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Kachroo AH, Vandeloo M, Greco BM, Abdullah M. Humanized yeast to model human biology, disease and evolution. Dis Model Mech 2022; 15:275614. [PMID: 35661208 PMCID: PMC9194483 DOI: 10.1242/dmm.049309] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.
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O'Boyle N, Boyd A. Validation of a random Vibrio parahaemolyticus genomic library by selection of quinolone resistance in a heterologous host. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536738 DOI: 10.1099/mic.0.001189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vibrio parahaemolyticus is a shellfish-borne pathogen that is a highly prevalent causative agent of inflammatory gastroenteritis in humans. Genomic libraries have proven useful for the identification of novel gene functions in many bacterial species. In this study we prepared a library containing 40 kb fragments of randomly sheared V. parahaemolyticus genomic DNA and introduced this into Escherichia coli HB101 using a commercially available low copy cosmid system. In order to estimate coverage and suitability of the library and potentially identify novel antimicrobial resistance determinants, we screened for the acquisition of resistance to the fluoroquinolone norfloxacin - a phenotype exhibited by V. parahaemolyticus but not the heterologous E. coli host. Upon selection on solid medium containing norfloxacin, 0.52% of the library population was resistant, consistent with the selection of a single resistance locus. End-sequencing identified six distinct insert fragments. All clones displayed fourfold increased norfloxacin MIC compared with E. coli HB101 carrying an empty vector. The common locus contained within resistant clones included qnr, a previously described quinolone resistance gene. These results indicate that the library was unbiased, of sufficient coverage and that heterologous expression was possible. While we hope that this library proves useful for identifying the genetic determinants of complex phenotypes such as those related to virulence, not all norfloxacin resistance genes were detected in our screen. As such, we discuss the benefits and limitations of this approach for identifying the genetic basis of uncharacterized bacterial phenotypes.
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Affiliation(s)
- Nicky O'Boyle
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, T12 K8AF, Ireland
| | - Aoife Boyd
- Discipline of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
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Abbasi MN, Fu J, Bian X, Wang H, Zhang Y, Li A. Recombineering for Genetic Engineering of Natural Product Biosynthetic Pathways. Trends Biotechnol 2020; 38:715-728. [PMID: 31973879 DOI: 10.1016/j.tibtech.2019.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 01/21/2023]
Abstract
Microbial genomes encode many cryptic and uncharacterized biosynthetic gene clusters (BGCs). Exploiting this unexplored genetic wealth to discover microbial novel natural products (NPs) remains a challenging issue. We review homologous recombination (HR)-based recombineering, mediated by the recombinases RecE/RecT from Rac prophage and Redα/Redβ from lambda phage, which has developed into a highly inclusive tool for direct cloning of large DNA up to 100 kb, seamless mutation, multifragment assembly, and heterologous expression of microbial NP BGCs. Its utilization in the refactoring, engineering, and functional expression of long BGCs for NP biosynthesis makes it easy to elucidate NP-producing potential in microbes. This review also highlights various applications of recombineering in NP-derived drug discovery.
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Affiliation(s)
- Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Hailong Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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Yoshimura M, Ueta Y. Advanced genetic and viral methods for labelling and manipulation of oxytocin and vasopressin neurones in rats. Cell Tissue Res 2018; 375:311-327. [PMID: 30338378 DOI: 10.1007/s00441-018-2932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Rats have been widely used as one of the most common laboratory animals for biological research, because their physiology, pathology, and behavioral characteristics are highly similar to humans. Recent developments in rat genetic modification techniques have now led to further their utility for a broad range of research questions, including the ability to specifically label individual neurones, and even manipulate neuronal function in rats. We have succeeded in generating several transgenic rat lines that enable visualization of specific neurones due to their expression of fluorescently-tagged oxytocin, vasopressin, and c-fos protein. Furthermore, we have been able to generate novel transgenic rat lines in which we can activate vasopressin neurones using optogenetic and chemogenetic techniques. In this review, we will summarize the techniques of genetic modification for labeling and manipulating the specific neurones. Successful examples of generating transgenic rat lines in our lab and usefulness of these rats will also be introduced. These transgenic rat lines enable the interrogation of neuronal function and physiology in a way that was not possible in the past, providing novel insights into neuronal mechanisms both in vivo and ex vivo.
