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Murugan C, Subbian S, Kaliyaperumal S, Sadasivuni KK, Siddiqui MIH, Muthusamy S, Rosen MA, Prakash C, Chan CK. An event triggered control scheme for enhanced production of Escherichia coli and biomass concentration during fed-batch cultivation. Heliyon 2024; 10:e32210. [PMID: 38975212 PMCID: PMC11226784 DOI: 10.1016/j.heliyon.2024.e32210] [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: 01/19/2024] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
Control of a bioprocess is a challenging task mainly due to the nonlinearity of the process, the complex nature of microorganisms, and variations in critical parameters such as temperature, pH, and agitator speed. Generally, the optimum values chosen for critical parameters during Escherichia coli (E.coli) K-12fed-batch fermentation are37 ᵒC for temperature, 7 for pH, and 35 % for Dissolved Oxygen (DO). The objective of this research is to enhance biomass concentration while minimizing energy consumption. To achieve this, an Event-Triggered Control (ETC) scheme based on feedback-feed forward control is proposed. The ETC system dynamically adjusts the substrate feed rate in response to variations in critical parameters. We compare the performance of classical Proportional Integral (PI) controllers and advanced Model Predictive Control (MPC) controllers in terms of bioprocess yield. Initially, the data are collected from a laboratory-scaled 3L bioreactor setup under fed-batch operating conditions, and data-driven models are developed using system identification techniques. Then, classical Proportional Integral (PI) and advanced Model Predictive Control (MPC) based feedback controllers are developed for controlling the yield of bioprocess by manipulating substrate flow rate, and their performances are compared. PI and MPC-based Event Triggered Feed Forward Controllers are designed to increase the yield and to suppress the effect of known disturbances due to critical parameters. Whenever there is a variation in the value of a critical parameter, it is considered an event, and ETC initiates a control action by manipulating the substrate feed rate. PI and MPC-based ETC controllers are developed in simulation, and their closed-loop performances are compared. It is observed that the Integral Square Error (ISE) is notably minimized to 4.668 for MPC with disturbance and 4.742 for MPC with Feed Forward Control. Similarly, the Integral Absolute Error (IAE) reduces to 2.453 for MPC with disturbance and 0.8124 for MPC with Feed Forward Control. The simulation results reveal that the MPC-based ETC control scheme enhances the biomass yield by 7 %, and this result is verified experimentally. This system dynamically adjusts the substrate feed rate in response to variations in critical parameters, which is a novel approach in the field of bioprocess control. Also, the proposed control schemes help reduce the frequency of communication between controller and actuator, which reduces power consumption.
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Affiliation(s)
- Chitra Murugan
- Department of Electronics and Communication Engineering, Bharath Institute of Higher Education and Research (Deemed to be University), Chennai, Tamil Nadu, India
| | - Sutha Subbian
- Department of Instrumentation Engineering, Madras Institute of Technology Campus, Anna University Chennai, Tamil Nadu, India
| | - Saravanan Kaliyaperumal
- Department of Electrical and Electronics Engineering, SRM Institute of Science and Technology (Deemed to be University), Kattankulathur, Chennai, Tamil Nadu, India
| | - Kishor Kumar Sadasivuni
- Centre for Advanced Materials, Qatar University, Qatar
- Department of Mechanical and Industrial Engineering, Qatar University, Qatar
| | | | - Suresh Muthusamy
- Department of Electrical and Electronics Engineering, Kongu Engineering College (Autonomous), Perundurai, Erode, Tamil Nadu, India
| | - Marc A. Rosen
- Department of Mechanical and Manufacturing Engineering, Faculty of Engineering and Applied Sciences, University of Ontario Institute of Technology, Oshawa, Canada
- Centre for Research Impact and Outcomes, Chitkara University, Rajpura, Punjab, India
| | - Chander Prakash
- Faculty of Engineering and Quantity Surveying, INTI International University, Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Choon Kit Chan
- Faculty of Engineering and Quantity Surveying, INTI International University, Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
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Rothkranz B, Rieb M, Unrau EL, Frindi-Wosch I, Hemmerich J, Sehl T, Rother D. High Cell Density Cultivation Combined with high Specific Enzyme Activity: Cultivation Protocol for the Production of an Amine Transaminase from Bacillus megaterium in E. coli. Chembiochem 2024; 25:e202400006. [PMID: 38457364 DOI: 10.1002/cbic.202400006] [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: 01/10/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High cell density cultivation is an established method for the production of various industrially important products such as recombinant proteins. However, these protocols are not always suitable for biocatalytic processes as the focus often lies on biomass production rather than high specific activities of the enzyme inside the cells. In contrast, a range of shake flask protocols are well known with high specific activities but rather low cell densities. To overcome this gap, we established a tailor-made fed-batch protocol combining both aspects: high cell density and high specific activities of heterologously produced enzyme. Using the example of an industrially relevant amine transaminase from Bacillus megaterium, we describe a strategy to optimize the cultivation yield based on the feed rate, IPTG concentration, and post-induction temperature. By adjusting these key parameters, we were able to increase the specific activity by 2.6-fold and the wet cell weight by even 17-fold compared to shake flasks. Finally, we were able to verify our established protocol by transferring it to another experimenter. With that, our optimization strategy can serve as a template for the production of high titers of heterologously produced, active enzymes and might enable the availability of these catalysts for upscaling biocatalytic processes.
