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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. SCIENCE ADVANCES 2024; 10:eadn6603. [PMID: 38838146 PMCID: PMC11152119 DOI: 10.1126/sciadv.adn6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Standard zebrafish transgenesis involves random transgene integration with resource-intensive screening. While phiC31 integrase-based attP/attB recombination has streamlined transgenesis in mice and Drosophila, validated attP-based landing sites for universal applications are lacking in zebrafish. Here, we developed phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET) as transgenesis approach, with two attP landing sites pIGLET14a and pIGLET24b from well-validated Tol2 transgenes. Both sites facilitate diverse transgenesis applications including reporters and Cre/loxP transgenes. The pIGLET14a and pIGLET24b landing sites consistently yield 25 to 50% germline transmission, substantially reducing the resources needed for transgenic line generation. Transgenesis into these sites enables reproducible expression patterns in F0 zebrafish embryos for enhancer discovery and testing of gene regulatory variants. Together, our new landing sites streamline targeted, reproducible zebrafish transgenesis as a robust platform for various applications while minimizing the workload for generating transgenic lines.
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Affiliation(s)
| | | | - Cassie L. Kemmler
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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2
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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401797. [PMID: 38728624 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Mudi Meng Honors College, China Pharmaceutical University, Nanjing, 210009, China
| | - Jianping Kong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Gongyu Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhaoxing Li
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
| | - Yibei Xiao
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
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3
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Cortez CT, Murphy RO, Owens IM, Beckmann JF. Use of Drosophila Transgenics to Identify Functions for Symbiont Effectors. Methods Mol Biol 2024; 2739:301-320. [PMID: 38006559 DOI: 10.1007/978-1-0716-3553-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Wolbachia, one of the most successful and studied insect symbionts, and Drosophila, one of the most understood model insects, can be exploited as complementary tools to unravel mechanisms of insect symbiosis. Although Wolbachia itself cannot be grown axenically as clonal isolates or genetically manipulated by standard methods, its reproductive phenotypes, including cytoplasmic incompatibility (CI), have been elucidated using well-developed molecular tools and precise transgenic manipulations available for Drosophila melanogaster. Current research only scratches the surface of how Drosophila can provide a tool for understanding Wolbachia's evolutionary success and the molecular roles of its genetic elements. Here, we briefly outline basic methodologies inherent to transgenic Drosophila systems that have already contributed significant advances in understanding CI, but may be unfamiliar to those who lack experience in Drosophila genetics. In the future, these approaches will continue providing significant insights into Wolbachia that undoubtedly will be extended to other insect symbionts and their biological capabilities.
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Affiliation(s)
- Carai T Cortez
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Richard O Murphy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Isabella M Owens
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.
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4
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Chen YW, Su BY, Van Duyne GD, Fogg P, Fan HF. The influence of coiled-coil motif of serine recombinase toward the directionality regulation. Biophys J 2023; 122:4656-4669. [PMID: 37974397 PMCID: PMC10754689 DOI: 10.1016/j.bpj.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Serine integrases promote the recombination of two complementary DNA sequences, attP and attB, to create hybrid sequences, attL and attR. The reaction is unidirectional in the absence of an accessory protein called recombination directionality factor. We utilized tethered particle motion (TPM) experiments to investigate the reaction behaviors of two model serine integrases from Listeria innocua phage LI and Streptomyces coelicolor phage C31. Detailed kinetic analyses of wild-type and mutant proteins were carried out to verify the mechanisms of recombination directionality. In particular, we assessed the influence of a coiled-coil motif (CC) that is conserved in the C-terminal domain of serine integrases and is an important prerequisite for efficient recombination. Compared to wild type, we found that CC deletions in both serine integrases reduced the overall abundance of integrase (Int) att-site complexes and favored the formation of nonproductive complexes over recombination-competent complexes. Furthermore, the rate at which CC mutants formed productive synaptic complexes and disassembled aberrant nonproductive complexes was significantly reduced. It is notable that while the φC31 Int CC is essential for recombination, the LI Int CC plays an auxiliary role for recombination to stabilize protein-protein interactions and to control the directionality of the reaction.
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Affiliation(s)
- Yei-Wei Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan; Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Gregory D Van Duyne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Paul Fogg
- Biology Department and York Biomedical Research Institute (YBRI), University of York, York, United Kingdom.
| | - Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan; Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan.
