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Zhu Z, Ding X, Rang J, Xia L. Application and research progress of ARTP mutagenesis in actinomycetes breeding. Gene 2024; 929:148837. [PMID: 39127415 DOI: 10.1016/j.gene.2024.148837] [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: 04/17/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.
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Affiliation(s)
- Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jie Rang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China.
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Gao S, Li L, Wei Y, Wen L, Shao S, Wu J, Zong X. Research Progress of ARTP Mutagenesis Technology Based on Citespace Visualization Analysis. Mol Biotechnol 2024:10.1007/s12033-024-01231-5. [PMID: 38990498 DOI: 10.1007/s12033-024-01231-5] [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: 04/03/2024] [Accepted: 06/15/2024] [Indexed: 07/12/2024]
Abstract
Atmospheric and room temperature plasma (ARTP) mutagenesis technology has been developed rapidly in recent years because of its simple operation, safety, environmental friendliness, high mutation rate, and large mutation library capacity. It has been widely used in traditional fields such as food, agriculture, and medicine, and has been gradually applied in emerging fields such as environmental remediation, bioenergy, and microalgae utilization. In this paper, the Web of Science Core Collection (WOSCC) was used as the data source, and the keywords and core literature of ARTP mutagenesis technology were plotted by citespace software, and the research progress and research hotspots of ARTP mutagenesis technology were analyzed. Through citespace visualization analysis, it is concluded that the country with the largest number of studies is China, the institution with the largest number of studies is Jiangnan University, and the author of the most published papers is Jiangnan University. Through keyword analysis, it is concluded that the most widely used ARTP mutagenesis technology is fermentation-related majors, mainly for biosynthesis and microbial research at the molecular level. Among them, the most widely used microorganisms are Escherichia coli and Saccharomyces cerevisiae.
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Affiliation(s)
- Shun Gao
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
| | - Li Li
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
| | - Yonggong Wei
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
| | - Lei Wen
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
| | - Shujuan Shao
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China
| | - Jianhang Wu
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China.
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China.
| | - Xuyan Zong
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China.
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, 644000, Sichuan, China.
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Hua L, Shi H, Lin Q, Wang H, Gao Y, Zeng J, Lou K, Huo X. Selection and Genetic Analysis of High Polysaccharide-Producing Mutants in Inonotus obliquus. Microorganisms 2024; 12:1335. [PMID: 39065103 PMCID: PMC11278842 DOI: 10.3390/microorganisms12071335] [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: 05/29/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To enhance polysaccharide production of I. obliquus HS819, atmospheric and room temperature plasma (ARTP) technology was employed for mutagenesis of the protoplasts. Through liquid fermentation, 32 mutant strains exhibiting diverse characteristics in morphology, color of the fermentation broth, mycelial pellet size, and biomass were screened. Secondary screening identified mutant strain A27, which showed a significant increase in polysaccharide production up to 1.67 g/L and a mycelial dry weight of 17.6 g/L, representing 137.67% and 15% increases compared to the HS819 strain, respectively. Furthermore, the fermentation period was reduced by 2 days, and subsequent subculture cultivation demonstrated stable polysaccharide production and mycelial dry weight. The genome resequencing analysis of the HS819 strain and mutant strain A27 revealed 3790 InDel sites and mutations affecting 612 functional genes associated with polysaccharide synthesis. We predict that our findings will be helpful for high polysaccharide production through genetic engineering of I. obliquus.
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Affiliation(s)
- Lanlan Hua
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Hongling Shi
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Qing Lin
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Haozhong Wang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Yan Gao
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Jun Zeng
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Kai Lou
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
| | - Xiangdong Huo
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Xinjiang Laboratory of SpecialEnvironmental Microbiology, Urumqi 830091, China; (L.H.); (H.S.); (Q.L.); (Y.G.); (J.Z.)
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Asefi S, Nouri H, Pourmohammadi G, Moghimi H. Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering. Microb Cell Fact 2024; 23:180. [PMID: 38890644 PMCID: PMC11186258 DOI: 10.1186/s12934-024-02459-1] [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: 10/05/2023] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Nowadays, biofuels, especially bioethanol, are becoming increasingly popular as an alternative to fossil fuels. Zymomonas mobilis is a desirable species for bioethanol production due to its unique characteristics, such as low biomass production and high-rate glucose metabolism. However, several factors can interfere with the fermentation process and hinder microbial activity, including lignocellulosic hydrolysate inhibitors, high temperatures, an osmotic environment, and high ethanol concentration. Overcoming these limitations is critical for effective bioethanol production. In this review, the stress response mechanisms of Z. mobilis are discussed in comparison to other ethanol-producing microbes. The mechanism of stress response is divided into physiological (changes in growth, metabolism, intracellular components, and cell membrane structures) and molecular (up and down-regulation of specific genes and elements of the regulatory system and their role in expression of specific proteins and control of metabolic fluxes) changes. Systemic metabolic engineering approaches, such as gene manipulation, overexpression, and silencing, are successful methods for building new metabolic pathways. Therefore, this review discusses systems metabolic engineering in conjunction with systems biology and synthetic biology as an important method for developing new strains with an effective response mechanism to fermentation stresses during bioethanol production. Overall, understanding the stress response mechanisms of Z. mobilis can lead to more efficient and effective bioethanol production.
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Affiliation(s)
- Shaqayeq Asefi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hoda Nouri
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Golchehr Pourmohammadi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Moghimi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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Yarangsee P, Khacha-ananda S, Pitchakarn P, Intayoung U, Sriuan S, Karinchai J, Wijaikhum A, Boonyawan D. A Nonclinical Safety Evaluation of Cold Atmospheric Plasma for Medical Applications: The Role of Genotoxicity and Mutagenicity Studies. Life (Basel) 2024; 14:759. [PMID: 38929742 PMCID: PMC11204557 DOI: 10.3390/life14060759] [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: 05/06/2024] [Revised: 05/21/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Atmospheric nonthermal plasma (ANTP) has rapidly evolved as an innovative tool in biomedicine with various applications, especially in treating skin diseases. In particular, the formation of reactive oxygen species (ROS) and nitrogen species (RNS), which are generated by ANTP, plays an important role in the biological signaling pathways of human cells. Unfortunately, excessive amounts of these reactive species significantly result in cellular damage and cell death induction. To ensure the safe application of ANTP, preclinical in vitro studies must be conducted before proceeding to in vivo or clinical trials involving humans. Our study aimed to investigate adverse effects on genetic substances in murine fibroblast cells exposed to ANTP. Cell viability and proliferation were markedly reduced after exposing the cells with plasma. Both extracellular and intracellular reactive species, especially RNS, were significantly increased upon plasma exposure in the culture medium and the cells. Notably, significant DNA damage in the cells was observed in the cells exposed to plasma. However, plasma was not classified as a mutagen in the Ames test. This suggested that plasma led to the generation of both extracellular and intracellular reactive species, particularly nitrogen species, which affect cell proliferation and are also known to induce genetic damage in fibroblast cells. These results highlight the genotoxic and mutagenic effects of ANTP, emphasizing the need for the cautious selection of plasma intensity in specific applications to avoid adverse side effects resulting from reactive species production.
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Affiliation(s)
- Piimwara Yarangsee
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.Y.); (U.I.); (S.S.)
| | - Supakit Khacha-ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.Y.); (U.I.); (S.S.)
| | - Pornsiri Pitchakarn
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.P.); (J.K.)
| | - Unchisa Intayoung
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.Y.); (U.I.); (S.S.)
| | - Sirikhwan Sriuan
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.Y.); (U.I.); (S.S.)
| | - Jirarat Karinchai
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (P.P.); (J.K.)
| | - Apiwat Wijaikhum
- Research and Innovation Division, Electricity Generating Authority of Thailand, Nonthaburi 11130, Thailand;
| | - Dheerawan Boonyawan
- Plasma and Beam Physics Research Facility, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
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Xiong Z, Zhang Y, Chen X, Sha A, Xiao W, Luo Y, Han J, Li Q. Soil Microplastic Pollution and Microbial Breeding Techniques for Green Degradation: A Review. Microorganisms 2024; 12:1147. [PMID: 38930528 PMCID: PMC11205638 DOI: 10.3390/microorganisms12061147] [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: 05/14/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Microplastics (MPs), found in many places around the world, are thought to be more detrimental than other forms of plastics. At present, physical, chemical, and biological methods are being used to break down MPs. Compared with physical and chemical methods, biodegradation methods have been extensively studied by scholars because of their advantages of greenness and sustainability. There have been numerous reports in recent years summarizing the microorganisms capable of degrading MPs. However, there is a noticeable absence of a systematic summary on the technology for breeding strains that can degrade MPs. This paper summarizes the strain-breeding technology of MP-degrading strains for the first time in a systematic way, which provides a new idea for the breeding of efficient MP-degrading strains. Meanwhile, potential techniques for breeding bacteria that can degrade MPs are proposed, providing a new direction for selecting and breeding MP-degrading bacteria in the future. In addition, this paper reviews the sources and pollution status of soil MPs, discusses the current challenges related to the biodegradation of MPs, and emphasizes the safety of MP biodegradation.
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Affiliation(s)
| | | | | | | | | | | | - Jialiang Han
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, No. 2025, Chengluo Avenue, Longquanyi District, Chengdu 610106, China; (Z.X.); (Y.Z.); (X.C.); (A.S.); (W.X.); (Y.L.)