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Affiliation(s)
- Berit Rothkranz
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
| | - Matthias Rieb
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Evelin Lisa Unrau
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Ilona Frindi-Wosch
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Johannes Hemmerich
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- dsm-firmenich, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Torsten Sehl
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Dörte Rother
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
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3
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Guo Q, Peng QQ, Li YW, Yan F, Wang YT, Ye C, Shi TQ. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene. Crit Rev Biotechnol 2024; 44:337-351. [PMID: 36779332 DOI: 10.1080/07388551.2023.2166809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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4
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Wang J, Ma W, Ma W, Fang Z, Jiang Y, Jiang W, Kong X, Xin F, Zhang W, Jiang M. Strategies for the efficient biosynthesis of β-carotene through microbial fermentation. World J Microbiol Biotechnol 2024; 40:160. [PMID: 38607448 DOI: 10.1007/s11274-024-03955-7] [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: 01/26/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
β-Carotene is an orange fat-soluble compound, which has been widely used in fields such as food, medicine and cosmetics owing to its anticancer, antioxidant and cardiovascular disease prevention properties. Currently, natural β-carotene is mainly extracted from plants and algae, which cannot meet the growing market demand, while chemical synthesis of β-carotene cannot satisfy the pursuit for natural products of consumers. The β-carotene production through microbial fermentation has become a promising alternative owing to its high efficiency and environmental friendliness. With the rapid development of synthetic biology and in-depth study on the synthesis pathway of β-carotene, microbial fermentation has shown promising applications in the β-carotene synthesis. Accordingly, this review aims to summarize the research progress and strategies of natural carotenoid producing strain and metabolic engineering strategies in the heterologous synthesis of β-carotene by engineered microorganisms. Moreover, it also summarizes the adoption of inexpensive carbon sources to synthesize β-carotene as well as proposes new strategies that can further improve the β-carotene production.
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Affiliation(s)
- Jingnan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wenqi Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Weixu Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Zhanyang Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Xiangping Kong
- Key Laboratory for Crop and Animal Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, People's Republic of China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
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5
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Kinet R, Richelle A, Colle M, Demaegd D, von Stosch M, Sanders M, Sehrt H, Delvigne F, Goffin P. Giving the cells what they need when they need it: Biosensor-based feeding control. Biotechnol Bioeng 2024; 121:1271-1283. [PMID: 38258490 DOI: 10.1002/bit.28657] [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: 07/28/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
"Giving the cells exactly what they need, when they need it" is the core idea behind the proposed bioprocess control strategy: operating bioprocess based on the physiological behavior of the microbial population rather than exclusive monitoring of environmental parameters. We are envisioning to achieve this through the use of genetically encoded biosensors combined with online flow cytometry (FCM) to obtain a time-dependent "physiological fingerprint" of the population. We developed a biosensor based on the glnA promoter (glnAp) and applied it for monitoring the nitrogen-related nutritional state of Escherichia coli. The functionality of the biosensor was demonstrated through multiple cultivation runs performed at various scales-from microplate to 20 L bioreactor. We also developed a fully automated bioreactor-FCM interface for on-line monitoring of the microbial population. Finally, we validated the proposed strategy by performing a fed-batch experiment where the biosensor signal is used as the actuator for a nitrogen feeding feedback control. This new generation of process control, -based on the specific needs of the cells, -opens the possibility of improving process development on a short timescale and therewith, the robustness and performance of fermentation processes.
