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Yuan S, Shi J, Jiang J, Ma Y. Genome-scale top-down strategy to generate viable genome-reduced phages. Nucleic Acids Res 2022; 50:13183-13197. [PMID: 36511873 PMCID: PMC9825161 DOI: 10.1093/nar/gkac1168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Efforts have been made to reduce the genomes of living cells, but phage genome reduction remains challenging. It is of great interest to investigate whether genome reduction can make phages obtain new infectious properties. We developed a CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach and applied this to four distinct phages, thereby obtaining heterogeneous genome-reduced mutants. We isolated and sequenced 200 mutants with loss of up to 8-23% (3.3-35 kbp) of the original sequences. This allowed the identification of non-essential genes for phage propagation, although loss of these genes is mostly detrimental to phage fitness to various degrees. Notwithstanding this, mutants with higher infectious efficiency than their parental strains were characterized, indicating a trade-off between genome reduction and infectious fitness for phages. In conclusion, this study provides a foundation for future work to leverage the information generated by CiPGr in phage synthetic biology research.
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Affiliation(s)
- Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Shi
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianrong Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- To whom correspondence should be addressed. Tel: +86 755 8639 2674;
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2
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Tian J, Xing B, Li M, Xu C, Huo YX, Guo S. Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers. Int J Mol Sci 2022; 23:ijms23094853. [PMID: 35563243 PMCID: PMC9099979 DOI: 10.3390/ijms23094853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable host strains. Herein, we develop an efficient CRISPR-Cas9 method for large-scale and scarless genome engineering in the Bacillus subtilis genome, which can delete up to 134.3 kb DNA fragments, 3.5 times as long as the previous report, with a positivity rate of 100%. The effects of using a heterologous NHEJ system, linear donor DNA, and various donor DNA length on the engineering efficiencies were also investigated. The CRISPR-Cas9 method was then utilized for Bacillus subtilis genome simplification and construction of a series of individual and cumulative deletion mutants, which are further screened for overproducer of isobutanol, a new generation biofuel. These results suggest that the method is a powerful genome engineering tool for constructing and screening engineered host strains with enhanced capabilities, highlighting the potential for synthetic biology and metabolic engineering.
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3
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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4
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Yu H, Khokhlatchev AV, Chew C, Illendula A, Conaway M, Dryden K, Maeda DLNF, Rajasekaran V, Kester M, Zeichner SL. Minicells from Highly Genome Reduced Escherichia coli: Cytoplasmic and Surface Expression of Recombinant Proteins and Incorporation in the Minicells. ACS Synth Biol 2021; 10:2465-2477. [PMID: 34516078 DOI: 10.1021/acssynbio.1c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minicells, small cells lacking a chromosome, produced by bacteria with mutated min genes, which control cell division septum placement, have many potential uses. Minicells have contributed to basic bacterial physiology studies and can enable new biotechnological applications, including drug delivery and vaccines. Genome-reduced bacteria are another informative area of investigation. Investigators identified that with even almost 30% of the E. coli genome deleted, the bacteria still live. In biotechnology and synthetic biology, genome-reduced bacteria offer certain advantages. With genome-reduced bacteria, more recombinant genes can be placed into genome-reduced chromosomes and fewer cell resources are devoted to purposes apart from biotechnological goals. Here, we show that these two technologies can be combined: min mutants can be made in genome-reduced E. coli. The minC minD mutant genome-reduced E. coli produce minicells that concentrate engineered recombinant proteins within these spherical delivery systems. We expressed recombinant GFP protein in the cytoplasm of genome-reduced bacteria and showed that it is concentrated within the minicells. We also expressed proteins on the surfaces of minicells made from genome-reduced bacteria using a recombinant Gram-negative AIDA-I autotransporter expression cassette. Some autotransporters, like AIDA-I, are concentrated at the bacterial poles, where minicells bud. Recombinant proteins expressed on surfaces of the genome-reduced bacteria are concentrated on the minicells. Minicells made from genome-reduced bacteria may enable useful biotechnological innovations, such as drug delivery vehicles and vaccine immunogens.
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Affiliation(s)
- Hanna Yu
- Department of Pediatrics and Child Health Research Institute, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Andrei V. Khokhlatchev
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Claude Chew
- School of Medicine ORCA, Flow Cytometry Core Facility, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Anuradha Illendula
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Mark Conaway
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Kelly Dryden
- Department of Molecular Physiology and Biophysics, University of Virginia, Charlottesville, Virginia 22903, United States
| | | | - Vignesh Rajasekaran
- Department of Pediatrics and Child Health Research Institute, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Mark Kester
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22903, United States
- Director, nanoSTAR Institute, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Steven L. Zeichner
- Department of Pediatrics and Child Health Research Institute, University of Virginia, Charlottesville, Virginia 22903, United States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22903, United States
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5
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Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
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Simons M. Synthetic biology as a technoscience: The case of minimal genomes and essential genes. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 85:127-136. [PMID: 33966767 DOI: 10.1016/j.shpsa.2020.09.012] [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: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 06/12/2023]
Abstract
This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience.
