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Lou X, Shu W, Wang LC, Lim YT, Zhao T, Liu H, Sobota RM, Yang H. Metabolic and protein expression responses of Shewanella baltica in golden pomfret broths to slightly acidic electrolysed water. Food Chem 2025; 462:140991. [PMID: 39208721 DOI: 10.1016/j.foodchem.2024.140991] [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: 02/20/2024] [Revised: 08/05/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Shewanella baltica is a specific spoilage organism of golden pomfret. This study aims to explore the antibacterial mechanism of slightly acidic electrolysed water (SAEW) against S. baltica (strains ABa4, ABe2 and BBe1) in golden pomfret broths by metabolomics, proteomics and bioinformatics analyses. S. baltica was decreased by at least 3.94 log CFU/mL after SAEW treatment, and strain ABa4 had the highest resistance. Under SAEW stress, amino acids and organic acids in S. baltica decreased, and nucleotide related compounds degraded. Furthermore, 100 differentially expressed proteins (DEPs) were identified. Most DEPs of strains ABe2 and BBe1 were down-regulated, while some DEPs of strain ABa4 were up-regulated, especially those oxidative stress related proteins. These results suggest that the modes of SAEW against S. baltica can be traced to the inhibition of amino acid, carbon, nucleotide and sulphur metabolisms, and the loss of functional proteins for temperature regulation, translation, motility and protein folding.
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Affiliation(s)
- Xiaowei Lou
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore.
| | - Weichen Shu
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Loo Chien Wang
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Tianyun Zhao
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Hang Liu
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Hongshun Yang
- College of Light Industry and Food Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
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Sawada K, Hagihara H, Takimura Y, Kataoka M. Production and molecular weight variation of poly-γ-glutamic acid using a recombinant Bacillus subtilis with various Pgs-component ratios. Biosci Biotechnol Biochem 2024; 88:1217-1224. [PMID: 38955395 DOI: 10.1093/bbb/zbae093] [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: 05/07/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Poly-γ-glutamic acid (PGA) has been of interest as a sustainable biopolymer in industrial applications. PGA biosynthesis in Bacillus subtilis is catalyzed by a transmembrane protein complex comprising PgsB, PgsC, and PgsA. To determine the Pgs component responsible for PGA overproduction, we constructed recombinants in which the promoter of the host-derived pgs gene was replaced with another host-derived gene promoter. These recombinants were then transformed using high-copy-number plasmids with various pgs-gene combinations to enhance Pgs component in different ratios. Subsequently, PGA production was investigated in batch cultures with l-glutamate supplemented medium. The recombinant strain enhanced with pgsB alone significantly overproduced PGA (maximum production 35.8 g/L) than either the pgsC- or pgsA-enhanced strain. The molecular weight of the PGA produced with the pgsB-enhanced strain was also greater than that for the pgsC- or pgsA-enhanced strain (approximately 10-fold). Hence, PgsB enhancement alone contributes to PGA overproduction with increased molecular weight.
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Affiliation(s)
- Kazuhisa Sawada
- Global R&D-Biological Science Research, Kao Corporation, Haga, Tochigi, Japan
- Department of Biomedical Engineering, Graduate School of Shinshu University, Wakasato, Nagano, Japan
| | - Hiroshi Hagihara
- Global R&D-Biological Science Research, Kao Corporation, Haga, Tochigi, Japan
| | - Yasushi Takimura
- Global R&D-Biological Science Research, Kao Corporation, Haga, Tochigi, Japan
| | - Masakazu Kataoka
- Department of Biomedical Engineering, Graduate School of Shinshu University, Wakasato, Nagano, Japan
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3
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Jung YJ, Park KH, Jang TY, Yoo SM. Gene expression regulation by modulating Hfq expression in coordination with tailor-made sRNA-based knockdown in Escherichia coli. J Biotechnol 2024; 388:1-10. [PMID: 38616040 DOI: 10.1016/j.jbiotec.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: 02/26/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
The tailor-made synthetic sRNA-based gene expression knockdown system has demonstrated its efficacy in achieving pathway balancing in microbes, facilitating precise target gene repression and fine-tuned control of gene expression. This system operates under a competitive mode of gene regulation, wherein the tailor-made synthetic sRNA shares the intrinsic intracellular Hfq protein with other RNAs. The limited intracellular Hfq amount has the potential to become a constraining factor in the post-transcription regulation of sRNAs. To enhance the efficiency of the tailor-made sRNA gene expression regulation platform, we introduced an Hfq expression level modulation-coordinated sRNA-based gene knockdown system. This system comprises tailor-made sRNA expression cassettes that produce varying Hfq expression levels using different strength promoters. Modulating the expression levels of Hfq significantly improved the repressing capacity of sRNA, as evidenced by evaluations with four fluorescence proteins. In order to validate the practical application of this system, we applied the Hfq-modulated sRNA-based gene knockdown cassette to Escherichia coli strains producing 5-aminolevulinic acid and L-tyrosine. Diversifying the expression levels of metabolic enzymes through this cassette resulted in substantial increases of 74.6% in 5-aminolevulinic acid and 144% in L-tyrosine production. Tailor-made synthetic sRNA-based gene expression knockdown system, coupled with Hfq copy modulation, exhibits potential for optimizing metabolic fluxes through biosynthetic pathways, thereby enhancing the production yields of bioproducts.
