1
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Zhang C, Fei Q, Fu R, Lackner M, Zhou YJ, Tan T. Economic and sustainable revolution to facilitate one-carbon biomanufacturing. Nat Commun 2025; 16:4896. [PMID: 40425587 PMCID: PMC12117142 DOI: 10.1038/s41467-025-60247-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025] Open
Abstract
One-carbon (C1) biomanufacturing serves as a substitute for fossil-based feedstocks, aiming to de-fossilize chemical production and foster a circular carbon economy by recycling waste greenhouse gases. Here, we review the key economic and technical barriers associated with the commercialization of C1 biomanufacturing through case studies. Additionally, a viable roadmap to enhance cost competitiveness is unveiled, underscoring its potential to facilitate carbon neutrality as scalable and sustainable alternatives to traditional chemical production.
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Affiliation(s)
- Chenyue Zhang
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Qiang Fei
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China.
| | - Rongzhan Fu
- School of Chemical Engineering, Northwest University, Xi'an, China
| | | | - Yongjin J Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tianwei Tan
- State Key Laboratory of Green Biomanufacturing, Beijing University of Chemical Technology, Beijing, China.
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2
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Ricci L, Cen X, Zu Y, Antonicelli G, Chen Z, Fino D, Pirri FC, Stephanopoulos G, Woolston BM, Re A. Metabolic Engineering of E. coli for Enhanced Diols Production from Acetate. ACS Synth Biol 2025; 14:1204-1219. [PMID: 40103233 PMCID: PMC12012870 DOI: 10.1021/acssynbio.4c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 03/11/2025] [Accepted: 03/11/2025] [Indexed: 03/20/2025]
Abstract
Effective employment of renewable carbon sources is highly demanded to develop sustainable biobased manufacturing. Here, we developed Escherichia coli strains to produce 2,3-butanediol and acetoin (collectively referred to as diols) using acetate as the sole carbon source by stepwise metabolic engineering. When tested in fed-batch experiments, the strain overexpressing the entire acetate utilization pathway was found to consume acetate at a 15% faster rate (0.78 ± 0.05 g/g/h) and to produce a 35% higher diol titer (1.16 ± 0.01 g/L) than the baseline diols-producing strain. Moreover, singularly overexpressing the genes encoding alternative acetate uptake pathways as well as alternative isoforms of genes in the malate-to-pyruvate pathway unveiled that leveraging ackA-pta and maeA is more effective in enhancing acetate consumption and diols production, compared to acs and maeB. Finally, the increased substrate consumption rate and diol production obtained in flask-based experiments were confirmed in bench-scale bioreactors operated in fed-batch mode. Consequently, the highest titer of 1.56 g/L achieved in this configuration increased by over 30% compared to the only other similar effort carried out so far.
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Affiliation(s)
- Luca Ricci
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02142, United States
- Centre
for Sustainable Future Technologies, Fondazione
Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
- RINA
Consulting S.p.A., Energy Innovation Strategic
Centre, Via Antonio Cecchi,
6, 16129 Genoa, Italy
| | - Xuecong Cen
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02142, United States
- Department
of Chemical Engineering, Key Laboratory of Industrial Biocatalysis
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yuexuan Zu
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02142, United States
| | - Giacomo Antonicelli
- Centre
for Sustainable Future Technologies, Fondazione
Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy
- Department
of Environment, Land and Infrastructure Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
| | - Zhen Chen
- Department
of Chemical Engineering, Key Laboratory of Industrial Biocatalysis
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Debora Fino
- Centre
for Sustainable Future Technologies, Fondazione
Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
| | - Fabrizio C. Pirri
- Centre
for Sustainable Future Technologies, Fondazione
Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
| | - Gregory Stephanopoulos
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02142, United States
| | - Benjamin M. Woolston
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 223 Cullinane, Boston, Massachusetts 02115, United States
| | - Angela Re
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
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3
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Jiang J. Teaching system reform and practice of Industrial Microbiology in pharmaceutical engineering. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2025:e0000925. [PMID: 40237457 DOI: 10.1128/jmbe.00009-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 03/27/2025] [Indexed: 04/18/2025]
Abstract
Industrial Microbiology is a fundamental course in pharmaceutical engineering. This paper aims at the problems existing in the teaching practice of Industrial Microbiology for pharmaceutical engineering in our school. It discusses the formation of a teaching team primarily consisting of doctors/associate professors with biochemical and pharmaceutical background, supplemented by middle and senior pharmaceutical engineers. Individual students have a certain influence on the effectiveness of teaching reform. Problem-based learning (PBL) teaching significantly improves the teaching effect, and the average scores of males and females are increased by 3.66 points and 4.13 points, respectively, with an increase rate of 5.64% and 5.94%. Gender also has a significant impact on the effectiveness of PBL teaching, with females being more proactive and effective than males. The aim of this study is to establish a scientific and reasonable teaching system to provide reference for improving the teaching effect of Industrial Microbiology.
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4
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Altamira-Algarra B, Garcia J, Gonzalez-Flo E. Cyanobacteria microbiomes for bioplastic production: Critical review of key factors and challenges in scaling from laboratory to industry set-ups. BIORESOURCE TECHNOLOGY 2025; 422:132231. [PMID: 39956522 DOI: 10.1016/j.biortech.2025.132231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 01/24/2025] [Accepted: 02/13/2025] [Indexed: 02/18/2025]
Abstract
Cyanobacteria are photoautotrophic microorganisms capable of accumulating polyhydroxybutyrate (PHB). A novel approach for PHB production involves the exploration of cyanobacterial microbiomes, potentially reducing costs through non-sterile cultivation with non-pure substrates. Although still in its early stages, this approach shows promise for high yields and sustained synthesis. However, managing microbiome population dynamics in non-sterile environments requires effective monitoring and control. This review covers PHB production by cyanobacteria microbiomes, from sample procurement to laboratory-scale production. It highlights recent insights into optimizing cultivation parameters for enhanced biopolymer yield. Strategies to overcome challenges in PHB production are evaluated, emphasizing integrated molecular biology techniques with quantitative and qualitative PHB analysis. Finally, key challenges in scaling up production to industrial-scale scenarios are discussed, along with potential solutions to support the development of sustainable industrial processes. Cyanobacteria microbiomes show promise PHB production but challenges like managing non-sterile conditions and scaling up require optimized strategies and integrated approaches.
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Affiliation(s)
- Beatriz Altamira-Algarra
- GEMMA-Group of Environmental Engineering and Microbiology. Department of Civil and Environmental Engineering. Escola d'Enginyeria de Barcelona Est (EEBE). Universitat Politècnica de Catalunya-BarcelonaTech. Av. Eduard Maristany 16. Building C5.1. E-, 08019 Barcelona. Spain.
| | - Joan Garcia
- GEMMA-Group of Environmental Engineering and Microbiology. Department of Civil and Environmental Engineering. Universitat Politècnica de Catalunya-BarcelonaTech. c/ Jordi Girona 1-3. Building, D1. E-08034 Barcelona. Spain.
| | - Eva Gonzalez-Flo
- GEMMA-Group of Environmental Engineering and Microbiology. Department of Civil and Environmental Engineering. Escola d'Enginyeria de Barcelona Est (EEBE). Universitat Politècnica de Catalunya-BarcelonaTech. Av. Eduard Maristany 16. Building C5.1. E-, 08019 Barcelona. Spain.
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5
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Outram V, Yiakoumetti A, Green C, King R, Ward JM, Conradie A. Enhancing the stability of continuous fermentations for platform chemical production. iScience 2025; 28:111786. [PMID: 40034854 PMCID: PMC11875142 DOI: 10.1016/j.isci.2025.111786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 11/11/2024] [Accepted: 01/08/2025] [Indexed: 03/05/2025] Open
Abstract
A significant bottleneck of continuous fermentation is the stability of plasmid-based expression systems. This work tested five plasmid addiction systems based on essential gene complementation in continuous E. coli fermentation. The essential genes tested were infA, ssb, proBA, proC, and dapD and evaluated under phosphate-limited continuous fermentation at two dilution rates (0.033 h-1 and 0.1 h-1) and two temperatures (30°C and 37°C). Of these, plasmids stabilized by infA, ssb, and dapD complementation were segregationally stable under all operating conditions. While a lower dilution rate decreased structural stability, this could be remedied by lowering the temperature. At 0.033 h-1 and 30°C, addiction systems based on proC, dapD, and infA complementation conferred segregational stability with no detriment to structural stability, enabling higher yields at lower dilution rates. This work expands the potential of continuous fermentations for bio-based platform chemical production using plasmid addiction systems to ensure plasmid stability.
