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Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024; 74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [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: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Hongyu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark.
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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2
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Ding Q, Liu L. Reprogramming cellular metabolism to increase the efficiency of microbial cell factories. Crit Rev Biotechnol 2024; 44:892-909. [PMID: 37380349 DOI: 10.1080/07388551.2023.2208286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 06/30/2023]
Abstract
Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.
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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, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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3
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He SJ, Yang LH, Du YH, Tong LL, Wang Y, Guo DS. Development of a novel microplate for high-throughput screening and optimization of DHA producing strains based on CFD technology. Biotechnol J 2023; 18:e2300169. [PMID: 37466173 DOI: 10.1002/biot.202300169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Microtiter plates are suitable for screening and process development of most microorganisms. They are currently the container of choice for high-throughput and small-scale microbial culture, but require optimization for specific work. In this research, a novel type of microtiter plate was developed using computational fluid dynamics (CFD) technology. The new plate provided high oxygen supply and optimal mixing effects for the fermentation culture of docosahexaenoic acid (DHA) producing strains, surpassing the conventional method of strain screening with shake flasks, which was insufficient. The shape of the microtiter plate was modified, and baffles were introduced to improve mass transfer and oxygen supply effects in the vibrating bioreactor. CFD technology was used to model the new plate's characteristics, establishing the superiority of hexagonal microtiter plates with six baffles. Parameters in the incubation process, such as vibration frequency and liquid load, were optimized, and the final result achieved an oxygen transfer coefficient (KL a) of 0.61 s-1 and a volume power input of 2364 w m-3 , which was four to five times better than the original 96-well plate. The culture results optimized by the model were also verified. Therefore, this new microtiter plate provides a powerful tool for future high-throughput screening of strains.
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Affiliation(s)
- Shao-Jie He
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Lin-Hui Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yuan-Hang Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Ling-Ling Tong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Dong-Sheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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Ding Q, Ye C. Microbial engineering for shikimate biosynthesis. Enzyme Microb Technol 2023; 170:110306. [PMID: 37598506 DOI: 10.1016/j.enzmictec.2023.110306] [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: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China; Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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Du H, Qi Y, Qiao J, Li L, Wei L, Xu N, Shao L, Liu J. Transcription factor OxyR regulates sulfane sulfur removal and L-cysteine biosynthesis in Corynebacterium glutamicum. Appl Environ Microbiol 2023; 89:e0090423. [PMID: 37768042 PMCID: PMC10537588 DOI: 10.1128/aem.00904-23] [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: 05/31/2023] [Accepted: 07/09/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfane sulfur, a collective term for hydrogen polysulfide and organic persulfide, often damages cells at high concentrations. Cells can regulate intracellular sulfane sulfur levels through specific mechanisms, but these mechanisms are unclear in Corynebacterium glutamicum. OxyR is a transcription factor capable of sensing oxidative stress and is also responsive to sulfane sulfur. In this study, we found that OxyR functioned directly in regulating sulfane sulfur in C. glutamicum. OxyR binds to the promoter of katA and nrdH and regulates its expression, as revealed via in vitro electrophoretic mobility shift assay analysis, real-time quantitative PCR, and reporting systems. Overexpression of katA and nrdH reduced intracellular sulfane sulfur levels by over 30% and 20% in C. glutamicum, respectively. RNA-sequencing analysis showed that the lack of OxyR downregulated the expression of sulfur assimilation pathway genes and/or sulfur transcription factors, which may reduce the rate of sulfur assimilation. In addition, OxyR also affected the biosynthesis of L-cysteine in C. glutamicum. OxyR overexpression strain Cg-2 accumulated 183 mg/L of L-cysteine, increased by approximately 30% compared with the control (142 mg/L). In summary, OxyR not only regulated sulfane sulfur levels by controlling the expression of katA and nrdH in C. glutamicum but also facilitated the sulfur assimilation and L-cysteine synthesis pathways, providing a potential target for constructing robust cell factories of sulfur-containing amino acids and their derivatives. IMPORTANCE C. glutamicum is an important industrial microorganism used to produce various amino acids. In the production of sulfur-containing amino acids, cells inevitably accumulate a large amount of sulfane sulfur. However, few studies have focused on sulfane sulfur removal in C. glutamicum. In this study, we not only revealed the regulatory mechanism of OxyR on intracellular sulfane sulfur removal but also explored the effects of OxyR on the sulfur assimilation and L-cysteine synthesis pathways in C. glutamicum. This is the first study on the removal of sulfane sulfur in C. glutamicum. These results contribute to the understanding of sulfur regulatory mechanisms and may aid in the future optimization of C. glutamicum for biosynthesis of sulfur-containing amino acids.