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Affiliation(s)
- Yu Jung Jung
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Keun Ha Park
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Tae Yeong Jang
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
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4
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Zhang X, Liu L, Ma C, Zhang H, Liu H, Fang H. Improving the level of the cytidine biosynthesis in E. coli through atmospheric room temperature plasma mutagenesis and metabolic engineering. J Appl Microbiol 2024; 135:lxae133. [PMID: 38830792 DOI: 10.1093/jambio/lxae133] [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: 03/21/2024] [Revised: 05/09/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
AIMS Cytidine, as an important commercial precursor in the chemical synthesis of antiviral and antitumor drugs, is in great demand in the market. Therefore, the purpose of this study is to build a microbial cell factory with high cytidine production. METHODS AND RESULTS A mutant E. coli NXBG-11-F34 with high tolerance to uridine monophosphate structural analogs and good genetic stability was obtained by atmospheric room temperature plasma (ARTP) mutagenesis combined with high-throughput screening. Then, the udk and rihA genes involved in cytidine catabolism were knocked out by CRISPR/Cas9 gene editing technology, and the recombinant strain E. coli NXBG-13 was constructed. The titer, yield, and productivity of cytidine fermented in a 5 l bioreactor were 15.7 g l-1, 0.164 g g-1, and 0.327 g l-1 h-1, respectively. Transcriptome analysis of the original strain and the recombinant strain E. coli NXBG-13 showed that the gene expression profiles of the two strains changed significantly, and the cytidine de novo pathway gene of the recombinant strain was up-regulated significantly. CONCLUSIONS ARTP mutagenesis combined with metabolic engineering is an effective method to construct cytidine-producing strains.
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Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Lu Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Cong Ma
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haojie Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
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Lv T, Li J, Zhou L, Zhou T, Pritchard HW, Ren C, Chen J, Yan J, Pei J. Aging-Induced Reduction in Safflower Seed Germination via Impaired Energy Metabolism and Genetic Integrity Is Partially Restored by Sucrose and DA-6 Treatment. PLANTS (BASEL, SWITZERLAND) 2024; 13:659. [PMID: 38475505 DOI: 10.3390/plants13050659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.
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Affiliation(s)
- Tang Lv
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Juan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lanyu Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hugh W Pritchard
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, China
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, West Sussex, UK
| | - Chaoxiang Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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6
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Elbanna K, Alsulami FS, Neyaz LA, Abulreesh HH. Poly (γ) glutamic acid: a unique microbial biopolymer with diverse commercial applicability. Front Microbiol 2024; 15:1348411. [PMID: 38414762 PMCID: PMC10897055 DOI: 10.3389/fmicb.2024.1348411] [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: 12/02/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Microbial biopolymers have emerged as promising solutions for environmental pollution-related human health issues. Poly-γ-glutamic acid (γ-PGA), a natural anionic polymeric compound, is composed of highly viscous homo-polyamide of D and L-glutamic acid units. The extracellular water solubility of PGA biopolymer facilitates its complete biodegradation and makes it safe for humans. The unique properties have enabled its applications in healthcare, pharmaceuticals, water treatment, foods, and other domains. It is applied as a thickener, taste-masking agent, stabilizer, texture modifier, moisturizer, bitterness-reducing agent, probiotics cryoprotectant, and protein crystallization agent in food industries. γ-PGA is employed as a biological adhesive, drug carrier, and non-viral vector for safe gene delivery in tissue engineering, pharmaceuticals, and medicine. It is also used as a moisturizer to improve the quality of hair care and skincare cosmetic products. In agriculture, it serves as an ideal stabilizer, environment-friendly fertilizer synergist, plant-growth promoter, metal biosorbent in soil washing, and animal feed additive to reduce body fat and enhance egg-shell strength.
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Affiliation(s)
- Khaled Elbanna
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Fatimah S Alsulami
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Leena A Neyaz
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hussein H Abulreesh
- Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
- Research Laboratories Unit, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia
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7
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Xin Q, Jia H, Wang B, Pan L. CRISPR-dCpf1 mediated whole genome crRNA inhibition library for high-throughput screening of growth characteristic genes in Bacillus amyloliquefaciens LB1ba02. Int J Biol Macromol 2023; 253:127179. [PMID: 37802457 DOI: 10.1016/j.ijbiomac.2023.127179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/06/2023] [Accepted: 09/23/2023] [Indexed: 10/10/2023]
Abstract
Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, autolysis affects the growth of bacteria, further affecting the yield of target products. Besides, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which further leads to a lack of high-throughput screening tools. Here, we constructed a genome-wide crRNA inhibition library based on the CRISPR/dCpf1 system and high-throughput screening of related genes affecting the cell growth and autolysis using flow cytometry in B. amyloliquefaciens LB1ba02. The whole genome crRNA library was first validated for resistance to the toxic chemical 5-fluorouracil, and then used for validation of essential genes. In addition, seven gene loci (oppD, flil, tuaA, prmA, sigO, hslU, and GE03231) that affect the growth characteristics of LB1ba02 were screened. Among them, the Opp system had the greatest impact on growth. When the expression of operon oppA-oppB-oppC-oppD-oppF was inhibited, the cell growth difference was most significant. Inhibition of other sites could also promote rapid growth of bacteria to varying degrees; however, inhibition of GE03231 site accelerated cell autolysis. Therefore, the whole genome crRNA inhibition library is well suited for B. amyloliquefaciens LB1ba02 and can be further applied to high-throughput mining of other functional genes.
