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Mizutani M, Omori S, Yamane N, Suzuki Y, Glass JI, Chuang RY, Fukatsu T, Kakizawa S. Cloning and sequencing analysis of whole Spiroplasma genome in yeast. Front Microbiol 2024; 15:1411609. [PMID: 38881660 PMCID: PMC11176537 DOI: 10.3389/fmicb.2024.1411609] [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: 04/03/2024] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Cloning and transfer of long-stranded DNA in the size of a bacterial whole genome has become possible by recent advancements in synthetic biology. For the whole genome cloning and whole genome transplantation, bacteria with small genomes have been mainly used, such as mycoplasmas and related species. The key benefits of whole genome cloning include the effective maintenance and preservation of an organism's complete genome within a yeast host, the capability to modify these genome sequences through yeast-based genetic engineering systems, and the subsequent use of these cloned genomes for further experiments. This approach provides a versatile platform for in-depth genomic studies and applications in synthetic biology. Here, we cloned an entire genome of an insect-associated bacterium, Spiroplasma chrysopicola, in yeast. The 1.12 Mbp whole genome was successfully cloned in yeast, and sequences of several clones were confirmed by Illumina sequencing. The cloning efficiency was high, and the clones contained only a few mutations, averaging 1.2 nucleotides per clone with a mutation rate of 4 × 10-6. The cloned genomes could be distributed and used for further research. This study serves as an initial step in the synthetic biology approach to Spiroplasma.
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Affiliation(s)
- Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Sawako Omori
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Noriko Yamane
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yo Suzuki
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, CA, United States
| | - John I Glass
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, CA, United States
| | - Ray-Yuan Chuang
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, CA, United States
- Telesis Bio, San Diego, CA, United States
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shigeyuki Kakizawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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2
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Bittencourt DDC, Brown DM, Assad-Garcia N, Romero MR, Sun L, Palhares de Melo LAM, Freire M, Glass JI. Minimal Bacterial Cell JCVI-syn3B as a Chassis to Investigate Interactions between Bacteria and Mammalian Cells. ACS Synth Biol 2024; 13:1128-1141. [PMID: 38507598 PMCID: PMC11036491 DOI: 10.1021/acssynbio.3c00513] [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: 08/21/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Mycoplasmas are atypical bacteria with small genomes that necessitate colonization of their respective animal or plant hosts as obligate parasites, whether as pathogens, or commensals. Some can grow axenically in specialized complex media yet show only host-cell-dependent growth in cell culture, where they can survive chronically and often through interactions involving surface colonization or internalization. To develop a mycoplasma-based system to identify genes mediating such interactions, we exploited genetically tractable strains of the goat pathogen Mycoplasma mycoides (Mmc) with synthetic designer genomes representing the complete natural organism (minus virulence factors; JCVI-syn1.0) or its reduced counterpart (JCVI-syn3B) containing only those genes supporting axenic growth. By measuring growth of surviving organisms, physical association with cultured human cells (HEK-293T, HeLa), and induction of phagocytosis by human myeloid cells (dHL-60), we determined that JCVI-syn1.0 contained a set of eight genes (MMSYN1-0179 to MMSYN1-0186, dispensable for axenic growth) conferring survival, attachment, and phagocytosis phenotypes. JCVI-syn3B lacked these phenotypes, but insertion of these genes restored cell attachment and phagocytosis, although not survival. These results indicate that JCVI-syn3B may be a powerful living platform to analyze the role of specific gene sets, from any organism, on the interaction with diverse mammalian cells in culture.
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Affiliation(s)
- Daniela
Matias de C. Bittencourt
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - David M. Brown
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Nacyra Assad-Garcia
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Michaela R. Romero
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Lijie Sun
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Luis Alberto M. Palhares de Melo
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - Marcelo Freire
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - John I. Glass
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
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3
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Nucifora D, Mehta ND, Giguere DJ, Karas BJ. An Expanded Genetic Toolbox to Accelerate the Creation of Acholeplasma laidlawii Driven by Synthetic Genomes. ACS Synth Biol 2024; 13:45-53. [PMID: 38113213 PMCID: PMC10805103 DOI: 10.1021/acssynbio.3c00399] [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: 06/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
We have developed genetic tools for the atypical bacterium Acholeplasma laidlawii. A. laidlawii is a member of the class Mollicutes, which lacks cell walls, has small genomes, and has limited metabolic capabilities, requiring many metabolites from their hosts. Several of these traits have facilitated the development of genome transplantation for some Mollicutes, consequently enabling the generation of synthetic cells. Here, we propose the development of genome transplantation for A. laidlawii. We first investigated a donor-recipient relationship between two strains, PG-8A and PG-8195, through whole-genome sequencing. We then created multihost shuttle plasmids and used them to optimize an electroporation protocol. We also evolved a superior strain for DNA uptake via electroporation. We created a PG-8A donor strain with a Tn5 transposon carrying a tetracycline resistance gene. These tools will enhance Acholeplasma research and accelerate the effort toward creating A. laidlawii strains with synthetic genomes.
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Affiliation(s)
- Daniel
P. Nucifora
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Nidhi D. Mehta
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Daniel J. Giguere
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Bogumil J. Karas
- Department
of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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4
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Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine. Oncotarget 2023; 14:1009-1033. [PMID: 38147065 PMCID: PMC10750837 DOI: 10.18632/oncotarget.28546] [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: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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5
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Guesdon G, Gourgues G, Rideau F, Ipoutcha T, Manso-Silván L, Jules M, Sirand-Pugnet P, Blanchard A, Lartigue C. Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast. ACS Synth Biol 2023; 12:3252-3266. [PMID: 37843014 PMCID: PMC10662353 DOI: 10.1021/acssynbio.3c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Indexed: 10/17/2023]
Abstract
The genetic engineering of genome fragments larger than 100 kbp is challenging and requires both specific methods and cloning hosts. The yeast Saccharomyces cerevisiae is considered as a host of choice for cloning and engineering whole or partial genomes from viruses, bacteria, and algae. Several methods are now available to perform these manipulations, each with its own limitations. In order to extend the range of yeast cloning strategies, a new approach combining two already described methods, Fusion cloning and CReasPy-Cloning, was developed. The CReasPy-Fusion method allows the simultaneous cloning and engineering of megabase-sized genomes in yeast by the fusion of bacterial cells with yeast spheroplasts carrying the CRISPR-Cas9 system. With this new approach, we demonstrate the feasibility of cloning and editing whole genomes from several Mycoplasma species belonging to different phylogenetic groups. We also show that CReasPy-Fusion allows the capture of large genome fragments with high efficacy, resulting in the successful cloning of selected loci in yeast. We finally identify bacterial nuclease encoding genes as barriers for CReasPy-Fusion by showing that their removal from the donor genome improves the cloning efficacy.
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Affiliation(s)
- Gabrielle Guesdon
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Géraldine Gourgues
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Fabien Rideau
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Thomas Ipoutcha
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Lucía Manso-Silván
- CIRAD,
UMR ASTRE, F-34398 Montpellier, France
- ASTRE,
Univ. Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Matthieu Jules
- Université
Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, F-78350 Jouy-en-Josas, France
| | - Pascal Sirand-Pugnet
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Alain Blanchard
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Carole Lartigue
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
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6
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Zhao G, Lu D, Li M, Wang Y. Gene editing tools for mycoplasmas: references and future directions for efficient genome manipulation. Front Microbiol 2023; 14:1191812. [PMID: 37275127 PMCID: PMC10232828 DOI: 10.3389/fmicb.2023.1191812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Mycoplasmas are successful pathogens that cause debilitating diseases in humans and various animal hosts. Despite the exceptionally streamlined genomes, mycoplasmas have evolved specific mechanisms to access essential nutrients from host cells. The paucity of genetic tools to manipulate mycoplasma genomes has impeded studies of the virulence factors of pathogenic species and mechanisms to access nutrients. This review summarizes several strategies for editing of mycoplasma genomes, including homologous recombination, transposons, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and synthetic biology. In addition, the mechanisms and features of different tools are discussed to provide references and future directions for efficient manipulation of mycoplasma genomes.