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Affiliation(s)
- Huanmin Du
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Qi
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jinfang Qiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lingcong Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Wei
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Li Shao
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jun Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Jiang Z, Lu J, Tong Y, Yang H, Feng S. Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile. World J Microbiol Biotechnol 2023; 39:158. [PMID: 37046107 DOI: 10.1007/s11274-023-03613-4] [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: 02/24/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpAAc for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.
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Affiliation(s)
- Zhenming Jiang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jie Lu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, China
| | - Hailin Yang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shoushuai Feng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
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Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.
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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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Shi TQ, Darvishi F, Cao M, Ji B, Ji XJ. Editorial: Design and construction of microbial cell factories for the production of fuels and chemicals. Front Bioeng Biotechnol 2023; 11:1198317. [PMID: 37152641 PMCID: PMC10154672 DOI: 10.3389/fbioe.2023.1198317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Affiliation(s)
- Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- *Correspondence: Tian-Qiong Shi, ; Farshad Darvishi, , ; Mingfeng Cao, ; Boyang Ji, ; Xiao-Jun Ji,
| | - Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran
- *Correspondence: Tian-Qiong Shi, ; Farshad Darvishi, , ; Mingfeng Cao, ; Boyang Ji, ; Xiao-Jun Ji,
| | - Mingfeng Cao
- College of Chemistry and Chemical Engineering, Xiamen University, Fujian, China
- *Correspondence: Tian-Qiong Shi, ; Farshad Darvishi, , ; Mingfeng Cao, ; Boyang Ji, ; Xiao-Jun Ji,
| | - Boyang Ji
- BioInnovation InstituteCopenhagen, Denmark
- *Correspondence: Tian-Qiong Shi, ; Farshad Darvishi, , ; Mingfeng Cao, ; Boyang Ji, ; Xiao-Jun Ji,
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- *Correspondence: Tian-Qiong Shi, ; Farshad Darvishi, , ; Mingfeng Cao, ; Boyang Ji, ; Xiao-Jun Ji,
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Tóth GS, Siitonen V, Nikkanen L, Sovic L, Kallio P, Kourist R, Kosourov S, Allahverdiyeva Y. Photosynthetically produced sucrose by immobilized Synechocystis sp. PCC 6803 drives biotransformation in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:146. [PMID: 36575466 PMCID: PMC9795604 DOI: 10.1186/s13068-022-02248-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Whole-cell biotransformation is a promising emerging technology for the production of chemicals. When using heterotrophic organisms such as E. coli and yeast as biocatalysts, the dependence on organic carbon source impairs the sustainability and economic viability of the process. As a promising alternative, photosynthetic cyanobacteria with low nutrient requirements and versatile metabolism, could offer a sustainable platform for the heterologous production of organic compounds directly from sunlight and CO2. This strategy has been applied for the photoautotrophic production of sucrose by a genetically engineered cyanobacterium, Synechocystis sp. PCC 6803 strain S02. As the key concept in the current work, this can be further used to generate organic carbon compounds for different heterotrophic applications, including for the whole-cell biotransformation by yeast and bacteria. RESULTS Entrapment of Synechocystis S02 cells in Ca2+-cross-linked alginate hydrogel beads improves the specific sucrose productivity by 86% compared to suspension cultures during 7 days of cultivation under salt stress. The process was further prolonged by periodically changing the medium in the vials for up to 17 days of efficient production, giving the final sucrose yield slightly above 3000 mg l-1. We successfully demonstrated that the medium enriched with photosynthetically produced sucrose by immobilized Synechocystis S02 cells supports the biotransformation of cyclohexanone to ε-caprolactone by the E. coli WΔcscR Inv:Parvi strain engineered to (i) utilize low concentrations of sucrose and (ii) perform biotransformation of cyclohexanone to ε-caprolactone. CONCLUSION We conclude that cell entrapment in Ca2+-alginate beads is an effective method to prolong sucrose production by the engineered cyanobacteria, while allowing efficient separation of the cells from the medium. This advantage opens up novel possibilities to create advanced autotroph-heterotroph coupled cultivation systems for solar-driven production of chemicals via biotransformation, as demonstrated in this work by utilizing the photosynthetically produced sucrose to drive the conversion of cyclohexanone to ε-caprolactone by engineered E. coli.