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Affiliation(s)
- Qinglong Xin
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China
| | - Hang Jia
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China
| | - Bin Wang
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
| | - Li Pan
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
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Luo Z, Yan Y, Du S, Zhu Y, Pan F, Wang R, Xu Z, Xu X, Li S, Xu H. Recent advances and prospects of Bacillus amyloliquefaciens as microbial cell factories: from rational design to industrial applications. Crit Rev Biotechnol 2023; 43:1073-1091. [PMID: 35997331 DOI: 10.1080/07388551.2022.2095499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/02/2022] [Indexed: 11/03/2022]
Abstract
Bacillus amyloliquefaciens is one of the most characterized Gram-positive bacteria. This species has unique characteristics that are beneficial for industrial applications, including its utilization of: cheap carbon as a substrate, a transparent genetic background, and large-scale robustness in fermentation. Indeed, the productivity characteristics of B. amyloliquefaciens have been thoroughly analyzed and further optimized through systems biology and synthetic biology techniques. Following the analysis of multiple engineering design strategies, B. amyloliquefaciens is now considered an efficient cell factory capable of producing large quantities of multiple products from various raw materials. In this review, we discuss the significant potential advantages offered by B. amyloliquefaciens as a platform for metabolic engineering and industrial applications. In addition, we systematically summarize the recent laboratory research and industrial application of B. amyloliquefaciens, including: relevant advances in systems and synthetic biology, various strategies adopted to improve the cellular performances of synthetic chemicals, as well as the latest progress in the synthesis of certain important products by B. amyloliquefaciens. Finally, we propose the current challenges and essential strategies to usher in an era of broader B. amyloliquefaciens use as microbial cell factories.
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Affiliation(s)
- Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yifan Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Shanshan Du
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Fei Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiaoqi Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Zalila-Kolsi I, Ben-Mahmoud A, Al-Barazie R. Bacillus amyloliquefaciens: Harnessing Its Potential for Industrial, Medical, and Agricultural Applications-A Comprehensive Review. Microorganisms 2023; 11:2215. [PMID: 37764059 PMCID: PMC10536829 DOI: 10.3390/microorganisms11092215] [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: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillus amyloliquefaciens, a Gram-positive bacterium, has emerged as a versatile microorganism with significant applications in various fields, including industry, medicine, and agriculture. This comprehensive review aims to provide an in-depth understanding of the characteristics, genetic tools, and metabolic capabilities of B. amyloliquefaciens, while highlighting its potential as a chassis cell for synthetic biology, metabolic engineering, and protein expression. We discuss the bacterium's role in the production of chemicals, enzymes, and other industrial bioproducts, as well as its applications in medicine, such as combating infectious diseases and promoting gut health. In agriculture, B. amyloliquefaciens has demonstrated potential as a biofertilizer, biocontrol agent, and stress tolerance enhancer for various crops. Despite its numerous promising applications, B. amyloliquefaciens remains less studied than its Gram-negative counterpart, Escherichia coli. This review emphasizes the need for further research and development of advanced engineering techniques and genetic editing technologies tailored for B. amyloliquefaciens, ultimately unlocking its full potential in scientific and industrial contexts.
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Affiliation(s)
- Imen Zalila-Kolsi
- Faculty of Medical and Health Sciences, Liwa College, Abu Dhabi P.O. Box 41009, United Arab Emirates;
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar;
| | - Ray Al-Barazie
- Faculty of Medical and Health Sciences, Liwa College, Abu Dhabi P.O. Box 41009, United Arab Emirates;
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10
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Qian J, Wang Y, Liu X, Hu Z, Xu N, Wang Y, Shi T, Ye C. Improving acetoin production through construction of a genome-scale metabolic model. Comput Biol Med 2023; 158:106833. [PMID: 37015178 DOI: 10.1016/j.compbiomed.2023.106833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/15/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Acetoin was widely used in food, medicine, and other industries, because of its unique fragrance. Bacillus amyloliquefaciens was recognized as a safe strain and a promising acetoin producer in fermentation. However, due to the complexity of its metabolic network, it had not been fully utilized. Therefore, a genome-scale metabolic network model (iJYQ746) of B. amyloliquefaciens was constructed in this study, containing 746 genes, 1736 reactions, and 1611 metabolites. The results showed that Mg2+, Mn2+, and Fe2+ have inhibitory effects on acetoin. When the stirring speed was 400 rpm, the maximum titer was 49.8 g L-1. Minimization of metabolic adjustments (MOMA) was used to identify potential metabolic modification targets 2-oxoglutarate aminotransferase (serC, EC 2.6.1.52) and glucose-6-phosphate isomerase (pgi, EC 5.3.1.9). These targets could effectively accumulate acetoin by increasing pyruvate content, and the acetoin synthesis rate was increased by 610% and 10%, respectively. This provides a theoretical basis for metabolic engineering to reasonably transform B. amyloliquefaciens and produce acetoin.
