enhancing tryptophan production by balancing precursors in Escherichia coli. Biotechnol Bioeng 2021; 119:983-993. [PMID: 34936092 DOI: 10.1002/bit.28019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/20/2021] [Accepted: 11/27/2021] [Indexed: 11/11/2022]
Abstract
Tryptophan, an essential aromatic amino acid, is widely used in animal feed, food additives, and pharmaceuticals. Although sustainable and environmentally friendly, microbial tryptophan production from renewable feedstocks is limited by low biosynthesis and transport rates. Here, an Escherichia coli strain capable of efficient tryptophan production was generated by improving and balancing the supply of precursors and by engineering membrane transporters. Tryptophan biosynthesis was increased by eliminating negative regulatory factors, blocking competing pathways, and preventing tryptophan degradation. Promoter engineering balanced the supply of the precursors erythrose-4-phosphate and phosphoenolpyruvate, as well as the availability of serine. Finally, the engineering of tryptophan transporters prevented feedback inhibition and growth toxicity. Fed-batch fermentation of the final strain (TRP12) in a 5 L bioreactor produced 52.1 g·L-1 of tryptophan, with a yield of 0.171 g·g-1 glucose and productivity of 1.45 g·L-1 ·h-1 . The metabolic engineering strategy described here paves the way for high-performance microbial cell factories aimed at the production of tryptophan as well as other valuable chemicals.
Collapse
Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Shuang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| |
Collapse
|
14
|
Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [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: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
Collapse
|
15
|
Wei Z, Xu Y, Xu Q, Cao W, Huang H, Liu H. Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects. Front Bioeng Biotechnol 2021; 9:765685. [PMID: 34660563 PMCID: PMC8511312 DOI: 10.3389/fbioe.2021.765685] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Malic acid, a four-carbon dicarboxylic acid, is widely used in the food, chemical and medical industries. As an intermediate of the TCA cycle, malic acid is one of the most promising building block chemicals that can be produced from renewable sources. To date, chemical synthesis or enzymatic conversion of petrochemical feedstocks are still the dominant mode for malic acid production. However, with increasing concerns surrounding environmental issues in recent years, microbial fermentation for the production of L-malic acid was extensively explored as an eco-friendly production process. The rapid development of genetic engineering has resulted in some promising strains suitable for large-scale bio-based production of malic acid. This review offers a comprehensive overview of the most recent developments, including a spectrum of wild-type, mutant, laboratory-evolved and metabolically engineered microorganisms for malic acid production. The technological progress in the fermentative production of malic acid is presented. Metabolic engineering strategies for malic acid production in various microorganisms are particularly reviewed. Biosynthetic pathways, transport of malic acid, elimination of byproducts and enhancement of metabolic fluxes are discussed and compared as strategies for improving malic acid production, thus providing insights into the current state of malic acid production, as well as further research directions for more efficient and economical microbial malic acid production.
Collapse
Affiliation(s)
- Zhen Wei
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yongxue Xu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin, China
| |
Collapse
|
16
|
Tong T, Chen X, Hu G, Wang XL, Liu GQ, Liu L. Engineering microbial metabolic energy homeostasis for improved bioproduction. Biotechnol Adv 2021; 53:107841. [PMID: 34610353 DOI: 10.1016/j.biotechadv.2021.107841] [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: 06/16/2021] [Revised: 08/25/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.
Collapse
Affiliation(s)
- Tian Tong
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiao-Ling Wang
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
17
|
Metabolic engineering strategies to enable microbial utilization of C1 feedstocks. Nat Chem Biol 2021; 17:845-855. [PMID: 34312558 DOI: 10.1038/s41589-021-00836-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
One-carbon (C1) substrates are preferred feedstocks for the biomanufacturing industry and have recently gained attention owing to their natural abundance, low production cost and availability as industrial by-products. However, native pathways to utilize these substrates are absent in most biotechnologically relevant microorganisms. Recent advances in synthetic biology, genome engineering and laboratory evolution are enabling the first steps towards the creation of synthetic C1-utilizing microorganisms. Here, we briefly review the native metabolism of methane, methanol, CO2, CO and formate, and how these C1-utilizing pathways can be engineered into heterologous hosts. In addition, this review analyses the potential, the challenges and the perspectives of C1-based biomanufacturing.