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, No. 2025, Chengluo Avenue, Longquanyi District, Chengdu 610106, China; (Z.X.); (Y.Z.); (X.C.); (A.S.); (W.X.); (Y.L.)
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Yang S, Li K, Liu H, Lu J, Yang H, Wu D. Enhancing citric acid tolerance of Acetobacter tropicalis using chemical and physical mutagenesis and adaptive evolution to improve the quality of lemon fruit vinegar. J Food Sci 2024; 89:2581-2596. [PMID: 38551187 DOI: 10.1111/1750-3841.17031] [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: 12/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 05/19/2024]
Abstract
The high concentration of citric acid in lemons limits the production of lemon fruit vinegar because it inhibits the metabolism of acetic acid bacteria and reduces the utilization of raw materials. This study aimed to enhance the citric acid tolerance of Acetobacter tropicalis by using complex mutagenesis and adaptive laboratory evolution (ALE) and improving the quality of lemon fruit vinegar. After mutagenesis and ALE, A. tropicalis JY-135 grew well under 40 g/L citric acid, and it showed high physiological activity and excellent fermentation performance under high concentrations of citric acid. The survival rate and ATP content of JY-135 were 15.27 and 9.30 times higher than that of the original strain J-2736. In the fermentation of lemon fruit vinegar, the acid production and the number of aroma-active compounds were 1.61-fold and 2.17-fold than J-2736. In addition, we found that citric acid tolerance of JY-135 is related to the respiratory electron-transport chain and the tricarboxylic acid (TCA) cycle. This work is of great significance for the production of high-quality lemon fruit vinegar and the enrichment of seed resources of acetic acid bacteria.
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Affiliation(s)
- Shaojie Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Kang Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Hua Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Hua Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
| | - Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, P. R. China
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Li D, Shen J, Ding Q, Wu J, Chen X. Recent progress of atmospheric and room-temperature plasma as a new and promising mutagenesis technology. Cell Biochem Funct 2024; 42:e3991. [PMID: 38532652 DOI: 10.1002/cbf.3991] [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: 12/09/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
At present, atmospheric and room-temperature plasma (ARTP) is regarded as a new and powerful mutagenesis technology with the advantages of environment-friendliness, operation under mild conditions, and fast mutagenesis speed. Compared with traditional mutagenesis strategies, ARTP is used mainly to change the structure of microbial DNA, enzymes, and proteins through a series of physical, chemical, and electromagnetic effects with the organisms, leading to nucleotide breakage, conversion or inversion, causing various DNA damages, so as to screen out the microbial mutants with better biological characteristics. As a result, in recent years, ARTP mutagenesis and the combination of ARTP with traditional mutagenesis have been widely used in microbiology, showing great potential for application. In this review, the recent progress of ARTP mutagenesis in different application fields and bottlenecks of this technology are systematically summarized, with a view to providing a theoretical basis and technical support for better application. Finally, the outlook of ARTP mutagenesis is presented, and we identify the challenges in the field of microbial mutagenesis by ARTP.
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Affiliation(s)
- Dongao Li
- Institute of Plasma Physics, HFIPS, Chinese Academy of Sciences, Low Temperature Plasma Application Laboratory, Hefei, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Jie Shen
- Institute of Plasma Physics, HFIPS, Chinese Academy of Sciences, Low Temperature Plasma Application Laboratory, Hefei, China
| | - Qiang Ding
- Yichang Sanxia Pharmaceutical Co., Ltd., Yichang City, Hubei Province, China
| | - Jinyong Wu
- Institute of Plasma Physics, HFIPS, Chinese Academy of Sciences, Low Temperature Plasma Application Laboratory, Hefei, China
| | - Xiangsong Chen
- Institute of Plasma Physics, HFIPS, Chinese Academy of Sciences, Low Temperature Plasma Application Laboratory, Hefei, China
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Gao Q, Gao S, Zeng W, Li J, Zhou J. Enhancing (2S)-naringenin production in Saccharomyces cerevisiae by high-throughput screening method based on ARTP mutagenesis. 3 Biotech 2024; 14:85. [PMID: 38379664 PMCID: PMC10874921 DOI: 10.1007/s13205-023-03892-6] [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: 08/28/2023] [Accepted: 12/14/2023] [Indexed: 02/22/2024] Open
Abstract
(2S)-Naringenin, a dihydro-flavonoid, serves as a crucial precursor for flavonoid synthesis due to its extensive medicinal values and physiological functions. A pathway for the synthesis of (2S)-naringenin from glucose has previously been constructed in Saccharomyces cerevisiae through metabolic engineering. However, this synthetic pathway of (2S)-naringenin is lengthy, and the genes involved in the competitive pathway remain unknown, posing challenges in significantly enhancing (2S)-naringenin production through metabolic modification. To address this issue, a novel high-throughput screening (HTS) method based on color reaction combined with a random mutagenesis method called atmospheric room temperature plasma (ARTP), was established in this study. Through this approach, a mutant (B7-D9) with a higher titer of (2S)-naringenin was obtained from 9600 mutants. Notably, the titer was enhanced by 52.3% and 19.8% in shake flask and 5 L bioreactor respectively. This study demonstrates the successful establishment of an efficient HTS method that can be applied to screen for high-titer producers of (2S)-naringenin, thereby greatly improving screening efficiency and providing new insights and solutions for similar product screenings.
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Affiliation(s)
- Qian Gao
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Song Gao
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 China
| | - Jianghua Li
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education On Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
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10
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Ning Z, Ma C, Zhong W, Liu C, Niu J, Wang C, Wang Z. Compound mutation by ultraviolet and diethyl sulfate of protease producing thermophilic bacteria to hydrolyze excess sludge. BIORESOURCE TECHNOLOGY 2024; 395:130330. [PMID: 38224788 DOI: 10.1016/j.biortech.2024.130330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Excess sludge (ES), a resource-rich organic waste, can be solubilized by thermophilic enzymes to extract proteins for sludge reduction and resources recovery. To solve the problems of low hydrolysis effect of ES and low enzyme producing ability of wild thermophilic bacteria, ultraviolet and diethyl sulfate (UV-DES) were adopted to mutate thermophilic bacteria in this study. Mutation sites were detected and annotated by whole genome sequencing analysis. The results showed that UV-DES mutagenesis could effectively improve enzyme-producing capacity of thermophilic bacteria and promote the hydrolysis of ES. The protease activity of the mutant strain KT16 was 46.7 % higher than that of the original strain DC8. The protein extraction rate with enzyme produced by KT16 reached 83.3 %. The total content of proteins recycled through KT16 enzyme solution was 3539.6 mg·L-1, 18.4 % higher than that of DC8. This work provided a theoretical idea and technical guidance for the protein recovery from ES.
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Affiliation(s)
- Zhifang Ning
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Pollution Prevention Biotechnology Laboratory of Hebei Province, Shijiazhuang 050018, China
| | - Caiyun Ma
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Pollution Prevention Biotechnology Laboratory of Hebei Province, Shijiazhuang 050018, China
| | - Weizhang Zhong
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Pollution Prevention Biotechnology Laboratory of Hebei Province, Shijiazhuang 050018, China.
| | - Chun Liu
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Pollution Prevention Biotechnology Laboratory of Hebei Province, Shijiazhuang 050018, China
| | - Jianrui Niu
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Pollution Prevention Biotechnology Laboratory of Hebei Province, Shijiazhuang 050018, China
| | - Changwei Wang
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Zhaoyang Wang
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
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11
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Li M, Gao S, Yang P, Li H. Improvement of ribonucleic acid production in Cyberlindnera jadinii and optimization of fermentation medium. AMB Express 2024; 14:24. [PMID: 38358520 PMCID: PMC10869677 DOI: 10.1186/s13568-024-01679-3] [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: 06/19/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
To enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett-Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH2PO4) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH2PO4, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.
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Affiliation(s)
- Mengting Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuhong Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Pengcheng Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hejin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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12
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Li Q, Lu J, Liu J, Li J, Zhang G, Du G, Chen J. High-throughput droplet microfluidics screening and genome sequencing analysis for improved amylase-producing Aspergillus oryzae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:185. [PMID: 38031105 PMCID: PMC10685594 DOI: 10.1186/s13068-023-02437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND The exceptional protein secretion capacity, intricate post-translational modification processes, and inherent safety features of A. oryzae make it a promising expression system. However, heterologous protein expression levels of existing A. oryzae species cannot meet the requirement for industrial-scale production. Therefore, establishing an efficient screening technology is significant for the development of the A. oryzae expression system. RESULTS In this work, a high-throughput screening method suitable for A. oryzae has been established by combining the microfluidic system and flow cytometry. Its screening efficiency can reach 350 droplets per minute. The diameter of the microdroplet was enlarged to 290 µm to adapt to the polar growth of A. oryzae hyphae. Through enrichment and screening from approximately 450,000 droplets within 2 weeks, a high-producing strain with α-amylase increased by 6.6 times was successfully obtained. Furthermore, 29 mutated genes were identified by genome resequencing of high-yield strains, with 15 genes subjected to editing and validation. Two genes may individually influence α-amylase expression in A. oryzae by affecting membrane-associated multicellular processes and regulating the transcription of related genes. CONCLUSIONS The developed high-throughput screening strategy provides a reference for other filamentous fungi and Streptomyces. Besides, the strains with different excellent characteristics obtained by efficient screening can also provide materials for the analysis of genetic and regulatory mechanisms in the A. oryzae expression system.