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Affiliation(s)
- Victoria Outram
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Andrew Yiakoumetti
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Charlotte Green
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Rebekah King
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - John M. Ward
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, UK
| | - Alex Conradie
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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6
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Federici F, Luppino F, Aguilar-Vilar C, Mazaraki ME, Petersen LB, Ahonen L, Nikel PI. CIFR (Clone-Integrate-Flip-out-Repeat): A toolset for iterative genome and pathway engineering of Gram-negative bacteria. Metab Eng 2025; 88:180-195. [PMID: 39778677 DOI: 10.1016/j.ymben.2025.01.001] [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: 11/06/2024] [Revised: 01/01/2025] [Accepted: 01/05/2025] [Indexed: 01/11/2025]
Abstract
Advanced genome engineering enables precise and customizable modifications of bacterial species, and toolsets that exhibit broad-host compatibility are particularly valued owing to their portability. Tn5 transposon vectors have been widely used to establish random integrations of desired DNA sequences into bacterial genomes. However, the iteration of the procedure remains challenging because of the limited availability and reusability of selection markers. We addressed this challenge with CIFR, a mini-Tn5 integration system tailored for iterative genome engineering. The pCIFR vectors incorporate attP and attB sites flanking an antibiotic resistance marker used to select for the insertion. Subsequent removal of antibiotic determinants is facilitated by the Bxb1 integrase paired to a user-friendly counter-selection marker, both encoded in auxiliary plasmids. CIFR delivers engineered strains harboring stable DNA insertions and free of any antibiotic resistance cassette, allowing for the reusability of the tool. The system was validated in Pseudomonas putida, Escherichia coli, and Cupriavidus necator, underscoring its portability across diverse industrially relevant hosts. The CIFR toolbox was calibrated through combinatorial integrations of chromoprotein genes in P. putida, generating strains displaying a diverse color palette. We also introduced a carotenoid biosynthesis pathway in P. putida in a two-step engineering process, showcasing the potential of the tool for pathway balancing. The broad utility of the CIFR toolbox expands the toolkit for metabolic engineering, allowing for the construction of complex phenotypes while opening new possibilities in bacterial genetic manipulations.
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Affiliation(s)
- Filippo Federici
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Francesco Luppino
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Clara Aguilar-Vilar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria Eleni Mazaraki
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Boje Petersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Linda Ahonen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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7
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Xiong T, Gao Q, Liu W, Li W, Fan G. Biosynthesis of 2-phenylethanol from styrene using engineered Escherichia coli whole cells. Enzyme Microb Technol 2025; 184:110582. [PMID: 39798251 DOI: 10.1016/j.enzmictec.2025.110582] [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: 08/27/2024] [Revised: 12/19/2024] [Accepted: 01/07/2025] [Indexed: 01/15/2025]
Abstract
2-Phenylethanol, an aromatic alcohol with a rose scent, is widely used in the cosmetics, food, and pharmaceutical industries. We designed an efficient multi-enzyme cascade pathway for production of 2-phenylethanol from styrene as the substrate. Initially, 2-phenylethanol was produced by overexpression of styrene monooxygenase A (styA), styrene monooxygenase B (styB), styrene oxide isomerase (SOI), alcohol dehydrogenase (yahK), and glucose dehydrogenase (gdh) in Escherichia coli to give 6.28 mM 2-phenylethanol. Subsequently, plasmids with different copy numbers were employed to balance the expression of pathway enzymes to produce 10.28 mM 2-phenylethanol, resulting in a 63.7 % increase in the final yield. Furthermore, the pH and temperature of the whole-cell conversion reaction were optimized, the optimum pH and temperature are 7.5 and 35℃, respectively. Finally, whole-cell conversion experiment was conducted, and the production of 2-phenylethanol reached 48.17 mM within 10 h. This study provides a theoretical and practical foundation for production of 2-phenylethanol.
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Affiliation(s)
- Tianzhen Xiong
- Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan 464000, China; Henan Key Laboratory of Tea Plant Biology, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Qiuyue Gao
- College of Social Science, Xinyang University, 7th New Avenue West, Xinyang, Henan 464000, China
| | - Wei Liu
- Institute of Agricultural Quality Standards and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, Jilin 130000, China
| | - Wei Li
- Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan 464000, China
| | - Guangyan Fan
- Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan 464000, China
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8
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Zhou Z, Ding H, Shi C, Peng S, Zhu B, An X, Li H. Enhanced butanol tolerance and production from puerariae slag hydrolysate by Clostridium beijerinckii through metabolic engineering and process regulation strategies. BIORESOURCE TECHNOLOGY 2025; 419:132035. [PMID: 39755159 DOI: 10.1016/j.biortech.2025.132035] [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: 10/15/2024] [Revised: 12/21/2024] [Accepted: 01/01/2025] [Indexed: 01/06/2025]
Abstract
Butanol is a more desirable second-generation biomass energy source. Acetone-butanol-ethanol (ABE) fermentation using Clostridium spp. is a promising method for butanol production. However, the toxicity of butanol to the producing strains leading to its low yield and the high cost of feedstock are the main obstacles limiting the ABE fermentation industry. In this study, to enhance the butanol tolerance and production in Clostridium beijerinckii D9, the strategies of metabolic engineering and process regulation were employed. With this effort, a recombinant strain D9/pykA was successfully developed. Furthermore, the effect of exogenous fermentation waste streams and their two-stage addition strategy on ABE fermentation was also investigated. Under the optimal condition, the highest butanol and total solvent production of 11.20 ± 0.58 g/L and 13.65 ± 0.51 g/L was achieved in C. beijerinckii D9/pykA, representing increases of 40.70 % and 37.05 %, respectively, compared to the original strain D9. Additionally, the results of the physiological mechanism revealed that the two-stage fermentation waste stream addition improved NADH synthesis and upregulated key genes involved in butanol biosynthesis, and thus enhancing the production. These insights could provide a foundation for further optimization of ABE fermentation processes and offer promising avenues for improving other similar research.
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Affiliation(s)
- Zhiyou Zhou
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huanhuan Ding
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Chaoyue Shi
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Shuaiyin Peng
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Biao Zhu
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xuejiao An
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Hanguang Li
- College of Bioscience and Bioengineering, Institute of Applied Microbiology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China.
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9
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Guo C, Ling N, Tian H, Wang Z, Gao M, Chen Y, Ji C. Comprehensive review of extraction, purification, structural characteristics, pharmacological activities, structure-activity relationship and application of seabuckthorn protein and peptides. Int J Biol Macromol 2025; 294:139447. [PMID: 39756720 DOI: 10.1016/j.ijbiomac.2024.139447] [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: 11/26/2024] [Revised: 12/16/2024] [Accepted: 12/31/2024] [Indexed: 01/07/2025]
Abstract
Seabuckthorn (Hippophae rhamnoides) is an excellent plant that has the concomitant function of both medicine and foodstuff with high nutritional and health-promoting properties. As a pivotal bioactive component mainly existing in the seeds and leaves, seabuckthorn protein and its derived peptides have aroused wide attention owing to their multifaceted pharmacological activities, including anti-hypertensive, hypoglycemic, anti-obesity, anti-freeze, immunomodulatory, anti-inflammatory, sobriety, anti-oxidant and anti-neurodegenerative functions. Despite these promising attributes, the application of seabuckthorn peptides as functional food and medicines are impeded due to lack of a comprehensive understanding of pharmacological activities and intricate structure-activity relationship. Therefore, this review systematically summarizes the latest advancements in the extraction, purification, structural characteristics, pharmacological activities, digestion, absorption and transport, and application of seabuckthorn protein or peptides. Noteworthily, the structure-activity relationship is specifically delved into the hypoglycemic, anti-hypertensive, anti-obesity, anti-neurodegenerative and anti-oxidant peptides. Moreover, the shortcomings of current research and promising prospects are also highlighted. This comprehensive overview will provide a framework for future exploration and application of seabuckthorn protein or peptides in the realms of food and pharmaceuticals, offering a promising horizon for health benefits.
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Affiliation(s)
- Chunqiu Guo
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China
| | - Na Ling
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China.
| | - Haiyan Tian
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China
| | - Zihao Wang
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China
| | - Mingze Gao
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China
| | - Yin Chen
- School of Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Chenfeng Ji
- Pharmaceutical Engineering Technology Research Center, Harbin University of Commerce, Harbin 150076,China; Engineering Research Center for Natural Antitumor Drugs, Ministry of Education, Harbin University of Commerce, Harbin 150076, China.
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10
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Yook S, Alper HS. Bioconversion yields must account for all carbon: hidden biases from complex media. Trends Biotechnol 2025:S0167-7799(25)00035-6. [PMID: 39966066 DOI: 10.1016/j.tibtech.2025.01.010] [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: 12/08/2024] [Revised: 01/22/2025] [Accepted: 01/23/2025] [Indexed: 02/20/2025]
Abstract
Yield ratio is a critical parameter for quantifying bioprocess conversion efficiency. However, unquantified carbon in complex media formulations complicates yield calculations. We highlight the biases introduced by improperly neglecting all carbon-containing molecules. We recommend that yields be reported by accounting for all carbon and that media formulations are always stated.
