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Jureckova K, Nykrynova M, Slaninova E, Fleuriot-Blitman H, Amstutz V, Hermankova K, Bezdicek M, Mrazova K, Hrubanova K, Zinn M, Obruca S, Sedlar K. Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum. Comput Struct Biotechnol J 2024; 23:2681-2694. [PMID: 39035834 PMCID: PMC11259993 DOI: 10.1016/j.csbj.2024.06.023] [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: 03/15/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Eva Slaninova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Hugo Fleuriot-Blitman
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Véronique Amstutz
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Kristyna Hermankova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine – Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine – Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Mrazova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Kamila Hrubanova
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Manfred Zinn
- Institute of Life Technologies, University of Applied Sciences and Arts Western Switzerland Valais-Wallis (HES-SO Valais-Wallis), Sion, Switzerland
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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Zhu Q, Wang S, Fu G, Guo F, Huang W, Zhang T, Dong H, Jin Z, Zhang D. Highly flexible cell membranes are the key to efficient production of lipophilic compounds. J Lipid Res 2024; 65:100597. [PMID: 39029799 DOI: 10.1016/j.jlr.2024.100597] [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: 03/30/2024] [Revised: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
Lipophilic compounds have a variety of positive effects on human physiological functions and exhibit good effects in the prevention and treatment of clinical diseases. This has led to significant interest in the technical applications of synthetic biology for the production of lipophilic compounds. However, the strict selective permeability of the cell membrane and the hydrophobic nature of lipophilic compounds pose significant challenges to their production. During fermentation, lipophilic compounds tend to accumulate within cell membrane compartments rather than being secreted extracellularly. The toxic effects of excessive lipophilic compound accumulation can threaten cell viability, while the limited space within the cell membrane restricts further increases in production yield. Consequently, to achieve efficient production of lipophilic compounds, research is increasingly focused on constructing robust and multifunctional microbial cell factories. Utilizing membrane engineering techniques to construct highly flexible cell membranes is considered an effective strategy to break through the upper limit of lipophilic compound production. Currently, there are two main approaches to cell membrane modification: constructing artificial storage compartments for lipophilic compounds and engineering the cell membrane structure to facilitate product outflow. This review summarizes recent cell membrane engineering strategies applied in microbial cell factories for the production of liposoluble compounds, discussing the challenges and future prospects. These strategies enhance membrane flexibility and effectively promote the production of liposoluble compounds.
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Affiliation(s)
- Qiyao Zhu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sijia Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Fengming Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Wei Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tengyue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zhaoxia Jin
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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Wu T, Jiang J, Zhang H, Liu J, Ruan H. Transcending membrane barriers: advances in membrane engineering to enhance the production capacity of microbial cell factories. Microb Cell Fact 2024; 23:154. [PMID: 38796463 PMCID: PMC11128114 DOI: 10.1186/s12934-024-02436-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.
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Affiliation(s)
- Tao Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| | - Jingjing Jiang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Hongyang Zhang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Jiazhi Liu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
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Wang J, Ma W, Zhou J, Wang X, Zhao L. Microbial chassis design and engineering for production of gamma-aminobutyric acid. World J Microbiol Biotechnol 2024; 40:159. [PMID: 38607454 DOI: 10.1007/s11274-024-03951-x] [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: 12/11/2023] [Accepted: 03/10/2024] [Indexed: 04/13/2024]
Abstract
Gamma-aminobutyric acid (GABA) is a non-protein amino acid which is widely applied in agriculture and pharmaceutical additive industries. GABA is synthesized from glutamate through irreversible α-decarboxylation by glutamate decarboxylase. Recently, microbial synthesis has become an inevitable trend to produce GABA due to its sustainable characteristics. Therefore, reasonable microbial platform design and metabolic engineering strategies for improving production of GABA are arousing a considerable attraction. The strategies concentrate on microbial platform optimization, fermentation process optimization, rational metabolic engineering as key metabolic pathway modification, promoter optimization, site-directed mutagenesis, modular transporter engineering, and dynamic switch systems application. In this review, the microbial producers for GABA were summarized, including lactic acid bacteria, Corynebacterium glutamicum, and Escherichia coli, as well as the efficient strategies for optimizing them to improve the production of GABA.
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Affiliation(s)
- Jianli Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| | - Lei Zhao
- WuXi Biologics Co., Ltd., Wuxi, 214062, China
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Park H, Faulkner M, Toogood HS, Chen GQ, Scrutton N. Online Omics Platform Expedites Industrial Application of Halomonas bluephagenesis TD1.0. Bioinform Biol Insights 2023; 17:11779322231171779. [PMID: 37200674 PMCID: PMC10185862 DOI: 10.1177/11779322231171779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/07/2023] [Indexed: 05/20/2023] Open
Abstract
Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics. Here we introduce a user-friendly, interactive website hosting multi-omics data. Importantly, this new platform allows non-experts to explore questions in an industrially important chassis whose cellular dynamics are still largely unknown. The web platform contains a complete KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis derived from principal components analysis, an interactive bio-cluster heatmap analysis of genes, and the Halomonas TD1.0 genome-scale metabolic (GEM) model. As a case study of the effectiveness of this platform, we applied unsupervised machine learning to determine key differences between Halomonas bluephagenesis TD1.0 cultivated under varied conditions. Specifically, cell motility and flagella apparatus are identified to drive energy expenditure usage at different osmolarities, and predictions were verified experimentally using microscopy and fluorescence labelled flagella staining. As more omics projects are completed, this landing page will facilitate exploration and targeted engineering efforts of the robust, industrial chassis H bluephagenesis for researchers without extensive bioinformatics background.
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Affiliation(s)
- Helen Park
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Matthew Faulkner
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Helen S Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Nigel Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub and BBSRC Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, UK
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Kim S, Jang YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO 2. Microb Cell Fact 2022; 21:231. [PMCID: PMC9636797 DOI: 10.1186/s12934-022-01962-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO2) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO2 is still too low for commercialization. Results Here, we engineer the carbon fixation metabolism to improve CO2 utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO2—fixing metabolism and PHB production were investigated. Conclusions The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01962-7.
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Affiliation(s)
- Soyoung Kim
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Yong Jae Jang
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Sun-Mi Lee
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Kyoung Heon Kim
- grid.222754.40000 0001 0840 2678Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ja Kyong Ko
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
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