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11
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Zhu M, Zang Y, Zhang X, Shang S, Xue S, Chen J, Tang X. Insights into the regulation of energy metabolism during the seed-to-seedling transition in marine angiosperm Zostera marina L.: Integrated metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1130292. [PMID: 36968358 PMCID: PMC10036900 DOI: 10.3389/fpls.2023.1130292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Seed development is a crucial phase in the life cycle of seed-propagated plants. As the only group of angiosperms that evolved from terrestrial plants to complete their life cycle submerged in marine environments, the mechanisms underlying seed development in seagrasses are still largely unknown. In the present study, we attempted to combine transcriptomic, metabolomic, and physiological data to comprehensively analyze the molecular mechanism that regulates energy metabolism in Zostera marina seeds at the four major developmental stages. Our results demonstrated that seed metabolism was reprogrammed with significant alteration of starch and sucrose metabolism, glycolysis, the tricarboxylic acid cycle (TCA cycle), and the pentose phosphate pathway during the transition from seed formation to seedling establishment. The interconversion of starch and sugar provided energy storage substances in mature seeds and further acted as energy sources to support seed germination and seedling growth. The glycolysis pathway was active during Z. marina germination and seedling establishment, which provided pyruvate for TCA cycle by decomposing soluble sugar. Notably, the biological processes of glycolysis were severely inhibited during Z. marina seed maturation may have a positive effect on seed germination, maintaining a low level of metabolic activity during seed maturation to preserve seed viability. Increased acetyl-CoA and ATP contents were accompanied with the higher TCA cycle activity during seed germination and seedling establishment, indicating that the accumulations of precursor and intermediates metabolite that can strengthen the TCA cycle and facilitate energy supply for Z. marina seed germination and seedling growth. The large amount of oxidatively generated sugar phosphate promotes fructose 1,6-bisphosphate synthesis to feed back to glycolysis during seed germination, indicating that the pentose phosphate pathway not only provides energy for germination, but also complements the glycolytic pathway. Collectively, our findings suggest these energy metabolism pathways cooperate with each other in the process of seed transformation from maturity to seedling establishment, transforming seed from storage tissue to highly active metabolic tissue to meet the energy requirement seed development. These findings provide insights into the roles of the energy metabolism pathway in the complete developmental process of Z. marina seeds from different perspectives, which could facilitate habitat restoration of Z. marina meadows via seeds.
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Affiliation(s)
- Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, Shandong, China
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
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12
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Yeom J, Park JS, Jung SW, Lee S, Kwon H, Yoo SM. High-throughput genetic engineering tools for regulating gene expression in a microbial cell factory. Crit Rev Biotechnol 2023; 43:82-99. [PMID: 34957867 DOI: 10.1080/07388551.2021.2007351] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
With the rapid advances in biotechnological tools and strategies, microbial cell factory-constructing strategies have been established for the production of value-added compounds. However, optimizing the tradeoff between the biomass, yield, and titer remains a challenge in microbial production. Gene regulation is necessary to optimize and control metabolic fluxes in microorganisms for high-production performance. Various high-throughput genetic engineering tools have been developed for achieving rational gene regulation and genetic perturbation, diversifying the cellular phenotype and enhancing bioproduction performance. In this paper, we review the current high-throughput genetic engineering tools for gene regulation. In particular, technological approaches used in a diverse range of genetic tools for constructing microbial cell factories are introduced, and representative applications of these tools are presented. Finally, the prospects for high-throughput genetic engineering tools for gene regulation are discussed.
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Affiliation(s)
- Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Seung-Woon Jung
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Sumin Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Hyukjin Kwon
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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13
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Zhang S, Zhang X, Yuan Y, Li K, Liu H. Renewable biohydrogen production from Clostridium sp. LQ25 using different forms of ferric as electron acceptor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158911. [PMID: 36152847 DOI: 10.1016/j.scitotenv.2022.158911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Clostridium sp. LQ25 was cultured in different forms of ferric (ferric citrate and ferric hydroxide) as electron acceptors to investigate growth, ferric reduction, hydrogen production, fermentation products and fermentation process. The growth of the strain LQ25 detected by protein was 82.8 ± 2.1 mg/L and 73.5 ± 1.7 mg/L using ferric citrate and ferric hydroxide as electron acceptors, which was 33.3 % and 18.4 % higher than without ferric, respectively. The accumulation concentration of Fe(II) was 9.0 ± 0.6 mg/L and 5.0 ± 0.2 mg/L when using ferric citrate and ferric hydroxide as electron acceptors, and ferric citrate was 1.8-fold higher than ferric hydroxide, which indicated that the ability of ferric reduction was higher using ferric citrate as electron acceptor. The hydrogen production of strain LQ25 was 238.0 ± 1.0 mmol/mol glucose and 113.0 ± 1.3 mmol/mol glucose under condition of ferric citrate and ferric hydroxide as electron acceptors, which was 2.6 and 1.2-fold higher than without ferric, respectively. The growth and hydrogen production of strain LQ25 was promoted by using ferric as electron acceptor, while the fermentation type of strain did not change and was always butyrate type. The differential expression of the genes of strain LQ25 was significant when using ferric as electron acceptor, mainly in NADH and PFL pathway. This study provided preliminary evidence for hydrogen production by Clostridium sp. LQ25 in the presence of electron acceptor.