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Affiliation(s)
- Sangdo Yook
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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11
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Germann SM, Holtz M, Jensen MK, Acevedo-Rocha CG. Debottlenecking cytochrome P450-dependent metabolic pathways for the biosynthesis of commercial natural products. Nat Prod Rep 2024; 41:1846-1857. [PMID: 39552440 DOI: 10.1039/d4np00027g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Covering: 2016 to the end of 2024This highlight article aims to provide a perspective on the challenges that novel biotechnological processes face in the biomanufacturing of natural products (NPs) whose biosynthesis pathways rely on cytochrome P450 monooxygenases. This enzyme superfamily is one of the most versatile in the biosynthesis of a plethora of NPs finding use across the food, nutrition, medicine, chemical and cosmetics industries. These enzymes often exhibit excellent regio- and stereoselectivity, but they can suffer from low activity and instability, which are serious issues impairing the development of high performing bioprocesses. We start with a brief introduction to industrial biotechnology and the importance of looking for alternative means for producing NPs independently from unsustainable fossil fuels or plant extractions. We then discuss the challenges and implemented solutions during the development of commercial NP processes focusing on the P450-dependent steps primarily in yeast cell factories. Our main focus is to highlight the challenges often encountered when utilizing P450-dependent NP pathways, and how protein engineering can be used for debottlenecking them. Finally, we briefly touch upon the importance of artificial intelligence and machine learning for guiding engineering efforts.
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Affiliation(s)
| | - Maxence Holtz
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | | | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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12
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Park JE, Kim J, Baek M, An HJ, Park CS, Jung JY, Kim SY, Kim YH. Assessment of safety: In vitro reverse mutation and in vivo acute oral toxicity tests of three biomass products from amino acid-producing Corynebacterium glutamicum. Toxicol Rep 2024; 13:101741. [PMID: 39380689 PMCID: PMC11458549 DOI: 10.1016/j.toxrep.2024.101741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/04/2024] [Accepted: 09/16/2024] [Indexed: 10/10/2024] Open
Abstract
Microbial fermentation has emerged as a pivotal process for sustainable production of essential goods and chemicals. Corynebacterium glutamicum is a proficient platform organism that contributes significantly to amino acid production through microbial fermentation. Despite its recognized safety, challenges persist in efficiently biosynthesizing natural products compared with other organisms. This study evaluated the safety of biomass products from bioengineered C. glutamicum through two different toxicological studies: a bacterial reverse mutation test (AMES test) and an acute oral toxicity test in rats. Three types of dried fermentation biomass products, each engineered for the enhanced production of specific amino acids (L-lysine, L-threonine, and L-tryptophan), were examined. The tests were conducted in compliance with Organization for Economic Co-operation and Development guidelines and revealed no mutagenicity or acute toxicity at the tested doses. These findings suggest the safety of biomass products from bioengineered C. glutamicum as potential feed materials, although further toxicity studies are recommended for comprehensive evaluation. This study underscores the importance of stringent safety assessments for advancing biotechnological applications and provides valuable insights into the potential utilization of microbial fermentation products in various industries. Moreover, this study highlights the significance of regulatory compliance and adherence to international standards to ensure the safety and efficacy of novel biotechnological products.
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Affiliation(s)
- Ji-Eun Park
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
| | - Jiyeon Kim
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
| | - MiNa Baek
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
| | - Hyo-Jin An
- Advanced Toxicity Evaluation Center, Biotoxtech, Chungju-si, Chungchungbuk-do 28115, Republic of Korea
| | - Chan-Sung Park
- Toxicity Evaluation Team, Biotoxtech, Chungju-si, Chungchungbuk-do 28115, Republic of Korea
| | - Joon Young Jung
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
| | - So-Young Kim
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
| | - Yang Hee Kim
- Institute of Biotechnology, CJ CheilJedang, Suwon-si, Gyeonggi-do 16495, Republic of Korea
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13
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Konzock O, Nielsen J. TRYing to evaluate production costs in microbial biotechnology. Trends Biotechnol 2024; 42:1339-1347. [PMID: 38806369 DOI: 10.1016/j.tibtech.2024.04.007] [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: 02/18/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
Microbial fermentations offer the opportunity to produce a wide range of chemicals in a sustainable fashion, but it is important to carefully evaluate the production costs. This can be done on the basis of evaluation of the titer, rate, and yield (TRY) of the fermentation process. Here we describe how the three TRY metrics impact the technoeconomics of a microbial fermentation process, and we illustrate the use of these for evaluation of different processes in the production of two commodity chemicals, 1,3-propanediol (PDO) and ethanol, as well as for the fine chemical penicillin. On the basis of our discussions, we provide some recommendations on how the TRY metrics should be reported when new processes are described.
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Affiliation(s)
- Oliver Konzock
- Department of Life Sciences, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE41296 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark.
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Koshiba A, Nakano M, Hirata Y, Konishi R, Matsuoka Y, Miwa Y, Mori A, Kondo A, Tanaka T. Enhanced production of isobutyl and isoamyl acetate using Yarrowia lipolytica. Biotechnol Prog 2024; 40:e3499. [PMID: 39056525 DOI: 10.1002/btpr.3499] [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: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Short-chain esters, particularly isobutyl acetate and isoamyl acetate, hold significant industrial value due to their wide-ranging applications in flavors, fragrances, solvents, and biofuels. In this study, we demonstrated the biosynthesis of acetate esters using Yarrowia lipolytica as a host by feeding alcohols to the yeast culture. Initially, we screened for optimal alcohol acyltransferases for ester biosynthesis in Y. lipolytica. Strains of Y. lipolytica expressing atf1 from Saccharomyces cerevisiae, produced 251 or 613 mg/L of isobutyl acetate or of isoamyl acetate, respectively. We found that introducing additional copies of ATF1 enhanced ester production. Furthermore, by increasing the supply of acetyl-CoA and refining the culture conditions, we achieved high production of isoamyl acetate, reaching titers of 3404 mg/L. We expanded our study to include the synthesis of a range of acetate esters, facilitated by enriching the culture medium with various alcohols. This study underscores the versatility and potential of Y. lipolytica in the industrial production of acetate esters.
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Affiliation(s)
- Ayumi Koshiba
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Mariko Nakano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Rie Konishi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Yuta Matsuoka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Yuta Miwa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Ayana Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Hyogo, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
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15
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Chen Z, Wang Z, Cao Y, Shi X, Xu B, Li X, Li J, Zhang Y, Qiao Y. PungentDB: Bridging traditional Chinese medicine of medicine food homology and modern food flavor chemistry. Food Chem X 2024; 23:101742. [PMID: 39253011 PMCID: PMC11381829 DOI: 10.1016/j.fochx.2024.101742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Merging traditional Chinese medicine's (TCM) principles of medicine-food homology with modern flavor chemistry, this research unveils PungentDB (http://www.pungentdb.org.cn/home), a database documenting 205 unique pungent flavor compounds from 231 TCMs. It provides detailed insights into their chemical attributes, biological targets (including IC50/EC50 values), and molecular structures (2D/3D), enriched with visualizations of target organ distribution and protein structures, exploring the pungent flavor space with the help of a feature-rich visual interface. This collection, derived from over 3249 sources and highlighting 9129 targets, delves into the compounds' unique pungent flavors-taste, aroma, and thermal sensations-and their interaction with taste and olfactory receptors. PungentDB bridges ancient wisdom and culinary innovation, offering a nuanced exploration of pungent flavors' role in enhancing food quality, safety, and sensory experiences. This initiative propels flavor chemistry forward, serving as a pivotal resource for food science advancement and the innovative application of pungent flavors.
