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Yin J, Wang H, Li R, Ravichandran V, Bian X, Li A, Tu Q, Francis Stewart A, Fu J, Zhang Y. A Practical Guide to Recombineering in Photorhabdus and Xenorhabdus. Curr Top Microbiol Immunol 2016; 402:195-213. [PMID: 28154939 DOI: 10.1007/82_2016_57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluent genetic manipulation of prokaryote genomes is still limited to only a few commonly used hosts. Ideally the advanced technologies available for cloning into recombinant Escherichia coli should also be applicable in other prokaryotes. In particular, 'recombineering' is mediated by the lambda Red operon that permits fluent and precise engineering of the E. coli genome and associated recombinant DNA. The major limitation is that host-specific phage-derived recombination systems are also required in more distant species. Recently, an endogenous Red-like operon Pluγβα has been reported to be effective in both Photorhabdus and Xenorhabdus bacteria. The Pluγβα recombineering system is based on three host-specific phage proteins from Photorhabdus luminescens, Plu2935, Plu2936, and Plu2934, which are functional analogs of Redβ, Redα, and Redγ, respectively. In this chapter, we provide a comprehensive and up-to-date method for P. luminescens and Xenorhabdus stockiae genome engineering via the Pluγβα recombineering system. In order to facilitate the rapid construction of knock-in vectors, recET-mediated recombineering is incorporated in the pipeline. Concerted recET system in E. coli with Pluγβα system in Photorhabdus and Xenorhabdus could promote reverse genetics, functional genomics, and bioprospecting research for these two genera.
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Affiliation(s)
- Jia Yin
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Hailong Wang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Ruijuan Li
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Vinothkannan Ravichandran
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Aiying Li
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - Qiang Tu
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China
| | - A Francis Stewart
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307, Dresden, Germany
| | - Jun Fu
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China. .,Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307, Dresden, Germany.
| | - Youming Zhang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, Jinan, 250100, People's Republic of China.
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Abstract
ABSTRACT
Since the discovery of restriction enzymes and the generation of the first recombinant DNA molecule over 40 years ago, molecular biology has evolved into a multidisciplinary field that has democratized the conversion of a digitized DNA sequence stored in a computer into its biological counterpart, usually as a plasmid, stored in a living cell. In this article, we summarize the most relevant tools that allow the swift assembly of DNA sequences into useful plasmids for biotechnological purposes. We cover the main components and stages in a typical DNA assembly workflow, namely
in silico
design,
de novo
gene synthesis, and
in vitro
and
in vivo
sequence assembly methodologies.
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Abi-Ghanem J, Chusainow J, Karimova M, Spiegel C, Hofmann-Sieber H, Hauber J, Buchholz F, Pisabarro MT. Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach. Nucleic Acids Res 2012; 41:2394-403. [PMID: 23275541 PMCID: PMC3575804 DOI: 10.1093/nar/gks1308] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Site-specific recombinases (SSRs) can perform DNA rearrangements, including deletions, inversions and translocations when their naive target sequences are placed strategically into the genome of an organism. Hence, in order to employ SSRs in heterologous hosts, their target sites have to be introduced into the genome of an organism before the enzyme can be practically employed. Engineered SSRs hold great promise for biotechnology and advanced biomedical applications, as they promise to extend the usefulness of SSRs to allow efficient and specific recombination of pre-existing, natural genomic sequences. However, the generation of enzymes with desired properties remains challenging. Here, we use substrate-linked directed evolution in combination with molecular modeling to rationally engineer an efficient and specific recombinase (sTre) that readily and specifically recombines a sequence present in the HIV-1 genome. We elucidate the role of key residues implicated in the molecular recognition mechanism and we present a rationale for sTre’s enhanced specificity. Combining evolutionary and rational approaches should help in accelerating the generation of enzymes with desired properties for use in biotechnology and biomedicine.
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Affiliation(s)
- Josephine Abi-Ghanem
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg 47-51, 01037 Dresden, Germany
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Karimova M, Abi-Ghanem J, Berger N, Surendranath V, Pisabarro MT, Buchholz F. Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system. Nucleic Acids Res 2012; 41:e37. [PMID: 23143104 PMCID: PMC3553980 DOI: 10.1093/nar/gks1037] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the 'genetic toolbox' that can be used alone or in combination with other SSRs in heterologous hosts.