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Affiliation(s)
- Gang Zhao
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Yinchuan, China
- School of Life Sciences, Ningxia University, Yinchuan, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Doukun Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Min Li
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Yinchuan, China
- School of Life Sciences, Ningxia University, Yinchuan, China
| | - Yujiong Wang
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Yinchuan, China
- School of Life Sciences, Ningxia University, Yinchuan, China
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7
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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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8
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Talenton V, Baby V, Gourgues G, Mouden C, Claverol S, Vashee S, Blanchard A, Labroussaa F, Jores J, Arfi Y, Sirand-Pugnet P, Lartigue C. Genome Engineering of the Fast-Growing Mycoplasma feriruminatoris toward a Live Vaccine Chassis. ACS Synth Biol 2022; 11:1919-1930. [PMID: 35511588 PMCID: PMC9128628 DOI: 10.1021/acssynbio.2c00062] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Development of a new generation of vaccines is a key challenge for the control of infectious diseases affecting both humans and animals. Synthetic biology methods offer new ways to engineer bacterial chassis that can be used as vectors to present heterologous antigens and train the immune system against pathogens. Here, we describe the construction of a bacterial chassis based on the fast-growing Mycoplasma feriruminatoris, and the first steps toward its application as a live vaccine against contagious caprine pleuropneumonia (CCPP). To do so, the M. feriruminatoris genome was cloned in yeast, modified by iterative cycles of Cas9-mediated deletion of loci encoding virulence factors, and transplanted back in Mycoplasma capricolum subsp. capricolum recipient cells to produce the designed M. feriruminatoris chassis. Deleted genes encoded the glycerol transport and metabolism systems GtsABCD and GlpOKF and the Mycoplasma Ig binding protein-Mycoplasma Ig protease (MIB-MIP) immunoglobulin cleavage system. Phenotypic assays of the M. feriruminatoris chassis confirmed the corresponding loss of H2O2 production and IgG cleavage activities, while growth remained unaltered. The resulting mycoplasma chassis was further evaluated as a platform for the expression of heterologous surface proteins. A genome locus encoding an inactivated MIB-MIP system from the CCPP-causative agent Mycoplasma capricolum subsp. capripneumoniae was grafted in replacement of its homolog at the original locus in the chassis genome. Both heterologous proteins were detected in the resulting strain using proteomics, confirming their expression. This study demonstrates that advanced genome engineering methods are henceforth available for the fast-growing M. feriruminatoris, facilitating the development of novel vaccines, in particular against major mycoplasma diseases.
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Affiliation(s)
- Vincent Talenton
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | - Vincent Baby
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
- Département de Biologie, Université de Sherbrooke, J1K 2R1 Sherbrooke, Québec, Canada
| | - Geraldine Gourgues
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | | | - Stephane Claverol
- Plateforme Proteome, University of Bordeaux, F-33076 Bordeaux, France
| | - Sanjay Vashee
- J. Craig Venter Institute, Rockville, Maryland 20850, United States
| | - Alain Blanchard
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Joerg Jores
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Yonathan Arfi
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
| | | | - Carole Lartigue
- University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d’Ornon, France
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9
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Koster CC, Postma ED, Knibbe E, Cleij C, Daran-Lapujade P. Synthetic Genomics From a Yeast Perspective. Front Bioeng Biotechnol 2022; 10:869486. [PMID: 35387293 PMCID: PMC8979029 DOI: 10.3389/fbioe.2022.869486] [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: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Synthetic Genomics focuses on the construction of rationally designed chromosomes and genomes and offers novel approaches to study biology and to construct synthetic cell factories. Currently, progress in Synthetic Genomics is hindered by the inability to synthesize DNA molecules longer than a few hundred base pairs, while the size of the smallest genome of a self-replicating cell is several hundred thousand base pairs. Methods to assemble small fragments of DNA into large molecules are therefore required. Remarkably powerful at assembling DNA molecules, the unicellular eukaryote Saccharomyces cerevisiae has been pivotal in the establishment of Synthetic Genomics. Instrumental in the assembly of entire genomes of various organisms in the past decade, the S. cerevisiae genome foundry has a key role to play in future Synthetic Genomics developments.
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Affiliation(s)
- Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Eline D Postma
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Ewout Knibbe
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Céline Cleij
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
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10
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Brumwell SL, Van Belois KD, Giguere DJ, Edgell DR, Karas BJ. Conjugation-Based Genome Engineering in Deinococcus radiodurans. ACS Synth Biol 2022; 11:1068-1076. [PMID: 35254818 PMCID: PMC8939323 DOI: 10.1021/acssynbio.1c00524] [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] [Indexed: 11/28/2022]
Abstract
Deinococcus radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based DNA transfer method from E. coli to D. radiodurans, allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by targeting restriction-modification genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facilitate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.
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Affiliation(s)
- Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Katherine D Van Belois
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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11
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Rees-Garbutt J, Rightmyer J, Chalkley O, Marucci L, Grierson C. Testing Theoretical Minimal Genomes Using Whole-Cell Models. ACS Synth Biol 2021; 10:1598-1604. [PMID: 34111356 DOI: 10.1021/acssynbio.0c00515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The minimal gene set for life has often been theorized, with at least ten produced for Mycoplasma genitalium (M. genitalium). Due to the difficulty of using M. genitalium in the lab, combined with its long replication time of 12-15 h, none of these theoretical minimal genomes have been tested, even with modern techniques. The publication of the M. genitalium whole-cell model provided the first opportunity to test them, simulating the genome edits in silico. We simulated minimal gene sets from the literature, finding that they produced in silico cells that did not divide. Using knowledge from previous research, we reintroduced specific essential and low essential genes in silico; enabling cellular division. This reinforces the need to identify species-specific low essential genes and their interactions. Any genome designs created using the currently incomplete and fragmented gene essentiality information will very likely require in vivo reintroductions to correct issues and produce dividing cells.
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Affiliation(s)
- Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Jake Rightmyer
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Oliver Chalkley
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
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12
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Abstract
DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , , .,Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY 11201, USA
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13
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Belda I, Williams TC, de Celis M, Paulsen IT, Pretorius IS. Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell. Nat Commun 2021; 12:1599. [PMID: 33707418 PMCID: PMC7952416 DOI: 10.1038/s41467-021-21877-y] [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] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
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Affiliation(s)
- Ignacio Belda
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Thomas C. Williams
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Miguel de Celis
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Ian T. Paulsen
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Isak S. Pretorius
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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14
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Postma ED, Dashko S, van Breemen L, Taylor Parkins SK, van den Broek M, Daran JM, Daran-Lapujade P. A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae. Nucleic Acids Res 2021; 49:1769-1783. [PMID: 33423048 PMCID: PMC7897487 DOI: 10.1093/nar/gkaa1167] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 11/10/2020] [Accepted: 12/14/2020] [Indexed: 12/02/2022] Open
Abstract
The construction of microbial cell factories for sustainable production of chemicals and pharmaceuticals requires extensive genome engineering. Using Saccharomyces cerevisiae, this study proposes synthetic neochromosomes as orthogonal expression platforms for rewiring native cellular processes and implementing new functionalities. Capitalizing the powerful homologous recombination capability of S. cerevisiae, modular neochromosomes of 50 and 100 kb were fully assembled de novo from up to 44 transcriptional-unit-sized fragments in a single transformation. These assemblies were remarkably efficient and faithful to their in silico design. Neochromosomes made of non-coding DNA were stably replicated and segregated irrespective of their size without affecting the physiology of their host. These non-coding neochromosomes were successfully used as landing pad and as exclusive expression platform for the essential glycolytic pathway. This work pushes the limit of DNA assembly in S. cerevisiae and paves the way for de novo designer chromosomes as modular genome engineering platforms in S. cerevisiae.