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Affiliation(s)
- Mitsuhiro Yoshimura
- Department of Physiology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Yoichi Ueta
- Department of Physiology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
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Amemiya CT, Wagner GP. Francis (Frank) Hugh Ruddle (1929-2013). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:273-5. [PMID: 23650107 DOI: 10.1002/jez.b.22509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 04/07/2013] [Accepted: 04/09/2013] [Indexed: 11/06/2022]
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6
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Simplifying protein expression with ligation-free, traceless and tag-switching plasmids. Protein Expr Purif 2012; 85:9-17. [DOI: 10.1016/j.pep.2012.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023]
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7
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Kitazono AA. Optimized protocols and plasmids for in vivo cloning in yeast. Gene 2011; 484:86-9. [DOI: 10.1016/j.gene.2011.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 05/24/2011] [Accepted: 06/07/2011] [Indexed: 01/17/2023]
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Bentley KL, Stranford S, Liao S, Mounzer RM, Ruddle FH, Ruddle NH. High endothelial venule reporter mice to probe regulation of lymph node vasculature. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 691:35-44. [PMID: 21153307 DOI: 10.1007/978-1-4419-6612-4_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Kevin L Bentley
- Department of Epidemiology and Public Health, Yale University School of Medicine, 10 Amistad Street, P.O. Box 208089, New Haven, CT 06520, USA.
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Bentley KL, Shashikant CS, Wang W, Ruddle NH, Ruddle FH. A yeast-based recombinogenic targeting toolset for transgenic analysis of human disease genes. Ann N Y Acad Sci 2010; 1207 Suppl 1:E58-68. [PMID: 20961307 DOI: 10.1111/j.1749-6632.2010.05712.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transgenic mouse models are valuable resources for analyzing functions of genes involved in human diseases. Mouse models provide critical insights into biological processes, including in vivo visualization of vasculature critical to our understanding of the immune system. Generating transgenic mice requires the capture and modification of large-insert DNAs representing genes of interest. We have developed a methodology using a yeast-bacterial shuttle vector, pClasper, that enables the capture and modification of bacterial artificial chromosomes (BAC)-sized DNA inserts. Numerous improvements and technical advances in the original pClasper vector have allowed greater flexibility and utility in this system. Examples of such pClasper mediated gene modifications include: Claspette-mediated capture of large-insert genomic fragments from BACs-human polycystic kidney disease-1 (PKD1); modification of pClasperA clones by the RareGap method-PKD1 mutations; Claspette-mediated modification of pClasper clones-mouse albumin-1 gene; and, of most relevance to our interest in lymph node vasculature-Claspimer-mediated modification of pClasper clones-high endothelial venule and lymphatic vessel genes. Mice that have been generated with these methods include mice with fluorescent high endothelial venules.
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Affiliation(s)
- Kevin L Bentley
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520-8089, USA
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Noskov VN, Segall-Shapiro TH, Chuang RY. Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast. Nucleic Acids Res 2010; 38:2570-6. [PMID: 20228123 PMCID: PMC2860121 DOI: 10.1093/nar/gkq099] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The complete synthetic Mycoplasma genitalium genome (∼583 kb) has been assembled and cloned as a circular plasmid in the yeast Saccharomyces cerevisiae. Attempts to engineer the cloned genome by standard genetic methods involving the URA3/5-fluoroorotic acid (5-FOA) counter-selection have shown a high background of 5-FOA resistant clones derived from spontaneous deletions of the bacterial genome maintained in yeast. Here, we report a method that can seamlessly modify the bacterial genome in yeast with high efficiency. This method requires two sequential homologous recombination events. First, the target region is replaced with a mutagenesis cassette that consists of a knock-out CORE (an18-bp I-SceI recognition site, the SCEI gene under the control of the GAL1 promoter, and the URA3 marker) and a DNA fragment homologous to the sequence upstream of the target site. The replacement generates tandem repeat sequences flanking the CORE. Second, galactose induces the expression of I-SceI, which generates a double-strand break (DSB) at the recognition site. This DSB promotes intra-molecular homologous recombination between the repeat sequences, and leads to an excision of the CORE. As a result, a seamless modification is generated. This method can be adapted for a variety of genomic modifications and may provide an important tool to modify and design natural or synthetic genomes propagated in yeast.
