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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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Yuan H, Zheng Y, Yan X, Wang H, Zhang Y, Ma J, Fu J. Direct cloning of a herpesvirus genome for rapid generation of infectious BAC clones. J Adv Res 2022; 43:97-107. [PMID: 36585118 PMCID: PMC9811322 DOI: 10.1016/j.jare.2022.02.012] [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: 11/29/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION The herpesviridae are DNA viruses with large and complicated genomes. The herpesvirus bacterial artificial chromosomes (BACs) have been useful for generating recombinant viruses to study the biology and pathogenesis. However, the conventional method using homologous recombination is not only time consuming but also prone to accumulate attenuating mutations during serial passage of the virus in cells. Elimination of the BAC vector from the recombinant viral genome requires additional step for phenotypically consistence with the original strain. OBJECTIVES To generate a streamlined approach for generating infectious BAC clones of herpesvirus. METHODS The 142-kb pseudorabies virus genome was directly cloned into a bacterial artificial chromosome (BAC) in Escherichia coli by Exonuclease Combined with RecET recombination (ExoCET). Placement of the BAC vector at the terminus of the linear virus genome enabled excision of the BAC backbone from the viral genome by restriction endonuclease for delivery into mammalian cells, with the subsequent rapid rescue of virus that was genetically identical to the original strain. RESULTS This new approach for molecular cloning of the genome from a large DNA virus and isolation of pure virus lacking the BAC vector from transfected mammalian cells bypass the tedious and time-consuming method of multiple rounds of plaque purification. The viral BAC was stable in E. coli, allowing further mutagenesis mediated by the Red system or various site-specific recombination methods. CONCLUSION An efficient method for construction of infectious clones of herpesvirus was established. It is expected to be potentially useful for other viruses with large double-stranded DNA genomes.
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Affiliation(s)
- Hengxing Yuan
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yaoyao Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoling Yan
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hailong Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China,Corresponding authors.
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China,Corresponding authors.
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China,Corresponding authors.
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Gelatin methacrylate hydrogels culture model for glioblastoma cells enriches for mesenchymal-like state and models interactions with immune cells. Sci Rep 2021; 11:17727. [PMID: 34489494 PMCID: PMC8421368 DOI: 10.1038/s41598-021-97059-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma is the most lethal primary malignant brain tumor in adults. Simplified two-dimensional (2D) cell culture and neurospheres in vitro models fail to recapitulate the complexity of the tumor microenvironment, limiting its ability to predict therapeutic response. Three-dimensional (3D) scaffold-based models have emerged as a promising alternative for addressing these concerns. One such 3D system is gelatin methacrylate (GelMA) hydrogels, and we aimed to understand the suitability of using this system to mimic treatment-resistant glioblastoma cells that reside in specific niches. We characterized the phenotype of patient-derived glioma cells cultured in GelMA hydrogels (3D-GMH) for their tumorigenic properties using invasion and chemoresponse assays. In addition, we used integrated single-cell and spatial transcriptome analysis to compare cells cultured in 3D-GMH to neoplastic cells in vivo. Finally, we assessed tumor-immune cell interactions with a macrophage infiltration assay and a cytokine array. We show that the 3D-GMH system enriches treatment-resistant mesenchymal cells that are not represented in neurosphere cultures. Cells cultured in 3D-GMH resemble a mesenchymal-like cellular phenotype found in perivascular and hypoxic regions and recruit macrophages by secreting cytokines, a hallmark of the mesenchymal phenotype. Our 3D-GMH model effectively mimics the phenotype of glioma cells that are found in the perivascular and hypoxic niches of the glioblastoma core in situ, in contrast to the neurosphere cultures that enrich cells of the infiltrative edge of the tumor. This contrast highlights the need for due diligence in selecting an appropriate model when designing a study's objectives.
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Guo JC, Tang YD, Zhao K, Wang TY, Liu JT, Gao JC, Chang XB, Cui HY, Tian ZJ, Cai XH, An TQ. Highly Efficient CRISPR/Cas9-Mediated Homologous Recombination Promotes the Rapid Generation of Bacterial Artificial Chromosomes of Pseudorabies Virus. Front Microbiol 2016; 7:2110. [PMID: 28066407 PMCID: PMC5179515 DOI: 10.3389/fmicb.2016.02110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022] Open
Abstract
Bacterial artificial chromosomes (BACs) are powerful tools for the manipulation of the large genomes of DNA viruses, such as herpesviruses. However, the methods currently used to construct the recombinant viruses, an important intermediate link in the generation of BACs, involve the laborious process of multiple plaque purifications. Moreover, some fastidious viruses may be lost or damaged during these processes, making it impossible to generate BACs from these large-genome DNA viruses. Here, we introduce the CRISPR/Cas9 as a site-specific gene knock-in instrument that promotes the homologs recombination of a linearized transfer vector and the Pseudorabies virus genome through double incisions. The efficiency of recombination is as high as 86%. To our knowledge, this is the highest efficiency ever reported for Pseudorabies virus recombination. We also demonstrate that the positions and distances of the CRISPR/Cas9 single guide RNAs from the homology arms correlate with the efficiency of homologous recombination. Our work show a simple and fast cloning method of BACs with large genome inserted by greatly enhancing the HR efficiencies through CRISPR/Cas9-mediated homology-directed repair mechanism, and this method could be of helpful for manipulating large DNA viruses, and will provide a successful model for insertion of large DNA fragments into other viruses.