Collapse
|
18
|
Guo L, Lu J, Gao C, Zhang L, Liu L, Chen X. Dynamic control of the distribution of carbon flux between cell growth and butyrate biosynthesis in Escherichia coli. Appl Microbiol Biotechnol 2021; 105:5173-5187. [PMID: 34115183 DOI: 10.1007/s00253-021-11385-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/05/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
Microbial cell factories offer an economic and environmentally friendly method for the biosynthesis of acetyl-CoA-derived chemicals. However, the static control of carbon flux can cause direct and indirect competition for acetyl-CoA between cell growth and chemical biosynthesis, limiting the efficiency of microbial cell factories. Herein, recombinase-based genetic circuits were developed to achieve the optimal distribution of acetyl-CoA between cell growth and butyrate biosynthesis. First, three dynamic devices-a turn-on switch, a turn-off switch, and a recombinase-based inverter (RBI)-were constructed based on Bxb1 recombinase. Then, the turn-on switch was used to dynamically control the butyrate biosynthetic pathway, which directly improved the consumption of acetyl-CoA. Next, the turn-off switch was applied to dynamically control cell growth, which indirectly enhanced the supply of acetyl-CoA. Finally, an RBI was adopted for the dynamic dual control of the distribution of acetyl-CoA between cell growth and butyrate biosynthesis. The final butyrate production rate was increased to 34 g/L, with a productivity of 0.405 g/L/h. The strategy described herein will pave the way for the development of high-performance microbial cell factories for the production of other desirable chemicals. KEY POINTS: • Competition for acetyl-CoA between cell growth and synthesis limits productivity. • Recombinase-based genetic circuits were developed to dynamic control of acetyl-CoA. • Optimal distribution of acetyl-CoA between cell growth and synthesis was achieved.
Collapse
Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jiaxin Lu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Linpei Zhang
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
19
|
Ji L, Wang J, Luo Q, Ding Q, Tang W, Chen X, Liu L. Enhancing L-malate production of Aspergillus oryzae by nitrogen regulation strategy. Appl Microbiol Biotechnol 2021; 105:3101-3113. [PMID: 33818672 DOI: 10.1007/s00253-021-11149-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/14/2021] [Accepted: 01/26/2021] [Indexed: 12/01/2022]
Abstract
Regulating morphology engineering and fermentation of Aspergillus oryzae makes it possible to increase the titer of L-malate. However, the existing L-malate-producing strain has limited L-malate production capacity and the fermentation process is insufficiently mature, which cannot meet the needs of industrial L-malate production. To further increase the L-malate production capacity of A. oryzae, we screened out a mutant strain (FMME-S-38) that produced 79.8 g/L L-malate in 250-mL shake flasks, using a newly developed screening system based on colony morphology on the plate. We further compared the extracellular nitrogen (N1) and intracellular nitrogen (N2) contents of the control and mutant strain (FMME-S-38) to determine the relationship between the curve of nitrogen content (N1 and N2) and the L-malate titer. This correlation was then used to optimize the conditions for developing a novel nitrogen supply strategy (initial tryptone concentration of 6.5 g/L and feeding with 3 g/L tryptone at 24 h). Fermentation in a 7.5-L fermentor under the optimized conditions further increased the titer and productivity of L-malate to 143.3 g/L and 1.19 g/L/h, respectively, corresponding to 164.9 g/L and 1.14 g/L/h in a 30-L fermentor. This nitrogen regulation-based strategy cannot only enhance industrial-scale L-malate production but also has generalizability and the potential to increase the production of similar metabolites.Key Points• Construction of a new screening system based on colony morphology on the plate.• A novel nitrogen regulation strategy used to regulate the production of L-malate.• A nitrogen supply strategy used to maximize the production of L-malate.