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Affiliation(s)
| | | | | | | | | | | | - Hannah Sehrt
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Philippe Goffin
- Molecular and Cellular Biology, University of Brussels, Brussels, Belgium
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6
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Melchor-Moncada JJ, García-Barco A, Zuluaga-Vélez A, Veloza LA, Sepúlveda-Arias JC. Scale-Up of the Fermentation Process for the Production and Purification of Serratiopeptidase Using Silkworm Pupae as a Substrate. Methods Protoc 2024; 7:19. [PMID: 38525777 PMCID: PMC10961818 DOI: 10.3390/mps7020019] [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: 01/26/2024] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Serratiopeptidase, a bacterial metalloprotease known for its pain-relieving and anti-inflammatory properties, can be produced through fermentation with S. marcescens. This study aimed to identify key factors related to nutrient composition and physicochemical conditions for production in Erlenmeyer flasks and to scale up the mixture to a bioreactor to obtain the maximum proteolytic activity. A Plackett-Burman design was used to determine whether the presence of silkworm pupae (at 1.5%) was a significant parameter for serratiopeptidase production. Along with the variables pH, temperature, and time, they were optimized using a Taguchi experimental design, resulting in values of 7, 25 °C, and 36 h, respectively. Scaling up with a kLa of 25.45 ± 3.12 h-1 showed the highest serratiopeptidase production at 24 h. A factorial design was used for ultrafiltration, resulting in an LMH (liters per square meter per hour) of 960 L/m2h, a TMP (transmembrane pressure) of 15 psi, and a concentration factor of five, with a specific activity of 24,325.81 ± 1515.69 U/mg. Afterward, the retentate was purified using strong anion exchange chromatography and ultrafiltration, yielding a 19.94 ± 3.07% recovery and a purification factor of 1.59 ± 0.31. In conclusion, waste from the sericulture industry can be used for serratiopeptidase production.
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Affiliation(s)
- Jhon Jairo Melchor-Moncada
- Grupo Infección e Inmunidad, Departamento de Ciencias Básicas, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.J.M.-M.); (A.G.-B.); (A.Z.-V.)
| | - Alejandra García-Barco
- Grupo Infección e Inmunidad, Departamento de Ciencias Básicas, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.J.M.-M.); (A.G.-B.); (A.Z.-V.)
| | - Augusto Zuluaga-Vélez
- Grupo Infección e Inmunidad, Departamento de Ciencias Básicas, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.J.M.-M.); (A.G.-B.); (A.Z.-V.)
| | - Luz Angela Veloza
- Grupo Polifenoles, Facultad de Tecnología, Escuela de Tecnología Química, Universidad Tecnológica de Pereira, Pereira 660003, Colombia;
| | - Juan Carlos Sepúlveda-Arias
- Grupo Infección e Inmunidad, Departamento de Ciencias Básicas, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.J.M.-M.); (A.G.-B.); (A.Z.-V.)
