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Liu Y, Xue B, Liu H, Wang S, Su H. Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform. Biotechnol Adv 2024; 72:108348. [PMID: 38531490 DOI: 10.1016/j.biotechadv.2024.108348] [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: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield. However, research on synthetic consortia is still in its infancy, with numerous challenges regarding the design and construction of stable synthetic consortia. This review provides a comprehensive comparison of the advantages and disadvantages of mono-culture systems and synthetic consortia. Key considerations for engineering synthetic consortia based on recent advances are summarized, and simulation and computational tools for guiding the advancement of synthetic consortia are discussed. Moreover, further development of more efficient and cost-effective synthetic consortia with emerging technologies such as artificial intelligence and machine learning is highlighted.
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Affiliation(s)
- Yu Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Boyuan Xue
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Hao Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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Gu S, Zhu F, Zhang L, Wen J. Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5555-5573. [PMID: 38442481 DOI: 10.1021/acs.jafc.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.
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Affiliation(s)
- Shanna Gu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
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Kaya C, Uğurlar F, Ashraf M, Hou D, Kirkham MB, Bolan N. Microbial consortia-mediated arsenic bioremediation in agricultural soils: Current status, challenges, and solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170297. [PMID: 38272079 DOI: 10.1016/j.scitotenv.2024.170297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/01/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Arsenic poisoning in agricultural soil is caused by both natural and man-made processes, and it poses a major risk to crop production and human health. Soil quality, agricultural production, runoff, ingestion, leaching, and absorption by plants are all influenced by these processes. Microbial consortia have become a feasible bioremediation technique in response to the urgent need for appropriate remediation solutions. These diverse microbial populations collaborate to combat arsenic poisoning in soil by facilitating mechanisms including oxidation-reduction, methylation-demethylation, volatilization, immobilization, and arsenic mobilization. The current state, problems, and remedies for employing microbial consortia in arsenic bioremediation in agricultural soils are examined in this review. Among the elements affecting their success include diversity, activity, community organization, and environmental conditions. Also, we emphasize the sensitivity and accuracy limits of existing assessment techniques. While earlier reviews have addressed a variety of arsenic remediation options, this study stands out by concentrating on microbial consortia as a viable strategy for arsenic removal and presents performance evaluation and technical problems. This work gives vital insights for tackling the major issue of arsenic pollution in agricultural soils by explaining the potential methods and components involved in microbial consortium-mediated arsenic bioremediation.
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Affiliation(s)
- Cengiz Kaya
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa, Turkey.
| | - Ferhat Uğurlar
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa, Turkey
| | - Muhammed Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
| | - Mary Beth Kirkham
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
| | - Nanthi Bolan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
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Zhou SP, Ke X, Jin LQ, Xue YP, Zheng YG. Sustainable management and valorization of biomass wastes using synthetic microbial consortia. BIORESOURCE TECHNOLOGY 2024; 395:130391. [PMID: 38307483 DOI: 10.1016/j.biortech.2024.130391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
In response to the persistent expansion of global resource demands, considerable attention has been directed toward the synthetic microbial consortia (SMC) within the domain of microbial engineering, aiming to address the sustainable management and valorization of biomass wastes. This comprehensive review systematically encapsulates the most recent advancements in research and technological applications concerning the utilization of SMC for biomass waste treatment. The construction strategies of SMC are briefly outlined, and the diverse applications of SMC in biomass wastes treatment are explored, with particular emphasis on its potential advantages in waste degradation, hazardous substances control, and high value-added products conversion. Finally, recommendations for the future development of SMC technology are proposed, and prospects for its sustainable application are discussed.
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Affiliation(s)
- Shi-Peng Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xia Ke
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Li-Qun Jin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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