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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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Chaudhary S, Ali Z, Mahfouz M. Molecular farming for sustainable production of clinical-grade antimicrobial peptides. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2282-2300. [PMID: 38685599 PMCID: PMC11258990 DOI: 10.1111/pbi.14344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024]
Abstract
Antimicrobial peptides (AMPs) are emerging as next-generation therapeutics due to their broad-spectrum activity against drug-resistant bacterial strains and their ability to eradicate biofilms, modulate immune responses, exert anti-inflammatory effects and improve disease management. They are produced through solid-phase peptide synthesis or in bacterial or yeast cells. Molecular farming, i.e. the production of biologics in plants, offers a low-cost, non-toxic, scalable and simple alternative platform to produce AMPs at a sustainable cost. In this review, we discuss the advantages of molecular farming for producing clinical-grade AMPs, advances in expression and purification systems and the cost advantage for industrial-scale production. We further review how 'green' production is filling the sustainability gap, streamlining patent and regulatory approvals and enabling successful clinical translations that demonstrate the future potential of AMPs produced by molecular farming. Finally, we discuss the regulatory challenges that need to be addressed to fully realize the potential of molecular farming-based AMP production for therapeutics.
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Affiliation(s)
- Shahid Chaudhary
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
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3
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Li Y, Liu M, Yang C, Fu H, Wang J. Engineering microbial metabolic homeostasis for chemicals production. Crit Rev Biotechnol 2024:1-20. [PMID: 39004513 DOI: 10.1080/07388551.2024.2371465] [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: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024]
Abstract
Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.
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Affiliation(s)
- Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Mingxiong Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Changyang Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
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Ji L, Zhang W, Zhang Y, Nian B, Hu Y. Functionalized Ionic Liquids-Modified Metal-Organic Framework Material Boosted the Enzymatic Performance of Lipase. Molecules 2024; 29:2381. [PMID: 38792242 PMCID: PMC11124374 DOI: 10.3390/molecules29102381] [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: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
The development of immobilized enzymes with high activity and stability is critical. Metal-organic frameworks (MOFs) have attracted much academic and industrial interest in the field of enzyme immobilization due to their unique properties. In this study, the amino-functionalized ionic liquid (NIL)-modified metal-organic framework (UiO-66-NH2) was prepared to immobilize Candida rugosa lipase (CRL), using dialdehyde starch (DAS) as the cross-linker. The results of the Fourier transform infrared (FT-IR) spectra, X-ray powder diffraction (XRD), and scanning electronic microscopy (SEM) confirmed that the NIL was successfully grafted to UiO-66-NH2. The CRL immobilized on NIL-modified UiO-66-NH2 (UiO-66-NH2-NIL-DAS@CRL) exhibited satisfactory activity recovery (79.33%), stability, reusability, and excellent organic solvent tolerance. The research results indicated that ionic liquid-modified UiO-66-NH2 had practical potential for application in enzyme immobilization.
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Affiliation(s)
| | | | | | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (L.J.); (W.Z.); (Y.Z.)
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China; (L.J.); (W.Z.); (Y.Z.)
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Zhou T, Wu J, Tang H, Liu D, Jeon BH, Jin W, Wang Y, Zheng Y, Khan A, Han H, Li X. Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer. NPJ Biofilms Microbiomes 2024; 10:6. [PMID: 38245564 PMCID: PMC10799920 DOI: 10.1038/s41522-024-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jingyuan Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Haibo Tang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Korea
| | - Weilin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yiqing Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | | | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huawen Han
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China.
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China.
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Lyu X, Nuhu M, Candry P, Wolfanger J, Betenbaugh M, Saldivar A, Zuniga C, Wang Y, Shrestha S. Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. J Ind Microbiol Biotechnol 2024; 51:kuae025. [PMID: 39003244 PMCID: PMC11287213 DOI: 10.1093/jimb/kuae025] [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: 04/11/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. ONE-SENTENCE SUMMARY This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.