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7
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Robles-Iglesias R, Fernández-Blanco C, Nicaud JM, Veiga MC, Kennes C. Unlocking the potential of one-carbon gases (CO 2, CO) for concomitant bioproduction of β-carotene and lipids. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 271:115950. [PMID: 38211510 DOI: 10.1016/j.ecoenv.2024.115950] [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: 08/18/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
This study investigates the use of a Yarrowia lipolytica strain for the bioconversion of syngas-derived acetic acid into β-carotene and lipids. A two-stage process was employed, starting with the acetogenic fermentation of syngas by Clostridium aceticum, metabolising CO, CO2, H2, to produce acetic acid, which is then utilized by Y. lipolytica for simultaneous lipid and β-carotene synthesis. The research demonstrates that acetic acid concentration plays a pivotal role in modulating lipid profiles and enhancing β-carotene production, with increased acetic acid consumption leading to higher yields of these compounds. This approach showcases the potential of using one-carbon gases as substrates in bioprocesses for generating valuable bioproducts, providing a sustainable and cost-effective alternative to more conventional feedstocks and substrates, such as sugars.
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Affiliation(s)
- Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Carla Fernández-Blanco
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, Rúa da Fraga 10, La Coruña 15008, Spain.
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8
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Gu L, Xiao X, Yup Lee S, Lai B, Solem C. Superior anodic electro-fermentation by enhancing capacity for extracellular electron transfer. BIORESOURCE TECHNOLOGY 2023; 389:129813. [PMID: 37776913 DOI: 10.1016/j.biortech.2023.129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Anodic electro-fermentation (AEF), where an anode replaces the terminal electron acceptor, shows great promise. Recently a Lactococcus lactis strain blocked in NAD+ regeneration was demonstrated to use ferricyanide as an alternative electron acceptor to support fast growth, but the need for high concentrations of this non-regenerated electron acceptor limits practical applications. To address this, growth of this L. lactis strain, and an adaptively evolved (ALE) mutant with enhanced ferricyanide respiration capacity were investigated using an anode as electron acceptor in a bioelectrochemical system (BES) setup. Both strains grew well, however, the ALE mutant significantly faster. The ALE mutant almost exclusively generated 2,3-butanediol, whereas its parent strain mainly produced acetoin. The ALE mutant interacted efficiently with the anode, achieving a record high current density of 0.81 ± 0.05 mA/cm2. It is surprising that a Lactic Acid Bacterium, with fermentative metabolism, interacts so well with an anode, which demonstrates the potential of AEF.
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Affiliation(s)
- Liuyan Gu
- National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Xinxin Xiao
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Bin Lai
- BMBF junior research group Biophotovoltaics, Helmholtz Center for Environmental Research - UFZ, Leipzig 04318, Germany.
| | - Christian Solem
- National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
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9
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Bi H, Xu C, Bao Y, Zhang C, Wang K, Zhang Y, Wang M, Chen B, Fang Y, Tan T. Enhancing precursor supply and modulating metabolism to achieve high-level production of β-farnesene in Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2023; 382:129171. [PMID: 37196740 DOI: 10.1016/j.biortech.2023.129171] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
β-Farnesene is a sesquiterpene commonly found in essential oils of plants, with applications spanning from agricultural pest control and biofuels to industrial chemicals. The use of renewable substrates in microbial cell factories offers a sustainable approach to β-farnesene biosynthesis. In this study, malic enzyme from Mucor circinelloides was examined for NADPH regeneration, concomitant with the augmentation of cytosolic acetyl-CoA supply by expressing ATP-citrate lyase from Mus musculus and manipulating the citrate pathway via AMP deaminase and isocitrate dehydrogenase. Carbon flux was modulated through the elimination of native 6-phosphofructokinase, while the incorporation of an exogenous non-oxidative glycolysis pathway served to bridge the pentose phosphate pathway with the mevalonate pathway. The resulting orthogonal precursor supply pathway facilitated β-farnesene production, reaching 810 mg/L in shake-flask fermentation. Employing optimal fermentation conditions and feeding strategy, a titer of 28.9 g/L of β-farnesene was attained in a 2 L bioreactor.
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Affiliation(s)
- Haoran Bi
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Chenchen Xu
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yufei Bao
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Changwei Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Kai Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yang Zhang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Meng Wang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
| | - Biqiang Chen
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Yunming Fang
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China
| | - Tianwei Tan
- National Energy R&D Center of Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P.R. China.