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Affiliation(s)
- Eline D Postma
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Sofia Dashko
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Lars van Breemen
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Shannara K Taylor Parkins
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627HZ Delft, The Netherlands
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15
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Coradini ALV, Hull CB, Ehrenreich IM. Building genomes to understand biology. Nat Commun 2020; 11:6177. [PMID: 33268788 PMCID: PMC7710724 DOI: 10.1038/s41467-020-19753-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.
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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, 90089-2910, USA
| | - Cara B Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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16
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Matteau D, Lachance J, Grenier F, Gauthier S, Daubenspeck JM, Dybvig K, Garneau D, Knight TF, Jacques P, Rodrigue S. Integrative characterization of the near-minimal bacterium Mesoplasma florum. Mol Syst Biol 2020; 16:e9844. [PMID: 33331123 PMCID: PMC7745072 DOI: 10.15252/msb.20209844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
The near-minimal bacterium Mesoplasma florum is an interesting model for synthetic genomics and systems biology due to its small genome (~ 800 kb), fast growth rate, and lack of pathogenic potential. However, fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. We investigated several physical and physiological parameters of this bacterium, including cell size, growth kinetics, and biomass composition of the cell. We also performed the first genome-wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein-coding sequences. We converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts provide a strong experimental foundation for the development of a genome-scale model for M. florum and will guide future genome engineering endeavors in this simple organism.
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Affiliation(s)
- Dominick Matteau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Frédéric Grenier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Samuel Gauthier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | | | - Kevin Dybvig
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamALUSA
| | - Daniel Garneau
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
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17
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Vashee S, Arfi Y, Lartigue C. Budding yeast as a factory to engineer partial and complete microbial genomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 24:1-8. [PMID: 33015421 PMCID: PMC7523139 DOI: 10.1016/j.coisb.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Yeast cells have long been used as hosts to propagate exogenous DNA. Recent progress in genome editing opens new avenues in synthetic biology. These developments allow the efficient engineering of microbial genomes in Saccharomyces cerevisiae that can then be rescued to yield modified bacteria/viruses. Recent examples show that the ability to quickly synthesize, assemble, and/or modify viral and bacterial genomes may be a critical factor to respond to emerging pathogens. However, this process has some limitations. DNA molecules much larger than two megabase pairs are complex to clone, bacterial genomes have proven to be difficult to rescue, and the dual-use potential of these technologies must be carefully considered. Regardless, the use of yeast as a factory has enormous appeal for biological applications.
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Affiliation(s)
| | - Yonathan Arfi
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, Villenave d'Ornon, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, Villenave d'Ornon, France
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18
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Rees-Garbutt J, Chalkley O, Grierson C, Marucci L. Minimal Genome Design Algorithms Using Whole-Cell Models. Methods Mol Biol 2020; 2189:183-198. [PMID: 33180302 DOI: 10.1007/978-1-0716-0822-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Synthetic biologists engineer cells and cellular functions using design-build-test cycles; when the task is to extensively engineer entire genomes, the lack of appropriate design tools and biological knowledge about each gene in a cell can lengthen the process, requiring time-consuming and expensive experimental iterations.Whole-cell models represent a new avenue for genome design; the bacteria Mycoplasma genitalium has the first (and currently only published) whole-cell model which combines 28 cellular submodels and represents the integrated functions of every gene and molecule in a cell.We created two minimal genome design algorithms, GAMA and Minesweeper, that produced 1000s of in silico minimal genomes by running simulations on multiple supercomputers. Here we describe the steps to produce in silico cells with reduced genomes, combining minimisation algorithms with whole-cell model simulations.We foresee that the combination of similar algorithms and whole-cell models could later be used for a broad spectrum of genome design applications across cellular species when appropriate models become available.
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Affiliation(s)
- Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Oliver Chalkley
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.,Bristol Centre for Complexity Science, University of Bristol, Bristol, UK
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol, UK. .,School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol, UK. .,Department of Engineering Mathematics, University of Bristol, Bristol, UK. .,School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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19
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Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology. Bioengineering (Basel) 2020; 7:bioengineering7040137. [PMID: 33138080 PMCID: PMC7711850 DOI: 10.3390/bioengineering7040137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
The field of genetic engineering was born in 1973 with the “construction of biologically functional bacterial plasmids in vitro”. Since then, a vast number of technologies have been developed allowing large-scale reading and writing of DNA, as well as tools for complex modifications and alterations of the genetic code. Natural genomes can be seen as software version 1.0; synthetic genomics aims to rewrite this software with “build to understand” and “build to apply” philosophies. One of the predominant model organisms is the baker’s yeast Saccharomyces cerevisiae. Its importance ranges from ancient biotechnologies such as baking and brewing, to high-end valuable compound synthesis on industrial scales. This tiny sugar fungus contributed greatly to enabling humankind to reach its current development status. This review discusses recent developments in the field of genetic engineering for budding yeast S. cerevisiae, and its application in biotechnology. The article highlights advances from Sc1.0 to the developments in synthetic genomics paving the way towards Sc2.0. With the synthetic genome of Sc2.0 nearing completion, the article also aims to propose perspectives for potential Sc3.0 and subsequent versions as well as its implications for basic and applied research.
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20
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Cochrane RR, Brumwell SL, Shrestha A, Giguere DJ, Hamadache S, Gloor GB, Edgell DR, Karas BJ. Cloning of Thalassiosira pseudonana's Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli. BIOLOGY 2020; 9:E358. [PMID: 33114477 PMCID: PMC7693118 DOI: 10.3390/biology9110358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/30/2023]
Abstract
Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana's mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.
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Affiliation(s)
| | | | | | | | | | | | | | - Bogumil J. Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada; (R.R.C.); (S.L.B.); (A.S.); (D.J.G.); (S.H.); (G.B.G.); (D.R.E.)
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21
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Contagious Bovine and Caprine Pleuropneumonia: a research community's recommendations for the development of better vaccines. NPJ Vaccines 2020; 5:66. [PMID: 32728480 PMCID: PMC7381681 DOI: 10.1038/s41541-020-00214-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/03/2020] [Indexed: 12/26/2022] Open
Abstract
Contagious bovine pleuropneumonia (CBPP) and contagious caprine pleuropneumonia (CCPP) are major infectious diseases of ruminants caused by mycoplasmas in Africa and Asia. In contrast with the limited pathology in the respiratory tract of humans infected with mycoplasmas, CBPP and CCPP are devastating diseases associated with high morbidity and mortality. Beyond their obvious impact on animal health, CBPP and CCPP negatively impact the livelihood and wellbeing of a substantial proportion of livestock-dependent people affecting their culture, economy, trade and nutrition. The causative agents of CBPP and CCPP are Mycoplasma mycoides subspecies mycoides and Mycoplasma capricolum subspecies capripneumoniae, respectively, which have been eradicated in most of the developed world. The current vaccines used for disease control consist of a live attenuated CBPP vaccine and a bacterin vaccine for CCPP, which were developed in the 1960s and 1980s, respectively. Both of these vaccines have many limitations, so better vaccines are urgently needed to improve disease control. In this article the research community prioritized biomedical research needs related to challenge models, rational vaccine design and protective immune responses. Therefore, we scrutinized the current vaccines as well as the challenge-, pathogenicity- and immunity models. We highlight research gaps and provide recommendations towards developing safer and more efficacious vaccines against CBPP and CCPP.
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22
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Piñero-Lambea C, Garcia-Ramallo E, Martinez S, Delgado J, Serrano L, Lluch-Senar M. Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection. ACS Synth Biol 2020; 9:1693-1704. [PMID: 32502342 PMCID: PMC7372593 DOI: 10.1021/acssynbio.0c00022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Mycoplasma species
share a set of features, such as lack of a cell
wall, streamlined genomes, simplified metabolism, and the use of a
deviant genetic code, that make them attractive approximations of
what a chassis strain should ideally be. Among them, Mycoplasma
pneumoniae arises as a candidate for synthetic biology projects,
as it is one of the most deeply characterized bacteria. However, the
historical paucity of tools for editing Mycoplasma genomes has precluded
the establishment of M. pneumoniae as a suitable
chassis strain. Here, we developed an oligonucleotide recombineering
method for this strain based on GP35, a ssDNA recombinase originally
encoded by a Bacillus subtilis-associated phage.