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Affiliation(s)
- Zhao Chen
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Zhixin Wang
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
- Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang, 330115, China
| | - Yanfeng Cao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Xinyuan Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Bing Xu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Xi Li
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
- School of Pharmacy, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jing Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Yanling Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
| | - Yanjiang Qiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of China, Beijing, 102488, China
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16
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Tan JC, Hu Q, Scrutton NS. A growth-coupling strategy for improving the stability of terpenoid bioproduction in Escherichia coli. Microb Cell Fact 2024; 23:279. [PMID: 39415159 PMCID: PMC11481808 DOI: 10.1186/s12934-024-02548-1] [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: 05/01/2024] [Accepted: 09/30/2024] [Indexed: 10/18/2024] Open
Abstract
BACKGROUND Achieving cost-competitiveness remains challenging for industrial biomanufacturing. With whole-cell biocatalysis, inefficiency presents when individual cells vary in their production levels. The problem exacerbates when the basis for such production heterogeneity is heritable. Here, evolution selects for the low- and non-producers, as they have lowered/abolished the cost of bioproduction to fitness. With the scale of population expansion required for industrial bioproduction, the asymmetrical enrichment can be severe enough to compromise the performance, and hence commercial viability of the bioprocess. Clearly, addressing production heterogeneity is crucial, especially in improving the stability of bioproduction across the cell generations. In this respect, we designed a growth-coupling strategy for terpenoid bioproduction in Escherichia coli. By knocking out the native 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and introducing the heterologous mevalonate pathway, we created a chassis that relies solely on the latter for synthesis of all terpenoids. We hypothesise that the need to sustain the biosynthesis of endogenous life-sustaining terpenoids will impose a minimum level of productivity, which concomitantly improves the bioproduction of our target terpenoid. RESULTS Following the confirmation of lethality of a dxr knockout, we challenged the strains with a continuous plasmid-based bioproduction of linalool. The Δdxr strain achieved an improved productivity profile in the first three days post-inoculation when compared to the parental strain. Productivity of the Δdxr strain remained observable near the end of 12 days, and after a disruption in nutrient and oxygen supply in a separate run. Unlike the parental strain, the Δdxr strain did not evolve the same deleterious mutations in the mevalonate pathway, nor a viable subgroup that had lost its resistance to the antibiotic selection pressure (a plausible plasmid loss event). We believe that this divergence in the evolution trajectories is indicative of a successful growth-coupling. CONCLUSION We have demonstrated a proof of concept of a growth-coupling strategy that improves the performance, and stability of terpenoid bioproduction across cell generations. The strategy is relatively broad in scope, and easy to implement in the background as a 'fail-safe' against a fall in productivity below the imposed minimum. We thus believe this work will find widespread utility in our collective effort towards industrial bioproduction.
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Affiliation(s)
- Jing Chong Tan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Qitiao Hu
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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Bozkurt EU, Ørsted EC, Volke DC, Nikel PI. Accelerating enzyme discovery and engineering with high-throughput screening. Nat Prod Rep 2024. [PMID: 39403004 DOI: 10.1039/d4np00031e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Covering: up to August 2024Enzymes play an essential role in synthesizing value-added chemicals with high specificity and selectivity. Since enzymes utilize substrates derived from renewable resources, biocatalysis offers a pathway to an efficient bioeconomy with reduced environmental footprint. However, enzymes have evolved over millions of years to meet the needs of their host organisms, which often do not align with industrial requirements. As a result, enzymes frequently need to be tailored for specific industrial applications. Combining enzyme engineering with high-throughput screening has emerged as a key approach for developing novel biocatalysts, but several challenges are yet to be addressed. In this review, we explore emergent strategies and methods for isolating, creating, and characterizing enzymes optimized for bioproduction. We discuss fundamental approaches to discovering and generating enzyme variants and identifying those best suited for specific applications. Additionally, we cover techniques for creating libraries using automated systems and highlight innovative high-throughput screening methods that have been successfully employed to develop novel biocatalysts for natural product synthesis.
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Affiliation(s)
- Eray U Bozkurt
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Emil C Ørsted
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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18
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Guang C, Du Z, Meng J, Zhu Y, Zhu Y, Mu W. Recent Progress in Physiological Significance and Biosynthesis of Lacto- N-triose II: Insights into a Crucial Biomolecule. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19539-19548. [PMID: 39188079 DOI: 10.1021/acs.jafc.4c04284] [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: 08/28/2024]
Abstract
Lacto-N-triose II (LNTri II), an important precursor for human milk oligosaccharide (HMOs) synthesis, has garnered significant attention due to its structural features and physiological properties. Composed of galactose (Gal), N-acetylglucosamine (GlcNAc), and glucose (Glc), with the chemical structure GlcNAcβ1,3Galβ1,4Glc, the distinctive structure of LNTri II confers various physiological functions such as promoting the growth of beneficial bacteria, regulating the infant immune system, and preventing certain gastrointestinal diseases. Extensive research efforts have been dedicated to elucidating efficient enzymatic synthesis pathways for LNTri II production, with particular emphasis on the transglycosylation activity of β-N-acetylhexosaminidases and the action of β-1,3-N-acetylglucosaminyltransferases. Additionally, metabolic engineering and cell factory approaches have been explored, harnessing the potential of engineered microbial hosts for the large-scale biosynthesis of LNTri II. This review summarizes the structure, derivatives, physiological effects, and biosynthesis of LNTri II.
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Affiliation(s)
- Cuie Guang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Zhihui Du
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Jiawei Meng
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yunqi Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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19
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Son A, Park J, Kim W, Lee W, Yoon Y, Ji J, Kim H. Integrating Computational Design and Experimental Approaches for Next-Generation Biologics. Biomolecules 2024; 14:1073. [PMID: 39334841 PMCID: PMC11430650 DOI: 10.3390/biom14091073] [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: 07/23/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Therapeutic protein engineering has revolutionized medicine by enabling the development of highly specific and potent treatments for a wide range of diseases. This review examines recent advances in computational and experimental approaches for engineering improved protein therapeutics. Key areas of focus include antibody engineering, enzyme replacement therapies, and cytokine-based drugs. Computational methods like structure-based design, machine learning integration, and protein language models have dramatically enhanced our ability to predict protein properties and guide engineering efforts. Experimental techniques such as directed evolution and rational design approaches continue to evolve, with high-throughput methods accelerating the discovery process. Applications of these methods have led to breakthroughs in affinity maturation, bispecific antibodies, enzyme stability enhancement, and the development of conditionally active cytokines. Emerging approaches like intracellular protein delivery, stimulus-responsive proteins, and de novo designed therapeutic proteins offer exciting new possibilities. However, challenges remain in predicting in vivo behavior, scalable manufacturing, immunogenicity mitigation, and targeted delivery. Addressing these challenges will require continued integration of computational and experimental methods, as well as a deeper understanding of protein behavior in complex physiological environments. As the field advances, we can anticipate increasingly sophisticated and effective protein therapeutics for treating human diseases.
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Affiliation(s)
- Ahrum Son
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA;
| | - Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Woojin Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Wonseok Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Yoonki Yoon
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Jaeho Ji
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea;
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea;
- Protein AI Design Institute, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- SCICS (Sciences for Panomics), 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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20
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Hu R, Teng X, Li Y. Unleashing plant synthetic capacity: navigating regulatory mechanisms for enhanced bioproduction and secondary metabolite discovery. Curr Opin Biotechnol 2024; 88:103148. [PMID: 38843577 PMCID: PMC11531776 DOI: 10.1016/j.copbio.2024.103148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/21/2024] [Accepted: 05/12/2024] [Indexed: 08/11/2024]
Abstract
Plant natural products (PNPs) hold significant pharmaceutical importance. The sessile nature of plants has led to the evolution of chemical defense mechanisms over millions of years to combat environmental challenges, making it a crucial and essential defense weapon. Despite their importance, the abundance of these bioactive molecules in plants is typically low, and conventional methods are time-consuming for enhancing production. Moreover, there is a pressing need for novel drug leads, exemplified by the shortage of antibiotics and anticancer drugs. Understanding how plants respond to stress and regulate metabolism to produce these molecules presents an opportunity to explore new avenues for discovering compounds that are typically under the detection limit or not naturally produced. Additionally, this knowledge can contribute to the advancement of plant engineering, enabling the development of new chassis for the biomanufacturing of these valuable molecules. In this perspective, we explore the intricate regulation of PNP biosynthesis in plants, and discuss the biotechnology strategies that have been and can be utilized for the discovery and production enhancement of PNPs in plants.
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Affiliation(s)
- Rongbin Hu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Xiaoxuan Teng
- Program of Chemical Engineering, Department of Nanongineering, University of California, San Diego, CA 92093, USA
| | - Yanran Li
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California, San Diego, CA 92093, USA.
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21
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Nielsen J. Autotrophic yeast. Nat Commun 2024; 15:5948. [PMID: 39013898 PMCID: PMC11252251 DOI: 10.1038/s41467-024-49586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Jens Nielsen
- BioInnovation Institute, DK2200 Copenhagen, Denmark and Department of Life Sciences, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
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22
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Matyja K, Lech M. Dynamic Energy Budget model for E. coli growth in carbon and nitrogen limitation conditions. Appl Microbiol Biotechnol 2024; 108:408. [PMID: 38967685 PMCID: PMC11226513 DOI: 10.1007/s00253-024-13245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
The simulations and predictions obtained from mathematical models of bioprocesses conducted by microorganisms are not overvalued. Mechanistic models are bringing a better process understanding and the possibility of simulating unmeasurable variables. The Dynamic Energy Budget (DEB) model is an energy balance that can be formulated for any living organism and can be classified as a structured model. In this study, the DEB model was used to describe E. coli growth in a batch reactor in carbon and nitrogen substrate limitation conditions. The DEB model provides a possibility to follow the changes in the microbes' cells including their elemental composition and content of some important cell ingredients in different growth phases in substrate limitation conditions which makes it more informative compared to Monod's model. The model can be used as an optimal choice between Monod-like models and flux-based approaches. KEY POINTS: • The DEB model can be used to catch changes in elemental composition of E. coli • Bacteria batch culture growth phases can be explained by the DEB model • The DEB model is more informative compared to Monod's based models.