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10
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Integrated pathway engineering and transcriptome analysis for improved astaxanthin biosynthesis in Yarrowia lipolytica. Synth Syst Biotechnol 2022; 7:1133-1141. [PMID: 36092272 PMCID: PMC9428815 DOI: 10.1016/j.synbio.2022.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Astaxanthin is a high value carotenoid with a broad range of commercial applications due to its superior antioxidant properties. In this study, β-carotene-producing Yarrowia lipolytica XK17 constructed in the lab was employed for astaxanthin biosynthesis. The catalytic effects of β-carotene ketolase CrtW and β-carotene hydroxylase CrtZ from various species were investigated. The PspCrtW from Paracoccus sp. and HpCrtZ# from Haematococcus pluvialis were confirmed to be the best combination in converting β-carotene. Several key bottlenecks in biomass and astaxanthin biosynthesis were effectively eliminated by optimizing the expression of the above enzymes and restoring uracil/leucine biosynthesis. In addition, the effects of astaxanthin biosynthesis on cell metabolism were investigated by integrated analysis of pathway modification and transcriptome information. After further optimization, strain DN30 was able to synthesize up to 730.3 mg/L astaxanthin in laboratory 5-L fermenter. This study provides a good metabolic strategy and a sustainable development platform for high-value carotenoid production.
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Arnesen JA, Borodina I. Engineering of Yarrowia lipolytica for terpenoid production. Metab Eng Commun 2022; 15:e00213. [PMID: 36387772 PMCID: PMC9663531 DOI: 10.1016/j.mec.2022.e00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
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12
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Shen D, He X, Weng P, Liu Y, Wu Z. A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation. FEMS Yeast Res 2022; 22:6775076. [PMID: 36288242 DOI: 10.1093/femsyr/foac050] [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: 07/17/2022] [Revised: 09/21/2022] [Accepted: 10/22/2022] [Indexed: 01/07/2023] Open
Abstract
Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.
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Affiliation(s)
- Dongxu Shen
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Xiaoli He
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Peifang Weng
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
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13
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Scale-Up of Capsular Polysaccharide Production Process by Haemophilus influenzae Type b Using kLa Criterion. Bioengineering (Basel) 2022; 9:bioengineering9090415. [PMID: 36134961 PMCID: PMC9495314 DOI: 10.3390/bioengineering9090415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
Polyribosyl-ribitol-phosphate (PRP) from Haemophilus influenzae type b (Hib) is an active immunizing molecule used in the production of the vaccine against H. influenzae, and industrial production could contribute to satisfying a world demand especially in developing countries. In this sense, the aim of this study was to establish a scale-up process using the constant oxygen mass transfer coefficient (kLa) such as the criterion for production of PRP in three different sizes of bioreactor systems. Three different kLa values (24, 52 and 80 h−1) were evaluated in which the biological influence in a 1.5 L bioreactor and 52 h−1 was selected to scale-up the production process until a 75 L pilot-scale bioreactor was achieved. Finally, the fed-batch phase was started under a dissolved oxygen concentration (pO2) at 30% of the saturation in the 75 L bioreactor to avoid oxygen limitation; the performance of production presented high efficiency (9.0 g/L DCW-dry cell weight and 1.4 g/L PRP) in comparison with previous scale-up studies. The yields, productivity and kinetic behavior were similar in the three-size bioreactor systems in the batch mode indicating that kLa is possible to use for PRP production at large scales. This process operated under two stages and successfully produced DCW and PRP in the pilot scale and could be beneficial for future bioprocess operations that may lead to higher production and less operative cost.