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Affiliation(s)
- Vladimir N Noskov
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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Kitazono AA. Improved gap-repair cloning method that uses oligonucleotides to target cognate sequences. Yeast 2009; 26:497-505. [PMID: 19621470 DOI: 10.1002/yea.1680] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In vivo or gap-repair cloning in yeast has been widely recognized as one of the most efficient means for error-free construction of plasmids. A protocol is described here that allows easy and efficient gap-repair cloning that is based on two major modifications. Instead of subcloning, the targeting plasmids are constructed using oligonucleotides from sequences derived from the upstream and downstream sequences of the fragment to be cloned. These sequences are selected so that they can lead to the generation of recognition sites for restriction enzymes that produce blunt ends. Accordingly, this procedure can be applied to any DNA fragment, regardless of whether these include unique restriction sites to generate the targeting ends. With the strategy described, approximately 50 bp upstream and downstream targeting ends are generated that allow efficient cloning. Further, to allow easy identification of the positive clones, the annealed oligonucleotides are cloned in frame with the lacZ fragment present in the plasmid. Accordingly, these plasmids produce blue Escherichia coli colonies on media containing X-Gal. On the other hand, plasmids rescued from yeast that have acquired the respective cognate sequences produce white colonies. To demonstrate the efficiency of the method, this report includes the cloning of fragments harbouring the CDC28, CAK1, CIN5 and CLB2 genes. We found that 30-100% of the analysed plasmids carried the expected inserts.
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Affiliation(s)
- Ana A Kitazono
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840, USA.
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Tian Y, Jiang W, Zhao G, Qin Z. In vivo conjugation-coupled recombinational cloning of a Streptomyces lividans chromosomal telomeric DNA using a linear plasmid. Biotechnol Lett 2009; 31:1253-8. [PMID: 19404745 DOI: 10.1007/s10529-009-0005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 03/25/2009] [Accepted: 03/27/2009] [Indexed: 11/24/2022]
Abstract
The high efficiency of homologous recombination in yeast and bacteria makes it useful for recombinational cloning of large genomic segments in vivo. The low efficiency of homologous recombination in Streptomyces has hindered the development of this cloning method. Unlike the inefficient mobilization of chromosomal markers, conjugative plasmid transfer is very efficient in Streptomyces. Here we report that the conjugation-coupled recombination procedure can be used to transfer a 10 kb chromosomal telomeric segment of Streptomyces lividans into a linear plasmid. The plasmid predominated in the population of cells after transfer into recipients. These results may promote the development of the recombinational cloning of large chromosomal segments in Streptomyces in vivo.
