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Schindler D, Walker RSK, Cai Y. Methodological advances enabled by the construction of a synthetic yeast genome. Cell Rep Methods 2024; 4:100761. [PMID: 38653205 PMCID: PMC11046031 DOI: 10.1016/j.crmeth.2024.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
The international Synthetic Yeast Project (Sc2.0) aims to construct the first synthetic designer eukaryote genome. Over the past few years, the Sc2.0 consortium has achieved several significant milestones by synthesizing and characterizing all 16 nuclear chromosomes of the yeast Saccharomyces cerevisiae, as well as a 17thde novo neochromosome containing all nuclear tRNA genes. In this commentary, we discuss the recent technological advances achieved in this project and provide a perspective on how they will impact the emerging field of synthetic genomics in the future.
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Affiliation(s)
- Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany.
| | - Roy S K Walker
- School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
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Coradini ALV, Ville CN, Krieger ZA, Roemer J, Hull C, Yang S, Lusk DT, Ehrenreich IM. Building synthetic chromosomes from natural DNA. Nat Commun 2023; 14:8337. [PMID: 38123566 PMCID: PMC10733283 DOI: 10.1038/s41467-023-44112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
De novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We use CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment reveals that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Christopher Ne Ville
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zachary A Krieger
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joshua Roemer
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Cara Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shawn Yang
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daniel T Lusk
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S, Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. Cell Genom 2023; 3:100439. [PMID: 38020967 PMCID: PMC10667551 DOI: 10.1016/j.xgen.2023.100439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.
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Affiliation(s)
- Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Biochemistry, Cellular and Molecular Biology Graduate program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | - Guillaume Mercy
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Jonna Heldrich
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mingyu Kenneth Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Kun Yang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Jitong Cai
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Giovanni Stracquadanio
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David B. Kaback
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, International Center for Public Health, Newark, NJ 07101-1709, USA
| | - Joel S. Bader
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Julien Mozziconacci
- Structure and instability of Genomes Lab, UMR 7196, Muséum National d'Histoire Naturelle (MNHN), 75005 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | | | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, Tandon School of Engineering, Brooklyn, NY 11201, USA
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