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Deeba F, Kiran Kumar K, Ali Wani S, Kumar Singh A, Sharma J, Gaur NA. Enhanced biodiesel and β-carotene production in Rhodotorula pacifica INDKK using sugarcane bagasse and molasses by an integrated biorefinery framework. BIORESOURCE TECHNOLOGY 2022; 351:127067. [PMID: 35351564 DOI: 10.1016/j.biortech.2022.127067] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Dependency on fossil fuels raises an economic and ecological concern that has urged to look for alternative sources of energy. Bio-refinery concept is one of the alternate frameworks for the biomass conversion into biofuel and other value-added by-products. The present work illustrates importance of an oleaginous yeast Rhodotorula pacifica INDKK in an integrated bio-refinery field by utilizing renewable sugars generated from lignocellulosic biomass. The maximum 11.8 g/L lipid titer, 210.4 mg/L β-carotene and 7.1 g animal feed were produced by R. pacifica INDKK in bioreactor containing 5% (v/v) molasses supplemented with enzymatically hydrolyzed and alkali-pretreated sugarcane bagasse hydrolysate (35% v/v). Furthermore, xylooligosaccharides (20.6 g/L), a beneficial prebiotics were also produced from the hemicellulosic fraction separated after alkali pretreatment of bagasse. This novel concept of integrated yeast bio-refinery for concomitant production of biodiesel and multiple value-added products with minimum waste generation is proposed as a sustainable and profitable process.
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Affiliation(s)
- Farha Deeba
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Kukkala Kiran Kumar
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Shahid Ali Wani
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Anup Kumar Singh
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Juhi Sharma
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Naseem A Gaur
- Yeast Biofuel Group, DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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15
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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Improved production of D-pantothenic acid in Escherichia coli by integrated strain engineering and fermentation strategies. J Biotechnol 2021; 339:65-72. [PMID: 34352344 DOI: 10.1016/j.jbiotec.2021.07.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022]
Abstract
D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in medicine, food, and animal feed. Microbial production of D-PA from natural renewable resources is attractive and challenging. In this study, both strain improvements and fermentation process strategies were applied to achieve high-level D-PA production in Escherichia coli. First, a D-PA-producing strain was developed through deletion of the aceF and mdh genes combined with the overexpression of the gene ppnk. The obtained engineered E. coli DPA02/pT-ppnk accumulated 6.89 ± 0.11 g/L of D-PA in shake flask fermentation, which was 79.9 % higher than the control strain. Moreover, the cultivation process contributed greatly to D-PA production with respect to titer and productivity by betaine supplementation and dissolved oxygen (DO)-feedback feeding framework. Under optimal conditions, 68.3 g/L of D-PA, the specific productivity of 0.794 g/L h and the yield of 0.36 g/g glucose in 5 L fermenter were achieved. Overall, this research successfully exploited advanced strategies to lay the foundation for bio-based D-PA production in industrial applications.
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Liu TT, Zhong JJ. Impact of oxygen supply on production of a novel ganoderic acid in Saccharomyces cerevisiae fermentation. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mamaev D, Zvyagilskaya R. Yarrowia lipolytica: a multitalented yeast species of ecological significance. FEMS Yeast Res 2021; 21:6141120. [PMID: 33595651 DOI: 10.1093/femsyr/foab008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Yarrowia lipolytica is characterized by GRAS (Generally regarded as safe) status, the versatile substrate utilization profile, rapid utilization rates, metabolic diversity and flexibility, the unique abilities to tolerate to extreme environments (acidic, alkaline, hypersaline, heavy metal-pollutions and others) and elevated biosynthesis and secreting capacities. These advantages of Y. lipolytica allow us to consider it as having great ecological significance. Unfortunately, there is still a paucity of relevant review data. This mini-review highlights ecological ubiquity of Y. lipolytica species, their ability to diversify and colonize specialized niches. Different Y. lipolytica strains, native and engineered, are beneficial in degrading many environmental pollutants causing serious ecological problems worldwide. In agriculture has a potential to be a bio-control agent by stimulating plant defense response, and an eco-friendly bio-fertilizer. Engineered strains of Y. lipolytica have become a very promising platform for eco-friendly production of biofuel, commodities, chemicals and secondary metabolites of plant origin, obtaining which by other method were limited or economically infeasible, or were accompanied by stringent environmental problems. Perspectives to use potential of Y. lipolytica's capacities for industrial scale production of valuable compounds in an eco-friendly manner are proposed.
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Affiliation(s)
- Dmitry Mamaev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
| | - Renata Zvyagilskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
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