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Affiliation(s)
- Yongqiang Tian
- Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Liao S, Bentley K, Lebrun M, Lesslauer W, Ruddle FH, Ruddle NH. Transgenic LacZ under control of Hec-6st regulatory sequences recapitulates endogenous gene expression on high endothelial venules. Proc Natl Acad Sci U S A 2007; 104:4577-82. [PMID: 17360566 PMCID: PMC1838643 DOI: 10.1073/pnas.0700334104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Indexed: 11/18/2022] Open
Abstract
Hec-6st is a highly specific high endothelial venule (HEV) gene that is crucial for regulating lymphocyte homing to lymph nodes (LN). The enzyme is also expressed in HEV-like vessels in tertiary lymphoid organs that form in chronic inflammation in autoimmunity, graft rejection, and microbial infection. Understanding the molecular nature of Hec-6st regulation is crucial for elucidating its function in development and disease. However, studies of HEV are limited because of the difficulties in isolating and maintaining the unique characteristics of these vessels in vitro. The novel pClasper yeast homologous recombination technique was used to isolate from a BAC clone a 60-kb DNA fragment that included the Hec-6st (Chst4) gene with flanking sequences. Transgenic mice were generated with the beta-galactosidase (LacZ) reporter gene inserted in-frame in the exon II of Hec-6st within the isolated BAC DNA fragment. LacZ was expressed specifically on HEV in LN, as indicated by its colocalization with peripheral node vascular addressin. LacZ was increased in nasal-associated lymphoid tissue during development and was reduced in LN and nasal-associated lymphoid tissue by LTbetaR-Ig (lymphotoxin-beta receptor human Ig fusion protein) treatment in a manner identical to the endogenous gene. The transgene was expressed at high levels in lymphoid accumulations with characteristics of tertiary lymphoid organs in the salivary glands of aged mice. Thus, the Hec-6s-LacZ construct faithfully reproduces Hec-6st tissue-specific expression and can be used in further studies to drive expression of reporter or effector genes, which could visualize or inhibit HEV in autoimmunity.
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Affiliation(s)
- Shan Liao
- *Department of Epidemiology and Public Health and
| | - Kevin Bentley
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06510
| | - Marielle Lebrun
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06510
| | | | - Frank H. Ruddle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06510
| | - Nancy H. Ruddle
- *Department of Epidemiology and Public Health and
- Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06520; and
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Sassi HE, Renihan S, Spence AM, Cooperstock RL. Gene CATCHR--gene cloning and tagging for Caenorhabditis elegans using yeast homologous recombination: a novel approach for the analysis of gene expression. Nucleic Acids Res 2005; 33:e163. [PMID: 16254074 PMCID: PMC1270953 DOI: 10.1093/nar/gni164] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Expression patterns of gene products provide important insights into gene function. Reporter constructs are frequently used to analyze gene expression in Caenorhabditis elegans, but the sequence context of a given gene is inevitably altered in such constructs. As a result, these transgenes may lack regulatory elements required for proper gene expression. We developed Gene Catchr, a novel method of generating reporter constructs that exploits yeast homologous recombination (YHR) to subclone and tag worm genes while preserving their local sequence context. YHR facilitates the cloning of large genomic regions, allowing the isolation of regulatory sequences in promoters, introns, untranslated regions and flanking DNA. The endogenous regulatory context of a given gene is thus preserved, producing expression patterns that are as accurate as possible. Gene Catchr is flexible: any tag can be inserted at any position without introducing extra sequence. Each step is simple and can be adapted to process multiple genes in parallel. We show that expression patterns derived from Gene Catchr transgenes are consistent with previous reports and also describe novel expression data. Mutant rescue assays demonstrate that Gene Catchr-generated transgenes are functional. Our results validate the use of Gene Catchr as a valuable tool to study spatiotemporal gene expression.