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Affiliation(s)
- Massimiliano Simons
- Ghent University, Department of Philosophy and Moral Sciences, Blandijnberg 2, BE-9000, Ghent, Belgium.
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7
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Fan X, Zhang Y, Zhao F, Liu Y, Zhao Y, Wang S, Liu R, Yang C. Genome reduction enhances production of polyhydroxyalkanoate and alginate oligosaccharide in Pseudomonas mendocina. Int J Biol Macromol 2020; 163:2023-2031. [DOI: 10.1016/j.ijbiomac.2020.09.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/11/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
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8
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Chi H, Wang X, Shao Y, Qin Y, Deng Z, Wang L, Chen S. Engineering and modification of microbial chassis for systems and synthetic biology. Synth Syst Biotechnol 2019; 4:25-33. [PMID: 30560208 PMCID: PMC6290258 DOI: 10.1016/j.synbio.2018.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The 'Minimum genome factory' (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The 'cell factory' project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the 'secretome' [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications.
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Affiliation(s)
- Haotian Chi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiaoli Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yue Shao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Ying Qin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
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9
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Rustad M, Eastlund A, Jardine P, Noireaux V. Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction. Synth Biol (Oxf) 2018; 3:ysy002. [PMID: 32995511 PMCID: PMC7445788 DOI: 10.1093/synbio/ysy002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 11/30/2022] Open
Abstract
The bottom-up construction of biological entities from genetic information provides a broad range of opportunities to better understand fundamental processes within living cells, as well as holding great promise for the development of novel biomedical applications. Cell-free transcription–translation (TXTL) systems have become suitable platforms to tackle such topics because they recapitulate the process of gene expression. TXTL systems have advanced to where the in vitro construction of viable, complex, self-assembling deoxyribonucleic acid-programmed biological entities is now possible. Previously, we demonstrated the cell-free synthesis of three bacteriophages from their genomes: MS2, ΦX174, T7. In this work, we present the complete synthesis of the phage T4 from its 169-kbp genome in one-pot TXTL reactions. This achievement, for one of the largest coliphages, demonstrates the integration of complex gene regulation, metabolism and self-assembly, and brings the bottom-up synthesis of biological systems to a new level.
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Affiliation(s)
- Mark Rustad
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Allen Eastlund
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Paul Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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Abstract
Genome sequences have become the new phenotype for microbial evolutionists. The patterns of diversity revealed in the first 100 bacterial genomes fostered development of a comprehensive framework that can explain their contents, organization, and evolution.
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Affiliation(s)
- Howard Ochman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
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11
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Comparative bacterial genomics: defining the minimal core genome. Antonie van Leeuwenhoek 2012; 103:385-98. [DOI: 10.1007/s10482-012-9819-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
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12
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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Liu X, Wang SY, Wang J. A statistical feature of Hurst exponents of essential genes in bacterial genomes. Integr Biol (Camb) 2011; 4:93-8. [PMID: 22108754 DOI: 10.1039/c1ib00030f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
At present, methods for determining essential genes depend on biochemical experiments. There is therefore a demand for the development of analysis methods and software for identifying essential genes, based on the common features of these genes. In this study, we employed the Hurst exponent as a characteristic parameter and analyzed its distribution among nine bacterial species. We found that most of the significance levels of the Hurst exponents of essential genes were higher than those of the corresponding full-gene-set. Conversely, most of the significance levels of the Hurst exponents of nonessential genes remained unchanged or only increased slightly. Therefore, we propose that this feature represents a restraint for pre- or post-design checking of bacterial essential genes in computer-aided design.
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Affiliation(s)
- Xiao Liu
- College of Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing, 400044, China.
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Synthetic biology: From the first synthetic cell to see its current situation and future development. ACTA ACUST UNITED AC 2011; 56:229-237. [PMID: 32214738 PMCID: PMC7088918 DOI: 10.1007/s11434-010-4304-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/19/2010] [Indexed: 10/31/2022]
Abstract
Synthetic biology is an emerging field, which, since its birth, has shown great value and potential in many fields including medicine, energy, environment and agriculture. It is also important for the study of the origin and evolution of life. Since the publication of the first synthetic cell in May, 2010, synthetic biology again attracts high attention and leads to extensive discussions all over the world. There have been a number of researches and achievements on synthetic biology in the United States and European countries. While in China, so far there is no systematic research on synthetic biology. In order to promote the development of this new discipline in China, we organized this review to systematically introduce the concept and research content of synthetic biology, summarize the achievements, and investigate the current situation in both China and abroad. We also analyzed the opportunities and challenges in synthetic biology, and looked forward to the future development of synthetic biology, especially its future development in China.
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