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Affiliation(s)
- Konrad Matyja
- Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Magdalena Lech
- Faculty of Chemistry, Department of Micro, Nano, and Bioprocess Engineering, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
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23
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Mousavi S, Esfandiar R, Najafpour-Darzi G. Hyaluronic acid production by Streptococcus zooepidemicus MW26985 using potato peel waste hydrolyzate. Bioprocess Biosyst Eng 2024; 47:1003-1015. [PMID: 38811468 DOI: 10.1007/s00449-024-03007-2] [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: 11/29/2023] [Accepted: 03/20/2024] [Indexed: 05/31/2024]
Abstract
In this research, we examined the production of hyaluronic acid (HA) by Streptococcus zooepidemicus strain MW26985 using different substrates and potato peel waste (PPW) as an affordable substrate. First, culture medium components, including carbon and nitrogen sources, were optimized for bacterial HA production. Five different carbon sources (glucose, sucrose, lactose, sago starch, and potato starch, at a concentration of 30 g/L) and three distinct nitrogen sources (peptone, yeast extract, and ammonium sulfate, at a concentration of 10 g/L) were investigated. Glucose, among the carbon sources, and yeast extract, among nitrogen sources, produced the most HA which was determined as 1.41 g/L. Afterward, potato peel sugars were extracted by dilute acid and enzymatic hydrolysis and then employed as a cost-effective carbon source for the growth of S. zooepidemicus. Based on the results, the fermentation process yielded 0.59 g/L HA from potato peel sugars through acid hydrolysis and 0.92 g/L HA from those released by enzymatic hydrolysis. The supplementation of both hydrolyzates with glucose as an additional carbon source enhanced HA production to 0.95 g/L and 1.18 g/L using acidic and enzymatic hydrolyzates, respectively. The cetyltrimethylammonium bromide (CTAB) turbidimetric method was used to evaluate the concentration of HA in the fermentation broth using the colorimetric method. Also, the peaks observed by Fourier transform infrared (FTIR) spectroscopy confirmed that the exopolysaccharide (EPS) was composed of HA. These observations demonstrate that potato peel residues can be a novel alternative as a carbon source for the economical production of HA by S. zooepidemicus.
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Affiliation(s)
- Seyedali Mousavi
- Biotechnology Research Laboratory, Department of Biochemical Engineering, Faculty of Chemical Engineering, Babol Noshirvani University of Technology, P.O. Box 47148-71167, Babol, Iran
| | - Razieh Esfandiar
- Biotechnology Research Laboratory, Department of Biochemical Engineering, Faculty of Chemical Engineering, Babol Noshirvani University of Technology, P.O. Box 47148-71167, Babol, Iran
| | - Ghasem Najafpour-Darzi
- Biotechnology Research Laboratory, Department of Biochemical Engineering, Faculty of Chemical Engineering, Babol Noshirvani University of Technology, P.O. Box 47148-71167, Babol, Iran.
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24
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Li DX, Guo Q, Yang YX, Jiang SJ, Ji XJ, Ye C, Wang YT, Shi TQ. Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica. ACS Synth Biol 2024; 13:1647-1662. [PMID: 38860708 DOI: 10.1021/acssynbio.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Monoterpenoids are an important subclass of terpenoids that play important roles in the energy, cosmetics, pharmaceuticals, and fragrances fields. With the development of biotechnology, microbial synthesis of monoterpenoids has received great attention. Yeasts such Saccharomyces cerevisiae and Yarrowia lipolytica are emerging as potential hosts for monoterpenoids production because of unique advantages including rapid growth cycles, mature gene editing tools, and clear genetic background. Recently, advancements in metabolic engineering and fermentation engineering have significantly enhanced the accumulation of monoterpenoids in cell factories. First, this review introduces the biosynthetic pathway of monoterpenoids and comprehensively summarizes the latest production strategies, which encompass enhancing precursor flux, modulating the expression of rate-limited enzymes, suppressing competitive pathway flux, mitigating cytotoxicity, optimizing substrate utilization, and refining the fermentation process. Subsequently, this review introduces four representative monoterpenoids. Finally, we outline the future prospects for efficient construction cell factories tailored for the production of monoterpenoids and other terpenoids.
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Affiliation(s)
- Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Shun-Jie Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
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25
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Hari A, Doddapaneni TRKC, Kikas T. Common operational issues and possible solutions for sustainable biosurfactant production from lignocellulosic feedstock. ENVIRONMENTAL RESEARCH 2024; 251:118665. [PMID: 38493851 DOI: 10.1016/j.envres.2024.118665] [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: 10/13/2023] [Revised: 02/06/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Surfactants are compounds with high surface activity and emulsifying property. These compounds find application in food, medical, pharmaceutical, and petroleum industries, as well as in agriculture, bioremediation, cleaning, cosmetics, and personal care product formulations. Due to their widespread use and environmental persistence, ensuring biodegradability and sustainability is necessary so as not to harm the environment. Biosurfactants, i.e., surfactants of plant or microbial origin produced from lignocellulosic feedstock, perform better than their petrochemically derived counterparts on the scale of net-carbon-negativity. Although many biosurfactants are commercially available, their high cost of production justifies their application only in expensive pharmaceuticals and cosmetics. Besides, the annual number of new biosurfactant compounds reported is less, compared to that of chemical surfactants. Multiple operational issues persist in the biosurfactant value chain. In this review, we have categorized some of these issues based on their relative position in the value chain - hurdles occurring during planning, upstream processes, production stage, and downstream processes - alongside plausible solutions. Moreover, we have presented the available paths forward for this industry in terms of process development and integrated pretreatment, combining conventional tried-and-tested strategies, such as reactor designing and statistical optimization with cutting-edge technologies including metabolic modeling and artificial intelligence. The development of techno-economically feasible biosurfactant production processes would be instrumental in the complete substitution of petrochemical surfactants, rather than mere supplementation.
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Affiliation(s)
- Anjana Hari
- Chair of Biosystems Engineering, Institute of Forestry and Engineering, Estonian University of Life Sciences, Kreutzwaldi 56, Tartu, 51014, Estonia.
| | - Tharaka Rama Krishna C Doddapaneni
- Chair of Biosystems Engineering, Institute of Forestry and Engineering, Estonian University of Life Sciences, Kreutzwaldi 56, Tartu, 51014, Estonia
| | - Timo Kikas
- Chair of Biosystems Engineering, Institute of Forestry and Engineering, Estonian University of Life Sciences, Kreutzwaldi 56, Tartu, 51014, Estonia
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26
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Etit D, Meramo S, Ögmundarson Ó, Jensen MK, Sukumara S. Can biotechnology lead the way toward a sustainable pharmaceutical industry? Curr Opin Biotechnol 2024; 87:103100. [PMID: 38471403 DOI: 10.1016/j.copbio.2024.103100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
The impact-intensive and rapidly growing pharmaceutical industry must ensure its sustainability. This study reveals that environmental sustainability assessments have been conducted for only around 0.2% of pharmaceuticals, environmental impacts have significant variations among the assessed products, and different impact categories have not been consistently studied. Highly varied impacts require assessing more products to understand the industry's sustainability status. Reporting all impact categories will be crucial, especially when comparing production technologies. Biological production of (semi)synthetic pharmaceuticals could reduce their environmental costs, though the high impacts of biologically produced monoclonal antibodies should also be optimized. Considering the sustainability potential of biopharmaceuticals from economic, environmental, and social perspectives, collaboratively guiding their immense market growth would lead to the industry's sustainability transition.