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Affiliation(s)
- Madina Karimova
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, University of Technology, Fetscherstrasse 74, 01307 Dresden, Germany
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Bi Y, Qiao X, Hua Z, Zhang L, Liu X, Li L, Hua W, Xiao H, Zhou J, Wei Q, Zheng X. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy. BMC Biotechnol 2012; 12:39. [PMID: 22768962 PMCID: PMC3408372 DOI: 10.1186/1472-6750-12-39] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/06/2012] [Indexed: 12/24/2022] Open
Abstract
Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN) promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i) rapid and highly efficient; (ii) native DNA cloning without introduction of extra bases; (iii) restriction-free; (iv) easy positioning of directional and site-specific recombination owing to formulated primer design. ABI-REC is a novel approach to DNA engineering and gene functional analysis.
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Affiliation(s)
- Yanzhen Bi
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Science, Wuhan 430064, China.
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Retallack DM, Jin H, Chew L. Reliable protein production in a Pseudomonas fluorescens expression system. Protein Expr Purif 2012; 81:157-65. [DOI: 10.1016/j.pep.2011.09.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 09/20/2011] [Accepted: 09/20/2011] [Indexed: 10/17/2022]
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Anastassiadis K, Fu J, Patsch C, Hu S, Weidlich S, Duerschke K, Buchholz F, Edenhofer F, Stewart AF. Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice. Dis Model Mech 2009; 2:508-15. [PMID: 19692579 DOI: 10.1242/dmm.003087] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Tyrosine site-specific recombinases (SSRs) including Cre and FLP are essential tools for DNA and genome engineering. Cre has long been recognized as the best SSR for genome engineering, particularly in mice. Obtaining another SSR that is as good as Cre will be a valuable addition to the genomic toolbox. To this end, we have developed and validated reagents for the Dre-rox system. These include an Escherichia coli-inducible expression vector based on the temperature-sensitive pSC101 plasmid, a mammalian expression vector based on the CAGGs promoter, a rox-lacZ reporter embryonic stem (ES) cell line based on targeting at the Rosa26 locus, the accompanying Rosa26-rox reporter mouse line, and a CAGGs-Dre deleter mouse line. We also show that a Dre-progesterone receptor shows good ligand-responsive induction properties. Furthermore, we show that there is no crossover recombination between Cre-rox or Dre-loxP. Hence, we add another set of efficient tools to the genomic toolbox, which will enable the development of more sophisticated mouse models for the analysis of gene function and disease.
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Affiliation(s)
- Konstantinos Anastassiadis
- Center for Regenerative Therapies Dresden, BioInnovationsZentrum Technische Universitaet Dresden, Am Tatzberg 47, 01307 Dresden, Germany
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Navrátilová A, Koblížková A, Macas J. Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC PLANT BIOLOGY 2008; 8:90. [PMID: 18721471 PMCID: PMC2543021 DOI: 10.1186/1471-2229-8-90] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 08/22/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes. RESULTS We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths. CONCLUSION This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.
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Affiliation(s)
- Alice Navrátilová
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Andrea Koblížková
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
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Sektas M, Specht M. Limited use of the Cre/loxP recombination system in efficient production of loxP-containing minicircles in vivo. Plasmid 2004; 53:148-63. [PMID: 15737402 DOI: 10.1016/j.plasmid.2004.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Revised: 04/08/2004] [Accepted: 04/08/2004] [Indexed: 11/26/2022]
Abstract
The Cre/loxP recombination system of bacteriophage P1 is one of the most powerful tools in genome engineering. We report, however, that the activity of the Cre/loxP system interferes with the stability of the multicopy loxP-bearing plasmids in Escherichia coli recA bacteria. Due to the predominantly unidirectional Cre-mediated high-order multimer formation of these plasmids, the number of their copies (overall yield) gradually decreases. Intermolecular recombination reduces the copy number of plasmids and eventually increases their segregational instability. We have found that in the presence of even the slightest amount of Cre activity, loxP-bearing plasmids continuously undergo multimerization, which very rapidly leads to loxP-plasmid free cells. Our results are compatible with the hypothesis of the multimer catastrophe [Cell, 1984 (36), 1097].
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Affiliation(s)
- Marian Sektas
- Department of Microbiology, University of Gdansk, 80-822 Gdansk, ul.Kladki 24, Poland.
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