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Affiliation(s)
- Holly E. Sassi
- Department of Medical Genetics and Microbiology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
- Collaborative Program in Developmental Biology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
| | - Stephanie Renihan
- Department of Medical Genetics and Microbiology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
| | - Andrew M. Spence
- Department of Medical Genetics and Microbiology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
- Collaborative Program in Developmental Biology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
| | - Ramona L. Cooperstock
- Department of Medical Genetics and Microbiology, University of Toronto1 King's College Circle, Toronto, Canada, M5S 1A8
- To whom correspondence should be addressed. Tel: +1 416 946 7917; Fax: +1 416 978 6885;
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Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A 2005; 102:547-52. [PMID: 15647345 PMCID: PMC545576 DOI: 10.1073/pnas.0408782102] [Citation(s) in RCA: 334] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the increasing availability of genome sequences from many human pathogens, the production of complete proteomes remains at a bottleneck. To address this need, a high-throughput PCR recombination cloning and expression platform has been developed that allows hundreds of genes to be batch-processed by using ordinary laboratory procedures without robotics. The method relies on high-throughput amplification of each predicted ORF by using gene specific primers, followed by in vivo homologous recombination into a T7 expression vector. The proteins are expressed in an Escherichia coli-based cell-free in vitro transcription/translation system, and the crude reactions containing expressed proteins are printed directly onto nitrocellulose microarrays without purification. The protein microarrays are useful for determining the complete antigen-specific humoral immune-response profile from vaccinated or infected humans and animals. The system was verified by cloning, expressing, and printing a vaccinia virus proteome consisting of 185 individual viral proteins. The chips were used to determine Ab profiles in serum from vaccinia virus-immunized humans, primates, and mice. Human serum has high titers of anti-E. coli Abs that require blocking to unmask vaccinia-specific responses. Naive humans exhibit reactivity against a subset of 13 antigens that were not associated with vaccinia immunization. Naive mice and primates lacked this background reactivity. The specific profiles between the three species differed, although a common subset of antigens was reactive after vaccinia immunization. These results verify this platform as a rapid way to comprehensively scan humoral immunity from vaccinated or infected humans and animals.
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Affiliation(s)
- D Huw Davies
- Center for Virus Research, University of California, Irvine, CA 92697, USA
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Wilson JW, Figurski DH, Nickerson CA. VEX-capture: a new technique that allows in vivo excision, cloning, and broad-host-range transfer of large bacterial genomic DNA segments. J Microbiol Methods 2004; 57:297-308. [PMID: 15134879 DOI: 10.1016/j.mimet.2004.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 12/10/2003] [Accepted: 01/06/2004] [Indexed: 11/21/2022]
Abstract
We have developed a novel and easily performed procedure for the targeted excision, cloning, and broad-host-range transfer of large bacterial genomic DNA segments. This procedure, called Vector-mediated excision and Capture (VEX-Capture), represents a new molecular tool for the convenient manipulation and exchange of large (20-40+ kb) bacterial genomic fragments. VEX-Capture utilizes lox/Cre-mediated site-specific recombination for excision of the targeted genomic segment and homologous recombination for cloning of the excised DNA section onto a self-transmissible, broad-host-range IncP plasmid. The "captured" genomic DNA segment can then be transferred to a wide variety of Gram-negative hosts for basic research and bioengineering purposes. To demonstrate the utility and function of VEX-Capture, we have excised and cloned three separate genomic islands from the Salmonella typhimurium chromosome ranging in size from 26.7 to 40.0 kb. To test the ability of these islands to be established in different bacterial hosts, we transferred them to six other Gram-negative species and monitored their establishment via phenotypic and molecular analysis. RT-PCR was used to assay the expression of selected S. typhimurium island genes in the different species. This analysis led to the discovery that an island-encoded master regulator of S. typhimurium virulence functions is expressed in a species-specific manner. Our results demonstrate the potential for VEX-Capture to be used as a convenient genetic technique for fundamental biological applications in a wide variety of bacterial species.
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Affiliation(s)
- James W Wilson
- Program in Molecular Pathogenesis and Immunity, Department of Microbiology and Immunology, SL38 Tulane University Medical School, 1430 Tulane Avenue Rm. 5728, New Orleans, LA 70112, USA.
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Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells. BMC Mol Biol 2003; 4:1. [PMID: 12530927 PMCID: PMC149363 DOI: 10.1186/1471-2199-4-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Accepted: 01/16/2003] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The phage protein pairs, RecE/RecT from Rac or Redalpha/Redbeta from lambda, initiate efficient double strand break repair (DSBR) in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. RESULTS Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR) at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redalpha) but only requires a phage annealing protein (RecT or Redbeta). Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. CONCLUSION Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redalpha/Redbeta.
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Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2002; 133:609-46. [PMID: 12470823 DOI: 10.1016/s1096-4959(02)00167-7] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.