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Affiliation(s)
- Deniz Etit
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Samir Meramo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ólafur Ögmundarson
- Faculty of Food Science and Nutrition, University of Iceland, Nýi Garður, Sæmundargata 2, 102 Reykjavík, Iceland
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Sumesh Sukumara
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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27
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Adams J, Clark DS. Techno-Economic Assessment of Electromicrobial Production of n-Butanol from Air-Captured CO 2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7302-7313. [PMID: 38621294 PMCID: PMC11064224 DOI: 10.1021/acs.est.3c08748] [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: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Electromicrobial production (EMP), where electrochemically generated substrates (e.g., H2) are used as energy sources for microbial processes, has garnered significant interest as a method of producing fuels and other value-added chemicals from CO2. Combining these processes with direct air capture (DAC) has the potential to enable a truly circular carbon economy. Here, we analyze the economics of a hypothetical system that combines adsorbent-based DAC with EMP to produce n-butanol, a potential replacement for fossil fuels. First-principles-based modeling is used to predict the performance of the DAC and bioprocess components. A process model is then developed to map material and energy flows, and a techno-economic assessment is performed to determine the minimum fuel selling price. Beyond assessing a specific set of conditions, this analytical framework provides a tool to reveal potential pathways toward the economic viability of this process. We show that an EMP system utilizing an engineered knallgas bacterium can achieve butanol production costs of <$6/gal ($1.58/L) if a set of optimistic assumptions can be realized.
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Affiliation(s)
- Jeremy
David Adams
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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28
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Wang H, Chen Y, Yang Z, Deng H, Liu Y, Wei P, Zhu Z, Jiang L. Metabolic and Bioprocess Engineering of Clostridium tyrobutyricum for Butyl Butyrate Production on Xylose and Shrimp Shell Waste. Foods 2024; 13:1009. [PMID: 38611315 PMCID: PMC11011809 DOI: 10.3390/foods13071009] [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: 02/29/2024] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Microbial conversion of agri-food waste to valuable compounds offers a sustainable route to develop the bioeconomy and contribute to sustainable biorefinery. Clostridium tyrobutyricum displays a series of native traits suitable for high productivity conversion of agri-food waste, which make it a promising host for the production of various compounds, such as the short-chain fatty acids and their derivative esters products. In this study, a butanol synthetic pathway was constructed in C. tyrobutyricum, and then efficient butyl butyrate production through in situ esterification was achieved by the supplementation of lipase into the fermentation. The butyryl-CoA/acyl-CoA transferase (cat1) was overexpressed to balance the ratio between precursors butyrate and butanol. Then, a suitable fermentation medium for butyl butyrate production was obtained with xylose as the sole carbon source and shrimp shell waste as the sole nitrogen source. Ultimately, 5.9 g/L of butyl butyrate with a selectivity of 100%, and a productivity of 0.03 g/L·h was achieved under xylose and shrimp shell waste with batch fermentation in a 5 L bioreactor. Transcriptome analyses exhibited an increase in the expression of genes related to the xylose metabolism, nitrogen metabolism, and amino acid metabolism and transport, which reveal the mechanism for the synergistic utilization of xylose and shrimp shell waste. This study presents a novel approach for utilizing xylose and shrimp shell waste to produce butyl butyrate by using an anaerobic fermentative platform based on C. tyrobutyricum. This innovative fermentation medium could save the cost of nitrogen sources (~97%) and open up possibilities for converting agri-food waste into other high-value products.
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Affiliation(s)
- Hao Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (H.W.); (Y.C.); (Z.Y.); (P.W.)
| | - Yingli Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (H.W.); (Y.C.); (Z.Y.); (P.W.)
| | - Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (H.W.); (Y.C.); (Z.Y.); (P.W.)
| | - Haijun Deng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; (H.D.); (Y.L.)
| | - Yiran Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; (H.D.); (Y.L.)
| | - Ping Wei
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (H.W.); (Y.C.); (Z.Y.); (P.W.)
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; (H.D.); (Y.L.)
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; (H.D.); (Y.L.)
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
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29
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Kinose K, Shinoda K, Konishi T, Kawasaki H. Mutational analysis in Corynebacterium stationis MFS transporters for improving nucleotide bioproduction. Appl Microbiol Biotechnol 2024; 108:251. [PMID: 38436751 PMCID: PMC10912292 DOI: 10.1007/s00253-024-13080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Product secretion from an engineered cell can be advantageous for microbial cell factories. Extensive work on nucleotide manufacturing, one of the most successful microbial fermentation processes, has enabled Corynebacterium stationis to transport nucleotides outside the cell by random mutagenesis; however, the underlying mechanism has not been elucidated, hindering its applications in transporter engineering. Herein, we report the nucleotide-exporting major facilitator superfamily (MFS) transporter from the C. stationis genome and its hyperactive mutation at the G64 residue. Structural estimation and molecular dynamics simulations suggested that the activity of this transporter improved via two mechanisms: (1) enhancing interactions between transmembrane helices through the conserved "RxxQG" motif along with substrate binding and (2) trapping substrate-interacting residue for easier release from the cavity. Our results provide novel insights into how MFS transporters change their conformation from inward- to outward-facing states upon substrate binding to facilitate efflux and can contribute to the development of rational design approaches for efflux improvements in microbial cell factories. KEYPOINTS: • An MFS transporter from C. stationis genome and its mutation at residue G64 were assessed • It enhanced the transporter activity by strengthening transmembrane helix interactions and trapped substrate-interacting residues • Our results contribute to rational design approach development for efflux improvement.
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Affiliation(s)
- Keita Kinose
- Agro-Biotechnology Research Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- Nagahama Institute for Biochemical Science, Oriental Yeast Co., Ltd., Nagahama, Shiga, Japan
| | - Keiko Shinoda
- Agro-Biotechnology Research Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
- Research Organization of Information and Systems, The Institute of Statistical Mathematics, Tachikawa, Japan
| | - Tomoyuki Konishi
- Agro-Biotechnology Research Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kawasaki
- Agro-Biotechnology Research Center, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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30
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Pignataro E, Pini F, Barbanente A, Arnesano F, Palazzo A, Marsano RM. Flying toward a plastic-free world: Can Drosophila serve as a model organism to develop new strategies of plastic waste management? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169942. [PMID: 38199375 DOI: 10.1016/j.scitotenv.2024.169942] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
The last century was dominated by the widespread use of plastics, both in terms of invention and increased usage. The environmental challenge we currently face is not just about reducing plastic usage but finding new ways to manage plastic waste. Recycling is growing but remains a small part of the solution. There is increasing focus on studying organisms and processes that can break down plastics, offering a modern approach to addressing the environmental crisis. Here, we provide an overview of the organisms associated with plastics biodegradation, and we explore the potential of harnessing and integrating their genetic and biochemical features into a single organism, such as Drosophila melanogaster. The remarkable genetic engineering and microbiota manipulation tools available for this organism suggest that multiple features could be amalgamated and modeled in the fruit fly. We outline feasible genetic engineering and gut microbiome engraftment strategies to develop a new class of plastic-degrading organisms and discuss of both the potential benefits and the limitations of developing such engineered Drosophila melanogaster strains.
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Affiliation(s)
- Eugenia Pignataro
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - Francesco Pini
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - Alessandra Barbanente
- Department of Chemistry, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.
| | - Fabio Arnesano
- Department of Chemistry, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.
| | - Antonio Palazzo
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
| | - René Massimiliano Marsano
- Department of Biosciences, Biotechnology and Environment, University of Bari "Aldo Moro" via Orabona 4, 70125 Bari, Italy.
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31
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Fang H, Zhao J, Zhao X, Dong N, Zhao Y, Zhang D. Standardized Iterative Genome Editing Method for Escherichia coli Based on CRISPR-Cas9. ACS Synth Biol 2024; 13:613-623. [PMID: 38243901 DOI: 10.1021/acssynbio.3c00585] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The introduction of complex biosynthetic pathways into the hosts' chromosomes is gaining attention with the development of synthetic biology. While CRISPR-Cas9 has been widely employed for gene knock-in, the process of multigene insertion remains cumbersome due to laborious and empirical gene cloning procedures. To address this, we devised a standardized iterative genome editing system for Escherichia coli, harnessing the power of CRISPR-Cas9 and MetClo assembly. This comprehensive toolkit comprises two fundamental elements based on the Golden Gate standard for modular assembly of sgRNA or CRISPR arrays and donor DNAs. We achieved a gene insertion efficiency of up to 100%, targeting a single locus. Expression of tracrRNA using a strong promoter enhances multiplex genomic insertion efficiency to 7.3%, compared with 0.76% when a native promoter is used. To demonstrate the robust capabilities of this genome editing toolbox, we successfully integrated 5-10 genes from the coenzyme B12 biosynthetic pathway ranging from 5.3 to 8 Kb in length into the chromosome of E. coli chassis cells, resulting in 14 antibiotic-free, plasmid-free producers. Following an extensive screening process involving genes from diverse sources, cistronic design modifications, and chromosome repositioning, we obtained a recombinant strain yielding 1.49 mg L-1 coenzyme B12, the highest known titer achieved by using E. coli as the producer. Illuminating its user-friendliness, this genome editing system is an exceedingly versatile tool for expediently integrating complex biosynthetic pathway genes into hosts' genomes, thus facilitating pathway optimization for chemical production.
