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Chang F, Wang Y, Zhang J, Tu T, Luo H, Huang H, Bai Y, Qin X, Wang Y, Yao B, Wang Y, Wang X. Efficient production of γ-aminobutyric acid using engineered Escherichia coli whole-cell catalyst. Enzyme Microb Technol 2024; 174:110379. [PMID: 38103484 DOI: 10.1016/j.enzmictec.2023.110379] [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: 10/31/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
γ-Aminobutyric acid (GABA) has been widely used in the food, feed, pharmaceutical, and chemical industry fields. Previously, we developed a whole-cell catalyst capable of converting L-glutamate (L-Glu) into GABA by overexpressing the glutamate decarboxylase gene (gadz11) from Bacillus sp. Z11 in Escherichia coli BL21(DE3). However, to enhance cell permeability, a freeze-thaw treatment is required, and to enhance GADZ11 activity, pyridoxal 5'-phosphate (PLP) must be added to the reaction system. The aim of this study is to provide a more efficient approach for GABA production by engineering the recombinant E. coli above. First, the inducible expression conditions of the gadz11 in E. coli were optimized to 37 °C for 6 h. Next, an ideal engineered strain was produced via increasing cell permeability by overexpressing sulA and eliminating PLP dependence by constructing a self-sufficient system. Furthermore, an efficient whole-cell biocatalytic process was optimized. The optimal substrate concentration, cell density, and reaction temperature were 1.0 mol/L (the molecular ratio of L-Glu to L-monosodium glutamate (L-MSG) was 4:1), 15 and 37 °C, respectively. Finally, a whole-cell bioconversion procedure was performed in a 3-L bioreactor under optimal conditions. The strain could be reused for at least two cycles with GABA yield, productivity and conversion ratio of 206.2 g/L, 117.8 g/L/h and 100.0%, respectively. This is currently the highest GABA productivity from a mixture of L-Glu and L-MSG reported without the addition of cofactors or additional treatment of cells. This work demonstrates that the novel engineered E. coli strain has the potential for application in large-scale industrial GABA production.
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Affiliation(s)
- Fangfang Chang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuheng Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Wang L, Luo H, Yao B, Yao J, Zhang J. Optimizing Hexose Utilization Pathways of Cupriavidus necator for Improving Growth and L-Alanine Production under Heterotrophic and Autotrophic Conditions. Int J Mol Sci 2023; 25:548. [PMID: 38203719 PMCID: PMC10778655 DOI: 10.3390/ijms25010548] [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: 12/06/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Cupriavidus necator is a versatile microbial chassis to produce high-value products. Blocking the poly-β-hydroxybutyrate synthesis pathway (encoded by the phaC1AB1 operon) can effectively enhance the production of C. necator, but usually decreases cell density in the stationary phase. To address this problem, we modified the hexose utilization pathways of C. necator in this study by implementing strategies such as blocking the Entner-Doudoroff pathway, completing the phosphopentose pathway by expressing the gnd gene (encoding 6-phosphogluconate dehydrogenase), and completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene (encoding 6-phosphofructokinase). During heterotrophic fermentation, the OD600 of the phaC1AB1-knockout strain increased by 44.8% with pfkA gene expression alone, and by 93.1% with gnd and pfkA genes expressing simultaneously. During autotrophic fermentation, gnd and pfkA genes raised the OD600 of phaC1AB1-knockout strains by 19.4% and 12.0%, respectively. To explore the effect of the pfkA gene on the production of C. necator, an alanine-producing C. necator was constructed by expressing the NADPH-dependent L-alanine dehydrogenase, alanine exporter, and knocking out the phaC1AB1 operon. The alanine-producing strain had maximum alanine titer and yield of 784 mg/L and 11.0%, respectively. And these values were significantly improved to 998 mg/L and 13.4% by expressing the pfkA gene. The results indicate that completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene is an effective method to improve the growth and production of C. necator.
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Affiliation(s)
- Lei Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Bin Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
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Tang R, Yuan X, Yang J. Problems and corresponding strategies for converting CO 2 into value-added products in Cupriavidus necator H16 cell factories. Biotechnol Adv 2023; 67:108183. [PMID: 37286176 DOI: 10.1016/j.biotechadv.2023.108183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.