GP35-mediated oligo recombineering is able to carry out point mutations
in the M. pneumoniae genome with an efficiency as
high as 2.7 × 10–2, outperforming oligo recombineering
protocols developed for other bacteria. Gene deletions of different
sizes showed a decreasing power trend between efficiency and the scale
of the attempted edition. However, the editing rates for all modifications
increased when CRISPR/Cas9 was used to counterselect nonedited cells.
This allowed edited clones carrying chromosomal deletions of up to
1.8 kb to be recovered with little to no screening of survivor cells.
We envision this technology as a major step toward the use of M. pneumoniae, and possibly other Mycoplasmas, as synthetic
biology chassis strains.
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Affiliation(s)
- Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Garcia-Ramallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Sira Martinez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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23
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Thi Nhu Thao T, Labroussaa F, Ebert N, V'kovski P, Stalder H, Portmann J, Kelly J, Steiner S, Holwerda M, Kratzel A, Gultom M, Schmied K, Laloli L, Hüsser L, Wider M, Pfaender S, Hirt D, Cippà V, Crespo-Pomar S, Schröder S, Muth D, Niemeyer D, Corman VM, Müller MA, Drosten C, Dijkman R, Jores J, Thiel V. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature 2020; 582:561-565. [PMID: 32365353 DOI: 10.1038/s41586-020-2294-9] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Reverse genetics has been an indispensable tool to gain insights into viral pathogenesis and vaccine development. The genomes of large RNA viruses, such as those from coronaviruses, are cumbersome to clone and manipulate in Escherichia coli owing to the size and occasional instability of the genome1-3. Therefore, an alternative rapid and robust reverse-genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Pneumoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples or synthetic DNA, and these fragments were then reassembled in one step in Saccharomyces cerevisiae using transformation-associated recombination cloning to maintain the genome as a yeast artificial chromosome. T7 RNA polymerase was then used to generate infectious RNA to rescue viable virus. Using this platform, we were able to engineer and generate chemically synthesized clones of the virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)4, which has caused the recent pandemic of coronavirus disease (COVID-19), in only a week after receipt of the synthetic DNA fragments. The technical advance that we describe here facilitates rapid responses to emerging viruses as it enables the real-time generation and functional characterization of evolving RNA virus variants during an outbreak.
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Affiliation(s)
- Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Melle Holwerda
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Mitra Gultom
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Laura Laloli
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Linda Hüsser
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manon Wider
- Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Department for Molecular and Medical Virology, Ruhr-Universität Bochum, Bochum, Germany
| | - Dagny Hirt
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valentina Cippà
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvia Crespo-Pomar
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Simon Schröder
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Doreen Muth
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Insitute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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24
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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25
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Dawe RK. Charting the path to fully synthetic plant chromosomes. Exp Cell Res 2020; 390:111951. [PMID: 32151492 DOI: 10.1016/j.yexcr.2020.111951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.
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Affiliation(s)
- R Kelly Dawe
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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26
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Selective isolation of large segments from individual microbial genomes and environmental DNA samples using transformation-associated recombination cloning in yeast. Nat Protoc 2020; 15:734-749. [PMID: 32005981 DOI: 10.1038/s41596-019-0280-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/05/2019] [Indexed: 11/08/2022]
Abstract
Here, we describe an extension of our original transformation-associated recombination (TAR) cloning protocol, enabling selective isolation of DNA segments from microbial genomes. The technique is based on the previously described TAR cloning procedure developed for isolation of a desirable region from mammalian genomes that are enriched in autonomously replicating sequence (ARS)-like sequences, elements that function as the origin of replication in yeast. Such sequences are not common in microbial genomes. In this Protocol Extension, an ARS is inserted into the TAR vector along with a counter-selectable marker, allowing for selection of cloning events against vector circularization. Pre-treatment of microbial DNA with CRISPR-Cas9 to generate double-stranded breaks near the targeted sequences greatly increases the yield of region-positive colonies. In comparison to other available methods, this Protocol Extension allows selective isolation of any region from microbial genomes as well as from environmental DNA samples. The entire procedure can be completed in 10 d.
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27
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Brown DM, Glass JI. Technology used to build and transfer mammalian chromosomes. Exp Cell Res 2020; 388:111851. [PMID: 31952951 DOI: 10.1016/j.yexcr.2020.111851] [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: 11/08/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 01/05/2023]
Abstract
In the near twenty-year existence of the human and mammalian artificial chromosome field, the technologies for artificial chromosome construction and installation into desired cell types or organisms have evolved with the rest of modern molecular and synthetic biology. Medical, industrial, pharmaceutical, agricultural, and basic research scientists seek the as yet unrealized promise of human and mammalian artificial chromosomes. Existing technologies for both top-down and bottom-up approaches to construct these artificial chromosomes for use in higher eukaryotes are very different but aspire to achieve similar results. New capacity for production of chromosome sized synthetic DNA will likely shift the field towards more bottom-up approaches, but not completely. Similarly, new approaches to install human and mammalian artificial chromosomes in target cells will compete with the microcell mediated cell transfer methods that currently dominate the field.
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Ruiz E, Talenton V, Dubrana MP, Guesdon G, Lluch-Senar M, Salin F, Sirand-Pugnet P, Arfi Y, Lartigue C. CReasPy-Cloning: A Method for Simultaneous Cloning and Engineering of Megabase-Sized Genomes in Yeast Using the CRISPR-Cas9 System. ACS Synth Biol 2019; 8:2547-2557. [PMID: 31663334 DOI: 10.1021/acssynbio.9b00224] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the past decade, a new strategy was developed to bypass the difficulties to genetically engineer some microbial species by transferring (or "cloning") their genome into another organism that is amenable to efficient genetic modifications and therefore acts as a living workbench. As such, the yeast Saccharomyces cerevisiae has been used to clone and engineer genomes from viruses, bacteria, and algae. The cloning step requires the insertion of yeast genetic elements in the genome of interest, in order to drive its replication and maintenance as an artificial chromosome in the host cell. Current methods used to introduce these genetic elements are still unsatisfactory, due either to their random nature (transposon) or the requirement for unique restriction sites at specific positions (TAR cloning). Here we describe the CReasPy-cloning, a new method that combines both the ability of Cas9 to cleave DNA at a user-specified locus and the yeast's highly efficient homologous recombination to simultaneously clone and engineer a bacterial chromosome in yeast. Using the 0.816 Mbp genome of Mycoplasma pneumoniae as a proof of concept, we demonstrate that our method can be used to introduce the yeast genetic element at any location in the bacterial chromosome while simultaneously deleting various genes or group of genes. We also show that CReasPy-cloning can be used to edit up to three independent genomic loci at the same time with an efficiency high enough to warrant the screening of a small (<50) number of clones, allowing for significantly shortened genome engineering cycle times.
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Affiliation(s)
- Estelle Ruiz
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Vincent Talenton
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Marie-Pierre Dubrana
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Gabrielle Guesdon
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG) , The Barcelona Institute of Science and Technology , Dr Aiguader 88 , Barcelona 08003 , Spain
- Universitat Pompeu Fabra (UPF) , 08003 Barcelona , Spain
| | - Franck Salin
- BIOGECO, INRA , Univ. Bordeaux , 33610 Cestas , France
| | - Pascal Sirand-Pugnet
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Yonathan Arfi
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
| | - Carole Lartigue
- INRA , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
- Univ. Bordeaux , UMR 1332 de Biologie du Fruit et Pathologie , F-33140 Villenave d'Ornon , France
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29
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Labroussaa F, Baby V, Rodrigue S, Lartigue C. [Whole genome transplantation: bringing natural or synthetic bacterial genomes back to life]. Med Sci (Paris) 2019; 35:761-770. [PMID: 31625898 DOI: 10.1051/medsci/2019154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The development of synthetic genomics (SG) allowed the emergence of several groundbreaking techniques including the synthesis, assembly and engineering of whole bacterial genomes. The successful implantation of those methods, which culminated in the creation of JCVI-syn3.0 the first nearly minimal bacterium with a synthetic genome, mainly results from the use of the yeast Saccharomyces cerevisiae as a transient host for bacterial genome replication and modification. Another method played a key role in the resounding success of this project: bacterial genome transplantation (GT). GT consists in the transfer of bacterial genomes cloned in yeast, back into a cellular environment suitable for the expression of their genetic content. While successful using many mycoplasma species, a complete understanding of the factors governing GT will most certainly help unleash the power of the entire SG pipeline to other genetically intractable bacteria.