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Affiliation(s)
- Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Science, Beijing 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jianghua Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Science, Beijing 100049, China
| | - Xinfang Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Ning Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Ying Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Science, Beijing 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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32
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Zhang J, Yan X, Park H, Scrutton NS, Chen T, Chen GQ. Nonsterile microbial production of chemicals based on Halomonas spp. Curr Opin Biotechnol 2024; 85:103064. [PMID: 38262074 DOI: 10.1016/j.copbio.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/09/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
The use of extremophile organisms such as Halomomas spp. can eliminate the need for fermentation sterilization, significantly reducing process costs. Microbial fermentation is considered a pivotal strategy to reduce reliance on fossil fuel resources; however, sustainable processes continue to incur higher costs than their chemical industry counterparts. Most organisms require equipment sterilization to prevent contamination, a practice that introduces complexity and financial strain. Fermentations involving extremophile organisms can eliminate the sterilization process, relying instead on conditions that are conductive solely to the growth of the desired organism. This review discusses current challenges in pilot- and industrial-scale bioproduction when using the extremophile bacteria Halomomas spp. under nonsterile conditions.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
| | - Xu Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing 100084, China; EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing 100084, China.
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33
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Chainani Y, Bonnanzio G, Tyo KE, Broadbelt LJ. Coupling chemistry and biology for the synthesis of advanced bioproducts. Curr Opin Biotechnol 2023; 84:102992. [PMID: 37688985 DOI: 10.1016/j.copbio.2023.102992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 09/11/2023]
Abstract
Chemical and biological syntheses can both lead to a myriad of compounds. Biology enables us to harness the metabolism of microbial cell factories to produce key target molecules from renewable biomass-derived substrates. Although bio-based feedstocks are sustainably sourced and more benign than the rapidly depleting fossil fuels that chemical processes have historically relied on, limiting pathways solely to biological reactions may not equate to a greener process overall. In fact, bioreactors rely on substantial quantities of water and can be inefficient since organisms typically operate around ambient conditions and are sensitive to perturbations in their environment. Hybridizing biosynthetic pathways with green chemistry can instead be a more potent strategy to reduce our net manufacturing footprint. Emerging chemistries have demonstrated considerable success in performing complex transformations on biological feedstocks without significant solvent use. Many of these transformations would be too slow to perform enzymatically or infeasible altogether. Here, we put forth the concept that by carefully considering the merits and drawbacks of synthetic biology and chemistry as well as one's own use case, there exist many opportunities for coupling the two. Merging these syntheses can unlock a wider suite of functional group transformations, thereby enabling future manufacturing processes to sustainably access a larger space of valuable, platform chemicals.
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Affiliation(s)
- Yash Chainani
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Geoffrey Bonnanzio
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Keith Ej Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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34
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Kulakowski S, Banerjee D, Scown CD, Mukhopadhyay A. Improving microbial bioproduction under low-oxygen conditions. Curr Opin Biotechnol 2023; 84:103016. [PMID: 37924688 DOI: 10.1016/j.copbio.2023.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 11/06/2023]
Abstract
Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.
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Affiliation(s)
- Shawn Kulakowski
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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35
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François JM. Progress advances in the production of bio-sourced methionine and its hydroxyl analogues. Biotechnol Adv 2023; 69:108259. [PMID: 37734648 DOI: 10.1016/j.biotechadv.2023.108259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.
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Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, 31077 Toulouse, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, 31077 Toulouse, France.
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36
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Orsi E, Nikel PI, Nielsen LK, Donati S. Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy. Nat Commun 2023; 14:6673. [PMID: 37865689 PMCID: PMC10590403 DOI: 10.1038/s41467-023-42166-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g. CO2, formate, methanol, etc.) are converted by microbial cell factories into value-added goods (i.e. food, feed, and chemicals). To render C1-based biomanufacturing cost-competitive, we must adapt microbial metabolism to perform chemical conversions at high rates and yields. To this end, the biotechnology community has undertaken two (seemingly opposing) paths: optimizing natural C1-trophic microorganisms versus engineering synthetic C1-assimilation de novo in model microorganisms. Here, we pose how these approaches can instead create synergies for strengthening the competitiveness of C1-based biomanufacturing as a whole.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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37
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Wowra K, Hegel E, Scharf A, Grünberger A, Rosenthal K. Estimating environmental impacts of early-stage bioprocesses. Trends Biotechnol 2023; 41:1199-1212. [PMID: 37188575 DOI: 10.1016/j.tibtech.2023.03.011] [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: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 05/17/2023]
Abstract
The use of bioprocesses in industrial production promises resource- and energy-efficient processes starting from renewable, nonfossil feedstocks. Thus, the environmental benefits must be demonstrated, ideally in the early development phase with standardized methods such as life cycle assessment (LCA). Herein we discuss selected LCA studies of early-stage bioprocesses, highlighting their potential and contribution to estimating environmental impacts and decision support in bioprocess development. However, LCAs are rarely performed among bioprocess engineers due to challenges such as data availability and process uncertainties. To address this issue, recommendations are provided for conducting LCAs of early-stage bioprocesses. Opportunities are identified to facilitate future applicability, for example, by establishing dedicated bioprocess databases that could enable the use of LCAs as standard tools for bioprocess engineers.
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Affiliation(s)
- Karoline Wowra
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Esther Hegel
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Andreas Scharf
- Subdivision Biotechnology, Dechema e.V., Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Alexander Grünberger
- Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Rosenthal
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany.
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38
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Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
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Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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39
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Nielsen J. Engineering yeast to produce plant-derived anti-obesity agent. Nat Chem 2023; 15:1204-1205. [PMID: 37640851 DOI: 10.1038/s41557-023-01292-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- Jens Nielsen
- BioInnovation Institute, Copenhagen, Denmark.
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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40
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Satoh Y, Fukui K, Koma D, Shen N, Lee TS. Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:115. [PMID: 37464414 DOI: 10.1186/s13068-023-02365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/02/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Aromatic compounds derived from tyrosine are important and diverse chemicals that have industrial and commercial applications. Although these aromatic compounds can be obtained by extraction from natural producers, their growth is slow, and their content is low. To overcome these problems, many of them have been chemically synthesized from petroleum-based feedstocks. However, because of the environmental burden and depleting availability of feedstock, microbial cell factories are attracting much attention as sustainable and environmentally friendly processes. RESULTS To facilitate development of microbial cell factories for producing tyrosine derivatives, we developed simple and convenient tyrosine-producing Escherichia coli platforms with a bacterial phenylalanine hydroxylase, which converted phenylalanine to tyrosine with tetrahydromonapterin as a cofactor, using a synthetic biology approach. By introducing a tetrahydrobiopterin-regeneration system, the tyrosine titer of the plasmid-based engineered strain was 4.63 g/L in a medium supplemented with 5.00 g/L phenylalanine with a test tube. The strains were successfully used to produce industrially attractive compounds, such as tyrosol with a yield of 1.58 g/L by installing a tyrosol-producing module consisting of genes encoding tyrosine decarboxylase and tyramine oxidase on a plasmid. Gene integration into E. coli chromosomes has an advantage over the use of plasmids because it increases genetic stability without antibiotic feeding to the culture media and enables more flexible pathway engineering by accepting more plasmids with artificial pathway genes. Therefore, we constructed a plasmid-free tyrosine-producing platform by integrating five modules, comprising genes encoding the phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system, into the chromosome. The platform strain could produce 1.04 g/L of 3,4-dihydroxyphenylalanine, a drug medicine, by installing a gene encoding tyrosine hydroxylase and the tetrahydrobiopterin-regeneration system on a plasmid. Moreover, by installing the tyrosol-producing module, tyrosol was produced with a yield of 1.28 g/L. CONCLUSIONS We developed novel E. coli platforms for producing tyrosine from phenylalanine at multi-gram-per-liter levels in test-tube cultivation. The platforms allowed development and evaluation of microbial cell factories installing various designed tyrosine-derivative biosynthetic pathways at multi-grams-per-liter levels in test tubes.
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Affiliation(s)
- Yasuharu Satoh
- Faculty of Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Keita Fukui
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kanagawa, 210-8681, Japan
| | - Daisuke Koma
- Osaka Research Institute of Industrial Science and Technology, Osaka, 536-8553, Japan
| | - Ning Shen
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Taek Soon Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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41
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Zhu J, Wang S, Wang C, Wang Z, Luo G, Li J, Zhan Y, Cai D, Chen S. Microbial synthesis of bacitracin: Recent progress, challenges, and prospects. Synth Syst Biotechnol 2023; 8:314-322. [PMID: 37122958 PMCID: PMC10130698 DOI: 10.1016/j.synbio.2023.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Microorganisms are important sources of various natural products that have been commercialized for human medicine and animal healthcare. Bacitracin is an important antibacterial natural product predominantly produced by Bacillus licheniformis and Bacillus subtilis, and it is characterized by a broad antimicrobial spectrum, strong activity and low resistance, thus bacitracin is extensively applied in animal feed and veterinary medicine industries. In recent years, various strategies have been proposed to improve bacitracin production. Herein, we systematically describe the regulation of bacitracin biosynthesis in genus Bacillus and its associated mechanism, to provide a theoretical basis for bacitracin overproduction. The metabolic engineering strategies applied for bacitracin production are explored, including improving substrate utilization, using an enlarged precursor amino acid pool, increasing ATP supply and NADPH generation, and engineering transcription regulators. We also present several approaches of fermentation process optimization to facilitate the industrial large-scale production of bacitracin. Finally, the challenges and prospects associated with microbial bacitracin synthesis are discussed to facilitate the establishment of high-yield and low-cost biological factories.