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Affiliation(s)
- Jin-Chao Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Kuan Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Ji-Ting Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Jia-Cong Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Xiao-Bo Chang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Hong-Yu Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Tong-Qing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
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Liu Y, Luo M, Xiang X, Chen C, Ji X, Chen L, He Z. A graphene oxide and exonuclease-aided amplification immuno-sensor for antigen detection. Chem Commun (Camb) 2014; 50:2679-81. [PMID: 24473576 DOI: 10.1039/c4cc00128a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have developed a novel immuno-sensor applied to protein detection based on exonuclease III (Exo III)-induced signal amplification, multiplex binding of the biotin-streptavidin system and the fluorescence quenching ability of graphene oxide.
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Affiliation(s)
- Yufei Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.
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Liu Y, Luo M, Yan J, Xiang X, Ji X, Zhou G, He Z. An ultrasensitive biosensor for DNA detection based on hybridization chain reaction coupled with the efficient quenching of a ruthenium complex to CdTe quantum dots. Chem Commun (Camb) 2014; 49:7424-6. [PMID: 23863907 DOI: 10.1039/c3cc42639d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly sensitive and selective DNA biosensor based on hybridization chain reaction is described, which combines CdTe quantum dots (QDs) and a ruthenium complex. Based on the variation of fluorescence signals of the CdTe QDs, the target DNA is determined.
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Affiliation(s)
- Yufei Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
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Jiao K, Rashid A, Basu SK, Zhu S, Brown BD, Guerciolini R, Fambrough DM. Quantitative Analysis of Dicer Substrate Oligonucleotides in Mouse Liver by Ultra-High-Performance Liquid Chromatography–Electrospray Ionization Tandem Mass Spectrometry. Assay Drug Dev Technol 2012; 10:278-88. [DOI: 10.1089/adt.2011.0435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
| | - Aftab Rashid
- Dicerna Pharmaceuticals, Watertown, Massachusetts
| | | | - Shuhao Zhu
- Dicerna Pharmaceuticals, Watertown, Massachusetts
| | - Bob D. Brown
- Dicerna Pharmaceuticals, Watertown, Massachusetts
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Paredes AM, Yu D. Human cytomegalovirus: bacterial artificial chromosome (BAC) cloning and genetic manipulation. CURRENT PROTOCOLS IN MICROBIOLOGY 2012; Chapter 14:Unit14E.4. [PMID: 22307551 DOI: 10.1002/9780471729259.mc14e04s24] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The understanding of human cytomegalovirus (HCMV) biology was long hindered by the inability to perform efficient viral genetic analysis. This hurdle was recently overcome when the genomes of multiple HCMV strains were cloned as infectious bacterial artificial chromosomes (BACs). The BAC system takes advantage of the single-copy F plasmid of E. coli that can stably carry large pieces of foreign DNA. In this system, a recombinant HCMV virus carrying a modified F plasmid is first generated in eukaryotic cells. Recombinant viral genomes are then isolated and recovered in E. coli as BAC clones. BAC-captured viral genomes can be manipulated using prokaryotic genetics, and recombinant virus can be reconstituted from BAC transfection in eukaryotic cells. The BAC reverse genetic system provides a reliable and efficient method to introduce genetic alterations into the viral genome in E.coli and subsequently analyze their effects on virus biology in eukaryotic cells.
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Affiliation(s)
- Anne M Paredes
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Back to BAC: the use of infectious clone technologies for viral mutagenesis. Viruses 2012; 4:211-35. [PMID: 22470833 PMCID: PMC3315213 DOI: 10.3390/v4020211] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 12/18/2022] Open
Abstract
Bacterial artificial chromosome (BAC) vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC) using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses.