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Affiliation(s)
- Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, PO Box, CH-3001 Bern, Suisse
| | - Vincent Baby
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, 2500 boulevard de l'université, Sherbrooke, Québec, Canada
| | - Carole Lartigue
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
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30
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Kouprina N, Larionov V. TAR Cloning: Perspectives for Functional Genomics, Biomedicine, and Biotechnology. Mol Ther Methods Clin Dev 2019; 14:16-26. [PMID: 31276008 PMCID: PMC6586605 DOI: 10.1016/j.omtm.2019.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Completion of the human genome sequence and recent advances in engineering technologies have enabled an unprecedented level of understanding of DNA variations and their contribution to human diseases and cellular functions. However, in some cases, long-read sequencing technologies do not allow determination of the genomic region carrying a specific mutation (e.g., a mutation located in large segmental duplications). Transformation-associated recombination (TAR) cloning allows selective, most accurate, efficient, and rapid isolation of a given genomic fragment or a full-length gene from simple and complex genomes. Moreover, this method is the only way to simultaneously isolate the same genomic region from multiple individuals. As such, TAR technology is currently in a leading position to create a library of the individual genes that comprise the human genome and physically characterize the sites of chromosomal alterations (copy number variations [CNVs], inversions, translocations) in the human population, associated with the predisposition to different diseases, including cancer. It is our belief that such a library and analysis of the human genome will be of great importance to the growing field of gene therapy, new drug design methods, and genomic research. In this review, we detail the motivation for TAR cloning for human genome studies, biotechnology, and biomedicine, discuss the recent progress of some TAR-based projects, and describe how TAR technology in combination with HAC (human artificial chromosome)-based and CRISPR-based technologies may contribute in the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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31
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Brumwell SL, MacLeod MR, Huang T, Cochrane RR, Meaney RS, Zamani M, Matysiakiewicz O, Dan KN, Janakirama P, Edgell DR, Charles TC, Finan TM, Karas BJ. Designer Sinorhizobium meliloti strains and multi-functional vectors enable direct inter-kingdom DNA transfer. PLoS One 2019; 14:e0206781. [PMID: 31206509 PMCID: PMC6576745 DOI: 10.1371/journal.pone.0206781] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
Storage, manipulation and delivery of DNA fragments is crucial for synthetic biology applications, subsequently allowing organisms of interest to be engineered with genes or pathways to produce desirable phenotypes such as disease or drought resistance in plants, or for synthesis of a specific chemical product. However, DNA with high G+C content can be unstable in many host organisms including Saccharomyces cerevisiae. Here, we report the development of Sinorhizobium meliloti, a nitrogen-fixing plant symbioticα-Proteobacterium, as a novel host that can store DNA, and mobilize DNA to E. coli, S. cerevisiae, and the eukaryotic microalgae Phaeodactylum tricornutum. To achieve this, we deleted the hsdR restriction-system in multiple reduced genome strains of S. meliloti that enable DNA transformation with up to 1.4 x 105 and 2.1 x 103 CFU μg-1 of DNA efficiency using electroporation and a newly developed polyethylene glycol transformation method, respectively. Multi-host and multi-functional shuttle vectors (MHS) were constructed and stably propagated in S. meliloti, E. coli, S. cerevisiae, and P. tricornutum. We also developed protocols and demonstrated direct transfer of these MHS vectors via conjugation from S. meliloti to E. coli, S. cerevisiae, and P. tricornutum. The development of S. meliloti as a new host for inter-kingdom DNA transfer will be invaluable for synthetic biology research and applications, including the installation and study of genes and biosynthetic pathways into organisms of interest in industry and agriculture.
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Affiliation(s)
- Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Tony Huang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ryan R Cochrane
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Kaitlyn N Dan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Designer Microbes Inc., London, ON, Canada
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32
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Attenuation of a Pathogenic Mycoplasma Strain by Modification of the obg Gene by Using Synthetic Biology Approaches. mSphere 2019; 4:4/3/e00030-19. [PMID: 31118296 PMCID: PMC6531878 DOI: 10.1128/msphere.00030-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Animal diseases due to mycoplasmas are a major cause of morbidity and mortality associated with economic losses for farmers all over the world. Currently used mycoplasma vaccines exhibit several drawbacks, including low efficacy, short time of protection, adverse reactions, and difficulty in differentiating infected from vaccinated animals. Therefore, there is a need for improved vaccines to control animal mycoplasmoses. Here, we used genome engineering tools derived from synthetic biology approaches to produce targeted mutations in the essential GTPase-encoding obg gene of Mycoplasma mycoides subsp. capri. Some of the resulting mutants exhibited a marked temperature-sensitive phenotype. The virulence of one of the obg mutants was evaluated in a caprine septicemia model and found to be strongly reduced. Although the obg mutant reverted to a virulent phenotype in one infected animal, we believe that these results contribute to a strategy that should help in building new vaccines against animal mycoplasmoses. Mycoplasma species are responsible for several economically significant livestock diseases for which there is a need for new and improved vaccines. Most of the existing mycoplasma vaccines are attenuated strains that have been empirically obtained by serial passages or by chemical mutagenesis. The recent development of synthetic biology approaches has opened the way for the engineering of live mycoplasma vaccines. Using these tools, the essential GTPase-encoding gene obg was modified directly on the Mycoplasma mycoides subsp. capri genome cloned in yeast, reproducing mutations suspected to induce a temperature-sensitive (TS+) phenotype. After transplantation of modified genomes into a recipient cell, the phenotype of the resulting M. mycoides subsp. capri mutants was characterized. Single-point obg mutations did not result in a strong TS+ phenotype in M. mycoides subsp. capri, but a clone presenting three obg mutations was shown to grow with difficulty at temperatures of ≥40°C. This particular mutant was then tested in a caprine septicemia model of M. mycoides subsp. capri infection. Five out of eight goats infected with the parental strain had to be euthanized, in contrast to one out of eight goats infected with the obg mutant, demonstrating an attenuation of virulence in the mutant. Moreover, the strain isolated from the euthanized animal in the group infected with the obg mutant was shown to carry a reversion in the obg gene associated with the loss of the TS+ phenotype. This study demonstrates the feasibility of building attenuated strains of mycoplasma that could contribute to the design of novel vaccines with improved safety. IMPORTANCE Animal diseases due to mycoplasmas are a major cause of morbidity and mortality associated with economic losses for farmers all over the world. Currently used mycoplasma vaccines exhibit several drawbacks, including low efficacy, short time of protection, adverse reactions, and difficulty in differentiating infected from vaccinated animals. Therefore, there is a need for improved vaccines to control animal mycoplasmoses. Here, we used genome engineering tools derived from synthetic biology approaches to produce targeted mutations in the essential GTPase-encoding obg gene of Mycoplasma mycoides subsp. capri. Some of the resulting mutants exhibited a marked temperature-sensitive phenotype. The virulence of one of the obg mutants was evaluated in a caprine septicemia model and found to be strongly reduced. Although the obg mutant reverted to a virulent phenotype in one infected animal, we believe that these results contribute to a strategy that should help in building new vaccines against animal mycoplasmoses.
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33
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Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. THE NEW PHYTOLOGIST 2019; 222:628-640. [PMID: 30521109 DOI: 10.1111/nph.15625] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 09/20/2018] [Indexed: 06/09/2023]
Abstract
High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Ariel Cerda
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomás Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Anthony West
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Fernán Federici
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Affiliation(s)
- Volker Thiel
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
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35
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Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J, Koszul R. Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C. Mol Syst Biol 2018; 14:e8293. [PMID: 30012718 PMCID: PMC6047084 DOI: 10.15252/msb.20188293] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/29/2022] Open
Abstract
In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies, allowing to propose a robust definition of a Hi-C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene-arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8-delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.