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Affiliation(s)
- Gábor Szilveszter Tóth
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Vilja Siitonen
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lauri Nikkanen
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lucija Sovic
- grid.410413.30000 0001 2294 748XCell and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Pauli Kallio
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Robert Kourist
- grid.410413.30000 0001 2294 748XCell and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Sergey Kosourov
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Yagut Allahverdiyeva
- grid.1374.10000 0001 2097 1371Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
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11
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Liu X, Luo H, Yu D, Tan J, Yuan J, Li H. Synthetic biology promotes the capture of CO2 to produce fatty acid derivatives in microbial cell factories. BIORESOUR BIOPROCESS 2022; 9:124. [PMID: 38647643 PMCID: PMC10992411 DOI: 10.1186/s40643-022-00615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/27/2022] [Indexed: 12/07/2022] Open
Abstract
Environmental problems such as greenhouse effect, the consumption of fossil energy, and the increase of human demand for energy are becoming more and more serious, which force researcher to turn their attention to the reduction of CO2 and the development of renewable energy. Unsafety, easy to lead to secondary environmental pollution, cost inefficiency, and other problems limit the development of conventional CO2 capture technology. In recent years, many microorganisms have attracted much attention to capture CO2 and synthesize valuable products directly. Fatty acid derivatives (e.g., fatty acid esters, fatty alcohols, and aliphatic hydrocarbons), which can be used as a kind of environmentally friendly and renewable biofuels, are sustainable substitutes for fossil energy. In this review, conventional CO2 capture techniques pathways, microbial CO2 concentration mechanisms and fixation pathways were introduced. Then, the metabolic pathway and progress of direct production of fatty acid derivatives from CO2 in microbial cell factories were discussed. The synthetic biology means used to design engineering microorganisms and optimize their metabolic pathways were depicted, with final discussion on the potential of optoelectronic-microbial integrated capture and production systems.
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Affiliation(s)
- Xiaofang Liu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China.
| | - Hangyu Luo
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Dayong Yu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Jinyu Tan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Junfa Yuan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Hu Li
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China.
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12
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Wang J, Yang J, Shi G, Li W, Ju Y, Wei L, Liu J, Xu N. Transcriptome profiles of high-lysine adaptation reveal insights into osmotic stress response in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 10:933325. [PMID: 36017356 PMCID: PMC9395588 DOI: 10.3389/fbioe.2022.933325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/06/2022] [Indexed: 12/05/2022] Open
Abstract
Corynebacterium glutamicum has been widely and effectively used for fermentative production of l-lysine on an industrial scale. However, high-level accumulation of end products inevitably leads to osmotic stress and hinders further increase of l-lysine production. At present, the underlying mechanism by which C. glutamicum cells adapt to high-lysine-induced osmotic stress is still unclear. In this study, we conducted a comparative transcriptomic analysis by RNA-seq to determine gene expression profiles under different high-lysine stress conditions. The results indicated that the increased expression of some metabolic pathways such as sulfur metabolism and specific amino acid biosynthesis might offer favorable benefits for high-lysine adaptation. Functional assays of 18 representative differentially expressed genes showed that the enhanced expression of multiple candidate genes, especially grpE chaperon, conferred high-lysine stress tolerance in C. glutamicum. Moreover, DNA repair component MutT and energy-transducing NADH dehydrogenase Ndh were also found to be important for protecting cells against high-lysine-induced osmotic stress. Taken together, these aforementioned findings provide broader views of transcriptome profiles and promising candidate targets of C. glutamicum for the adaptation of high-lysine stress during fermentation.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Jian Yang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Guoxin Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Weidong Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Yun Ju
- School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Ning Xu,
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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]
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Yang D, Park SY, Lee SY. Production of Rainbow Colorants by Metabolically Engineered Escherichia coli. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100743. [PMID: 34032018 PMCID: PMC8261500 DOI: 10.1002/advs.202100743] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/08/2021] [Indexed: 05/07/2023]
Abstract
There has been much interest in producing natural colorants to replace synthetic colorants of health concerns. Escherichia coli has been employed to produce natural colorants including carotenoids, indigo, anthocyanins, and violacein. However, production of natural green and navy colorants has not been reported. Many natural products are hydrophobic, which are accumulated inside or on the cell membrane. This causes cell growth limitation and consequently reduces production of target chemicals. Here, integrated membrane engineering strategies are reported for the enhanced production of rainbow colorants-three carotenoids and four violacein derivatives-as representative hydrophobic natural products in E. coli. By integration of systems metabolic engineering, cell morphology engineering, inner- and outer-membrane vesicle formation, and fermentation optimization, production of rainbow colorants are significantly enhanced to 322 mg L-1 of astaxanthin (red), 343 mg L-1 of β-carotene (orange), 218 mg L-1 of zeaxanthin (yellow), 1.42 g L-1 of proviolacein (green), 0.844 g L-1 of prodeoxyviolacein (blue), 6.19 g L-1 of violacein (navy), and 11.26 g L-1 of deoxyviolacein (purple). The membrane engineering strategies reported here are generally applicable to microbial production of a broader range of hydrophobic natural products, contributing to food, cosmetic, chemical, and pharmaceutical industries.
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Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
| | - Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
- BioInformatics Research CenterKAISTDaejeon34141Republic of Korea
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