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Affiliation(s)
- Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA.
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19
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Salvatori R, Fan X, Mullis PE, Haile A, Levine MA. Decreased expression of the GHRH receptor gene due to a mutation in a Pit-1 binding site. Mol Endocrinol 2002; 16:450-8. [PMID: 11875102 DOI: 10.1210/mend.16.3.0785] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A variety of mutations in the gene encoding the GHRH receptor (GHRHR) that are predicted to alter protein structure or function have been recently described in patients with isolated GH deficiency type IB. In the present report we describe a patient with isolated GH deficiency type IB who was heterozygous for two novel mutations in this gene: a missense mutation in codon 329 that replaces lysine with glutamic acid (K329E) and an A-->C transversion (position -124) in one of the two sites of the promoter region that binds the pituitary-specific transcription factor Pit-1, which is required for GHRHR expression. Chinese hamster ovary cells that were transfected with a cDNA encoding the K329E GHRHR expressed the receptor but failed to show a cAMP response after treatment with GHRH, confirming the lack of functionality. To test the effect of the A-->C mutation at position -124 of the promoter, we transfected rat GH3 pituitary cells, which express endogenous Pit-1, with plasmids in which the luciferase reporter gene was under the control of either the wild-type or the mutant promoter. GH3 cells expressing the mutant promoter showed significantly less luciferase activity than cells expressing the wild-type promoter. DNA-binding studies confirmed that the A-->C base change markedly reduces DNA binding to the Pit-1 protein. These results demonstrate that mutations in the GHRHR are not limited to the coding sequence and that promoter mutations that impair Pit-1 binding can reduce expression of the GHRHR gene.
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Affiliation(s)
- Roberto Salvatori
- Division of Endocrinology, and the Ilyssa Center for Molecular and Cellular Endocrinology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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20
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Ho Y, Elefant F, Cooke N, Liebhaber S. A defined locus control region determinant links chromatin domain acetylation with long-range gene activation. Mol Cell 2002; 9:291-302. [PMID: 11864603 DOI: 10.1016/s1097-2765(02)00447-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Gene activation in higher eukaryotes is often under the control of regulatory elements quite distant from their target promoters. It is unclear how such long-range control is mediated. Here we show that a single determinant of the human growth hormone locus control region (hGH LCR) located 14.5 kb 5prime prime or minute to the hGH-N promoter has a critical, specific, and nonredundant role in facilitating promoter trans factor binding and activating hGH-N transcription. Significantly, this same determinant plays an essential role in establishing a 32 kb acetylated domain that encompasses the entire hGH LCR and the contiguous hGH-N promoter. These data support a model for long-range gene activation via LCR-mediated targeting and extensive spreading of core histone acetylation.
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Affiliation(s)
- Yugong Ho
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Abstract
The completed draft of the human genome sequence has facilitated a revolution in neuroscience research. This sequence information and the development of new technologies used to analyze gene expression on a genomic scale provides a new and powerful means to investigate brain disorders of unknown etiology and to isolate novel drug targets for these disorders. The term functional genomics broadly describes a set of technologies and strategies directed at the problem of determining the function of genes, and understanding how the genome works together to generate whole patterns of biological function. The most powerful of these functional genomics approaches, expression profiling or DNA microarrays, can be used to analyze the expression of thousands of genes simultaneously. The results to date from the application of DNA microarray methods to postmortem diseased human brain tissue, animal models and cell culture models of brain disorders provide an exciting glimpse into the future of this field.
