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Bai S, Luo H, Tong H, Wu Y, Yuan Y. Advances on transfer and maintenance of large DNA in bacteria, fungi, and mammalian cells. Biotechnol Adv 2024; 76:108421. [PMID: 39127411 DOI: 10.1016/j.biotechadv.2024.108421] [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: 03/24/2023] [Revised: 05/07/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Advances in synthetic biology allow the design and manipulation of DNA from the scale of genes to genomes, enabling the engineering of complex genetic information for application in biomanufacturing, biomedicine and other areas. The transfer and subsequent maintenance of large DNA are two core steps in large scale genome rewriting. Compared to small DNA, the high molecular weight and fragility of large DNA make its transfer and maintenance a challenging process. This review outlines the methods currently available for transferring and maintaining large DNA in bacteria, fungi, and mammalian cells. It highlights their mechanisms, capabilities and applications. The transfer methods are categorized into general methods (e.g., electroporation, conjugative transfer, induced cell fusion-mediated transfer, and chemical transformation) and specialized methods (e.g., natural transformation, mating-based transfer, virus-mediated transfection) based on their applicability to recipient cells. The maintenance methods are classified into genomic integration (e.g., CRISPR/Cas-assisted insertion) and episomal maintenance (e.g., artificial chromosomes). Additionally, this review identifies the major technological advantages and disadvantages of each method and discusses the development for large DNA transfer and maintenance technologies.
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Affiliation(s)
- Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Han Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China. @tju.edu.cn
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Huang T, Fakurazi S, Cheah PS, Ling KH. Chromosomal and cellular therapeutic approaches for Down syndrome: A research update. Biochem Biophys Res Commun 2024; 735:150664. [PMID: 39260337 DOI: 10.1016/j.bbrc.2024.150664] [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: 06/01/2024] [Revised: 08/20/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024]
Abstract
In individuals with Down syndrome (DS), an additional HSA21 chromosome copy leads to the overexpression of a myriad of HSA21 genes, disrupting the transcription of the entire genome. This dysregulation in transcription and post-transcriptional modifications contributes to abnormal phenotypes across nearly all tissues and organs in DS individuals. The array of severe clinical symptoms associated with trisomy 21 poses a considerable challenge in the quest for a cure for DS. Fortunately, a wealth of research suggests that chromosome therapy, hinging on cutting-edge genome editing technologies, can potentially eliminate the extra copy of the human chromosome 21. Genome editing tools have demonstrated their efficacy in restoring trisomy to a normal diploid state in vitro DS cell models. Furthermore, we delve into the noteworthy findings in cellular therapy for DS, with recent studies showcasing the increasing feasibility of strategies involving stem cells and CAR T-cells to address corresponding clinical phenotypes.
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Affiliation(s)
- Tan Huang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Sharida Fakurazi
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Pike-See Cheah
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Malaysian Research Institute on Ageing (MyAgeing(TM)), Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Malaysian Research Institute on Ageing (MyAgeing(TM)), Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Bai S, Luo H, Tong H, Wu Y. Application and Technical Challenges in Design, Cloning, and Transfer of Large DNA. Bioengineering (Basel) 2023; 10:1425. [PMID: 38136016 PMCID: PMC10740618 DOI: 10.3390/bioengineering10121425] [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: 11/18/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In the field of synthetic biology, rapid advancements in DNA assembly and editing have made it possible to manipulate large DNA, even entire genomes. These advancements have facilitated the introduction of long metabolic pathways, the creation of large-scale disease models, and the design and assembly of synthetic mega-chromosomes. Generally, the introduction of large DNA in host cells encompasses three critical steps: design-cloning-transfer. This review provides a comprehensive overview of the three key steps involved in large DNA transfer to advance the field of synthetic genomics and large DNA engineering.
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Affiliation(s)
- Song Bai
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Han Luo
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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McCulloch LH, Sambasivam V, Hughes AL, Annaluru N, Ramalingam S, Fanfani V, Lobzaev E, Mitchell LA, Cai J, Jiang H, LaCava J, Taylor MS, Bishai WR, Stracquadanio G, Steinmetz LM, Bader JS, Zhang W, Boeke JD, Chandrasegaran S. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. CELL GENOMICS 2023; 3:100419. [PMID: 38020974 PMCID: PMC10667316 DOI: 10.1016/j.xgen.2023.100419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023]
Abstract
We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome, synIX (synthetic chromosome IX). Combined chromosome construction methods were used to synthesize and integrate its left arm (synIXL) into a strain containing previously described synIXR. We identified and resolved a bug affecting expression of EST3, a crucial gene for telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains, we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. Both steps of this chromosome substitution method were efficient. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these chromosomes.
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Affiliation(s)
- Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Vijayan Sambasivam
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amanda L. Hughes
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Narayana Annaluru
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sivaprakash Ramalingam
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
- School of Informatics, The University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY 10065, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY 10065, USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin S. Taylor
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - William R. Bishai
- Department of Medicine/Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Lars M. Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Srinivasan Chandrasegaran
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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He B, Ma Y, Tian F, Zhao GR, Wu Y, Yuan YJ. YLC-assembly: large DNA assembly via yeast life cycle. Nucleic Acids Res 2023; 51:8283-8292. [PMID: 37486765 PMCID: PMC10450165 DOI: 10.1093/nar/gkad599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023] Open
Abstract
As an enabling technique of synthetic biology, the scale of DNA assembly largely determines the scale of genetic manipulation. However, large DNA assembly technologies are generally cumbersome and inefficient. Here, we developed a YLC (yeast life cycle)-assembly method that enables in vivo iterative assembly of large DNA by nesting cell-cell transfer of assembled DNA in the cycle of yeast mating and sporulation. Using this method, we successfully assembled a hundred-kilobase (kb)-sized endogenous yeast DNA and a megabase (Mb)-sized exogenous DNA. For each round, over 104 positive colonies per 107 cells could be obtained, with an accuracy ranging from 67% to 100%. Compared with other Mb-sized DNA assembly methods, this method exhibits a higher success rate with an easy-to-operate workflow that avoid in vitro operations of large DNA. YLC-assembly lowers the technical difficulty of Mb-sized DNA assembly and could be a valuable tool for large-scale genome engineering and synthetic genomics.
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Affiliation(s)
- Bo He
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yuan Ma
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Fangfang Tian
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Guang-Rong Zhao
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Ying-Jin Yuan
- Frontiers 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
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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Zhu MC, Cui YZ, Wang JY, Xu H, Li BZ, Yuan YJ. Cross-species microbial genome transfer: a Review. Front Bioeng Biotechnol 2023; 11:1183354. [PMID: 37214278 PMCID: PMC10194841 DOI: 10.3389/fbioe.2023.1183354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Synthetic biology combines the disciplines of biology, chemistry, information science, and engineering, and has multiple applications in biomedicine, bioenergy, environmental studies, and other fields. Synthetic genomics is an important area of synthetic biology, and mainly includes genome design, synthesis, assembly, and transfer. Genome transfer technology has played an enormous role in the development of synthetic genomics, allowing the transfer of natural or synthetic genomes into cellular environments where the genome can be easily modified. A more comprehensive understanding of genome transfer technology can help to extend its applications to other microorganisms. Here, we summarize the three host platforms for microbial genome transfer, review the recent advances that have been made in genome transfer technology, and discuss the obstacles and prospects for the development of genome transfer.
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