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Affiliation(s)
- Ruohao Tang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Xianzheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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Takeno S, Hirata Y, Kitamura K, Ohtake T, Aoki K, Murata N, Hayashi M, Ikeda M. Metabolic engineering to produce palmitic acid or palmitoleic acid in an oleic acid-producing Corynebacterium glutamicum strain. Metab Eng 2023; 78:148-158. [PMID: 37286071 DOI: 10.1016/j.ymben.2023.06.002] [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: 02/20/2023] [Revised: 05/14/2023] [Accepted: 06/04/2023] [Indexed: 06/09/2023]
Abstract
Focusing on the differences in the catalytic properties of two type I fatty acid synthases FasA and FasB, the fasA gene was disrupted in an oleic acid-producing Corynebacterium glutamicum strain. The resulting oleic acid-requiring strain whose fatty acid synthesis depends only on FasB exhibited almost exclusive production (217 mg/L) of palmitic acid (C16:0) from 1% glucose under the conditions supplemented with the minimum concentration of sodium oleate for growth. Plasmid-mediated amplification of fasB led to a 1.47-fold increase in palmitic acid production (320 mg/L), while fasB disruption resulted in no fatty acid production, with excretion of malonic acid (30 mg/L). Next, aiming at conversion of the palmitic acid producer to a producer of palmitoleic acid (POA, C16:1Δ9), we introduced the Pseudomonas nitroreducens Δ9-desaturase genes desBC into the palmitic acid producer. Although this resulted in failure, we noticed the emergence of suppressor mutants that exhibited the oleic acid-non-requiring phenotype. Production experiments revealed that one such mutant M-1 undoubtedly produced POA (17 mg/L) together with palmitic acid (173 mg/L). Whole genomic analysis and subsequent genetic analysis identified the suppressor mutation of strain M-1 as a loss-of-function mutation for the DtxR protein, a global regulator of iron metabolism. Considering that DesBC are both iron-containing enzymes, we investigated the conditions for increased iron availability to improve the DesBC-dependent conversion ratio of palmitic acid to POA. Eventually, supplementation of both hemin and the iron chelator protocatechuic acid in the engineered strain dramatically enhanced POA production to 161 mg/L with a conversion ratio of 80.1%. Cellular fatty acid analysis revealed that the POA-producing cells were really equipped with unnatural membrane lipids comprised predominantly of palmitic acid (85.1% of total cellular fatty acids), followed by non-native POA (12.4%).
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Affiliation(s)
- Seiki Takeno
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Yosuke Hirata
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Kako Kitamura
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Tatsunori Ohtake
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Kuniyoshi Aoki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Noriko Murata
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Mikiro Hayashi
- Bioprocess Development Center, Kyowa Hakko Bio Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Masato Ikeda
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan.
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Wang X, Wang K, Wang L, Luo H, Wang Y, Wang Y, Tu T, Qin X, Su X, Bai Y, Yao B, Huang H, Zhang J. Engineering Cupriavidus necator H16 for heterotrophic and autotrophic production of myo-inositol. BIORESOURCE TECHNOLOGY 2023; 368:128321. [PMID: 36379295 DOI: 10.1016/j.biortech.2022.128321] [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] [Received: 10/19/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Bioconversion of sustainable feedstocks to commodity chemicals is considered as an effective solution for transforming the fossil-based economy into a carbon-neutral model. Here, the CO2-fixing bacterium Cupriavidus necator H16 was exploited for myo-inositol production from renewable substrates. First, by introducing the glucose transportation system, the glucose consumption route was established. Second, two key enzymes involved in myo-inositol biosynthesis were screened and evaluated. A myo-inositol-producing strain was constructed via overexpression of myo-inositol-3-phosphate synthase from Saccharomyces cerevisiae and inositol monophosphatase from Escherichia coli. Finally, carbon flux redirection was achieved through disruption of Entner-Doudoroff pathway and poly(3-hydroxybutyrate) synthesis pathway, resulting in a final myo-inositol production of 520.2, 1076.3 and 1054.8 mg/L from glucose, glycerol and CO2, respectively. The myo-inositol production level from CO2 achieved here set up the record. This study underlines the potential of C. necator to be utilized as microbial factory for upcycling the renewable feedstocks and CO2 to high-value biochemicals.
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Affiliation(s)
- Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kaikai Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lei Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Calvey CH, Sànchez I Nogué V, White AM, Kneucker CM, Woodworth SP, Alt HM, Eckert CA, Johnson CW. Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering. Metab Eng 2023; 75:78-90. [PMID: 36368470 DOI: 10.1016/j.ymben.2022.10.016] [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: 03/25/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Conversion of CO2 to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO2, has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. The metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ΔphcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.