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Affiliation(s)
- Héloïse Muller
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Vittore F Scolari
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Aurèle Piazza
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Agnès Thierry
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Guillaume Mercy
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Stéphane Descorps-Declere
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Luciana Lazar-Stefanita
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Olivier Espeli
- Centre Interdisciplinaire de Recherche en Biologie, Collège de France, UMR-CNRS 7241, INSERM U1050, Paris, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julien Mozziconacci
- Theoretical Physics for Condensed Matter Lab, CNRS UMR 7600, Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Romain Koszul
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
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36
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Baby V, Labroussaa F, Brodeur J, Matteau D, Gourgues G, Lartigue C, Rodrigue S. Cloning and Transplantation of the Mesoplasma florum Genome. ACS Synth Biol 2018; 7:209-217. [PMID: 28893065 DOI: 10.1021/acssynbio.7b00279] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cloning and transplantation of bacterial genomes is a powerful method for the creation of engineered microorganisms. However, much remains to be understood about the molecular mechanisms and limitations of this approach. We report the whole-genome cloning of Mesoplasma florum in Saccharomyces cerevisiae, and use this model to investigate the impact of a bacterial chromosome in yeast cells. Our results indicate that the cloned M. florum genome is subjected to weak transcriptional activity, and causes no significant impact on yeast growth. We also report that the M. florum genome can be transplanted into Mycoplasma capricolum without any negative impact from the putative restriction enzyme encoding gene mfl307. Using whole-genome sequencing, we observed that a small number of mutations appeared in all M. florum transplants. Mutations also arose, albeit at a lower frequency, when the M. capricolum genome was transplanted into M. capricolum recipient cells. These observations suggest that genome transplantation is mutagenic, and that this phenomenon is magnified by the use of genome donor and recipient cell belonging to different species. No difference in efficiency was detected after three successive rounds of genome transplantation, suggesting that the observed mutations were not selected during the procedure. Taken together, our results provide a more accurate picture of the events taking place during bacterial genome cloning and transplantation.
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Affiliation(s)
- Vincent Baby
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Fabien Labroussaa
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Joëlle Brodeur
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Dominick Matteau
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Géraldine Gourgues
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Sébastien Rodrigue
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
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Glass JI, Merryman C, Wise KS, Hutchison CA, Smith HO. Minimal Cells-Real and Imagined. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023861. [PMID: 28348033 DOI: 10.1101/cshperspect.a023861] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A minimal cell is one whose genome only encodes the minimal set of genes necessary for the cell to survive. Scientific reductionism postulates the best way to learn the first principles of cellular biology would be to use a minimal cell in which the functions of all genes and components are understood. The genes in a minimal cell are, by definition, essential. In 2016, synthesis of a genome comprised of only the set of essential and quasi-essential genes encoded by the bacterium Mycoplasma mycoides created a near-minimal bacterial cell. This organism performs the cellular functions common to all organisms. It replicates DNA, transcribes RNA, translates proteins, undergoes cell division, and little else. In this review, we examine this organism and contrast it with other bacteria that have been used as surrogates for a minimal cell.
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Affiliation(s)
- John I Glass
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Chuck Merryman
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Kim S Wise
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Clyde A Hutchison
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Hamilton O Smith
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
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38
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Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination. mSphere 2017; 2:mSphere00331-17. [PMID: 28989973 PMCID: PMC5628293 DOI: 10.1128/mspheredirect.00331-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 07/29/2017] [Indexed: 01/17/2023] Open
Abstract
The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. To overcome these limitations, we used synthetic biology tools to capture genomic fragments from viral DNA and assemble full-length genomes in yeast. Using an early passage of the HCMV isolate Toledo containing a mixture of wild-type and tissue culture-adapted virus. we directly cloned the majority sequence and recreated the minority sequence by simultaneous modification of multiple genomic regions. Thus, our novel approach provides a paradigm to not only efficiently engineer HCMV and other large DNA viruses on a genome-wide scale but also facilitates the cloning and genetic manipulation of primary isolates and provides a pathway to generating entirely synthetic genomes. Genetic engineering of cytomegalovirus (CMV) currently relies on generating a bacterial artificial chromosome (BAC) by introducing a bacterial origin of replication into the viral genome using in vivo recombination in virally infected tissue culture cells. However, this process is inefficient, results in adaptive mutations, and involves deletion of viral genes to avoid oversized genomes when inserting the BAC cassette. Moreover, BAC technology does not permit the simultaneous manipulation of multiple genome loci and cannot be used to construct synthetic genomes. To overcome these limitations, we adapted synthetic biology tools to clone CMV genomes in Saccharomyces cerevisiae. Using an early passage of the human CMV isolate Toledo, we first applied transformation-associated recombination (TAR) to clone 16 overlapping fragments covering the entire Toledo genome in Saccharomyces cerevisiae. Then, we assembled these fragments by TAR in a stepwise process until the entire genome was reconstituted in yeast. Since next-generation sequence analysis revealed that the low-passage-number isolate represented a mixture of parental and fibroblast-adapted genomes, we selectively modified individual DNA fragments of fibroblast-adapted Toledo (Toledo-F) and again used TAR assembly to recreate parental Toledo (Toledo-P). Linear, full-length HCMV genomes were transfected into human fibroblasts to recover virus. Unlike Toledo-F, Toledo-P displayed characteristics of primary isolates, including broad cellular tropism in vitro and the ability to establish latency and reactivation in humanized mice. Our novel strategy thus enables de novo cloning of CMV genomes, more-efficient genome-wide engineering, and the generation of viral genomes that are partially or completely derived from synthetic DNA. IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. To overcome these limitations, we used synthetic biology tools to capture genomic fragments from viral DNA and assemble full-length genomes in yeast. Using an early passage of the HCMV isolate Toledo containing a mixture of wild-type and tissue culture-adapted virus. we directly cloned the majority sequence and recreated the minority sequence by simultaneous modification of multiple genomic regions. Thus, our novel approach provides a paradigm to not only efficiently engineer HCMV and other large DNA viruses on a genome-wide scale but also facilitates the cloning and genetic manipulation of primary isolates and provides a pathway to generating entirely synthetic genomes.
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39
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Rideau F, Le Roy C, Descamps ECT, Renaudin H, Lartigue C, Bébéar C. Cloning, Stability, and Modification of Mycoplasma hominis Genome in Yeast. ACS Synth Biol 2017; 6:891-901. [PMID: 28118540 DOI: 10.1021/acssynbio.6b00379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mycoplasma hominis is a minimal human pathogen that is responsible for genital and neonatal infections. Despite many attempts, there is no efficient genetic tool to manipulate this bacterium, limiting most investigations of its pathogenicity and its uncommon energy metabolism that relies on arginine. The recent cloning and subsequent engineering of other mycoplasma genomes in yeast opens new possibilities for studies of the genomes of genetically intractable organisms. Here, we report the successful one-step cloning of the M. hominis PG21 genome in yeast using the transformation-associated recombination (TAR) cloning method. At low passages, the M. hominis genome cloned into yeast displayed a conserved size. However, after ∼60 generations in selective media, this stability was affected, and large degradation events were detected, raising questions regarding the stability of large heterologous DNA molecules cloned in yeast and the need to minimize host propagation. Taking these results into account, we selected early passage yeast clones and successfully modified the M. hominis PG21 genome using the CRISPR/Cas9 editing tool, available in Saccharomyces cerevisiae. Complete M. hominis PG21 genomes lacking the adhesion-related vaa gene were efficiently obtained.