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Affiliation(s)
- Qinghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jinchang Lu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingya Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guoqiang Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
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13
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Koh HG, Kim J, Rao CV, Park SJ, Jin YS. Construction of a Compact Array of Microplasma Jet Devices and Its Application for Random Mutagenesis of Rhodosporidium toruloides. ACS Synth Biol 2023; 12:3406-3413. [PMID: 37864563 DOI: 10.1021/acssynbio.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2023]
Abstract
A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides. Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm3) capable of generating an electron density of greater than 1013 cm-3 was constructed to produce reactive species (N2*, N2+, O, OH, and Hα) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. This compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.
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Affiliation(s)
- Hyun Gi Koh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jinhong Kim
- Laboratory for Optical Physics and Engineering, Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Christopher V Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Sung-Jin Park
- Laboratory for Optical Physics and Engineering, Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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14
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Yi X, Yang D, Xu X, Wang Y, Guo Y, Zhang M, Wang Y, He Y, Zhu J. Cold plasma pretreatment reinforces the lignocellulose-derived aldehyde inhibitors tolerance and bioethanol fermentability for Zymomonas mobilis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:102. [PMID: 37322470 DOI: 10.1186/s13068-023-02354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lignocellulose-derived aldehyde inhibitors seriously blocked the biorefinery of biofuels and biochemicals. To date, the economic production of lignocellulose-based products heavily relied on high productivities of fermenting strains. However, it was expensive and time-consuming for the achievable rational modification to strengthen stress tolerance robustness of aldehyde inhibitors. Here, it aimed to improve aldehyde inhibitors tolerance and cellulosic bioethanol fermentability for the chassis Zymomonas mobilis ZM4 pretreated using energy-efficient and eco-friendly cold plasma. RESULTS It was found that bioethanol fermentability was weaker in CSH (corn stover hydrolysates) than that in synthetic medium for Z. mobilis, and thus was attributed to the inhibition of the lignocellulose-derived aldehyde inhibitors in CSH. Convincingly, it further confirmed that the mixed aldehydes severely decreased bioethanol accumulation through additional aldehydes supplementary assays in synthetic medium. After assayed under different processing time (10-30 s), discharge power (80-160 W), and working pressure (120-180 Pa) using cold atmosphere plasma (CAP), it achieved the increased bioethanol fermentability for Z. mobilis after pretreated at the optimized parameters (20 s, 140 W and 165 Pa). It showed that cold plasma brought about three mutation sites including ZMO0694 (E220V), ZMO0843 (L471L) and ZMO0843 (P505H) via Genome resequencing-based SNPs (single nucleotide polymorphisms). A serial of differentially expressed genes (DEGs) were further identified as the potential contributors for stress tolerance via RNA-Seq sequencing, including ZMO0253 and ZMO_RS09265 (type I secretion outer membrane protein), ZMO1941 (Type IV secretory pathway protease TraF-like protein), ZMOr003 and ZMOr006 (16S ribosomal RNA), ZMO0375 and ZMO0374 (levansucrase) and ZMO1705 (thioredoxins). It enriched cellular process, followed by metabolic process and single-organism process for biological process. For KEGG analysis, the mutant was also referred to starch and sucrose metabolism, galactose metabolism and two-component system. Finally, but interestingly, it simultaneously achieved the enhanced stress tolerance capacity of aldehyde inhibitors and bioethanol fermentability in CSH for the mutant Z. mobilis. CONCLUSIONS Of several candidate genetic changes, the mutant Z. mobilis treated with cold plasma was conferred upon the facilitated aldehyde inhibitors tolerance and bioethanol production. This work would provide a strain biocatalyst for the efficient production of lignocellulosic biofuels and biochemicals.
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Affiliation(s)
- Xia Yi
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Dong Yang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Xiaoyan Xu
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Youjun Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yan Guo
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Meng Zhang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yilong Wang
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China
| | - Yucai He
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
| | - Jie Zhu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
- Institute of Urban and Rural Mining, Changzhou University, Changzhou, 213164, China.
- Changzhou Key Laboratory of Biomass Green, Safe & High Value Utilization Technology, Changzhou University, Changzhou, 213164, Jiangsu, China.
- School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China.
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15
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Sun L, Yue M, Yang L, Ding X, Wang Y, Liu Y, Sun W. Biosynthesis and physicochemical properties of low molecular weight gellan produced by a high-yield mutant of Sphingomonas paucimobilis ATCC 31461. Int J Biol Macromol 2023; 242:124899. [PMID: 37196715 DOI: 10.1016/j.ijbiomac.2023.124899] [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: 03/03/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Gellan gum (GG) is used in many industries. Here, we obtained a low molecular weight GG (L-GG) directly produced by M155, the high-yield mutant strain of Sphingomonas paucimobilis ATCC 31461, which was selected using UV-ARTP combined mutagenesis. The molecular weight of L-GG was 44.6 % lesser than that of the initial GG (I-GG), and the GG yield increased by 24 %. The monosaccharide composition and Fourier transform-infrared spectroscopic patterns of L-GG were similar to those of I-GG, which indicated that the decrease in the molecular weight of L-GG was probably because of reduction in the degree of polymerization. In addition, microstructural analysis revealed that the surface of L-GG was rougher, with smaller pores and tighter network, than that of I-GG. L-GG showed low hardness, gumminess, and chewiness, which are indicative of better taste. The results of rheological analysis revealed that the L-GG solution is a typical non-Newtonian fluid with low viscoelasticity, which exhibited stable dynamic viscoelasticity within 20-65 °C. To the best of our knowledge, this is the first report of direct biosynthesis of low molecular weight GG during fermentation, which will reduce the manufacturing costs. Our observations provide a reference for precise and expanded applications of GG.
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Affiliation(s)
- Ling Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Meixiang Yue
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lei Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xialiang Ding
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yazhen Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yuhan Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wenjing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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16
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Zhou K, Yu C, Liang N, Xiao W, Wang Y, Yao M, Yuan Y. Adaptive Evolution and Metabolic Engineering Boost Lycopene Production in Saccharomyces cerevisiae via Enhanced Precursors Supply and Utilization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3821-3831. [PMID: 36802623 DOI: 10.1021/acs.jafc.2c08579] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Lycopene is a red carotenoid with remarkable antioxidant activity, which has been widely used in food, cosmetics, medicine, and other industries. Production of lycopene in Saccharomyces cerevisiae provides an economic and sustainable means. Many efforts have been done in recent years, but the titer of lycopene seems to reach a ceiling. Enhancing the supply and utilization of farnesyl diphosphate (FPP) is generally regarded as an efficient strategy for terpenoid production. Herein, an integrated strategy by means of atmospheric and room-temperature plasma (ARTP) mutagenesis combined with H2O2-induced adaptive laboratory evolution (ALE) was proposed to improve the supply of upstream metabolic flux toward FPP. Enhancing the expression of CrtE and introducing an engineered CrtI mutant (Y160F&N576S) increased the utilization of FPP toward lycopene. Consequently, the titer of lycopene in the strain harboring the Ura3 marker was increased by 60% to 703 mg/L (89.3 mg/g DCW) at the shake-flask level. Eventually, the highest reported titer of 8.15 g/L of lycopene in S. cerevisiae was achieved in a 7 L bioreactor. The study highlights an effective strategy that the synergistic complementarity of metabolic engineering and adaptive evolution facilitates natural product synthesis.
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Affiliation(s)
- Kui Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chao Yu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- CABIO Biotech (Wuhan) Co., Ltd, Wuhan 430075, China
| | - Nan Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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17
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Gou Z, Li J, He F, Bamao Z, Li Z, Xu T. Screening of a high-yield strain of avermectin B 1a by colony analysis in situ. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2023; 26:123-133. [PMID: 36178644 DOI: 10.1007/s10123-022-00279-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 08/21/2022] [Accepted: 09/19/2022] [Indexed: 01/06/2023]
Abstract
Avermectin, an agricultural antibiotic, is widely used as an agricultural insecticide and an important lead compound of antibiotics. It is manufactured by Streptomyces avermitilis through fermentation. Manufacturers pay special attention to screening for strains with high fermentation capacity based on morphological properties of the colony and by the result of shake flask fermentation. These traditional screening methods are time-consuming and labor-intensive and require specialized equipment. Moreover, evaluation of colony appearance is highly subjective. To improve and accelerate the screening process, we developed a rapid in situ screening method. Forty-four strains isolated naturally from the spores of industrial high-yielding strains were studied. The data show that the colony fermentation titer is highly correlated with the yield from the shake flask fermentation of avermectin, and the Pearson's R is 0.990. The total titer of avermectins by shake flask fermentation is also highly correlated with the B1a titer (Pearson's R is 0.994). This result also shows that strains can be quickly screened by analyzing the colony titer. Pigment rings of the colonies that appeared after growing and maturing on the new medium plate were analyzed. The chosen colonies were directly marked and punched and then extracted with methanol. The fermentation ability can be evaluated by measuring the absorbance at 245 nm. This methodology can be applied in both natural breeding and mutation breeding conditions. By continuously breeding from 2008 to 2020, the flask titer of avermectin B1a increased from 4582 ± 483 to 9197 ± 1134 μg/mL.