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5
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570868. [PMID: 38106217 PMCID: PMC10723424 DOI: 10.1101/2023.12.08.570868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Standard methods for transgenesis in zebrafish depend on random transgene integration into the genome followed by resource-intensive screening and validation. Targeted vector integration into validated genomic loci using phiC31 integrase-based attP/attB recombination has transformed mouse and Drosophila transgenesis. However, while the phiC31 system functions in zebrafish, validated loci carrying attP-based landing or safe harbor sites suitable for universal transgenesis applications in zebrafish have not been established. Here, using CRISPR-Cas9, we converted two well-validated single insertion Tol2-based zebrafish transgenes with long-standing genetic stability into two attP landing sites, called phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET). Generating fluorescent reporters, loxP-based Switch lines, CreERT2 drivers, and gene-regulatory variant reporters in the pIGLET14a and pIGLET24b landing site alleles, we document their suitability for transgenesis applications across cell types and developmental stages. For both landing sites, we routinely achieve 25-50% germline transmission of targeted transgene integrations, drastically reducing the number of required animals and necessary resources to generate individual transgenic lines. We document that phiC31 integrase-based transgenesis into pIGLET14a and pIGLET24b reproducibly results in representative reporter expression patterns in injected F0 zebrafish embryos suitable for enhancer discovery and qualitative and quantitative comparison of gene-regulatory element variants. Taken together, our new phiC31 integrase-based transgene landing sites establish reproducible, targeted zebrafish transgenesis for numerous applications while greatly reducing the workload of generating new transgenic zebrafish lines.
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Affiliation(s)
- Robert L. Lalonde
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Harrison H. Wells
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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6
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Abioye J, Lawson-Williams M, Lecanda A, Calhoon B, McQue AL, Colloms SD, Stark WM, Olorunniji FJ. High fidelity one-pot DNA assembly using orthogonal serine integrases. Biotechnol J 2023; 18:e2200411. [PMID: 36504358 DOI: 10.1002/biot.202200411] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Large serine integrases (LSIs, derived from temperate phages) have been adapted for use in a multipart DNA assembly process in vitro, called serine integrase recombinational assembly (SIRA). The versatility, efficiency, and fidelity of SIRA is limited by lack of a sufficient number of LSIs whose activities have been characterized in vitro. METHODS AND MAJOR RESULTS In this report, we compared the activities in vitro of 10 orthogonal LSIs to explore their suitability for multiplex SIRA reactions. We found that Bxb1, ϕR4, and TG1 integrases were the most active among the set we studied, but several others were also usable. As proof of principle, we demonstrated high-efficiency one-pot assembly of six DNA fragments (made by PCR) into a 7.5 kb plasmid that expresses the enzymes of the β-carotenoid pathway in Escherichia coli, using six different LSIs. We further showed that a combined approach using a few highly active LSIs, each acting on multiple pairs of att sites with distinct central dinucleotides, can be used to scale up "poly-part" gene assembly and editing. CONCLUSIONS AND IMPLICATIONS We conclude that use of multiple orthogonal integrases may be the most predictable, efficient, and programmable approach for SIRA and other in vitro applications.
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Affiliation(s)
- Jumai Abioye
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Makeba Lawson-Williams
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
| | - Alicia Lecanda
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Brecken Calhoon
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Arlene L McQue
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Sean D Colloms
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - W Marshall Stark
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Femi J Olorunniji
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
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7
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van der Graaf K, Srivastav S, Singh P, McNew JA, Stern M. The Drosophila melanogaster attP40 docking site and derivatives are insertion mutations of msp-300. PLoS One 2022; 17:e0278598. [PMID: 36516171 PMCID: PMC9750024 DOI: 10.1371/journal.pone.0278598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
Abstract
The ɸC31 integrase system is widely used in Drosophila melanogaster to allow transgene targeting to specific loci. Over the years, flies bearing any of more than 100 attP docking sites have been constructed. One popular docking site, termed attP40, is located close to the Nesprin-1 orthologue msp-300 and lies upstream of certain msp-300 isoforms and within the first intron of others. Here we show that attP40 causes larval muscle nuclear clustering, which is a phenotype also conferred by msp-300 mutations. We also show that flies bearing insertions within attP40 can exhibit decreased msp-300 transcript levels in third instar larvae. Finally, chromosomes carrying certain "transgenic RNAi project" (TRiP) insertions into attP40 can confer pupal or adult inviability or infertility, or dominant nuclear clustering effects in certain genetic backgrounds. These phenotypes do not require transcription from the insertions within attP40. These results demonstrate that attP40 and insertion derivatives act as msp-300 insertional mutations. These findings should be considered when interpreting data from attP40-bearing flies.