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Bacterial artificial chromosome clones of viruses comprising the towne cytomegalovirus vaccine. J Biomed Biotechnol 2011; 2012:428498. [PMID: 22187535 PMCID: PMC3236503 DOI: 10.1155/2012/428498] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 08/24/2011] [Indexed: 12/18/2022] Open
Abstract
Bacterial artificial chromosome (BAC) clones have proven invaluable for genetic manipulation of herpesvirus genomes. BAC cloning can also be useful for capturing representative genomes that comprise a viral stock or mixture. The Towne live attenuated cytomegalovirus vaccine was developed in the 1970s by serial passage in cultured fibroblasts. Although its safety, immunogenicity, and efficacy have been evaluated in nearly a thousand human subjects, the vaccine itself has been little studied. Instead, genetic composition and in vitro growth properties have been inferred from studies of laboratory stocks that may not always accurately represent the viruses that comprise the vaccine. Here we describe the use of BAC cloning to define the genotypic and phenotypic properties of viruses from the Towne vaccine. Given the extensive safety history of the Towne vaccine, these BACs provide a logical starting point for the development of next-generation rationally engineered cytomegalovirus vaccines.
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Zhou F, Gao SJ. Recent advances in cloning herpesviral genomes as infectious bacterial artificial chromosomes. Cell Cycle 2011; 10:434-40. [PMID: 21245660 DOI: 10.4161/cc.10.3.14708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Herpesviruses are common but important pathogens in humans and animals. These viruses have large complex genomes encoding genes with diverse functions in different phases of their life cycle and associated diseases. In the last decade, genomes of herpesviruses cloned as infectious bacterial artificial chromosomes (BACs) have become powerful tools for delineating the functions of viral genes and understanding the pathogenesis of their associated diseases. Here we review the history of herpesviral genetics and recent advances in methods for cloning herpesviral genomes as infectious BACs.
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Affiliation(s)
- Fuchun Zhou
- Tumor virology Program, Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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Tovkach A, Zeevi V, Tzfira T. Expression, purification and characterization of cloning-grade zinc finger nuclease. J Biotechnol 2011; 151:1-8. [DOI: 10.1016/j.jbiotec.2010.10.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/10/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
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Sarid R, Gao SJ. Viruses and human cancer: from detection to causality. Cancer Lett 2010; 305:218-27. [PMID: 20971551 DOI: 10.1016/j.canlet.2010.09.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 09/15/2010] [Accepted: 09/22/2010] [Indexed: 01/21/2023]
Abstract
The study of cancer is incomplete without taking into consideration of tumorigenic viruses. Initially, searches for human cancer viruses were fruitless despite an expansion of our knowledge in the same period concerning acute-transforming retroviruses in animals. However, over the last 40 years, we have witnessed rapid progress in the tumor virology field. Currently, acknowledged human cancer viruses include Epstein-Barr virus, hepatitis B virus, hepatitis C virus, high-risk human papilloma viruses, human T-cell lymphotropic virus type 1 and Kaposi's sarcoma-associated herpesvirus. Extensive epidemiological and mechanistic studies have led to the development of novel preventive and therapeutic approaches for managing some of these infections and associated cancers. In addition, recent advances in molecular technologies have enabled the discovery of a new potential human tumor virus, Merkel cell polyomavirus, but its association with cancer remains to be validated. It is anticipated that in the next few decades many additional human cancer viruses will be discovered and the mechanisms underlying viral oncogenesis delineated. Thus, it can be expected that better tools for preventing and treating virus-associated cancer will be available in the near future.
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Affiliation(s)
- Ronit Sarid
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.
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Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, Chuang RY, Carrera W, Moodie M, Algire MA, Phan Q, Alperovich N, Vashee S, Merryman C, Venter JC, Smith HO, Glass JI, Hutchison CA. Cloning whole bacterial genomes in yeast. Nucleic Acids Res 2010; 38:2558-69. [PMID: 20211840 PMCID: PMC2860123 DOI: 10.1093/nar/gkq119] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/08/2010] [Accepted: 02/09/2010] [Indexed: 01/21/2023] Open
Abstract
Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation.
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Affiliation(s)
- Gwynedd A Benders
- Synthetic Biology and Bioenergy Group, The J. Craig Venter Institute, San Diego, CA 92121, USA.
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Cunningham C, Gatherer D, Hilfrich B, Baluchova K, Dargan DJ, Thomson M, Griffiths PD, Wilkinson GWG, Schulz TF, Davison AJ. Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol 2010; 91:605-15. [PMID: 19906940 PMCID: PMC2885759 DOI: 10.1099/vir.0.015891-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 11/09/2009] [Indexed: 12/14/2022] Open
Abstract
We have assessed two approaches to sequencing complete human cytomegalovirus (HCMV) genomes (236 kbp) in DNA extracted from infected cell cultures (strains 3157, HAN13, HAN20 and HAN38) or clinical specimens (strains JP and 3301). The first approach involved amplifying genomes from the DNA samples as overlapping PCR products, sequencing these by the Sanger method, acquiring reads from a capillary instrument and assembling these using the Staden programs. The second approach involved generating sequence data from the DNA samples by using an Illumina Genome Analyzer (IGA), processing the filtered reads by reference-independent (de novo) assembly, utilizing the resulting sequence to direct reference-dependent assembly of the same data and finishing by limited PCR sequencing. Both approaches were successful. In particular, the investigation demonstrated the utility of IGA data for efficiently sequencing genomes from clinical samples containing as little as 3 % HCMV DNA. Analysis of the genome sequences obtained showed that each of the strains grown in cell culture was a mutant. Certain of the mutations were shared among strains from independent clinical sources, thus suggesting that they may have arisen in a common ancestor during natural infection. Moreover, one of the strains (JP) sequenced directly from a clinical specimen was mutated in two genes, one of which encodes a proposed immune-evasion function, viral interleukin-10. These observations imply that HCMV mutants exist in human infections.