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Affiliation(s)
- Zhongxuan Gou
- Jiangsu Food & Pharmaceutical Science College, Huaian, 223003, Jiangsu, China. .,Hebei Veyong Biochemical Co., LTD, Shijiazhuang City, Hebei, 050011, China.
| | - Junhua Li
- Hebei Veyong Biochemical Co., LTD, Shijiazhuang City, Hebei, 050011, China
| | - Feng He
- Jiangsu Food & Pharmaceutical Science College, Huaian, 223003, Jiangsu, China
| | - Zhaxi Bamao
- Jiangsu Food & Pharmaceutical Science College, Huaian, 223003, Jiangsu, China
| | - Zixuan Li
- Jiangsu Food & Pharmaceutical Science College, Huaian, 223003, Jiangsu, China
| | - Tingyu Xu
- Jiangsu Food & Pharmaceutical Science College, Huaian, 223003, Jiangsu, China.,Hebei Veyong Biochemical Co., LTD, Shijiazhuang City, Hebei, 050011, China
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18
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Li C, Xia Y, Li M, Zhang T. ARTP mutagenesis of phospholipase D-producing strain Streptomyces hiroshimensis SK43.001, and its enzymatic properties. Heliyon 2022; 8:e12587. [PMID: 36619468 PMCID: PMC9816975 DOI: 10.1016/j.heliyon.2022.e12587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/16/2022] [Accepted: 12/14/2022] [Indexed: 12/26/2022] Open
Abstract
Phospholipase D (PLD) is a group of enzymes that act on phospholipid molecules, which is widely used in the fields of food and medicine. PLD is extracted from animals and plants with low transesterification activity and high price. Therefore, it is benefit to screen an efficient PLD producing strain from microorganisms. A highly productive strain of PLD with transphosphatidylation activity, named Streptomyces hiroshimensis SK43.001, was screened from soil in our laboratory and mutated using atmospheric room temperature plasma (ARTP). A mutant strain SK43.001-11 with the highest enzyme activity and superior genetic stability was obtained, and its fermentation enzyme activity was 5.3 U/mL, which was 82% increased comparing to wild strain. The purification of PLD showed that the specific enzyme activity increased to 49.48 U/mg, which was 54.37-fold higher than that of the crude enzyme, with a recovery of 32.31%. In addition, enzymatic properties of PLD have revealed that the optimal pH and temperature were 7.0 and 60 °C, respectively. Metal ion Mg2+ and surfactant Triton X-100 made the enzymatic activity increased by 16% and 100%, respectively. The reaction kinetic parameters showed that the mutant PLD had higher affinity for the substrate of egg PC and better catalytic efficiency with K m, V max and K cat of 30.20 mmol/L, 99.70 μmol/min and 76.33 s-1, respectively. This study may provide important inspiration for obtaining high enzyme activity strains with PLD.
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Affiliation(s)
- Chenchen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China,Corresponding author.
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19
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Rapid Screening of High-Yield Gellan Gum Mutants of Sphingomonas paucimobilis ATCC 31461 by Combining Atmospheric and Room Temperature Plasma Mutation with Near-Infrared Spectroscopy Monitoring. Foods 2022; 11:foods11244078. [PMID: 36553820 PMCID: PMC9777525 DOI: 10.3390/foods11244078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/23/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
In this study, an efficient mutagenesis and rapid screening method of high-yield gellan gum mutant by atmospheric and room temperature plasma (ARTP) treatment combined with Near-Infrared Spectroscopy (NIRS) was proposed. A NIRS model for the on-line detection of gellan gum yield was constructed by joint interval partial least squares (siPLS) regression on the basis of chemical determination and NIRS acquisition of gellan gum yield. Five genetically stable mutant strains were screened using the on-line NIRS detection of gellan gum yield in the fermentation from approximately 600 mutant strains induced by ARTP. Remarkably, compared with the original strain, the gellan gum yield of mutant strain 519 was 9.427 g/L (increased by 133.5%) under the optimal fermentation conditions, which was determined by single-factor and response surface optimization. Therefore, the method of ARTP mutation combined with the NIRS model can be used to screen high-yield mutant strains of gellan gum and other high-yield polysaccharide strains.
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20
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Elshobary ME, Zabed HM, Qi X, El-Shenody RA. Enhancing biomass and lipid productivity of a green microalga Parachlorella kessleri for biodiesel production using rapid mutation of atmospheric and room temperature plasma. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:122. [PMID: 36372889 PMCID: PMC9655907 DOI: 10.1186/s13068-022-02220-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microalgae, with their high adaptability to various stress conditions and rapid growth, are considered excellent biomass resources for lipid production and biodiesel feedstocks. However, lipid yield and productivity of the natural strains are common bottlenecks in their large-scale use for lipid production, which can be overcome by evolving new strains using conventional and advanced mutagenic techniques. It is challenging to generate microalgae strains capable of high lipid synthesis through natural selection. As a result, random mutagenesis is currently considered a viable option in many scenarios. The objective of this study was to explore atmospheric and room temperature plasma (ARTP) as a random mutagenesis technique to obtain high lipid-accumulating mutants of a green microalga for improved biodiesel production. RESULTS A green microalgal species was isolated from the Chinese Yellow Sea and identified as Parachlorella kessleri (OM758328). The isolated microalga was subsequently mutated by ARTP to obtain high lipid-accumulating mutants. Based on the growth rate and lipid content, 5 mutants (named M1, M2, M4, M5, and M8) were selected from 15 pre-selected mutants. These five mutants varied in their growth rate from 0.33 to 0.68 day-1, with the lipid content varying between 0.25 g/L in M2 to 0.30 g/L in M8 at 10th day of cultivation. Among the mutants, M8 showed the maximum biomass productivity (0.046 g/L/day) and lipid productivity (20.19 mg/L/day), which were 75% and 44% higher than the wild strain, respectively. The triglyceride (TAG) content of M8 was found to be 0.56 g/L at 16th day of cultivation, which was 1.77-fold higher than that of the wild strain. Furthermore, M8 had the highest saturated fatty acids (C16-18) with the lowermost polyunsaturated fatty acid content, which are favorable properties of a biodiesel feedstock according to international standards. CONCLUSION The mutant strain of P. kessleri developed by the ARTP technique exhibited significant improvements in biomass productivity, lipid content, and biodiesel quality. Therefore, the biomass of this mutant microalga could be a potential feedstock for biodiesel production.
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Affiliation(s)
- Mostafa E Elshobary
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Hossain M Zabed
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rania A El-Shenody
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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21
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Enhancing the antibacterial activity of Lactobacillus reuteri against Escherichia coli by random mutagenesis and delineating its mechanism. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Li YW, Yang CL, Peng H, Nie ZK, Shi TQ, Huang H. RETRACTED ARTICLE: Mutagenesis combined with fermentation optimization to enhance gibberellic acid GA3 yield in Fusarium fujikuroi. BIORESOUR BIOPROCESS 2022; 9:106. [PMID: 38647889 PMCID: PMC10991607 DOI: 10.1186/s40643-022-00595-3] [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: 07/31/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Gibberellic acid (GA3) is a plant growth hormone that plays an important role in the production of crops, fruits, and vegetables with a wide market share. Due to intrinsic advantages, liquid fermentation of Fusarium fujikuroi has become the sole method for industrial GA3 production, but the broader application of GA3 is hindered by low titer. In this study, we combined atmospheric and room-temperature plasma (ARTP) with ketoconazole-based screening to obtain the mutant strain 3-6-1 with high yield of GA3. Subsequently, the medium composition and fermentation parameters were systematically optimized to increase the titer of GA3, resulting in a 2.5-fold increase compared with the titer obtained under the initial conditions. Finally, considering that the strain is prone to substrate inhibition and glucose repression, a new strategy of fed-batch fermentation was adopted to increase the titer of GA3 to 575.13 mg/L, which was 13.86% higher than the control. The strategy of random mutagenesis combined with selection and fermentation optimization developed in this study provides a basis for subsequent research on the industrial production of GA3.
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Affiliation(s)
- Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Cai-Ling Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
| | - Hui Peng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Zhi-Kui Nie
- Jiangxi New Reyphon Biochemical Co., Ltd., Salt and Chemical Industry, Xingan, China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, 210023, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
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23
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Tang A, Ren Q, Wu Y, Wu C, Cheng Y. Investigation into the Antibacterial Mechanism of Biogenic Tellurium Nanoparticles and Precursor Tellurite. Int J Mol Sci 2022; 23:ijms231911697. [PMID: 36232999 PMCID: PMC9569536 DOI: 10.3390/ijms231911697] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Antibacterial tellurium nanoparticles have the advantages of high activity and biocompatibility. Microbial synthesis of Te nanoparticles is not only a green technology but builds new ecological relationships in diverse environments. However, the antibacterial mechanism of Te nanoparticles is largely unclear. In this study, we report the bacterial synthesis of rod-shaped Te nanoparticles (BioTe) with high antibacterial activity against Escherichia coli. Morphology and permeability examination indicates that membrane damage is the primary reason for the antibacterial activity of BioTe, rather than ROS production and DNA damage. Moreover, a comparison of transcriptome and relative phenotypes reveals the difference in antibacterial mechanisms between BioTe and tellurite. Based on our evidence, we propose an antibacterial mode of rod-shaped BioTe, in which positively charged BioTe interact with the cell membrane through electrostatic attraction and then penetrate the membrane by using their sharp ends. In contrast, tellurite toxicity might be involved in sulfur metabolism.