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Affiliation(s)
- Kevin van der Graaf
- Department of Biosciences, Program in Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Saurabh Srivastav
- Department of Biosciences, Program in Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Pratibha Singh
- Department of Biosciences, Program in Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - James A. McNew
- Department of Biosciences, Program in Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Michael Stern
- Department of Biosciences, Program in Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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8
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Yang Z, Liu C, Wang Y, Chen Y, Li Q, Zhang Y, Chen Q, Ju J, Ma J. MGCEP 1.0: A Genetic-Engineered Marine-Derived Chassis Cell for a Scaled Heterologous Expression Platform of Microbial Bioactive Metabolites. ACS Synth Biol 2022; 11:3772-3784. [PMID: 36241611 DOI: 10.1021/acssynbio.2c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Marine microorganisms produce a variety of bioactive secondary metabolites, which represent a significant source of novel antibiotics. Heterologous expression is a valuable tool for discovering marine microbial secondary metabolites; however, marine-derived chassis cell is very scarce. Here, we build an efficient plug-and-play marine-derived gene clusters expression platform 1.0 (MGCEP 1.0) by the systematic engineering of the deep-sea-derived Streptomyces atratus SCSIO ZH16. For a proof of concept, four families of microbial bioactive metabolite biosynthetic gene clusters (BGCs), including alkaloids, aminonucleosides, nonribosomal peptides, and polyketides, were efficiently expressed in this platform. Moreover, 19 compounds, including two new angucycline antibiotics, were produced in MGCEP 1.0. Dynamic patterns of global biosynthetic gene expression in MGCEP 1.0 with or without a heterologous gene cluster were revealed at the transcriptome level. The platform MGCEP 1.0 provides new possibilities for expressing microbial secondary metabolites, especially of marine origin.
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Affiliation(s)
- Zhijie Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Chunyu Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China
| | - Yuyang Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Yingying Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Yun Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Qi Chen
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, China.,College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
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9
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Caviglia S, Unterweger IA, Gasiūnaitė A, Vanoosthuyse AE, Cutrale F, Trinh LA, Fraser SE, Neuhauss SCF, Ober EA. FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development 2022; 149:276363. [DOI: 10.1242/dev.199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Visualizing cell shapes and interactions of differentiating cells is instrumental for understanding organ development and repair. Across species, strategies for stochastic multicolour labelling have greatly facilitated in vivo cell tracking and mapping neuronal connectivity. Yet integrating multi-fluorophore information into the context of developing zebrafish tissues is challenging given their cytoplasmic localization and spectral incompatibility with common fluorescent markers. Inspired by Drosophila Raeppli, we developed FRaeppli (Fish-Raeppli) by expressing bright membrane- or nuclear-targeted fluorescent proteins for efficient cell shape analysis and tracking. High spatiotemporal activation flexibility is provided by the Gal4/UAS system together with Cre/lox and/or PhiC31 integrase. The distinct spectra of the FRaeppli fluorescent proteins allow simultaneous imaging with GFP and infrared subcellular reporters or tissue landmarks. We demonstrate the suitability of FRaeppli for live imaging of complex internal organs, such as the liver, and have tailored hyperspectral protocols for time-efficient acquisition. Combining FRaeppli with polarity markers revealed previously unknown canalicular topologies between differentiating hepatocytes, reminiscent of the mammalian liver, suggesting common developmental mechanisms. The multispectral FRaeppli toolbox thus enables the comprehensive analysis of intricate cellular morphologies, topologies and lineages at single-cell resolution in zebrafish.
