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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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Liu Y, Wang K, Pan L, Chen X. Improved Production of ε-Poly-L-Lysine in Streptomyces albulus Using Genome Shuffling and Its High-Yield Mechanism Analysis. Front Microbiol 2022; 13:923526. [PMID: 35711770 PMCID: PMC9195005 DOI: 10.3389/fmicb.2022.923526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022] Open
Abstract
ε-Poly-L-lysine (ε-PL), a natural food preservative, has recently gained interest and mainly produced by Streptomyces albulus. Lacking of efficient breeding methods limit ε-PL production improving, knockout byproducts and increase of main product flux strategies as a logical solution to increase yield. However, removing byproduct formation and improving main product synthesis has seen limited success due to the genetic background of ε-PL producing organism is not clear. To overcome this limitation, random mutagenesis continues to be the best way towards improving strains for ε-PL production. Recent advances in Illumina sequencing opened new avenues to understand improved strains. In this work, we used genome shuffling on strains obtained by ribosome engineering to generate a better ε-PL producing strain. The mutant strain SG-86 produced 144.7% more ε-PL than the parent strain M-Z18. Except that SG-86 displayed obvious differences in morphology and ATP compared to parent strain M-Z18. Using Illumina sequencing, we mapped the genomic changes leading to the improved phenotype. Sequencing two strains showed that the genome of the mutant strain was about 2.1 M less than that of the parent strain, including a large number of metabolic pathways, secondary metabolic gene clusters, and gene deletions. In addition, there are many SNPs (single nucleotide polymorphisms) and InDels (insertions and deletions) in the mutant strain. Based on the results of data analysis, a mechanism of ε-PL overproduction in S. albulus SG-86 was preliminarily proposed. This study is of great significance for improving the fermentation performance and providing theoretical guidance for the metabolic engineering construction of ε-PL producing strains.
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Affiliation(s)
- Yongjuan Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Shandong Energy Institute, Qingdao, China.,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Kaifang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Long Pan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Xusheng Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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Li S, Mao Y, Zhang L, Wang M, Meng J, Liu X, Bai Y, Guo Y. Recent advances in microbial ε-poly-L-lysine fermentation and its diverse applications. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:65. [PMID: 35710433 PMCID: PMC9205021 DOI: 10.1186/s13068-022-02166-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The naturally occurring homo-polyamide biopolymer, ε-poly-L-lysine (ε-PL) consists of 25-35 L-lysine residues with amide linkages between α-carboxyl groups and ε-amino groups. ɛ-PL exhibits several useful properties because of its unusual structure, such as biodegradability, water solubility, no human toxicity, and broad-spectrum antibacterial activities; it is widely applied in the fields of food, medicine, clinical chemistry and electronics. However, current industrial production of ε-PL is only performed in a few countries. Based on an analysis of the physiological characteristics of ε-PL fermentation, current advances that enhance ε-PL fermentation, from strain improvement to product isolation are systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulatory mechanism of ε-PL synthesis; (2) enhancing biosynthetic performance through mutagenesis, fermentation optimization and metabolic engineering; and (3) understanding and improving the biological activity and functional properties of ε-PL. Finally, perspectives on engineering and exploiting ε-PL as a source material for the production of various advanced materials are also discussed, providing scientific guidelines for researchers to further improve the ε-PL fermentation process.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Yunren Mao
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Lifei Zhang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Miao Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Jinhao Meng
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Xiaoling Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Yunxia Bai
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Yuan Guo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, 530004, China.
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Wang L, Zhang C, Zhang J, Rao Z, Xu X, Mao Z, Chen X. Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications. Front Bioeng Biotechnol 2021; 9:748976. [PMID: 34650962 PMCID: PMC8506220 DOI: 10.3389/fbioe.2021.748976] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Abstract
ε-poly-L-lysine (ε-PL) is a naturally occurring poly(amino acid) of varying polymerization degree, which possesses excellent antimicrobial activity and has been widely used in food and pharmaceutical industries. To provide new perspectives from recent advances, this review compares several conventional and advanced strategies for the discovery of wild strains and development of high-producing strains, including isolation and culture-based traditional methods as well as genome mining and directed evolution. We also summarize process engineering approaches for improving production, including optimization of environmental conditions and utilization of industrial waste. Then, efficient downstream purification methods are described, including their drawbacks, followed by the brief introductions of proposed antimicrobial mechanisms of ε-PL and its recent applications. Finally, we discuss persistent challenges and future perspectives for the commercialization of ε-PL.
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Affiliation(s)
- Liang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Chongyang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jianhua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xueming Xu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Zhonggui Mao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xusheng Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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The Application of Ribosome Engineering to Natural Product Discovery and Yield Improvement in Streptomyces. Antibiotics (Basel) 2019; 8:antibiotics8030133. [PMID: 31480298 PMCID: PMC6784132 DOI: 10.3390/antibiotics8030133] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/10/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial natural product drug discovery and development has entered a new era, driven by microbial genomics and synthetic biology. Genome sequencing has revealed the vast potential to produce valuable secondary metabolites in bacteria and fungi. However, many of the biosynthetic gene clusters are silent under standard fermentation conditions. By rational screening for mutations in bacterial ribosomal proteins or RNA polymerases, ribosome engineering is a versatile approach to obtain mutants with improved titers for microbial product formation or new natural products through activating silent biosynthetic gene clusters. In this review, we discuss the mechanism of ribosome engineering and its application to natural product discovery and yield improvement in Streptomyces. Our analysis suggests that ribosome engineering is a rapid and cost-effective approach and could be adapted to speed up the discovery and development of natural product drug leads in the post-genomic era.
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Improvement of ε-poly-L-lysine production of Streptomyces albulus by continuous introduction of streptomycin resistance. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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