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Affiliation(s)
- Aiguo Tang
- School of Life Sciences, Anhui University, Hefei 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, China
| | - Qianwen Ren
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei 230109, China
| | - Yaling Wu
- School of Life Sciences, Anhui University, Hefei 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, China
| | - Chao Wu
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei 230109, China
| | - Yuanyuan Cheng
- School of Life Sciences, Anhui University, Hefei 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, China
- Correspondence:
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Wang J, Chen P, Li S, Zheng X, Zhang C, Zhao W. Mutagenesis of high-efficiency heterotrophic nitrifying-aerobic denitrifying bacterium Rhodococcus sp. strain CPZ 24. BIORESOURCE TECHNOLOGY 2022; 361:127692. [PMID: 35905881 DOI: 10.1016/j.biortech.2022.127692] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Breeding high-efficiency heterotrophic nitrifying-aerobic denitrifying (SND) bacteria is important for the removal of biological nitrogen in wastewater treatment. In this study, a high-efficiency SND mutant strain, ΔRhodococcus sp. CPZ 24, was obtained by ultraviolet-diethyl sulfate compound mutagenesis. The maximum nitrification and denitrification rates were 3.77 and 1.37 mg·L-1·h-1, respectively 30.30 % and 17.10 % higher than those of wild bacteria. Biolog technology and network model analysis revealed that ΔCPZ 24 significantly improved the utilisation ability and metabolic activity of organic carbon sources. Furthermore, the expression levels of the nitrogen removal function genes nxrA, nosZ, amoA, and norB in strain ΔCPZ 24 increased significantly. In actual sewage, mutant bacteria ΔCPZ 24 have a 95.05 % ammonia-nitrogen degradation rate and a 96.67 % nitrate-nitrogen degradation rate. These results suggested that UV-DES compound mutation was a successful strategy to improve the nitrogen removal performance of SND bacteria in wastewater treatment.
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Affiliation(s)
- Jingli Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Peizhen Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Shaopeng Li
- Tianjin Agricultural University, Tianjin 300392, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Wenjie Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
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Chen H, Wang J, Li Q, Xu X, Niu C, Zheng F, Liu C. Fed-Batch Fermentation of Saccharomyces pastorianus with High Ribonucleic Acid Yield. Foods 2022; 11:foods11182742. [PMID: 36140869 PMCID: PMC9497889 DOI: 10.3390/foods11182742] [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: 07/18/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The degradation products of ribonucleic acid (RNA)are widely used in the food and pharmaceutical industry for their flavoring and nutritional enhancement functions. Yeast is the main source for commercial RNA production, and an efficient strain is the key to reducing production costs; (2) Methods: A mutant Saccharomyces pastorianus G03H8 with a high RNA yield was developed via ARTP mutagenesis and fed-batch fermentation was applied to optimize production capacity. Genome sequencing analysis was used to reveal the underlying mechanism of higher RNA production genetic differences in the preferred mutant; (3) Results: Compared with the highest RNA content of the mutant strain, G03H8 increased by 40% compared with the parental strain G03 after response surface model optimization. Meanwhile, in fed-batch fermentation, G03H8′s dry cell weight (DCW) reached 60.58 g/L in 5 L fermenter by molasses flowing and RNA production reached up to 3.58 g/L. Genome sequencing showed that the ribosome biogenesis, yeast meiosis, RNA transport, and longevity regulating pathway were closely related to the metabolism of high RNA production; (4) Conclusion: S. pastorianus G03H8 was developed for RNA production and had the potential to greatly reduce the cost of RNA production and shorten the fermentation cycle. This work lays the foundation for efficient RNA content using S. pastorianus.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-0510-85918176
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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27
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Zhu Z, Chen W, Zhou H, Cheng H, Luo S, Zhou K, Zhou P, Xia L, Ding X. ARTP and NTG compound mutations improved Cry protein production and virulence of Bacillus thuringiensis X023. Appl Microbiol Biotechnol 2022; 106:4211-4221. [PMID: 35622123 DOI: 10.1007/s00253-022-11983-2] [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: 12/28/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 12/31/2022]
Abstract
A high production mutated strain Bacillus thuringiensis X023PN (BtX023PN) was screened from the wild strain Bacillus thuringiensis X023 (BtX023) after atmospheric and room temperature plasma (ARTP) and nitrosoguanidine (NTG) mutation. BtX023PN grows faster than the wild strain, and its lysis of mother cell was 6 h ahead BtX023, but the ability of sporulation was significantly reduced. Bioassay indicated that compared with the wild type strain, the virulence of BtX023PN against Plutella xylostella (P. xylostella) and Mythimna seperata (M. seperata) increased to 2.33-fold and 2.13-fold respectively. qRT-PCR and SDS-PAGE demonstrated that the production of Cry1Ac increased by 61%. Resequence indicated that the mutated sites enriched on the key carbohydrate metabolism and amino acid metabolism. This study provides a new strain resource for the development of Bt insecticides and a feasible technical strategy for the breeding of Bt. KEY POINTS: • Atmospheric and room temperature plasma used in breeding of Bacillus thuringiensis. • Less stationary phase time with more ICP production. • Semi-lethal concentration against Plutella xylostella reduced by about 57.
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Affiliation(s)
- Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Wenhui Chen
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Sisi Luo
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Kexuan Zhou
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Pengji Zhou
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, Hunan, China.
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28
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Enhanced Antibacterial Activity of Brevibacillus sp. SPR19 by Atmospheric and Room Temperature Plasma Mutagenesis (ARTP). Sci Pharm 2022. [DOI: 10.3390/scipharm90020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Antibiotic resistance is a major health concern worldwide. In our previous study, some bacterial isolates exhibited antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). However, the production of antibacterial substances by native microorganisms is limited by biosynthetic genes. This study aimed to improve the antibacterial activity of SPR19 using atmospheric and room temperature plasma mutagenesis (ARTP). The results showed that SPR19 belonged to the Brevibacillus genus. The growth curves and production kinetics of antibacterial substances were investigated. Argon-based ARTP was applied to SPR19, and the 469 mutants were preliminarily screened using agar overlay method. The remaining 25 mutants were confirmed by agar well diffusion assay against S. aureus TISTR 517 and MRSA isolates 142, 1096, and 2468. M285 exhibited the highest activity compared to the wild-type strain (10.34–13.59%) and this mutant was stable to produce the active substances throughout 15 generations consistently. The antibacterial substances from M285 were tolerant to various conditions (heat, enzyme, surfactant, and pH) while retaining more than 90% of their activities. Therefore, Brevibacillus sp. SPR19 is a potential source of antibacterial substances. ARTP mutagenesis is a powerful method for strain improvement that can be utilized to treat MRSA infection in the future.
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Peng Q, Xiao Y, Zhang S, Zhou C, Xie A, Li Z, Tan A, Zhou L, Xie Y, Zhao J, Wu C, Luo L, Huang J, He T, Sun R. Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability. PeerJ 2022; 10:e13076. [PMID: 35341057 PMCID: PMC8953557 DOI: 10.7717/peerj.13076] [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: 12/10/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background Phosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils. Methods In this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities. Results Compared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90-32, xj120-12, xj120-31, and xj180-22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120-12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains. Conclusions The results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains.
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Affiliation(s)
- Qiuju Peng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang, China
| | - Su Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China,Bureau of Agriculture and Rural Affairs, Xixiu District, Anshun, Guizou Province, China
| | - Changwei Zhou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Ailin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China,Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Aijuan Tan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Lihong Zhou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Yudan Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Jinyi Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Chenglin Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Lei Luo
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Jie Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
| | - Ran Sun
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizou Province, China
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Shen Q, Zhou XT, Guo Q, Xue YP, Zheng YG. Engineering laboratory/factory-specific phage-resistant strains of Escherichia coli by mutagenesis and screening. World J Microbiol Biotechnol 2022; 38:51. [DOI: 10.1007/s11274-022-03239-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022]
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Biosensor-assisted evolution for high-level production of 4-hydroxyphenylacetic acid in Escherichia coli. Metab Eng 2021; 70:1-11. [PMID: 34965469 DOI: 10.1016/j.ymben.2021.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022]
Abstract
4-Hydroxyphenylacetic acid (4HPAA) is an important building block for synthesizing drugs, agrochemicals, and biochemicals, and requires sustainable production to meet increasing demand. Here, we use a 4HPAA biosensor to overcome the difficulty of conventional library screening in identification of preferred mutants. Strains with higher 4HPAA production and tolerance are successfully obtained by atmospheric and room temperature plasma (ARTP) mutagenesis coupled with adaptive laboratory evolution using this biosensor. Genome shuffling integrates preferred properties in the strain GS-2-4, which produces 25.42 g/L 4HPAA. Chromosomal mutations of the strain GS-2-4 are identified by whole genome sequencing. Through comprehensive analysis and experimental validation, important genes, pathways and regulations are revealed. The best gene combination in inverse engineering, acrD-aroG, increases 4HPAA production of strain GS-2-4 by 37% further. These results emphasize precursor supply and stress resistance are keys to efficient 4HPAA biosynthesis. Our work shows the power of biosensor-assisted screening of mutants from libraries. The methods developed here can be easily adapted to construct cell factories for the production of other aromatic chemicals. Our work also provides many valuable target genes to build cell factories for efficient 4HPAA production in the future.
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Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2021.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021; 478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.