Collapse
Affiliation(s)
- Lihao Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ju Wang
- College of Food Engineering, Anhui Science and Technology University, Chuzhou, 233100, Anhui, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenxiu Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
20
|
Li W, Shen X, Wang J, Sun X, Yuan Q. Engineering microorganisms for the biosynthesis of dicarboxylic acids. Biotechnol Adv 2021; 48:107710. [PMID: 33582180 DOI: 10.1016/j.biotechadv.2021.107710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/26/2020] [Accepted: 02/02/2021] [Indexed: 01/02/2023]
Abstract
Dicarboxylic acids (DCAs) are important commodity chemicals which have been widely applied in polymer, food and pharmaceutical industries. Biosynthesis of DCAs from renewable carbon sources represents a promising alternative to chemical synthesis. Over the years, the recombinant strains have been constructed to produce an increasing number of DCAs. In this review, recent advances on the microbial synthesis of various DCAs have been summarized and categorized into three groups: the tricarboxylic acid cycle-derived, lysine metabolism-related, and aromatic compounds degradation-derived DCAs. We focused mainly on the metabolic engineering and synthetic biology strategies for improving the production efficiency, including metabolic flux analysis, fine-tuning of gene expression, cofactor balancing, metabolic compartmentalization, dynamic regulation and co-culture to regulate the production at multiple levels. The current challenges and perspectives have also been discussed.
Collapse
Affiliation(s)
- Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
21
|
Ding Q, Diao W, Gao C, Chen X, Liu L. Microbial cell engineering to improve cellular synthetic capacity. Biotechnol Adv 2020; 45:107649. [PMID: 33091485 DOI: 10.1016/j.biotechadv.2020.107649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.
Collapse
Affiliation(s)
- Qiang Ding
- 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
| | - Wenwen Diao
- 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
| | - Cong Gao
- 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
| | - 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
| | - 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; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
22
|
Ye C, Luo Q, Guo L, Gao C, Xu N, Zhang L, Liu L, Chen X. Improving lysine production through construction of an Escherichia coli enzyme-constrained model. Biotechnol Bioeng 2020; 117:3533-3544. [PMID: 32648933 DOI: 10.1002/bit.27485] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/28/2020] [Accepted: 07/09/2020] [Indexed: 12/28/2022]
Abstract
Microbial cell factories are widely used for the production of high-value chemicals. However, maximizing production titers is made difficult by the complicated regulatory mechanisms of these cell platforms. Here, kcat values were incorporated to construct an Escherichia coli enzyme-constrained model. The resulting ec_iML1515 model showed that the protein demand and protein synthesis rate were the key factors affecting lysine production. By optimizing the expression of the 20 top-demanded proteins, lysine titers reached 95.7 ± 0.7 g/L, with a 0.45 g/g glucose yield. Moreover, adjusting NH4 + and dissolved oxygen levels to regulate the synthesis rate of energy metabolism-related proteins caused lysine titers and glucose yields to increase to 193.6 ± 1.8 g/L and 0.74 g/g, respectively. The ec_iML1515 model provides insight into how enzymes required for the biosynthesis of certain products are distributed between and within metabolic pathways. This information can be used to accurately predict and rationally design lysine production.
Collapse
Affiliation(s)
- Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Li Zhang
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| |
Collapse
|
23
|
Ding Q, Ma D, Liu GQ, Li Y, Guo L, Gao C, Hu G, Ye C, Liu J, Liu L, Chen X. Light-powered Escherichia coli cell division for chemical production. Nat Commun 2020; 11:2262. [PMID: 32385264 PMCID: PMC7210317 DOI: 10.1038/s41467-020-16154-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/19/2020] [Indexed: 12/17/2022] Open
Abstract
Cell division can perturb the metabolic performance of industrial microbes. The C period of cell division starts from the initiation to the termination of DNA replication, whereas the D period is the bacterial division process. Here, we first shorten the C and D periods of E. coli by controlling the expression of the ribonucleotide reductase NrdAB and division proteins FtsZA through blue light and near-infrared light activation, respectively. It increases the specific surface area to 3.7 μm−1 and acetoin titer to 67.2 g·L−1. Next, we prolong the C and D periods of E. coli by regulating the expression of the ribonucleotide reductase NrdA and division protein inhibitor SulA through blue light activation-repression and near-infrared (NIR) light activation, respectively. It improves the cell volume to 52.6 μm3 and poly(lactate-co-3-hydroxybutyrate) titer to 14.31 g·L−1. Thus, the optogenetic-based cell division regulation strategy can improve the efficiency of microbial cell factories. Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).