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Affiliation(s)
- Paul D Shilling
- Department of Psychiatry, University of California at San Diego, and San Diego VA Healthcare System, La Jolla, 92093, USA
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22
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Affiliation(s)
- J P Muyrers
- Gene Expression Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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23
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Muyrers JP, Zhang Y, Stewart AF. Techniques: Recombinogenic engineering--new options for cloning and manipulating DNA. Trends Biochem Sci 2001; 26:325-31. [PMID: 11343926 DOI: 10.1016/s0968-0004(00)01757-6] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Driven by the needs of functional genomics, DNA engineering by homologous recombination in Escherichia coli has emerged as a major addition to existing technologies. Two alternative approaches, RecA-dependent engineering and ET recombination, allow a wide variety of DNA modifications, including some which are virtually impossible by conventional methods. These approaches do not rely on the presence of suitable restriction sites and can be used to insert, delete or substitute DNA sequences at any desired position on a target molecule. Furthermore, ET recombination can be used for direct subcloning and cloning of DNA sequences from complex mixtures, including bacterial artificial chromosomes and genomic DNA preparations. The strategies reviewed in this article are applicable to modification of DNA molecules of any size, including very large ones, and present powerful new avenues for DNA manipulation in general.
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Affiliation(s)
- J P Muyrers
- Gene Bridges GmbH, Laerchenweg 3, D-69181 Leimen, Germany
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24
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Zhang Y, Muyrers JP, Testa G, Stewart AF. DNA cloning by homologous recombination in Escherichia coli. Nat Biotechnol 2000; 18:1314-7. [PMID: 11101815 DOI: 10.1038/82449] [Citation(s) in RCA: 292] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The cloning of foreign DNA in Escherichia coli episomes is a cornerstone of molecular biology. The pioneering work in the early 1970s, using DNA ligases to paste DNA into episomal vectors, is still the most widely used approach. Here we describe a different principle, using ET recombination, for directed cloning and subcloning, which offers a variety of advantages. Most prominently, a chosen DNA region can be cloned from a complex mixture without prior isolation. Hence cloning by ET recombination resembles PCR in that both involve the amplification of a DNA region between two chosen points. We apply the strategy to subclone chosen DNA regions from several target molecules resident in E. coli hosts, and to clone chosen DNA regions from genomic DNA preparations. Here we analyze basic aspects of the approach and present several examples that illustrate its simplicity, flexibility, and remarkable efficiency.
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Affiliation(s)
- Y Zhang
- Gene Expression Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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25
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Celis JE, Kruhøffer M, Gromova I, Frederiksen C, Ostergaard M, Thykjaer T, Gromov P, Yu J, Pálsdóttir H, Magnusson N, Orntoft TF. Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett 2000; 480:2-16. [PMID: 10967322 DOI: 10.1016/s0014-5793(00)01771-3] [Citation(s) in RCA: 229] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel and powerful technologies such as DNA microarrays and proteomics have made possible the analysis of the expression levels of multiple genes simultaneously both in health and disease. In combination, these technologies promise to revolutionize biology, in particular in the area of molecular medicine as they are expected to reveal gene regulation events involved in disease progression as well as to pinpoint potential targets for drug discovery and diagnostics. Here, we review the current status of these technologies and highlight some studies in which they have been applied in concert to the analysis of biopsy specimens.
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Affiliation(s)
- J E Celis
- Department of Medical Biochemistry and Danish Centre for Human Genome Research, University of Aarhus, Denmark.
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26
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Hill F, Benes V, Thomasova D, Stewart AF, Kafatos FC, Ansorge W. BAC trimming: minimizing clone overlaps. Genomics 2000; 64:111-3. [PMID: 10708525 DOI: 10.1006/geno.1999.6106] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial vectors containing large inserts of genomic DNA are now the standard substrates for large-scale genomic sequencing. Long overlaps between some clones lead to considerable redundant effort. A method for deleting defined regions from bacterial artificial chromosome (BAC) inserts, using homologous recombination, was applied to minimize the overlap between successive BAC clones. This procedure, called trimming, was carried out in the recA(-) BAC host. We have precisely deleted up to 70 kb of DNA from BACs that were to be sequenced. This method requires minimal prior characterization of the clones: collections of BAC end sequences or STS-based maps will accelerate the process. BAC trimming will be useful in both small and large genome sequencing projects and will be of particular utility for gap closure in finishing phases.
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Affiliation(s)
- F Hill
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany.