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Patenall BL, Hathaway HJ, Laabei M, Young AE, Thet NT, Jenkins ATA, Short RD, Allinson SL. Assessment of mutations induced by cold atmospheric plasma jet treatment relative to known mutagens in Escherichia coli. Mutagenesis 2021; 36:380-387. [PMID: 34459491 DOI: 10.1093/mutage/geab030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/29/2021] [Indexed: 11/12/2022] Open
Abstract
The main bactericidal components of cold atmospheric plasma (CAP) are thought to be reactive oxygen and nitrogen species (RONS) and UV-radiation, both of which have the capacity to cause DNA damage and mutations. Here, the mutagenic effects of CAP on Escherichia coli were assessed in comparison to X- and UV-irradiation. DNA damage and mutagenesis were screened for using a diffusion-based DNA fragmentation assay and modified Ames test, respectively. Mutant colonies obtained from the latter were quantitated and sequenced. CAP was found to elicit a similar mutation spectrum to X-irradiation, which did not resemble that for UV implying that CAP-produced RONS are more likely the mutagenic component of CAP. CAP treatment was also shown to promote resistance to the antibiotic ciprofloxacin. Our data suggest that CAP treatment has mutagenic effects that may have important phenotypic consequences.
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Affiliation(s)
| | - Hollie J Hathaway
- Department of Chemistry, Faculty of Science and Technology, Lancaster University, Lancaster, LA1 4YB, UK
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AX, UK
| | - Amber E Young
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 1UD, UK
| | - Naing T Thet
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
| | | | - Robert D Short
- Department of Chemistry, Faculty of Science and Technology, Lancaster University, Lancaster, LA1 4YB, UK
| | - Sarah L Allinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
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Shang YT, Qin J, Gong JS, Wang ZK, Li H, Li H, Shi JS, Xu ZH. High-throughput screening of a nicotinate dehydrogenase producing Pseudomonas putida mutant for efficient biosynthesis of 6-hydroxynicotinic acid. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Madhavan A, Arun KB, Binod P, Sirohi R, Tarafdar A, Reshmy R, Kumar Awasthi M, Sindhu R. Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology. BIORESOURCE TECHNOLOGY 2021; 325:124617. [PMID: 33450638 DOI: 10.1016/j.biortech.2020.124617] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| | - Ranjna Sirohi
- The Center for Energy and Environmental Sustainability, Lucknow 226 010, Uttar Pradesh, India
| | - Ayon Tarafdar
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India.
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Liu T, Huang Z, Gui X, Xiang W, Jin Y, Chen J, Zhao J. Multi-omics Comparative Analysis of Streptomyces Mutants Obtained by Iterative Atmosphere and Room-Temperature Plasma Mutagenesis. Front Microbiol 2021; 11:630309. [PMID: 33584595 PMCID: PMC7876522 DOI: 10.3389/fmicb.2020.630309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Sponges, the most primitive multicellular animals, contain a large number of unique microbial communities. Sponge-associated microorganisms, particularly actinomyces, have the potential to produce diverse active natural products. However, a large number of silent secondary metabolic gene clusters have failed to be revived under laboratory culture conditions. In this study, iterative atmospheric room-temperature plasma. (ARTP) mutagenesis coupled with multi-omics conjoint analysis was adopted to activate the inactive wild Streptomyces strain. The desirable exposure time employed in this study was 75 s to obtain the appropriate lethality rate (94%) and mutation positive rate (40.94%). After three iterations of ARTP mutagenesis, the proportion of mutants exhibiting antibacterial activities significantly increased by 75%. Transcriptome analysis further demonstrated that the differential gene expression levels of encoding type I lasso peptide aborycin had a significant upward trend in active mutants compared with wild-type strains, which was confirmed by LC-MS results with a relative molecular mass of 1082.43 ([M + 2H]2+ at m/z = 2164.86). Moreover, metabolome comparative analysis of the mutant and wild-type strains showed that four spectra or mass peaks presented obvious differences in terms of the total ion count or extracting ion current profiles with each peak corresponding to a specific compound exhibiting moderate antibacterial activity against Gram-positive indicators. Taken together, our data suggest that the ARTP treatment method coupled with multi-omics profiling analysis could be used to estimate the valid active molecules of metabolites from microbial crudes without requiring a time-consuming isolation process.
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Affiliation(s)
- Tan Liu
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Zhiyong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xi Gui
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Xiang
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yubo Jin
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jun Chen
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jing Zhao
- College of Ocean and Earth Science, Xiamen University, Xiamen, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
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Cai M, Wu Y, Qi H, He J, Wu Z, Xu H, Qiao M. Improving the Level of the Tyrosine Biosynthesis Pathway in Saccharomyces cerevisiae through HTZ1 Knockout and Atmospheric and Room Temperature Plasma (ARTP) Mutagenesis. ACS Synth Biol 2021; 10:49-62. [PMID: 33395268 DOI: 10.1021/acssynbio.0c00448] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many studies have been conducted on the expression of multiple aromatic compounds by Saccharomyces cerevisiae. The concentration of l-tyrosine, as a precursor of such valuable compounds, is crucial for the biosynthesis of aromatic metabolites. In this study, a novel function of HTZ1 was found to be related to tyrosine biosynthesis, which has not yet been reported. Knockout of this gene could significantly improve the ability of yeast cells to synthesize tyrosine, and its p-coumaric acid (p-CA) titer was approximately 3.9-fold higher than that of the wild-type strain BY4742. Subsequently, this strain was selected for random mutagenesis through an emerging mutagenesis technique, namely, atmospheric and room temperature plasma (ARTP). After two rounds of mutagenesis, five tyrosine high-producing mutants were obtained. The highest production of p-CA was 7.6-fold higher than that of the wild-type strain. Finally, transcriptome data of the htz1Δ strain and the five mutants were analyzed. The genome of mutagenic strains was also resequenced to reveal the mechanism underlying the high titer of tyrosine. This system of target engineering combined with random mutagenesis to screen excellent mutants provides a new basis for synthetic biology.
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Affiliation(s)
- Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Yuzhen Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Hang Qi
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Jiaze He
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Zhenzhou Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
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Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate. mBio 2021; 12:mBio.02373-20. [PMID: 33436432 PMCID: PMC7844537 DOI: 10.1128/mbio.02373-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The signal recognition particle (SRP) is conserved in all living organisms, and it cotranslationally delivers proteins to the inner membrane or endoplasmic reticulum. Recently, SRP loss was found not to be lethal in either the eukaryote Saccharomyces cerevisiae or the prokaryote Streptococcus mutans In Escherichia coli, the role of SRP in mediating inner membrane protein (IMP) targeting has long been studied. However, the essentiality of SRP remains a controversial topic, partly hindered by the lack of strains in which SRP is completely absent. Here we show that the SRP was nonessential in E. coli by suppressor screening. We identified two classes of extragenic suppressors-two translation initiation factors and a ribosomal protein-all of which are involved in translation initiation. The translation rate and inner membrane proteomic analyses were combined to define the mechanism that compensates for the lack of SRP. The primary factor that contributes to the efficiency of IMP targeting is the extension of the time window for targeting by pausing the initiation of translation, which further reduces translation initiation and elongation rates. Furthermore, we found that easily predictable features in the nascent chain determine the specificity of protein targeting. Our results show why the loss of the SRP pathway does not lead to lethality. We report a new paradigm in which the time delay in translation initiation is beneficial during protein targeting in the absence of SRP.IMPORTANCE Inner membrane proteins (IMPs) are cotranslationally inserted into the inner membrane or endoplasmic reticulum by the signal recognition particle (SRP). Generally, the deletion of SRP can result in protein targeting defects in Escherichia coli Suppressor screening for loss of SRP reveals that pausing at the translation start site is likely to be critical in allowing IMP targeting and avoiding aggregation. In this work, we found for the first time that SRP is nonessential in E. coli The time delay in initiation is different from the previous mechanism that only slows down the elongation rate. It not only maximizes the opportunity for untranslated ribosomes to be near the inner membrane but also extends the time window for targeting translating ribosomes by decreasing the speed of translation. We anticipate that our work will be a starting point for a more delicate regulatory mechanism of protein targeting.
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Zhang C, Li Y, Zhang T, Zhao H. Increasing chitosanase production in Bacillus cereus by a novel mutagenesis and screen method. Bioengineered 2021; 12:266-277. [PMID: 33356788 PMCID: PMC8806256 DOI: 10.1080/21655979.2020.1869438] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Chitosan hydrolysis by chitosanase is one of the most effective methods to produce chitosan oligosaccharides. One of the prerequisites of enzyme fermentation production is to select and breed enzyme-producing cells with good performance. So in the process of fermentation production, the low yield of chitosanase cannot meet the current requirement. In this paper, a strain producing chitosanase was screened and identified, and a novel mutagenesis system (Atmospheric and Room Temperature Plasma (ARTP)) was selected to increase the yield of chitosanase. Then, the fermentation medium was optimized to further improve the enzyme activity of the strain. A strain of Bacillus cereus capable of producing chitosanase was screened and identified from soil samples. A mutant strain of B.cereus was obtained by Atmospheric and Room Temperature Plasma mutagenesis and bioscreening method, and chitosanase activity was 2.49 folds that of the original bacterium. After an optimized fermentation medium, the enzyme activity of the mutant strain was 1.47 folds that of the original bacterium. Combined with all the above optimization experiments, the enzyme activity of mutant strain increased by 3.66 times. The results showed that the Atmospheric and Room Temperature Plasma mutagenesis and bioscreening method could significantly increase the yield of chitosanase in B.cereus, and had little effect on the properties of the enzyme. These findings have potential applications in the mutagenesis of other enzyme-producing microorganisms.