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Affiliation(s)
- Sara Caviglia
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Iris A. Unterweger
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Akvilė Gasiūnaitė
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Alexandre E. Vanoosthuyse
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Stephan C. F. Neuhauss
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Elke A. Ober
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
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10
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Montaño ET, Nideffer JF, Brumage L, Erb M, Busch J, Fernandez L, Derman AI, Davis JP, Estrada E, Fu S, Le D, Vuppala A, Tran C, Luterstein E, Lakkaraju S, Panchagnula S, Ren C, Doan J, Tran S, Soriano J, Fujita Y, Gutala P, Fujii Q, Lee M, Bui A, Villarreal C, Shing SR, Kim S, Freeman D, Racha V, Ho A, Kumar P, Falah K, Dawson T, Enustun E, Prichard A, Gomez A, Khanna K, Trigg S, Pogliano K, Pogliano J. Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PLoS One 2022; 17:e0262354. [PMID: 35061755 PMCID: PMC8782336 DOI: 10.1371/journal.pone.0262354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare's most potent antibiotics are becoming obsolete. Approximately two-thirds of the world's antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 104 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
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Affiliation(s)
- Elizabeth T. Montaño
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jason F. Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marcella Erb
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Julia Busch
- Department of Immunology, Duke University, Durham, North Carolina, United Stated of America
| | - Lynley Fernandez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alan I. Derman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - John Paul Davis
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elena Estrada
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Fu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Le
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aishwarya Vuppala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Cassidy Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elaine Luterstein
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shivani Lakkaraju
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sriya Panchagnula
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Caroline Ren
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer Doan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jamielyn Soriano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Yuya Fujita
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Pranathi Gutala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Quinn Fujii
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Minda Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Anthony Bui
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Carleen Villarreal
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel R. Shing
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sean Kim
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Freeman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Vipula Racha
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alicia Ho
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Prianka Kumar
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kian Falah
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Thomas Dawson
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Amy Prichard
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Ana Gomez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shelly Trigg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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11
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Hao N, Sullivan AE, Shearwin KE, Dodd IB. The loopometer: a quantitative in vivo assay for DNA-looping proteins. Nucleic Acids Res 2021; 49:e39. [PMID: 33511418 PMCID: PMC8053113 DOI: 10.1093/nar/gkaa1284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/22/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Adrienne E Sullivan
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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12
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Askora A, Kawasaki T, Fujie M, Yamada T. In vitro characterization of the site-specific recombination system based on genus Habenivirus ϕRSM small serine integrase. Mol Genet Genomics 2021; 296:551-559. [PMID: 33575837 DOI: 10.1007/s00438-021-01762-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/27/2021] [Indexed: 10/22/2022]
Abstract
The genus Habenivirus which includes Ralstonia virus ϕRSM encodes a site-specific integrase of a small serine recombinase belonging to the resolvase/invertase family. Here we describe the integrative/excisive recombination reactions mediated by ϕRSM integrase using in vitro assays. The products of attP/attB recombination, i.e. attL and attR, were exactly identical to those found in the prophage ϕRSM in R. solanacearum strains. The minimum size of attB required for integration was determined to be 37 bp, containing a 13 bp core and flanking sequences of 4 bp on the left and 20 bp on the right. ϕRSM integrative recombination proceeds efficiently in vitro in the absence of additional proteins or high-energy cofactors. Excision of a functional phage genome from a prophage fragment was demonstrated in vitro, demonstrating two-way activity of ϕRSM1 integrase. This is the first example of a small serine recombinase from the resolvase/invertase group that functions in integrative and excisive recombination for filamentous phages. This serine integrase could be used as a tool for several genome engineering applications.
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Affiliation(s)
- Ahmed Askora
- Department of Botany and Microbiology, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Takeru Kawasaki
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan
| | - Makoto Fujie
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan
| | - Takashi Yamada
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan. .,Hiroshima Study Center, The Open University of Japan, Naka-ku, Hiroshima, 730-0053, Japan.