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Affiliation(s)
- Fabien Rideau
- Univ. Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections
in Humans, F-33000 Bordeaux, France
- INRA, USC-EA3671
Mycoplasmal and Chlamydial Infections in Humans, F-33000 Bordeaux, France
| | - Chloé Le Roy
- Univ. Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections
in Humans, F-33000 Bordeaux, France
- INRA, USC-EA3671
Mycoplasmal and Chlamydial Infections in Humans, F-33000 Bordeaux, France
| | - Elodie C. T. Descamps
- Univ. Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections
in Humans, F-33000 Bordeaux, France
- INRA, USC-EA3671
Mycoplasmal and Chlamydial Infections in Humans, F-33000 Bordeaux, France
| | - Hélène Renaudin
- Univ. Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections
in Humans, F-33000 Bordeaux, France
- INRA, USC-EA3671
Mycoplasmal and Chlamydial Infections in Humans, F-33000 Bordeaux, France
| | - Carole Lartigue
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Cécile Bébéar
- Univ. Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections
in Humans, F-33000 Bordeaux, France
- INRA, USC-EA3671
Mycoplasmal and Chlamydial Infections in Humans, F-33000 Bordeaux, France
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40
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Development of oriC-Based Plasmids for Mesoplasma florum. Appl Environ Microbiol 2017; 83:AEM.03374-16. [PMID: 28115382 DOI: 10.1128/aem.03374-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
The near-minimal bacterium Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted M. florum chromosomal origin of replication (oriC) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both rpmH-dnaA and dnaA-dnaN intergenic regions, interspaced or not with a copy of the dnaA gene, resulted in a frequency of ∼4.1 × 10-6 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one M. florumoriC intergenic region or the heterologous oriC region of Mycoplasma capricolum, Mycoplasma mycoides, or Spiroplasma citri failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from Escherichia coli, reaching frequencies up to 7.87 × 10-6 and 8.44 × 10-7 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in M. florum Taken together, these valuable genetic tools will facilitate efforts toward building an M. florum-based near-minimal cellular chassis for synthetic biology.IMPORTANCEMesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. M. florum is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, M. florum shows higher growth rates than other Mollicutes, has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of M. florum in order to modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.
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Messerschmidt SJ, Schindler D, Zumkeller CM, Kemter FS, Schallopp N, Waldminghaus T. Optimization and Characterization of the Synthetic Secondary Chromosome synVicII in Escherichia coli. Front Bioeng Biotechnol 2016; 4:96. [PMID: 28066763 PMCID: PMC5179572 DOI: 10.3389/fbioe.2016.00096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/09/2016] [Indexed: 11/15/2022] Open
Abstract
Learning by building is one of the core ideas of synthetic biology research. Consequently, building synthetic chromosomes is the way to fully understand chromosome characteristics. The last years have seen exciting synthetic chromosome studies. We had previously introduced the synthetic secondary chromosome synVicII in Escherichia coli. It is based on the replication mechanism of the secondary chromosome in Vibrio cholerae. Here, we present a detailed analysis of its genetic characteristics and a selection approach to optimize replicon stability. We probe the origin diversity of secondary chromosomes from Vibrionaceae by construction of several new respective replicons. Finally, we present a synVicII version 2.0 with several innovations including its full compatibility with the popular modular cloning (MoClo) assembly system.
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Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Daniel Schindler
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Celine M Zumkeller
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Franziska S Kemter
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg , Marburg , Germany
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42
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Labroussaa F, Lebaudy A, Baby V, Gourgues G, Matteau D, Vashee S, Sirand-Pugnet P, Rodrigue S, Lartigue C. Impact of donor-recipient phylogenetic distance on bacterial genome transplantation. Nucleic Acids Res 2016; 44:8501-11. [PMID: 27488189 PMCID: PMC5041484 DOI: 10.1093/nar/gkw688] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022] Open
Abstract
Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting organisms to adopt the genotype and the phenotype conferred by the donor cells. This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and economically important microbial species. So far, this process has only been reported using two closely related bacteria, Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma capricolum subsp. capricolum (Mcap), and the main factors driving the compatibility between a donor genome and a recipient cell are poorly understood. Here, we investigated the impact of the evolutionary distance between donor and recipient species on the efficiency of GT. Using Mcap as the recipient cell, we successfully transplanted the genome of six bacteria belonging to the Spiroplasma phylogenetic group but including species of two distinct genera. Our results demonstrate that GT efficiency is inversely correlated with the phylogenetic distance between donor and recipient bacteria but also suggest that other species-specific barriers to GT exist. This work constitutes an important step toward understanding the cellular factors governing the GT process in order to better define and eventually extend the existing genome compatibility limit.
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Affiliation(s)
- Fabien Labroussaa
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Anne Lebaudy
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Vincent Baby
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | - Géraldine Gourgues
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Dominick Matteau
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | | | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Université de Sherbrooke, Département de biologie, 2500 boulevard Université Sherbrooke (Québec), J1K 2R1, Canada
| | - Carole Lartigue
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
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43
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Kannan K, Tsvetanova B, Chuang RY, Noskov VN, Assad-Garcia N, Ma L, Hutchison Iii CA, Smith HO, Glass JI, Merryman C, Venter JC, Gibson DG. One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9. Sci Rep 2016; 6:30714. [PMID: 27489041 PMCID: PMC4973257 DOI: 10.1038/srep30714] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 01/04/2023] Open
Abstract
Bacteria are indispensable for the study of fundamental molecular biology processes due to their relatively simple gene and genome architecture. The ability to engineer bacterial chromosomes is quintessential for understanding gene functions. Here we demonstrate the engineering of the small-ribosomal subunit (16S) RNA of Mycoplasma mycoides, by combining the CRISPR/Cas9 system and the yeast recombination machinery. We cloned the entire genome of M. mycoides in yeast and used constitutively expressed Cas9 together with in vitro transcribed guide-RNAs to introduce engineered 16S rRNA genes. By testing the function of the engineered 16S rRNA genes through genome transplantation, we observed surprising resilience of this gene to addition of genetic elements or helix substitutions with phylogenetically-distant bacteria. While this system could be further used to study the function of the 16S rRNA, one could envision the “simple” M. mycoides genome being used in this setting to study other genetic structures and functions to answer fundamental questions of life.
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Affiliation(s)
| | | | | | | | | | - Li Ma
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Hamilton O Smith
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - J Craig Venter
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Daniel G Gibson
- Synthetic Genomics, Inc., La Jolla, CA 92037, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
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44
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CORDOVA CAIOM, HOELTGEBAUM DANIELAL, MACHADO LAÍSD, SANTOS LARISSADOS. Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell. ACTA ACUST UNITED AC 2016; 88 Suppl 1:599-607. [DOI: 10.1590/0001-3765201620150164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 11/21/2022]
Abstract
ABSTRACT Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.
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45
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Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology. Chromosoma 2016; 125:621-32. [PMID: 27116033 DOI: 10.1007/s00412-016-0588-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 12/25/2022]
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool for isolation and manipulation of large DNA molecules. The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. So far, TAR cloning is the only method available to selectively recover chromosomal segments up to 300 kb in length from complex and simple genomes. In addition, TAR cloning allows the assembly and cloning of entire microbe genomes up to several Mb as well as engineering of large metabolic pathways. In this review, we summarize applications of TAR cloning for functional/structural genomics and synthetic biology.
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46
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Tsarmpopoulos I, Gourgues G, Blanchard A, Vashee S, Jores J, Lartigue C, Sirand-Pugnet P. In-Yeast Engineering of a Bacterial Genome Using CRISPR/Cas9. ACS Synth Biol 2016; 5:104-9. [PMID: 26592087 DOI: 10.1021/acssynbio.5b00196] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One remarkable achievement in synthetic biology was the reconstruction of mycoplasma genomes and their cloning in yeast where they can be modified using available genetic tools. Recently, CRISPR/Cas9 editing tools were developed for yeast mutagenesis. Here, we report their adaptation for the engineering of bacterial genomes cloned in yeast. A seamless deletion of the mycoplasma glycerol-3-phosphate oxidase-encoding gene (glpO) was achieved without selection in one step, using 90 nt paired oligonucleotides as templates to drive recombination. Screening of the resulting clones revealed that more than 20% contained the desired deletion. After manipulation, the overall integrity of the cloned mycoplasma genome was verified by multiplex PCR and PFGE. Finally, the edited genome was back-transplanted into a mycoplasma recipient cell. In accordance with the deletion of glpO, the mutant mycoplasma was affected in the production of H2O2. This work paves the way to high-throughput manipulation of natural or synthetic genomes in yeast.