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Affiliation(s)
- Xuejiao Lyu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mujaheed Nuhu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pieter Candry
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jenna Wolfanger
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexis Saldivar
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Cristal Zuniga
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ying Wang
- Department of Soil and Crop Sciences, Texas A&M University, TX 77843, USA
| | - Shilva Shrestha
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Liu K, Yang P, Zhang X, Zhang D, Wu L, Zhang L, Zhang H, Li G, Li R, Rong L. Metabolic cross-feeding enhances branched-chain aldehydes production in a synthetic community of fermented sausages. Int J Food Microbiol 2023; 407:110373. [PMID: 37696140 DOI: 10.1016/j.ijfoodmicro.2023.110373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/30/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Microbial interactions play an important role in regulating the metabolic function of fermented food communities, especially the production of key flavor compounds. However, little is known about specific molecular mechanisms that regulate the production of key flavor compounds through microbial interactions. Here, we designed a synthetic consortium containing Debaryomyces hansenii D1, Staphylococcus xylosus S1, and Pediococcus pentosaceus PP1 to explore the mechanism of the microbial interactions underlying the branched-chain aldehydes production. In this consortium, firstly, D. hansenii secreted amino acids that promoted the growth of P. pentosaceus and S. xylosus. Specifically, D. hansenii D1 secreted alanine, aspartate, glutamate, glutamine, glycine, phenylalanine, serine, and threonine, which were the primary nutrients for bacterial growth. P. pentosaceus PP1 utilized all these eight amino acids through cross-feeding, whereas S. xylosus S1 did not utilize aspartate and serine. Furthermore, D. hansenii D1 promoted the production of branched-chain aldehydes from S. xylosus and P. pentosaceus through cross-feeding of α-keto acids (intermediate metabolites). Thus, the accumulation of 2-methyl-butanal was promoted in all co-culture. Overall, this work revealed the mechanism by which D. hansenii and bacteria cross-feed to produce branched-chain aldehydes in fermented sausages.
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Affiliation(s)
- Kaihao Liu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Peng Yang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Xudong Zhang
- Comprehensive Technology Service Center of Jinzhou Customs, Jinzhou, Liaoning 121013, China
| | - Di Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Liu Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Lan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China
| | - Huan Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Ruren Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
| | - Liangyan Rong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China.
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Li W, Huang X, Liu H, Lian H, Xu B, Zhang W, Sun X, Wang W, Jia S, Zhong C. Improvement in bacterial cellulose production by co-culturing Bacillus cereus and Komagataeibacter xylinus. Carbohydr Polym 2023; 313:120892. [PMID: 37182977 DOI: 10.1016/j.carbpol.2023.120892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023]
Abstract
Bacterial cellulose (BC) is a bio-produced nanostructure material widely used in biomedical, food, and paper-manufacturing industries. However, low production efficiency and high-cost have limited its industrial applications. This study aimed to examine the level of improvement in BC production by co-culturing Bacillus cereus and Komagataeibacter xylinus. The BC yield in corn stover enzymatic hydrolysate was found to be obviously enhanced from 1.2 to 4.4 g/L after the aforementioned co-culturing. The evidence indicated that acetoin (AC) and 2,3-butanediol (2,3-BD) produced by B. cereus were the key factors dominating BC increment. The mechanism underlying BC increment was that AC and 2,3-BD increased the specific activity of AC dehydrogenase and the contents of adenosine triphosphate (ATP) and acetyl coenzyme A (acetyl-CoA), thus promoting the growth and energy level of K. xylinus. Meanwhile, the immobilization of BC could also facilitate oxygen acquisition in B. cereus under static conditions. This study was novel in reporting that the co-culture could effectively enhance BC production from the lignocellulosic enzymatic hydrolysate.
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Affiliation(s)
- Wenchao Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Xinxin Huang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Huan Liu
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Hao Lian
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Bin Xu
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Wenjin Zhang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Xuewen Sun
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Wei Wang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Shiru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, 300457 Tianjin, PR China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science & Technology, 300457 Tianjin, PR China.