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13
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Fan HF, Su BY, Ma CH, Rowley PA, Jayaram M. A bipartite thermodynamic-kinetic contribution by an activating mutation to RDF-independent excision by a phage serine integrase. Nucleic Acids Res 2020; 48:6413-6430. [PMID: 32479633 PMCID: PMC7337939 DOI: 10.1093/nar/gkaa401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/02/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022] Open
Abstract
Streptomyces phage ϕC31 integrase (Int)—a large serine site-specific recombinase—is autonomous for phage integration (attP x attB recombination) but is dependent on the phage coded gp3, a recombination directionality factor (RDF), for prophage excision (attL x attR recombination). A previously described activating mutation, E449K, induces Int to perform attL x attR recombination in the absence of gp3, albeit with lower efficiency. E449K has no adverse effect on the competence of Int for attP x attB recombination. Int(E449K) resembles Int in gp3 mediated stimulation of attL x attR recombination and inhibition of attP x attB recombination. Using single-molecule analyses, we examined the mechanism by which E449K activates Int for gp3-independent attL x attR recombination. The contribution of E449K is both thermodynamic and kinetic. First, the mutation modulates the relative abundance of Int bound attL-attR site complexes, favoring pre-synaptic (PS) complexes over non-productively bound complexes. Roughly half of the synaptic complexes formed from Int(E449K) pre-synaptic complexes are recombination competent. By contrast, Int yields only inactive synapses. Second, E449K accelerates the dissociation of non-productively bound complexes and inactive synaptic complexes formed by Int. The extra opportunities afforded to Int(E499K) in reattempting synapse formation enhances the probability of success at fruitful synapsis.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan.,Department of Chemistry, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan.,Aerosol Science Research Center, National Sun Yat-sen University, Sizihwan, Kaohsiung 804, Taiwan
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chien-Hui Ma
- Department of Molecular Biosciences, UT Austin, Austin, TX 78712, USA
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, UT Austin, Austin, TX 78712, USA
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14
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Genomics-driven discovery of the biosynthetic gene cluster of maduramicin and its overproduction in Actinomadura sp. J1-007. ACTA ACUST UNITED AC 2020; 47:275-285. [DOI: 10.1007/s10295-019-02256-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Abstract
Maduramicin is the most efficient and possesses the largest market share of all anti-coccidiosis polyether antibiotics (ionophore); however, its biosynthetic gene cluster (BGC) has yet to been identified, and the associated strains have not been genetically engineered. Herein, we performed whole-genome sequencing of a maduramicin-producing industrial strain of Actinomadura sp. J1-007 and identified its BGC. Additionally, we analyzed the identified BGCs in silico to predict the biosynthetic pathway of maduramicin. We then developed a conjugation method for the non-spore-forming Actinomadura sp. J1-007, consisting of a site-specific integration method for gene overexpression. The maduramicin titer increased by 30% to 7.16 g/L in shake-flask fermentation following overexpression of type II thioesterase MadTE that is the highest titer at present. Our findings provide insights into the biosynthetic mechanism of polyethers and provide a platform for the metabolic engineering of maduramicin-producing microorganisms for overproduction and development of maduramicin analogs in the future.
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15
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Fogg PCM, Younger E, Fernando BD, Khaleel T, Stark WM, Smith MCM. Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif. Nucleic Acids Res 2019; 46:1308-1320. [PMID: 29228292 PMCID: PMC5814800 DOI: 10.1093/nar/gkx1233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/29/2017] [Indexed: 11/24/2022] Open
Abstract
To establish a prophage state, the genomic DNA of temperate bacteriophages normally becomes integrated into the genome of their host bacterium by integrase-mediated, site-specific DNA recombination. Serine integrases catalyse a single crossover between an attachment site in the host (attB) and a phage attachment site (attP) on the circularized phage genome to generate the integrated prophage DNA flanked by recombinant attachment sites, attL and attR. Exiting the prophage state and entry into the lytic growth cycle requires an additional phage-encoded protein, the recombination directionality factor or RDF, to mediate recombination between attL and attR and excision of the phage genome. The RDF is known to bind integrase and switch its activity from integration (attP x attB) to excision (attL x attR) but its precise mechanism is unclear. Here, we identify amino acid residues in the RDF, gp3, encoded by the Streptomyces phage ϕC31 and within the ϕC31 integrase itself that affect the gp3:Int interaction. We show that residue substitutions in integrase that reduce gp3 binding adversely affect both excision and integration reactions. The mutant integrase phenotypes are consistent with a model in which the RDF binds to a hinge region at the base of the coiled-coil motif in ϕC31 integrase.