Collapse
Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Danlei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, 410004, Changsha, China
| | - Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 214122, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, Wuxi, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122, Wuxi, China.
| |
Collapse
|
24
|
Gao C, Guo L, Ding Q, Hu G, Ye C, Liu J, Chen X, Liu L. Dynamic consolidated bioprocessing for direct production of xylonate and shikimate from xylan by Escherichia coli. Metab Eng 2020; 60:128-137. [PMID: 32315760 DOI: 10.1016/j.ymben.2020.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/21/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Numerous value-added chemicals can be produced using xylan as a feedstock. However, the product yields are limited by low xylan utilization efficiency, as well as by carbon flux competition between biomass production and biosynthesis. Herein, a dynamic consolidated bioprocessing strategy was developed, which coupled xylan utilization and yield optimization modules. Specifically, we achieved the efficient conversion of xylan to valuable chemicals in a fully consolidated manner by optimizing the expression level of xylanases and xylose transporter in the xylan utilization module. Moreover, a cell density-dependent, and Cre-triggered dynamic system that enabled the dynamic decoupling of biosynthesis and biomass production was constructed in the yield optimization module. The final shake flask-scale titers of xylonate, produced through an exogenous pathway, and shikimate, produced through an endogenous pathway, reached 16.85 and 3.2 g L-1, respectively. This study not only provides an efficient microbial platform for the utilization of xylan, but also opens up the possibility for the large-scale production of high value-added chemicals from renewable feedstocks.
Collapse
Affiliation(s)
- Cong Gao
- 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
| | - Liang Guo
- 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
| | - Qiang Ding
- 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
| | - 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
| | - 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
| | - Jia 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
| | - 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
| | - 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.
| |
Collapse
|
25
|
Liu Z, Wang K, Chen Y, Tan T, Nielsen J. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat Catal 2020. [DOI: 10.1038/s41929-019-0421-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
26
|
Guo L, Diao W, Gao C, Hu G, Ding Q, Ye C, Chen X, Liu J, Liu L. Engineering Escherichia coli lifespan for enhancing chemical production. Nat Catal 2020. [DOI: 10.1038/s41929-019-0411-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
27
|
Chen X, Ma D, Liu J, Luo Q, Liu L. Engineering the transmission efficiency of the noncyclic glyoxylate pathway for fumarate production in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:132. [PMID: 32760446 PMCID: PMC7379832 DOI: 10.1186/s13068-020-01771-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Fumarate is a multifunctional dicarboxylic acid in the tricarboxylic acid cycle, but microbial engineering for fumarate production is limited by the transmission efficiency of its biosynthetic pathway. RESULTS Here, pathway engineering was used to construct the noncyclic glyoxylate pathway for fumarate production. To improve the transmission efficiency of intermediate metabolites, pathway optimization was conducted by fluctuating gene expression levels to identify potential bottlenecks and then remove them, resulting in a large increase in fumarate production from 8.7 to 16.2 g/L. To further enhance its transmission efficiency of targeted metabolites, transporter engineering was used by screening the C4-dicarboxylate transporters and then strengthening the capacity of fumarate export, leading to fumarate production up to 18.9 g/L. Finally, the engineered strain E. coli W3110△4-P(H)CAI(H)SC produced 22.4 g/L fumarate in a 5-L fed-batch bioreactor. CONCLUSIONS In this study, we offered rational metabolic engineering and flux optimization strategies for efficient production of fumarate. These strategies have great potential in developing efficient microbial cell factories for production of high-value added chemicals.