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Affiliation(s)
- Shan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Xiaodan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Yuan Yuan
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Kaiqiang Li
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Hongyan Liu
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China.
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Nair P, Navale GR, Dharne MS. Poly-gamma-glutamic acid biopolymer: a sleeping giant with diverse applications and unique opportunities for commercialization. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:4555-4573. [PMID: 33824848 PMCID: PMC8016157 DOI: 10.1007/s13399-021-01467-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 05/06/2023]
Abstract
Poly-gamma-glutamic acid (γ-PGA) is a biodegradable, non-toxic, ecofriendly, and non-immunogenic biopolymer. Its phenomenal properties have gained immense attention in the field of regenerative medicine, the food industry, wastewater treatment, and even in 3D printing bio-ink. The γ-PGA has the potential to replace synthetic non-degradable counterparts, but the main obstacle is the high production cost and lower productivity. Extensive research has been carried out to reduce the production cost by using different waste; however, it is unable to match the commercialization needs. This review focuses on the biosynthetic mechanism of γ-PGA, its production using the synthetic medium as well as different wastes by L-glutamic acid-dependent and independent microbial strains. Furthermore, various metabolic engineering strategies and the recovery processes for γ-PGA and their possible applications are discussed. Finally, highlights on the challenges and unique approaches to reduce the production cost and to increase the productivity for commercialization of γ-PGA are also summarized.
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Affiliation(s)
- Pranav Nair
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, 411008 India
| | - Govinda R. Navale
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, 411008 India
| | - Mahesh S. Dharne
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory, Pune, 411008 India
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15
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Zhang Z, He P, Cai D, Chen S. Genetic and metabolic engineering for poly-γ-glutamic acid production: current progress, challenges, and prospects. World J Microbiol Biotechnol 2022; 38:208. [DOI: 10.1007/s11274-022-03390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/13/2022] [Indexed: 11/29/2022]
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16
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Gao W, Xie Y, Zuo M, Zhang G, Liu H. Improved genetic transformation by disarmament of type II Restriction-Modification system in Streptococcus zooepidemicus. 3 Biotech 2022; 12:192. [PMID: 35910286 PMCID: PMC9325941 DOI: 10.1007/s13205-022-03227-x] [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: 11/21/2021] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
Streptococcus zooepidemicus, group C Streptococci, is currently used for the industrial production of hyaluronic acid (HA). However, genetic manipulation of S. zooepidemicus is severely limited by its low transformation efficiency, which might be in part due to the Restriction-Modification (R-M) systems. The complete genome sequence of S. zooepidemicus ATCC39920 revealed the presence of two putative R-M systems, type I and type II. The putative type I R-M system is encoded by three closely linked genes: hsdR (SeseC_01315), hsdS, hsdM (SeseC_01318), and the putative type II R-M system consists of two closely linked genes: SeseC_02360 and yhdJ (SeseC_02362). Inactivation of hsdR, encoding the restriction endonuclease (REase) of the type I R-M system, showed no apparent effects on transformation efficiency, implying that disarmament of the type I R-M system alone is not sufficient for increasing transformation efficiency. However, inactivation of SeseC_02360, encoding the REase of the type II R-M system, improved transformation efficiency by 4.97 folds, indicating that type II R-M system is the major barrier that restricts genetic transformation in S. zooepidemicus. Furthermore, S. zooepidemicus strains lacking either of the two R-M systems are phenotypically indistinguishable from the wild-type in terms of cell growth and HA production. In summary, our study revealed that the type II R-M system is the main barrier to genetic transformation in S. zooepidemicus ATCC39920, and that the deletion of the type II R-M system renders S. zooepidemicus more transformable, thus facilitating metabolic engineering of this industrially important microorganism. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03227-x.