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Affiliation(s)
- Chaozheng Zhang
- Key Laboratory of Ministry of Education Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology , Tianjin, P. R. China
| | - Yi Li
- Key Laboratory of Ministry of Education Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology , Tianjin, P. R. China
| | - Tianshuang Zhang
- Key Laboratory of Ministry of Education Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology , Tianjin, P. R. China
| | - Hua Zhao
- Key Laboratory of Ministry of Education Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology , Tianjin, P. R. China
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Qiu L, Nie SX, Hu SJ, Wang SJ, Wang JJ, Guo K. Screening of Beauveria bassiana with high biocontrol potential based on ARTP mutagenesis and high-throughput FACS. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 171:104732. [PMID: 33357554 DOI: 10.1016/j.pestbp.2020.104732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Beauveria bassiana is a promising biocontrol agent due to its entomopathogenic activities and residue-free characteristics. However, its susceptibility to abiotic stresses and naturally low virulence limit the effective application of this fungus. To effectively obtain fungal strains with high biocontrol potential, fluorescence-activated cell sorting (FACS) was used to screen mutant libraries generated by atmospheric and room temperature plasma (ARTP). Among about 8000 mutants obtained by ARTP mutagenesis, six candidate mutants were selected according to the forward scatter (FSC) signal readings of FACS. B6, with a 37.4% higher FSC reading than wild-type (WT), showed a 32.6% increase in virulence. It also presented a 13.5% decrease in median germinating time (GT50) and a 12.1% increase in blastospore production. Comparative analysis between insect transcriptional responses to B6 and WT infection showed that the immune response coupled with protein digestion and absorption progress was highly activated in B6-infected Galleria mellonella larvae, while fatty acid synthesis was suppressed after 3 days of infection. Our results confirmed the feasibility of sorting B. bassiana with high biocontrol potential via the combination of ARTP and FACS and facilitated the understanding of insect-pathogen interactions, highlighting a new strategy for modifying entomopathogenic fungi to improve the efficiency of biological control.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China.
| | - Sheng-Xin Nie
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Shun-Juan Hu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Shou-Juan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Juan-Juan Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China.
| | - Kai Guo
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
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42
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Heslin C, Boehm D, Gilmore BF, Megaw J, Freeman TA, Hickok NJ, Cullen PJ, Bourke P. Biomolecules as Model Indicators of In Vitro and In Vivo Cold Plasma Safety. FRONTIERS IN PHYSICS 2021; 8:613046. [PMID: 37124146 PMCID: PMC10136044 DOI: 10.3389/fphy.2020.613046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The potential applications for cold plasma in medicine are extensive, from microbial inactivation and induction of apoptosis in cancer cells to stimulating wound healing and enhancing the blood coagulation cascade. The safe bio-medical application of cold plasma and subsequent effect on complex biological pathways requires precision and a distinct understanding of how physiological redox chemistry is manipulated. Chemical modification of biomolecules such as carbohydrates, proteins, and lipids treated with cold plasma have been characterized, however, the context of how alterations of these molecules affect cell behavior or in vivo functionality has not been determined. Thus, this study examines the cytotoxic and mutagenic effects of plasma-treated molecules in vitro using CHO-K1 cells and in vivo in Galleria mellonella larvae. Specifically, albumin, glucose, cholesterol, and arachidonic acid were chosen as representative biomolecules, with established involvement in diverse bioprocesses including; cellular respiration, intracellular transport, cell signaling or membrane structure. Long- and short-term effects depended strongly on the molecule type and the treatment milieu indicating the impact of chemical and physical modifications on downstream biological pathways. Importantly, absence of short-term toxicity did not always correlate with absence of longer-term effects, indicating the need to comprehensively assess ongoing effects for diverse biological applications.
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Affiliation(s)
- Caitlin Heslin
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
| | - Daniela Boehm
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
| | | | - Julianne Megaw
- School of Pharmacy, Queens University Belfast, Belfast, United Kingdom
| | - Theresa A. Freeman
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Jefferson University, Philadelphia, PA, United States
| | - Noreen J. Hickok
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Jefferson University, Philadelphia, PA, United States
| | - P. J. Cullen
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
- School of Chemical and Biomolecular Engineering, University of Sydney, Sydney, NSW, Australia
| | - Paula Bourke
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
- School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
- Plasma Research Group, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
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Xia XK, Zhang YE, Lei SJ, Hu B, Fu CX. Identification and iterative combinatorial mutagenesis of a new naringinase-producing strain, Aspergillus tubingensis MN589840. Lett Appl Microbiol 2020; 72:141-148. [PMID: 32870525 DOI: 10.1111/lam.13379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 01/20/2023]
Abstract
Naringinase was mainly obtained by microbial fermentation, and mutagenesis was a major way for obtaining excellent mutants. The aim of this study was to screen out a high naringinase yielding mutant to enhance the potential application value of its industrialization and compare the effects of different mutagenic methods on the enzyme activity of the strain. A novel producing naringinase strain, Aspergillus tubingensis MN589840, was isolated from mildewed pomelo peel, later subjected to mutagenesis including UV, ARTP and UV-ARTP. After five rounds iterative mutagenesis, the mutants U1, A6 and UA13 were screened out with 1448·49, 1848·71, 2475·16 U mg-1 enzyme activity, the naringinase productivity raised by 79·08, 123·56 and 206%, respectively. In addition, the naringinase activity of three mutants rose after each round of iterative mutagenesis. These results indicated that the mutagenesis efficiency of UV-ARTP was higher than that of single ARTP, and both are better than UV. In summary, the iterative UV-ARTP mutagenesis is an effective strategy for screening high naringinase-producing strains.
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Affiliation(s)
- X-K Xia
- College of Biological and Pharmaceutical, China Three Gorges University, Yichang, China
| | - Y-E Zhang
- College of Biological and Pharmaceutical, China Three Gorges University, Yichang, China
| | - S-J Lei
- College of Biological and Pharmaceutical, China Three Gorges University, Yichang, China
| | - B Hu
- College of Biological and Pharmaceutical, China Three Gorges University, Yichang, China
| | - C-X Fu
- Research and Development Center, Hubei Tulaohan Flavouring and Food Co., Ltd, Yichang, China
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44
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Li Y, Chen Y, Tian X, Chu J. Advances in sophorolipid-producing strain performance improvement and fermentation optimization technology. Appl Microbiol Biotechnol 2020; 104:10325-10337. [PMID: 33097965 DOI: 10.1007/s00253-020-10964-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/31/2022]
Abstract
Sophorolipids (SLs), currently one of the most promising biosurfactants, are secondary metabolites produced by many non-pathogenic yeasts, among which Candida bombicola ATCC 22214 is the main sophorolipid-producing strain. SLs have gained much attention since they exhibit anti-tumor, anti-bacterial, anti-inflammatory, and other beneficial biological activities. In addition, as biosurfactants, SLs have a low toxicity level and are easily degradable without polluting the environment. However, the production cost of SLs remains high, which hinders the industrialization process of SL production. This paper describes SL structure and the metabolic pathway of SL synthesis firstly. Furthermore, we analyze factors that contribute to the higher production cost of SLs and summarize current research status on the advancement of SL production based on two aspects: (1) the improvement of strain performance and (2) the optimization of fermentation process. Further prospects of lowering the cost of SL production are also discussed in order to achieve larger-scale SL production with a high yield at a low cost. KEY POINTS: • Review of advances in strain performance improvement and fermentation optimization. • High-throughput screening and metabolic engineering for high-performance strains. • Low-cost substrates and semi-continuous strategies for efficient SL production.
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Affiliation(s)
- Ya Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, P.O. Box 329, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yang Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, P.O. Box 329, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, P.O. Box 329, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, P.O. Box 329, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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45
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Wang L, Zhao H, He D, Wu Y, Jin L, Li G, Su N, Li H, Xing XH. Insights into the molecular-level effects of atmospheric and room-temperature plasma on mononucleotides and single-stranded homo- and hetero-oligonucleotides. Sci Rep 2020; 10:14298. [PMID: 32868795 PMCID: PMC7459345 DOI: 10.1038/s41598-020-71152-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/09/2020] [Indexed: 01/18/2023] Open
Abstract
Atmospheric and room-temperature plasma (ARTP) has been successfully developed as a useful mutation tool for mutation breeding of various microbes and plants as well animals by genetic alterations. However, understanding of the molecular mechanisms underlying the biological responses to ARTP irradiation is still limited. Therefore, to gain a molecular understanding of how irradiation with ARTP damages DNA, we irradiated the artificially synthesized mononucleotides of dATP, dTTP, dGTP, and dCTP, and the oligonucleotides of dA8, dT8, dG8, dC8, and dA2dT2dG2dC2 as chemical building blocks of DNA with ARTP for 1-4 min, identified the mononucleotide products using 31P- and 1H-nuclear magnetic resonance spectroscopy (NMR), and identified the oligonucleotide products using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) during ARTP treatment. The observed 31P-and 1H-NMR spectrum signals for the plasma-treated and untreated mononucleotides indicated that dATP was less stable to plasma irradiation than the other mononucleotides. The oligonucleotides after treatment with ARTP were found to have been broken into small fragments as shown by mass spectrometry, with the cleaved bonds and produced fragments identified according to their expected spectral m/z values or molecular weights derived from their m/z values. The stabilities of the oligonucleotides differed to ARTP irradiation, with dT8 being the most stable and was more beneficial to stabilizing single-stranded oligonucleotide structures compared to the other base groups (A, G, and C). This was consistent with the average potential energy level obtained by the molecular dynamic simulation of the oligonucleotides, i.e., dT8 > dC8 > dA8 > dG8 > dA2dT2dG2dC2. In summary, we found that ARTP treatment caused various structural changes to the oligonucleotides that may account for the wide and successful applications reported for ARTP-induced mutation breeding of various organisms.