Collapse
Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122 China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122 China
| | - Danlei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122 China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122 China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122 China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122 China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Wuxi Chenming Biotechnology Co. Ltd, Wuxi, 214100 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122 China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122 China
| |
Collapse
|
28
|
Programmable biomolecular switches for rewiring flux in Escherichia coli. Nat Commun 2019; 10:3751. [PMID: 31434894 PMCID: PMC6704175 DOI: 10.1038/s41467-019-11793-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022] Open
Abstract
Synthetic biology aims to develop programmable tools to perform complex functions such as redistributing metabolic flux in industrial microorganisms. However, development of protein-level circuits is limited by availability of designable, orthogonal, and composable tools. Here, with the aid of engineered viral proteases and proteolytic signals, we build two sets of controllable protein units, which can be rationally configured to three tools. Using a protease-based dynamic regulation circuit to fine-tune metabolic flow, we achieve 12.63 g L−1 shikimate titer in minimal medium without inducer. In addition, the carbon catabolite repression is alleviated by protease-based inverter-mediated flux redistribution under multiple carbon sources. By coordinating reaction rate using a protease-based oscillator in E. coli, we achieve d-xylonate productivity of 7.12 g L−1 h−1 with a titer of 199.44 g L−1. These results highlight the applicability of programmable protein switches to metabolic engineering for valuable chemicals production. Current flux rewiring technologies in metabolic engineering are mainly transcriptional regulation. Here, the authors build two sets of controllable protein units using engineered viral proteases and proteolytic signals, and utilize for increasing titers of shikimate and D-xylonate in E. coli.
Collapse
|
29
|
Yu T, Dabirian Y, Liu Q, Siewers V, Nielsen J. Strategies and challenges for metabolic rewiring. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
30
|
Abstract
Microbial synthesis represents an alternative approach for the sustainable production of chemicals, fuels, and medicines. However, construction of biosynthetic pathways always suffers from side reactions, toxicity of intermediates, or low efficiency of substrate channeling. Subcellular compartmentalization may contribute to a more efficient production of target products by reducing side reactions and toxic effects within a compact insular space. The peroxisome, a type of organelle that is involved in catabolism of fatty acids and reactive oxygen species, has attracted a great deal of attention in the construction of eukaryotic cell factories with little impact on essential cellular function. In this chapter, we will systematically review recent advances in peroxisomal compartmentalization for microbial production of valuable biomolecules. Additionally, detailed experimental designs and protocols are also described. We hope a comprehensive understanding of peroxisomes will promote their application in metabolic engineering and synthetic biology.
Collapse
Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| |
Collapse
|
31
|
Pang YY, Zhang C, Xu MJ, Huang GY, Cheng YX, Yang XZ. The transcriptome sequencing and functional analysis of eyestalk ganglions in Chinese mitten crab (Eriocheir sinensis) treated with different photoperiods. PLoS One 2019; 14:e0210414. [PMID: 30645610 PMCID: PMC6333377 DOI: 10.1371/journal.pone.0210414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Photoperiod plays an important role in individual growth, development, and metabolism in crustaceans. The growth and reproduction of crabs are closely related to the photoperiod. However, as of yet, there are still no transcriptomic reports of eyestalk ganglions treated under different photoperiods in the Chinese mitten crab (Eriocheir sinensis), which is a benthonic crab with high commercial value in Asia. In this study, we collected the eyestalk ganglions of crabs that were reared under different photoperiods, including a control group (L: D = 12 h: 12 h, named CC), a constant light group (L: D = 24 h: 0 h, named LL) and a constant darkness group (L: D = 0 h: 24 h, named DD). RNA sequencing was performed on these tissues in order to examine the effects of different photoperiods. The total numbers of clean reads from the CC, LL and DD groups were 48,772,584 bp, 53,943,281 bp and 53,815,178 bp, respectively. After de novo assembly, 161,380 unigenes were obtained and were matched with different databases. The DEGs were significantly enriched in phototransduction and energy metabolism pathways. Results from RT-qPCR showed that TRP channel protein (TRP) in the phototransduction pathway had a significantly higher level of expression in LL and DD groups than in the CC group. We found that the downregulation of the pyruvate dehydrogenase complex (PDC) gene and the upregulation phosphoenolpyruvate carboxykinase (PPC) gene were involved in energy metabolism processes in LL or DD. In addition, we also found that the upregulation of the expression level of the genes Gαq, pyruvate kinase (PK), NADH peroxidase (NADH) and ATPase is involved in phototransduction and energy metabolism. These results may shed some light on the molecular mechanism underlying the effect of photoperiod in physiological activity of E. sinensis.
Collapse
Affiliation(s)
- Yang-yang Pang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Cong Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Min-jie Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Gen-yong Huang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yong-xu Cheng
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- * E-mail: (XZY); (YXC)
| | - Xiao-zhen Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- * E-mail: (XZY); (YXC)
| |
Collapse
|