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Affiliation(s)
- Weixia Gao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
| | - Yaya Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
| | - Meng Zuo
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
| | - Guangtong Zhang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, 300457 People’s Republic of China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 People’s Republic of China
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Yeom J, Park JS, Jeon YM, Song BS, Yoo SM. Synthetic fused sRNA for the simultaneous repression of multiple genes. Appl Microbiol Biotechnol 2022; 106:2517-2527. [PMID: 35291022 DOI: 10.1007/s00253-022-11867-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/02/2022]
Abstract
Efficient control over multiple gene expression still presents a major challenge. Synthetic sRNA enables targeted gene expression control in trans without directly modifying the chromosome, but its use to simultaneously target multiple genes can often cause cell growth defects because of the need for additional energy for transcription and lowering of their repression efficiency by limiting the amount of Hfq protein. To address these limitations, we present fusion sRNA (fsRNA) that simultaneously regulates the translation of multiple genes efficiently. It is constructed by linking the mRNA-binding modules for multiple targeted genes in one sRNA scaffold via one-pot generation using overlap extension PCR. The repression capacity of fsRNA was demonstrated by the construction of sRNAs to target four endogenous genes: caiF, hybG, ytfR and minD in Escherichia coli. Their cross-reactivity and the effect on cell growth were also investigated. As practical applications, we applied fsRNA to violacein- and protocatechuic acid-producing strains, resulting in increases of 13% violacein and 81% protocatechuic acid, respectively. The developed fsRNA-mediated multiple gene expression regulation system thus enables rapid and efficient development of optimised cell factories for valuable chemicals without cell growth defects and limiting cellular resources.Key points• Synthetic fusion sRNA (fsRNA)-based system was constructed for the repression of multiple target genes.• fsRNA repressed multiple genes by only expressing a single sRNA while minimising the cellular burden.• The application of fsRNA showed the increased production titers of violacein (13%) and protocatechuic acid (81%).
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Affiliation(s)
- Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Yong Min Jeon
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Beom Seop Song
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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Li D, Hou L, Gao Y, Tian Z, Fan B, Wang F, Li S. Recent Advances in Microbial Synthesis of Poly-γ-Glutamic Acid: A Review. Foods 2022; 11:foods11050739. [PMID: 35267372 PMCID: PMC8909396 DOI: 10.3390/foods11050739] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/12/2022] [Accepted: 02/26/2022] [Indexed: 02/01/2023] Open
Abstract
Poly-γ-glutamic acid (γ-PGA) is a natural, safe, non-immunogenic, biodegradable, and environmentally friendly glutamic biopolymer. γ-PGA has been regarded as a promising bio-based materials in the food field, medical field, even in environmental engineering field, and other industrial fields. Microbial synthesis is an economical and effective way to synthesize γ-PGA. Bacillus species are the most widely studied producing strains. γ-PGA biosynthesis involves metabolic pathway of racemization, polymerization, transfer, and catabolism. Although microbial synthesis of γ-PGA has already been used extensively, productivity and yield remain the major constraints for its industrial application. Metabolic regulation is an attempt to solve the above bottleneck problems and meet the demands of commercialization. Therefore, it is important to understand critical factors that influence γ-PGA microbial synthesis in depth. This review focuses on production strains, biosynthetic pathway, and metabolic regulation. Moreover, it systematically summarizes the functional properties, purification procedure, and industrial application of γ-PGA.
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Affiliation(s)
- Danfeng Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
| | - Lizhen Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
| | - Yaxin Gao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
| | - Zhiliang Tian
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengzhong Wang
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (F.W.); (S.L.); Tel.: +86-010-62815977 (F.W.); +86-010-62810295 (S.L.)
| | - Shuying Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China; (D.L.); (L.H.); (Y.G.); (Z.T.); (B.F.)
- Correspondence: (F.W.); (S.L.); Tel.: +86-010-62815977 (F.W.); +86-010-62810295 (S.L.)
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19
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Wang L, Chen S, Yu B. Poly-γ-glutamic acid: Recent achievements, diverse applications and future perspectives. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Zhou C, Yang G, Zhang L, Zhang H, Zhou H, Lu F. Construction of an alkaline protease overproducer strain based on Bacillus licheniformis 2709 using an integrative approach. Int J Biol Macromol 2021; 193:1449-1456. [PMID: 34742839 DOI: 10.1016/j.ijbiomac.2021.10.208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Bacillus licheniformis 2709 is a potential cell factory for the production of alkaline protease AprE, which has important value in industrial application but still lacks sufficient production capacity. To address this problem, we investigated the effects of the secretory viscous materials on the synthesis of AprE, which might seriously affect the industrial fermentation. Furthermore, an iterative chromosomal integration strategy at various chromosomal loci was implemented to achieve stable high-level expression of AprE in B. licheniformis 2709. The host was genetically modified by disrupting the native pgs cluster controlling the biosynthesis of viscous poly-glutamic acid identified in the study by GC/MS, generating a mutant with significantly higher biomass and better bioreactor performance. We further enhanced the expression of alkaline protease by integrating two additional aprE expression cassettes into the genome, generating the integration mutant BL ∆UEP-3 with three aprE expression cassettes, whose AprE enzyme activity in shake flasks reached 25,736 ± 997 U/mL, which was 136% higher than that of the original strain, while the aprE transcription level increased 4.05 times. Thus, an AprE high-yielding strain with excellent fermentation traits was engineered, which was more suitable for bulk-production. Finally, the AprE titer was further increased in a 5-L fermenter, reaching 57,763 ± 1039 U/mL. In summary, genetic modification is an enabling technology for enhancing enzyme production by eliminating the unfavorable characteristics of the host and optimizing the expression of aprE through iterative chromosomal integration. We believe that the protocol developed in this study provides a valuable reference for chromosomal overexpression of proteins or bioactive molecules in other Bacillus species.