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Affiliation(s)
- Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Shiyi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Cheng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Zhi Wang
- Hubei Provincial Key Laboratory of Industrial Microbiology, Key Laboratory of Fermentation Engineering (Ministry of Education), School of Food and Biological Engineering, Hubei University of Technology, Wuhan, 430068, Hubei, PR China
| | - Gan Luo
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, PR China
| | - Junhui Li
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
- Corresponding author.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
- Corresponding author. 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, PR China.
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42
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Ploessl D, Zhao Y, Shao Z. Engineering of non-model eukaryotes for bioenergy and biochemical production. Curr Opin Biotechnol 2023; 79:102869. [PMID: 36584447 DOI: 10.1016/j.copbio.2022.102869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 12/29/2022]
Abstract
The prospect of leveraging naturally occurring phenotypes to overcome bottlenecks constraining the bioeconomy has marshalled increased exploration of nonconventional organisms. This review discusses the status of non-model eukaryotic species in bioproduction, the evaluation criteria for effectively matching a candidate host to a biosynthetic process, and the genetic engineering tools needed for host domestication. We present breakthroughs in genome editing and heterologous pathway design, delving into innovative spatiotemporal modulation strategies that potentiate more refined engineering capabilities. We cover current understanding of genetic instability and its ramifications for industrial scale-up, highlighting key factors and possible remedies. Finally, we propose future opportunities to expand the current collection of available hosts and provide guidance to benefit the broader bioeconomy.
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Affiliation(s)
- Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA; Bioeconomy Institute, Iowa State University, Ames, IA, USA; The Ames Laboratory, Ames, IA, USA.
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43
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Mellor SB, Behrendorff JBYH, Ipsen JØ, Crocoll C, Laursen T, Gillam EMJ, Pribil M. Exploiting photosynthesis-driven P450 activity to produce indican in tobacco chloroplasts. FRONTIERS IN PLANT SCIENCE 2023; 13:1049177. [PMID: 36743583 PMCID: PMC9890960 DOI: 10.3389/fpls.2022.1049177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/14/2022] [Indexed: 05/28/2023]
Abstract
Photosynthetic organelles offer attractive features for engineering small molecule bioproduction by their ability to convert solar energy into chemical energy required for metabolism. The possibility to couple biochemical production directly to photosynthetic assimilation as a source of energy and substrates has intrigued metabolic engineers. Specifically, the chemical diversity found in plants often relies on cytochrome P450-mediated hydroxylations that depend on reductant supply for catalysis and which often lead to metabolic bottlenecks for heterologous production of complex molecules. By directing P450 enzymes to plant chloroplasts one can elegantly deal with such redox prerequisites. In this study, we explore the capacity of the plant photosynthetic machinery to drive P450-dependent formation of the indigo precursor indoxyl-β-D-glucoside (indican) by targeting an engineered indican biosynthetic pathway to tobacco (Nicotiana benthamiana) chloroplasts. We show that both native and engineered variants belonging to the human CYP2 family are catalytically active in chloroplasts when driven by photosynthetic reducing power and optimize construct designs to improve productivity. However, while increasing supply of tryptophan leads to an increase in indole accumulation, it does not improve indican productivity, suggesting that P450 activity limits overall productivity. Co-expression of different redox partners also does not improve productivity, indicating that supply of reducing power is not a bottleneck. Finally, in vitro kinetic measurements showed that the different redox partners were efficiently reduced by photosystem I but plant ferredoxin provided the highest light-dependent P450 activity. This study demonstrates the inherent ability of photosynthesis to support P450-dependent metabolic pathways. Plants and photosynthetic microbes are therefore uniquely suited for engineering P450-dependent metabolic pathways regardless of enzyme origin. Our findings have implications for metabolic engineering in photosynthetic hosts for production of high-value chemicals or drug metabolites for pharmacological studies.
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Affiliation(s)
- Silas B. Mellor
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - James B. Y. H. Behrendorff
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
| | - Johan Ø. Ipsen
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Tomas Laursen
- Section for Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Mathias Pribil
- Section for Molecular Plant Biology, Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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44
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Maestroni L, Butti P, Senatore VG, Branduardi P. pCEC-red: a new vector for easier and faster CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. FEMS Yeast Res 2023; 23:foad002. [PMID: 36640150 PMCID: PMC9906608 DOI: 10.1093/femsyr/foad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023] Open
Abstract
CRISPR-Cas9 technology is widely used for precise and specific editing of Saccharomyces cerevisiae genome to obtain marker-free engineered hosts. Targeted double-strand breaks are controlled by a guide RNA (gRNA), a chimeric RNA containing a structural segment for Cas9 binding and a 20-mer guide sequence that hybridises to the genomic DNA target. Introducing the 20-mer guide sequence into gRNA expression vectors often requires complex, time-consuming, and/or expensive cloning procedures. We present a new plasmid for CRISPR-Cas9 genome editing in S. cerevisiae, pCEC-red. This tool allows to (i) transform yeast with both Cas9 and gRNA expression cassettes in a single plasmid and (ii) insert the 20-mer sequence in the plasmid with high efficiency, thanks to Golden Gate Assembly and (iii) a red chromoprotein-based screening to speed up the selection of correct plasmids. We tested genome-editing efficiency of pCEC-red by targeting the ADE2 gene. We chose three different 20-mer targets and designed two types of repair fragments to test pCEC-red for precision editing and for large DNA region replacement procedures. We obtained high efficiencies (∼90%) for both engineering procedures, suggesting that the pCEC system can be used for fast and reliable marker-free genome editing.
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Affiliation(s)
- Letizia Maestroni
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Pietro Butti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Vittorio Giorgio Senatore
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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45
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Haas R, Nikel PI. Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism. Trends Biotechnol 2023; 41:27-45. [PMID: 35786519 DOI: 10.1016/j.tibtech.2022.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
The relatively narrow spectrum of chemical elements within the microbial 'biochemical palate' limits the reach of biotechnology, because several added-value compounds can only be produced with traditional organic chemistry. Synthetic biology offers enabling tools to tackle this issue by facilitating 'biologization' of non-canonical chemical atoms. The interplay between xenobiology and synthetic metabolism multiplies routes for incorporating nonbiological atoms into engineered microbes. In this review, we survey natural assimilation routes for elements beyond the essential biology atoms [i.e., carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)], discussing how these mechanisms could be repurposed for biotechnology. Furthermore, we propose a computational framework to identify chemical elements amenable to biologization, ranking reactions suitable to build synthetic metabolism. When combined and deployed in robust microbial hosts, these approaches will offer sustainable alternatives for smart chemical production.
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Affiliation(s)
- Robert Haas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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46
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Chakraborty I, Edirippulige S, Ilavarasan PV. What is coming next in health technology startups? Some insights and practice guidelines. Digit Health 2023; 9:20552076231178435. [PMID: 38025116 PMCID: PMC10668566 DOI: 10.1177/20552076231178435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/10/2023] [Indexed: 12/01/2023] Open
Abstract
Health technology startups are experiencing a significant surge in growth, particularly since the COVID-19 pandemic, as they address gaps in the sector. However, despite their increasing prevalence, there is still relatively limited knowledge about this sector's evolution. This opinion article explores emerging trends in health startups, including their market size, growth, significant challenges, and guidelines for key stakeholders from a global healthcare service industry perspective. By gaining a better understanding of these trends, new research opportunities and evidence-based practices can be identified.
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Affiliation(s)
- Imon Chakraborty
- Centre for Online Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sisira Edirippulige
- Centre for Online Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
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47
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Jiang W, Li Y, Peng H. Engineering Biology of Yeast for Advanced Biomanufacturing. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 10:bioengineering10010010. [PMID: 36671581 PMCID: PMC9854945 DOI: 10.3390/bioengineering10010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Advanced biomanufacturing has been widely involved in people's daily life, such as the production of molecules used as pharmaceuticals, in foods and beverages, and in bio-fuels [...].
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Affiliation(s)
- Wei Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Huadong Peng
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence:
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