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Affiliation(s)
- Liyan Wang
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
- Biobreeding Center, Wuxi Research Institute of Applied Technologies, Tsinghua University, Wuxi, 214072, People's Republic of China
- TmaxTree Biotechnology Co. Ltd., Luoyang, 471023, People's Republic of China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Dong He
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Lihua Jin
- College of Bioengineering, Beijing Polytechnic, Beijing, 100176, People's Republic of China
| | - Guo Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Nan Su
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Heping Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
- Center for Synthetic and System Biology, Tsinghua University, Beijing, People's Republic of China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, People's Republic of China.
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46
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Dijksteel GS, Ulrich MMW, Vlig M, Sobota A, Middelkoop E, Boekema BKHL. Safety and bactericidal efficacy of cold atmospheric plasma generated by a flexible surface Dielectric Barrier Discharge device against Pseudomonas aeruginosa in vitro and in vivo. Ann Clin Microbiol Antimicrob 2020; 19:37. [PMID: 32814573 PMCID: PMC7439657 DOI: 10.1186/s12941-020-00381-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
Background Cold atmospheric plasma (CAP), which is ionized gas produced at atmospheric pressure, could be a novel and potent antimicrobial therapy for the treatment of infected wounds. Previously we have shown that CAP generated with a flexible surface Dielectric Barrier Discharge (sDBD) is highly effective against bacteria in vitro and in ex vivo burn wound models. In the current paper, we determined the in vitro and in vivo safety and efficacy of CAP generated by this sDBD device. Methods The effect of CAP on DNA mutations of V79 fibroblasts was measured using a hypoxanthine–guanine-phosphoribosyltransferase (HPRT) assay. Furthermore, effects on cell proliferation, apoptosis and DNA damage in ex vivo burn wound models (BWMs) were assessed using immunohistochemistry. Next, 105 colony forming units (CFU) P. aeruginosa strain PAO1 were exposed to CAP in a 3D collagen-elastin matrix environment to determine the number of surviving bacteria in vitro. Finally, rat excision wounds were inoculated with 107 CFU PAO1 for 24 h. The wounds received a single CAP treatment, repeated treatments on 4 consecutive days with CAP, 100 µL of 1% (wt/wt) silver sulfadiazine or no treatment. Wound swabs and punch biopsies were taken to determine the number of surviving bacteria. Results Exposure of V79 fibroblasts to CAP did not increase the numbers of mutated colonies. Additionally, the number of proliferative, apoptotic and DNA damaged cells in the BWMs was comparable to that of the unexposed control. Exposure of PAO1 to CAP for 2 min resulted in the complete elimination of bacteria in vitro. Contrarily, CAP treatment for 6 min of rat wounds colonized with PAO1 did not effectively reduce the in vivo bacterial count. Conclusions CAP treatment was safe but showed limited efficacy against PAO1 in our rat wound infection model.
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Affiliation(s)
- Gabrielle S Dijksteel
- Association of Dutch Burn Centres, Zeestraat 29, 1941 AJ, Beverwijk, The Netherlands. .,Dept. of Plastic, Reconstructive & Hand Surgery, Amsterdam Movement Sciences, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
| | - Magda M W Ulrich
- Association of Dutch Burn Centres, Zeestraat 29, 1941 AJ, Beverwijk, The Netherlands.,Dept. of Plastic, Reconstructive & Hand Surgery, Amsterdam Movement Sciences, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.,Dept. of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marcel Vlig
- Association of Dutch Burn Centres, Zeestraat 29, 1941 AJ, Beverwijk, The Netherlands
| | - Ana Sobota
- Dept. of Applied Physics, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Esther Middelkoop
- Association of Dutch Burn Centres, Zeestraat 29, 1941 AJ, Beverwijk, The Netherlands.,Dept. of Plastic, Reconstructive & Hand Surgery, Amsterdam Movement Sciences, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Bouke K H L Boekema
- Association of Dutch Burn Centres, Zeestraat 29, 1941 AJ, Beverwijk, The Netherlands
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47
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Connecting Microbial Genotype with Phenotype in the Omics Era. Methods Mol Biol 2020. [PMID: 32720157 DOI: 10.1007/978-1-0716-0195-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Although rational design-based metabolic engineering has been applied widely to obtain promising microbial biocatalysts, conventional strategies such as adaptive laboratory evolution (ALE) and mutagenesis are still efficient approaches to improve microorganisms for exceptional features such as a broad spectrum of substrate utilization, robustness of cell growth, as well as high titer, yield, and productivity of the target products. In this chapter, we describe the procedure to generate mutant strains with desired phenotypes using ALE and a new mutagenesis approach of Atmosphere and Room Temperature Plasma (ARTP). In addition, we discuss the methodology to combine next-generation sequencing (NGS)-based genome-resequencing and RNA-Seq transcriptomics approaches to characterize the mutant strains and connect the phenotypes with their corresponding genotypic changes.
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48
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Shu L, Si X, Yang X, Ma W, Sun J, Zhang J, Xue X, Wang D, Gao Q. Enhancement of Acid Protease Activity of Aspergillus oryzae Using Atmospheric and Room Temperature Plasma. Front Microbiol 2020; 11:1418. [PMID: 32670249 PMCID: PMC7332548 DOI: 10.3389/fmicb.2020.01418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/02/2020] [Indexed: 12/02/2022] Open
Abstract
Atmospheric and room temperature plasma (ARTP) system is a novel and efficient mutagenesis protocol for microbial breeding. In this study, ARTP was employed to treat spores of Aspergillus oryzae strain 3.042 for selection of high acid protease producers. With an irradiation time of 150 s at the lethal rate of 90%, 19 mutants with higher acid protease activity were initially selected based on different mutant colony morphology and ratio of the clarification halo of protease activity to the colony diameter. Measurements of the acid protease activity revealed that mutant strain B-2 is characterized by a steady hereditary stability with increased acid protease, neutral protease and total protease activities of 54.7, 17.3, and 8.5%, respectively, and decreased alkaline protease activity of 8.1%. In summary, the identified mutant strain B-2 exhibits great potential for the enhancement of the insufficient acid protease activity during the middle and later stages of soy sauce fermentation.
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Affiliation(s)
- Liang Shu
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaoguang Si
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,The Institute of Seawater Desalination and Multipurpose Utilization, Ministry of Natural Resources, Tianjin, China
| | - Xinda Yang
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wenyan Ma
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jinglan Sun
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jian Zhang
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Xianli Xue
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Depei Wang
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
| | - Qiang Gao
- Key Laboratory of Industrial Microbiology and Engineering Research Center of Food Biotechnology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Industrial Fermentation Microbiology, Tianjin, China.,Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
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Todhanakasem T, Wu B, Simeon S. Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production. World J Microbiol Biotechnol 2020; 36:112. [PMID: 32656581 DOI: 10.1007/s11274-020-02885-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.
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Affiliation(s)
- Tatsaporn Todhanakasem
- Department of Agro- Industry, Faculty of Biotechnology, Assumption University, Ramkhamhaeng Road, Bangkapi, Bangkok, 10240, Thailand.
| | - Bo Wu
- Biomass Energy Technology Research Center, Biogas Institute of Ministry of Agriculture and Rural Affairs, Renmin Rd. S 4-13, Chengdu, 610041, China
| | - Saw Simeon
- Absolute Clean Energy Public Company Limited, ITF Tower 7th Floor, Silom Road, Bang Rak, Bangkok, 10500, Thailand
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50
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Peng XL, Zhao WJ, Wang YS, Dai KL, Cen YK, Liu ZQ, Zheng YG. Enhancement of gibberellic acid production from Fusarium fujikuroi by mutation breeding and glycerol addition. 3 Biotech 2020; 10:312. [PMID: 32582509 DOI: 10.1007/s13205-020-02303-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022] Open
Abstract
Gibberellic acid (GA3) is a natural plant growth hormone that has been widely used in agriculture and horticulture. To obtain higher GA3 producing strains, the method of screening the strains for resistance to simvastatin was used after treatment with nitrosoguanidine (NTG) and gamma rays. The rationale for the strategy was that mutants showing simvastatin resistance were likely to be high GA3 producers, as their activity of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase is relatively more effective. GA3 yield of mutant S109 increased by 14.2% than that of the original strain. The GA3 production ability in mutant S109 remained relatively stable after ten generations. With the addition of 0.4 g glycerol on the 5th day during the fermentation process in Erlenmeyer flask, maximum GA3 production of 2.7 g/L was achieved by this mutant, exhibiting 28.6% increase compared with original strain. Furthermore, we also achieved 2.8 g/L GA3 and had a 33.3% increase with addition 20 g glycerol on the 5th day during the fermentation process in a 5-L bioreactor. Our results indicated efficient GA3 production could be achieved on the condition that the supply of glycerol at the suitable conditions. This study would lay a foundation for industrial production of GA3.
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