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Affiliation(s)
- Cuixia Zhou
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China.
| | - Lei Zhang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huiying Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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21
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Li B, Cai D, Chen S. Metabolic Engineering of Central Carbon Metabolism of Bacillus licheniformis for Enhanced Production of Poly-γ-glutamic Acid. Appl Biochem Biotechnol 2021; 193:3540-3552. [PMID: 34312784 DOI: 10.1007/s12010-021-03619-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 01/17/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) is an anionic polymer with wide-ranging applications in the areas of medicine, light chemical industry, wastewater treatment, and agriculture. However, the production cost of γ-PGA is high for the requirement of adding the expensive precursor L-glutamic acid during fermentation, which hinders its widespread application. In this study, in order to improve γ-PGA yield, central carbon metabolism was engineered to enhance the carbon flux of tricarboxylic acid (TCA) cycle and glutamic acid synthesis in a γ-PGA production strain Bacillus licheniformis WX-02. Firstly, pyruvate dehydrogenase (PdhABCD) and citrate synthase (CitA) were overexpressed to strengthen the flux of pyruvate into TCA cycle, resulting in 34.93% and 11.14% increase of γ-PGA yield in B. licheniformis WX-02, respectively. Secondly, the carbon flux to glyoxylate shunt was rewired via varying the expression of isocitrate lyase (AceA), and a 23.24% increase of γ-PGA yield was obtained in AceA down-regulated strain WXPbacAaceBA. Thirdly, deletion of pyruvate formate-lyase gene pflB led to a 30.70% increase of γ-PGA yield. Finally, combinatorial metabolic engineering was applied, and γ-PGA titer was enhanced to 12.02 g/L via overexpressing pdhABCD and citA, repressing aceA, and deleting pflB, with a 69.30% improvement compared to WX-02. Collectively, metabolic engineering of central carbon metabolism is an effective strategy for enhanced γ-PGA production in B. licheniformis, and this research provided a promising strain for industrial production of γ-PGA.
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Affiliation(s)
- Bichan Li
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of 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, People's Republic of China
| | - Shouwen Chen
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
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22
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Recent advances in tuning the expression and regulation of genes for constructing microbial cell factories. Biotechnol Adv 2021; 50:107767. [PMID: 33974979 DOI: 10.1016/j.biotechadv.2021.107767] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
To overcome environmental problems caused by the use of fossil resources, microbial cell factories have become a promising technique for the sustainable and eco-friendly development of valuable products from renewable resources. Constructing microbial cell factories with high titers, yields, and productivity requires a balance between growth and production; to this end, tuning gene expression and regulation is necessary to optimise and precisely control complicated metabolic fluxes. In this article, we review the current trends and advances in tuning gene expression and regulation and consider their engineering at each of the three stages of gene regulation: genomic, mRNA, and protein. In particular, the technological approaches utilised in a diverse range of genetic-engineering-based tools for the construction of microbial cell factories are reviewed and representative applications of these strategies are presented. Finally, the prospects for strategies and systems for tuning gene expression and regulation are discussed.
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γ-PGA-Rich Chungkookjang, Short-Term Fermented Soybeans: Prevents Memory Impairment by Modulating Brain Insulin Sensitivity, Neuro-Inflammation, and the Gut-Microbiome-Brain Axis. Foods 2021; 10:foods10020221. [PMID: 33494481 PMCID: PMC7911192 DOI: 10.3390/foods10020221] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Fermented soybean paste is an indigenous food for use in cooking in East and Southeast Asia. Korea developed and used its traditional fermented foods two thousand years ago. Chungkookjang has unique characteristics such as short-term fermentation (24–72 h) without salt, and fermentation mostly with Bacilli. Traditionally fermented chungkookjang (TFC) is whole cooked soybeans that are fermented predominantly by Bacillus species. However, Bacillus species are different in the environment according to the regions and seasons due to the specific bacteria. Bacillus species differently contribute to the bioactive components of chungkookjang, resulting in different functionalities. In this review, we evaluated the production process of poly-γ-glutamic acid (γ-PGA)-rich chungkookjang fermented with specific Bacillus species and their effects on memory function through the modulation of brain insulin resistance, neuroinflammation, and the gut–microbiome–brain axis. Bacillus species were isolated from the TFC made in Sunchang, Korea, and they included Bacillus (B.) subtilis, B. licheniformis, and B. amyloliquefaciens. Chungkookjang contains isoflavone aglycans, peptides, dietary fiber, γ-PGA, and Bacillus species. Chungkookjangs made with B. licheniformis and B. amyloliquefaciens have higher contents of γ-PGA, and they are more effective for improving glucose metabolism and memory function. Chungkookjang has better efficacy for reducing inflammation and oxidative stress than other fermented soy foods. Insulin sensitivity is improved, not only in systemic organs such as the liver and adipose tissues, but also in the brain. Chungkookjang intake prevents and alleviates memory impairment induced by Alzheimer’s disease and cerebral ischemia. This review suggests that the intake of chungkookjang (20–30 g/day) rich in γ-PGA acts as a synbiotic in humans and promotes memory function by suppressing brain insulin resistance and neuroinflammation and by modulating the gut–microbiome–brain axis.