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Affiliation(s)
- Charles Cunningham
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Derek Gatherer
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Birgitta Hilfrich
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Katarina Baluchova
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Derrick J. Dargan
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Marian Thomson
- The GenePool, Ashworth Laboratories, King's Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Paul D. Griffiths
- Centre for Virology, University College Medical School, Royal Free Campus, Rowland Hill Street, Hampstead, London NW3 2QG, UK
| | - Gavin W. G. Wilkinson
- Department of Medical Microbiology, Tenovus Building, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XX, UK
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Andrew J. Davison
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
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Autoexcision of bacterial artificial chromosome facilitated by terminal repeat-mediated homologous recombination: a novel approach for generating traceless genetic mutants of herpesviruses. J Virol 2010; 84:2871-80. [PMID: 20071577 DOI: 10.1128/jvi.01734-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Infectious bacterial artificial chromosomes (BACs) of herpesviruses are powerful tools for genetic manipulation. However, the presence of BAC vector sequence in the viral genomes often causes genetic and phenotypic alterations. While the excision of the BAC vector cassette can be achieved by homologous recombination between extra duplicate viral sequences or loxP site-mediated recombination, these methods either are inefficient or leave a loxP site mark in the viral genome. Here we describe the use of viral intrinsic repeat sequences, which are commonly present in herpesviral genomes, to excise the BAC vector cassette. Using a newly developed in vitro transposon-based cloning approach, we obtained an infectious BAC of rhesus rhadinovirus (RRV) strain RRV26-95 with the BAC vector cassette inserted in the terminal repeat (TR) region. We showed that the BAC vector cassette was rapidly excised upon reconstitution in cells predominantly through TR-mediated homologous recombination. Genetic and phenotypic analysis showed that the BAC-excised virus was reversed to wild-type RRV. Using this autoexcisable BAC clone, we successfully generated an RRV mutant with a deletion of Orf50, which encodes a replication and transcription activator (RTA) protein. Together, these results illustrate the usefulness of TR for genetic manipulation of herpesviruses when combined with the novel transposon-based cloning approach.
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Wussow F, Fickenscher H, Tischer BK. Red-mediated transposition and final release of the mini-F vector of a cloned infectious herpesvirus genome. PLoS One 2009; 4:e8178. [PMID: 19997639 PMCID: PMC2780728 DOI: 10.1371/journal.pone.0008178] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 11/08/2009] [Indexed: 01/06/2023] Open
Abstract
Bacterial artificial chromosomes (BACs) are well-established cloning vehicles for functional genomics and for constructing targeting vectors and infectious viral DNA clones. Red-recombination-based mutagenesis techniques have enabled the manipulation of BACs in Escherichia coli without any remaining operational sequences. Here, we describe that the F-factor-derived vector sequences can be inserted into a novel position and seamlessly removed from the present location of the BAC-cloned DNA via synchronous Red-recombination in E. coli in an en passant mutagenesis-based procedure. Using this technique, the mini-F elements of a cloned infectious varicella zoster virus (VZV) genome were specifically transposed into novel positions distributed over the viral DNA to generate six different BAC variants. In comparison to the other constructs, a BAC variant with mini-F sequences directly inserted into the junction of the genomic termini resulted in highly efficient viral DNA replication-mediated spontaneous vector excision upon virus reconstitution in transfected VZV-permissive eukaryotic cells. Moreover, the derived vector-free recombinant progeny exhibited virtually indistinguishable genome properties and replication kinetics to the wild-type virus. Thus, a sequence-independent, efficient, and easy-to-apply mini-F vector transposition procedure eliminates the last hurdle to perform virtually any kind of imaginable targeted BAC modifications in E. coli. The herpesviral terminal genomic junction was identified as an optimal mini-F vector integration site for the construction of an infectious BAC, which allows the rapid generation of mutant virus without any unwanted secondary genome alterations. The novel mini-F transposition technique can be a valuable tool to optimize, repair or restructure other established BACs as well and may facilitate the development of gene therapy or vaccine vectors.
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Affiliation(s)
- Felix Wussow
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- * E-mail: (HF); (BKT)
| | - B. Karsten Tischer
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- * E-mail: (HF); (BKT)
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