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Han YH, Kim G, Seo SW. Programmable synthetic biology tools for developing microbial cell factories. Curr Opin Biotechnol 2023; 79:102874. [PMID: 36610368 DOI: 10.1016/j.copbio.2022.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Microbial conversion to generate value-added chemicals from diverse biomass is one of the keystones of energy biotechnology. Programmable synthetic biology tools offer versatile, standardized options for developing microbial cell factories. These tools thus can be reprogrammed in a user-defined manner for flexible wiring of stimuli and response, highly efficient genome engineering, and extensive perturbation of metabolic flux and genetic circuits. They also can be modularly assembled to construct elaborate and unprecedented biological systems with unique features. This review highlights recent advances in programmable synthetic biology tools based on biosensors, CRISPR-Cas, and RNA devices for developing microbial cell factories that have the potential to be utilized for energy biotechnology.
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Affiliation(s)
- Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Giho Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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Yu W, Xu X, Jin K, Liu Y, Li J, Du G, Lv X, Liu L. Genetically encoded biosensors for microbial synthetic biology: From conceptual frameworks to practical applications. Biotechnol Adv 2023; 62:108077. [PMID: 36502964 DOI: 10.1016/j.biotechadv.2022.108077] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Genetically encoded biosensors are the vital components of synthetic biology and metabolic engineering, as they are regarded as powerful devices for the dynamic control of genotype metabolism and evolution/screening of desirable phenotypes. This review summarized the recent advances in the construction and applications of different genetically encoded biosensors, including fluorescent protein-based biosensors, nucleic acid-based biosensors, allosteric transcription factor-based biosensors and two-component system-based biosensors. First, the construction frameworks of these biosensors were outlined. Then, the recent progress of biosensor applications in creating versatile microbial cell factories for the bioproduction of high-value chemicals was summarized. Finally, the challenges and prospects for constructing robust and sophisticated biosensors were discussed. This review provided theoretical guidance for constructing genetically encoded biosensors to create desirable microbial cell factories for sustainable bioproduction.
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Affiliation(s)
- Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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Suo H, Geng X, Sun Y, Zhang L, Yang J, Yang F, Yan H, Hu Y, Xu L. Surface Modification of Magnetic ZIF-90 Nanoparticles Improves the Microenvironment of Immobilized Lipase and Its Application in Esterification. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15384-15393. [PMID: 36448653 DOI: 10.1021/acs.langmuir.2c02672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Interactions of enzymes with supports significantly affect the activity and stability of immobilized enzymes. Herein, amino-functionalized ionic liquid (IL)-grafted magnetic zeolitic imidazolate framework-90 (MZIF-90) was prepared and used to immobilize porcine pancreatic lipase (PPL). The nanocomposites were fully characterized; meanwhile, the interactions between ILs and ZIF-90 were calculated based on density functional theory. The prepared biocatalyst (PPL-ILs/MZIF-90) had a lipase loading of 178.3 mg/g and hydrolysis activity up to 287.5 U/g. When the biocatalyst was used to synthesize isoamyl acetate, the reaction media, molar ratio of alcohol/acid, temperature, and reaction time were optimized. Under the optimized reaction conditions (in hexane, alcohol/acid = 3:1, under 45 °C, reacted for 9 h), the ester yield reached 85.5%. The results of the stability test showed that PPL-ILs/MZIF-90 retained 88.7% of the initial activity after storing for 35 days and 92.5% of the initial activity after reusing for seven cycles for synthesizing isoamyl acetate. Moreover, the secondary structure analysis showed that the synthesized supports protected the active conformation of immobilized lipase, which lead to the enhanced catalytic performance. Additionally, the biocatalyst can be easily separated with a magnet, which facilitated the reusability. This study provides insights regarding the application of metal organic framework composites in the field of enzyme catalysis.
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Affiliation(s)
- Hongbo Suo
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Xinyue Geng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yinghui Sun
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Lu Zhang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Jie Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Fan Yang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China
| | - Lili Xu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, China
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Chiang CJ, Chang CH, Chao YP. Programmed cell-lysis system based on hybrid sigma factor-dependent promoters. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2022.104611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y, Tang H. Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. MLIFE 2022; 1:382-398. [PMID: 38818482 PMCID: PMC10989833 DOI: 10.1002/mlf2.12043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/01/2024]
Abstract
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
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Affiliation(s)
- Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Miaoxiao Wang
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyETH ZürichEawagSwitzerland
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yong Nie
- College of EngineeringPeking UniversityBeijingChina
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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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]
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15
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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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