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Guo J, Shi W, Li J, Zhai Z. Effects of poly-γ-glutamic acid and poly-γ-glutamic acid super absorbent polymer on the sandy loam soil hydro-physical properties. PLoS One 2021; 16:e0245365. [PMID: 33434231 PMCID: PMC7983855 DOI: 10.1371/journal.pone.0245365] [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: 09/23/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022] Open
Abstract
The main forms of poly-γ-glutamic acid (γ-PGA) applied in agriculture include
agricultural γ-PGA and γ-PGA super absorbent polymer (SAP). Laboratory
experiments were conducted with a check treatment CK (no γ-PGA added) and two
different forms of γ-PGA added to sandy loam soil (T and TM stand for γ-PGA and
γ-PGA SAP) at four different soil mass ratios (0.05% (1), 0.10% (2), 0.15% (3)
and 0.20% (4)) to determine their effects on sandy loam soil hydro-physical
properties. Both of them could reduce the cumulative infiltration of soil water.
The total available water (TAW) which the soil water content (SWC) from field
water capacity (FC) to permanent wilting point (PWP) after γ-PGA added into
sandy loam soil had no significant different compared with CK, and the TAW was
highest at the treatment of γ-PGA with 0.10% addition amount into sandy loam
soil. However, the TAW of sandy loam soil increased dramatically with the γ-PGA
SAP addition amount increasing. TM3 had the highest soil water absorption among
the treatments with γ-PGA SAP. The T1 to T4 treatments with γ-PGA addition
slightly prolonged retention time (RT) when SWC varied from FC to PWP compared
with CK. For γ-PGA SAP addition treatments, the time for SWC varied from FC to
PWP was 1.48 times (TM1), 1.88 times (TM2), 2.01 times (TM3) and 2.87 times
(TM4) longer than that of CK, respectively. The results of this study will
provide further information for the use of these materials in agricultural
application.
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Affiliation(s)
- Jianzhong Guo
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Wenjuan Shi
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jiake Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Zhongmin Zhai
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
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25
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Kubo Y, Kobori M, Nakagawa R, Yoshiura T, Asano T, Takeda A, Noguchi T. A high-accuracy method for quantifying poly-gamma-glutamic acid content in natto. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2021. [DOI: 10.3136/fstr.27.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuji Kubo
- Industrial Technology Innovation Center of Ibaraki Prefecture
| | - Masuko Kobori
- Food Research Institute, National Agriculture and Food Research Organization
| | - Rikio Nakagawa
- Industrial Technology Innovation Center of Ibaraki Prefecture
| | | | - Toshiyuki Asano
- Industrial Technology Innovation Center of Ibaraki Prefecture
| | - Ayanobu Takeda
- Industrial Technology Innovation Center of Ibaraki Prefecture
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26
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Li Y, Wang J, Liu N, Ke L, Zhao X, Qi G. Microbial synthesis of poly-γ-glutamic acid (γ-PGA) with fulvic acid powder, the waste from yeast molasses fermentation. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:180. [PMID: 33133238 PMCID: PMC7594462 DOI: 10.1186/s13068-020-01818-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Molasses is a wildly used feedstock for fermentation, but it also poses a severe wastewater-disposal problem worldwide. Recently, the wastewater from yeast molasses fermentation is being processed into fulvic acid (FA) powder as a fertilizer for crops, but it consequently induces a problem of soil acidification after being directly applied into soil. In this study, the low-cost FA powder was bioconverted into a value-added product of γ-PGA by a glutamate-independent producer of Bacillus velezensis GJ11. RESULTS FA power could partially substitute the high-cost substrates such as sodium glutamate and citrate sodium for producing γ-PGA. With FA powder in the fermentation medium, the amount of sodium glutamate and citrate sodium used for producing γ-PGA were both decreased around one-third. Moreover, FA powder could completely substitute Mg2+, Mn2+, Ca2+, and Fe3+ in the fermentation medium for producing γ-PGA. In the optimized medium with FA powder, the γ-PGA was produced at 42.55 g/L with a productivity of 1.15 g/(L·h), while only 2.87 g/L was produced in the medium without FA powder. Hydrolyzed γ-PGA could trigger induced systemic resistance (ISR), e.g., H2O2 accumulation and callose deposition, against the pathogen's infection in plants. Further investigations found that the ISR triggered by γ-PGA hydrolysates was dependent on the ethylene (ET) signaling and nonexpressor of pathogenesis-related proteins 1 (NPR1). CONCLUSIONS To our knowledge, this is the first report to use the industry waste, FA powder, as a sustainable substrate for microbial synthesis of γ-PGA. This bioprocess can not only develop a new way to use FA powder as a cheap feedstock for producing γ-PGA, but also help to reduce pollution from the wastewater of yeast molasses fermentation.
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Affiliation(s)
- Yazhou Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jianghan Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Na Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Luxin Ke
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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