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27
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Bhargava J, Shashikant CS, Carr JL, Juan H, Bentley KL, Ruddle FH. Direct cloning of genomic DNA by recombinogenic targeting method using a yeast-bacterial shuttle vector, pClasper. Genomics 1999; 62:285-8. [PMID: 10610723 DOI: 10.1006/geno.1999.6000] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a method to clone genomic DNA selectively into a yeast-bacterial shuttle vector, pClasper, by recombinogenic targeting in yeast. A gene-specific pClasper targeting vector was constructed with small recombinogenic ends (500 bp) derived from flanking sequences of the genomic region to be cloned. Linearized, recombinogenic pClasper targeting vector and native genomic DNA were cotransformed into yeast. The gene of interest is selectively cloned by recombination between the recombinogenic ends in the targeting vector and homologous regions in the genomic DNA. Here we demonstrate direct cloning of a stably integrated Hoxc8-LacZ-Ura3 reporter gene construct from a mouse embryo fibroblast cell line and single-copy genes from total human genomic DNA. The frequency of capture of the recombinant insert was 0.05-3% of transformants. In contrast to previous reports, we were able to clone genomic DNA directly with a vector containing yeast autonomous replicating sequences. This approach provides a powerful method with which to clone and modify genes precisely for functional analysis.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Cell Line
- Chromosomes, Bacterial/genetics
- Cloning, Molecular/methods
- DNA, Circular/genetics
- Gene Targeting/methods
- Genetic Vectors/chemistry
- Genetic Vectors/genetics
- Humans
- Mice
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Tumor Necrosis Factor/genetics
- Receptors, Tumor Necrosis Factor, Type I
- Recombination, Genetic
- Saccharomyces cerevisiae/genetics
- Transfection
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Affiliation(s)
- J Bhargava
- Genaissance Pharmaceuticals Inc., New Haven, Connecticut 06511, USA.
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Abstract
The third Siena proteomics conference held August 31-September 4, 1998, heralded a change in emphasis from technology development to using proteomics to assist in resolving biological questions. In this review, proteomics is placed in context with other major influences in the way discovery research is conducted in biology. The current status of genomics is examined in its broadest sense, including how such studies may influence the development of proteomics. It is suggested that we are entering a new phase in biology where information is no longer limiting and integration of different technologies is required to attack the big problems of biology. While much of the focus of funding bodies, both in the public and private sector, is on practical outcomes (new drugs, etc.), the new technologies are equally amenable to attacking long-standing fundamental challenges, such as cell division, cell patterning and morphogenesis.
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Affiliation(s)
- K L Williams
- Proteome Systems, North Ryde, Sydney, NSW, Australia.
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29
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Bhargava J, Shashikant CS, Carr JL, Bentley KL, Amemiya CT, Ruddle FH. pPAC-ResQ: A yeast-bacterial shuttle vector for capturing inserts from P1 and PAC clones by recombinogenic targeted cloning. Genomics 1999; 56:337-9. [PMID: 10087201 DOI: 10.1006/geno.1998.5710] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a method to capture inserts from P1 and P1 artificial chromosome (PAC) clones into a yeast-bacteria shuttle vector by using recombinogenic targeting. We have engineered a vector, pPAC-ResQ, a derivative of pClasper, which was previously used to capture inserts from yeast artificial chromosome clones. pPAC-ResQ contains DNA fragments flanking the inserts in P1 and PAC vectors as recombinogenic ends. When linearized pPAC-ResQ vector and P1 or PAC DNA are cotransformed into yeast, recombination between the two leads to the transfer of inserts into pPAC-ResQ. pPAC-ResQ clones thus obtained can be further modified in yeast for functional analysis and shuttled to Escherichia coli to produce large quantities of cloned DNA. This approach provides a rapid method to modify P1/PAC clones for functional analysis.
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Affiliation(s)
- J Bhargava
- Genaissance Pharmaceuticals Inc., 5 Science Park, New Haven, Connecticut, 06511, USA.
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