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Affiliation(s)
| | | | | | - Sanjay Vashee
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, 20850 Maryland United States,
| | - Joerg Jores
- International Livestock Research Institute (ILRI),
PO Box 30709, 00100 Nairobi, Kenya
- Institute
of Veterinary Bacteriology, University of Bern, Laenggass-Straße
122, CH-3001 Bern, Switzerland
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47
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48
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Karas BJ, Suzuki Y, Weyman PD. Strategies for cloning and manipulating natural and synthetic chromosomes. Chromosome Res 2015; 23:57-68. [PMID: 25596826 DOI: 10.1007/s10577-014-9455-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Advances in synthetic biology methods to assemble and edit DNA are enabling genome engineering at a previously impracticable scale and scope. The synthesis of the Mycoplasma mycoides genome followed by its transplantation to convert a related cell into M. mycoides has transformed strain engineering. This approach exemplifies the combination of newly emerging chromosome-scale genome editing strategies that can be defined in three main steps: (1) chromosome acquisition into a microbial engineering platform, (2) alteration and improvement of the acquired chromosome, and (3) installation of the modified chromosome into the original or alternative organism. In this review, we outline recent progress in methods for acquiring chromosomes and chromosome-scale DNA molecules in the workhorse organisms Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. We present overviews of important genetic strategies and tools for each of the three organisms, point out their respective strengths and weaknesses, and highlight how the host systems can be used in combination to facilitate chromosome assembly or engineering. Finally, we highlight efforts for the installation of the cloned/altered chromosomes or fragments into the target organism and present remaining challenges in expanding this powerful experimental approach to a wider range of target organisms.
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Affiliation(s)
- Bogumil J Karas
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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49
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Schieck E, Lartigue C, Frey J, Vozza N, Hegermann J, Miller RA, Valguarnera E, Muriuki C, Meens J, Nene V, Naessens J, Weber J, Lowary TL, Vashee S, Feldman MF, Jores J. Galactofuranose in Mycoplasma mycoides is important for membrane integrity and conceals adhesins but does not contribute to serum resistance. Mol Microbiol 2015; 99:55-70. [PMID: 26354009 DOI: 10.1111/mmi.13213] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 12/20/2022]
Abstract
Mycoplasma mycoides subsp. capri (Mmc) and subsp. mycoides (Mmm) are important ruminant pathogens worldwide causing diseases such as pleuropneumonia, mastitis and septicaemia. They express galactofuranose residues on their surface, but their role in pathogenesis has not yet been determined. The M. mycoides genomes contain up to several copies of the glf gene, which encodes an enzyme catalysing the last step in the synthesis of galactofuranose. We generated a deletion of the glf gene in a strain of Mmc using genome transplantation and tandem repeat endonuclease coupled cleavage (TREC) with yeast as an intermediary host for the genome editing. As expected, the resulting YCp1.1-Δglf strain did not produce the galactofuranose-containing glycans as shown by immunoblots and immuno-electronmicroscopy employing a galactofuranose specific monoclonal antibody. The mutant lacking galactofuranose exhibited a decreased growth rate and a significantly enhanced adhesion to small ruminant cells. The mutant was also 'leaking' as revealed by a β-galactosidase-based assay employing a membrane impermeable substrate. These findings indicate that galactofuranose-containing polysaccharides conceal adhesins and are important for membrane integrity. Unexpectedly, the mutant strain showed increased serum resistance.
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Affiliation(s)
- Elise Schieck
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Carole Lartigue
- UMR 1332 Biologie du Fruit et Pathologie, The French National Institute for Agricultural Research, INRA-Université Bordeaux, Segalen, 71, avenue Edouard Bourlaux, CS20032, F-33882, Villenave D'Ornon CEDEX, Bordeaux, France.,UMR 1332 de Biologie du Fruit et Pathologie, Université Bordeaux, F-33140, Villenave d'Ornon, Bordeaux, France
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, CH-3001, Bern, Switzerland
| | - Nicolas Vozza
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jan Hegermann
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany.,Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover, Germany
| | - Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY, USA
| | - Ezequiel Valguarnera
- Department of Molecular Microbiology, Washington University School of Medicine St Louis, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Cecilia Muriuki
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Vish Nene
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Jan Naessens
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya
| | - Johann Weber
- Center for Integrative Genomics, Lausanne Genomic Technologies Facility,University of Lausanne, Lausanne, Switzerland
| | - Todd L Lowary
- Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Sanjay Vashee
- J. Craig Venter Institute, 9704 Medical Center Drive, MD 20850, Rockville, USA
| | - Mario F Feldman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.,Department of Molecular Microbiology, Washington University School of Medicine St Louis, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Joerg Jores
- International Livestock Research Institute, Old Naivasha Road, P.O. Box 30709, 00100, Nairobi, Kenya.,Institute of Veterinary Bacteriology, University of Bern, CH-3001, Bern, Switzerland
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Nah HJ, Woo MW, Choi SS, Kim ES. Precise cloning and tandem integration of large polyketide biosynthetic gene cluster using Streptomyces artificial chromosome system. Microb Cell Fact 2015; 14:140. [PMID: 26377404 PMCID: PMC4573296 DOI: 10.1186/s12934-015-0325-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/27/2015] [Indexed: 11/29/2022] Open
Abstract
Background Direct cloning combined with heterologous expression of a secondary metabolite biosynthetic gene cluster has become a useful strategy for production improvement and pathway modification of potentially valuable natural products present at minute quantities in original isolates of actinomycetes. However, precise cloning and efficient overexpression of an entire biosynthetic gene cluster remains challenging due to the ineffectiveness of current genetic systems in manipulating large-sized gene clusters for heterologous as well as homologous expression. Results A versatile Escherichia coli-Streptomyces shuttle bacterial artificial chromosomal (BAC) conjugation vector, pSBAC, was used along with a cluster tandem integration approach to carry out homologous and heterologous overexpression of a large 80-kb polyketide biosynthetic pathway gene cluster of tautomycetin (TMC), which is a protein phosphatase PP1/PP2A inhibitor and T cell-specific immunosuppressant. Unique XbaI restriction sites were precisely inserted at both border regions of the TMC biosynthetic gene cluster within the chromosome of TMC-producing Streptomyces sp. CK4412, followed by site-specific recombination of pSBAC into the flanking region of the TMC gene cluster. The entire TMC gene cluster was then rescued as a single giant recombinant pSBAC by XbaI digestion of the chromosomal DNA as well as subsequent self-ligation. Next, the recombinant pSBAC construct containing the entire TMC cluster in E. coli was directly conjugated into model Streptomyces strains, resulting in rapid and enhanced TMC production. Moreover, introduction of the TMC cluster-containing pSBAC into wild-type Streptomyces sp. CK4412 as well as a recombinant S. coelicolor strain resulted in a chromosomal tandem repeat of the entire TMC cluster with 14-fold and 5.4-fold enhanced TMC productivities, respectively. Conclusions The 80-kb TMC biosynthetic gene cluster was isolated in a single integration vector, pSBAC. Introduction of TMC biosynthetic gene cluster in TMC non-producing strains has resulted in similar amount of TMC production yield. Moreover, over-expression of TMC biosynthetic gene cluster in original producing strain and recombinant S. coelicolor dramatically increased TMC production. Thus, this strategy can be employed to develop a custom overexpression scheme of entire metabolite pathway clusters present in actinomycetes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0325-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hee-Ju Nah
- Department of Biological Engineering, Inha University, Incheon, 402-751, Korea.
| | - Min-Woo Woo
- Department of Biological Engineering, Inha University, Incheon, 402-751, Korea.
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, 402-751, Korea.
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, 402-751, Korea.
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