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Affiliation(s)
- Christopher H Calvey
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Violeta Sànchez I Nogué
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Aleena M White
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Hannah M Alt
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Fu L, Ren Z, Si W, Ma Q, Huang W, Liao K, Huang Z, Wang Y, Li J, Xu P. Research progress on CO2 capture and utilization technology. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Wang X, Luo H, Wang Y, Wang Y, Tu T, Qin X, Su X, Huang H, Bai Y, Yao B, Zhang J. Direct conversion of carbon dioxide to glucose using metabolically engineered Cupriavidus necator. BIORESOURCE TECHNOLOGY 2022; 362:127806. [PMID: 36031135 DOI: 10.1016/j.biortech.2022.127806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Artificial synthesis of glucose, the monomer of starch, from renewable resources and CO2 is a promising method for addressing food crisis and alleviating climate change. Here, the construction of a microbial biocatalyst for glucose production from renewable resources and CO2 was reported. Initially, blocking the glucose catabolic pathway via deletion of glk gene generated a glucose-producing strain of Cupriavidus necator with titers of 24.7, 47.5 and 180.1 mg/L from fructose, glycerol and CO2, respectively. Subsequently, the Entner-Doudoroff pathway and polyhydroxybutyrate biosynthesis pathway were disrupted to further increase glucose accumulation. The maximum glucose titer and yield on biomass from CO2 reached 253.3 mg/L and 91.6 mg/L/OD600, respectively. Finally, the phosphatases that mediate the dephosphorylation of phosphorylated glucose were identified. Overexpression of HAD1 and cbbY2 could enhance glucose titer by 5.5-fold when fructose was used as sole carbon source. This study demonstrates a feasible route for microbial-based synthesis of glucose from CO2.
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Affiliation(s)
- Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Lin L, Huang H, Zhang X, Dong L, Chen Y. Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155559. [PMID: 35483467 DOI: 10.1016/j.scitotenv.2022.155559] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H2 and fix CO2 to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO2 capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.
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Affiliation(s)
- Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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Chen G, Harwood JL, Lemieux MJ, Stone SJ, Weselake RJ. Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control. Prog Lipid Res 2022; 88:101181. [PMID: 35820474 DOI: 10.1016/j.plipres.2022.101181] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022]
Abstract
Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.
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Affiliation(s)
- Guanqun Chen
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta, Membrane Protein Disease Research Group, Edmonton T6G 2H7, Canada
| | - Scot J Stone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
| | - Randall J Weselake
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta T6H 2P5, Canada
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Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
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Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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12
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Homayoonfar M, Roosta Azad R, Sardari S. Analytical methods in fatty acid analysis for microbial applications: the recent trends. Prep Biochem Biotechnol 2021; 51:937-952. [PMID: 34506247 DOI: 10.1080/10826068.2021.1881910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fatty acids are among the most important components of many biological systems and have been highlighted in many research fields in recent decades. In the food industry, it is important to check the amount and types of fatty acids in edible oils, beverages and other foods products, and checking the fatty acids parameters are among the quality control parameters for those products. In medical applications, investigation of fatty acids in biological samples and comparing imbalances in them can help to diagnose some diseases. On the other hand, the development of cell factories for the production of biofuels and other valuable chemicals requires the accurate analysis of fatty acids, which serve as precursors in development of those products. As a result, given all these different applications of fatty acids, rapid and accurate methods for characterization and quantification of fatty acids are essential. In recent years, various methods for the analysis of fatty acids have been proposed, which according to the specific purpose of the analysis, some of them can be used with consideration of speed, accuracy and cost. In this article, the available methods for the analysis of fatty acids are reviewed with a special emphasis on the analysis of microbial samples to pave the way for more widespread metabolic engineering research.
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Affiliation(s)
- Mohammad Homayoonfar
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Roosta Azad
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tahran, Iran
| | - Soroush Sardari
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Riley LA, Guss AM. Approaches to genetic tool development for rapid domestication of non-model microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:30. [PMID: 33494801 PMCID: PMC7830746 DOI: 10.1186/s13068-020-01872-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/30/2020] [Indexed: 05/04/2023]
Abstract
Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, "domestication" of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
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Affiliation(s)
- Lauren A Riley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Bredesen Center, University of Tennessee, Knoxville, TN, 37996, USA.
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Cho IJ, Choi KR, Lee SY. Microbial production of fatty acids and derivative chemicals. Curr Opin Biotechnol 2020; 65:129-141. [DOI: 10.1016/j.copbio.2020.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022]
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