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Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellen Younger
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Booshini D Fernando
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Thanafez Khaleel
- Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
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16
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Liu R, Deng Z, Liu T. Streptomyces species: Ideal chassis for natural product discovery and overproduction. Metab Eng 2018; 50:74-84. [DOI: 10.1016/j.ymben.2018.05.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/26/2022]
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17
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Makhija H, Roy S, Hoon S, Ghadessy FJ, Wong D, Jaiswal R, Campana D, Dröge P. A novel λ integrase-mediated seamless vector transgenesis platform for therapeutic protein expression. Nucleic Acids Res 2018; 46:e99. [PMID: 29893931 PMCID: PMC6144826 DOI: 10.1093/nar/gky500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/22/2018] [Indexed: 02/06/2023] Open
Abstract
Advances in stem cell engineering, gene therapy and molecular medicine often involve genome engineering at a cellular level. However, functionally large or multi transgene cassette insertion into the human genome still remains a challenge. Current practices such as random transgene integration or targeted endonuclease-based genome editing are suboptimal and might pose safety concerns. Taking this into consideration, we previously developed a transgenesis tool derived from phage λ integrase (Int) that precisely recombines large plasmid DNA into an endogenous sequence found in human Long INterspersed Elements-1 (LINE-1). Despite this advancement, biosafety concerns associated with bacterial components of plasmids, enhanced uptake and efficient transgene expression remained problematic. We therefore further improved and herein report a more superior Int-based transgenesis tool. This novel Int platform allows efficient and easy derivation of sufficient amounts of seamless supercoiled transgene vectors from conventional plasmids via intramolecular recombination as well as subsequent intermolecular site-specific genome integration into LINE-1. Furthermore, we identified certain LINE-1 as preferred insertion sites for Int-mediated seamless vector transgenesis, and showed that targeted anti-CD19 chimeric antigen receptor gene integration achieves high-level sustained transgene expression in human embryonic stem cell clones for potential downstream therapeutic applications.
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Affiliation(s)
- Harshyaa Makhija
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Suki Roy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Shawn Hoon
- Molecular Engineering Lab, Biomedical Sciences Institute, Agency for Science Technology and Research, 61 Biopolis Drive, Singapore 138673
| | | | - Desmond Wong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Rahul Jaiswal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Dario Campana
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Nanyang Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building (EMB), 59 Nanyang Drive, Singapore 636921
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18
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Fischer K, Kind A, Schnieke A. Assembling multiple xenoprotective transgenes in pigs. Xenotransplantation 2018; 25:e12431. [PMID: 30055014 DOI: 10.1111/xen.12431] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
This review gives a brief overview of the genetic modifications necessary for grafted porcine tissues and organs to overcome rejection in human recipients. It then focuses on the problem of generating and breeding herds of donor pigs carrying modified endogenous genes and multiple xenoprotective transgenes. A xenodonor pig optimised for human clinical use could well require the addition of ten or more xenoprotective transgenes. It is impractical to produce the required combination of transgene by cross-breeding animals bearing individual transgenes at unlinked genetic loci, because independent segregation means that huge numbers of pigs would be required to produce relatively few donor animals. A better approach is to colocate groups of transgenes at a single genomic locus. We outline current methods to assemble transgene arrays and consider their pros and cons. These include polycistronic expression systems, in vitro recombination of large DNA fragments in PAC and BAC vectors, transposon vectors, classical gene targeting by homologous recombination at permissive loci such as ROSA26, targeted transgene placement aided by gene editing systems such as CRISPR/Cas9, and transgene placement by site-specific recombination such as Min-tagging using the Bxb1recombinase.
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Affiliation(s)
- Konrad Fischer
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Alexander Kind
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
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19
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Evolution of a central neural circuit underlies Drosophila mate preferences. Nature 2018; 559:564-569. [PMID: 29995860 PMCID: PMC6276375 DOI: 10.1038/s41586-018-0322-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/05/2018] [Indexed: 01/20/2023]
Abstract
Courtship rituals serve to reinforce reproductive barriers between closely related species. Drosophila melanogaster and D. simulans exhibit reproductive isolation due, in part, to the fact that D. melanogaster females produce 7,11-heptacosadiene (7,11-HD), a pheromone that promotes courtship in D. melanogaster males but suppresses courtship in D. simulans males. Here we compare pheromone-processing pathways in D. melanogaster and D. simulans males to define how these sister species endow 7,11-HD with the opposite behavioral valence to underlie species discrimination. We show that males of both species detect 7,11-HD using the homologous peripheral sensory neurons but this signal is differentially propagated to the P1 neurons that control courtship behavior. A change in the balance of excitation and inhibition onto courtship-promoting neurons transforms an excitatory pheromonal cue in D. melanogaster into an inhibitory cue in D. simulans. Our results reveal how species-specific pheromone responses can emerge from conservation of peripheral detection mechanisms and diversification of central circuitry and illustrate how flexible nodes in neural circuits can contribute to behavioral evolution.
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20
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Bergmann T, Ehrke-Schulz E, Gao J, Schiwon M, Schildgen V, David S, Schildgen O, Ehrhardt A. Designer nuclease-mediated gene correction via homology-directed repair in an in vitro model of canine hemophilia B. J Gene Med 2018; 20:e3020. [PMID: 29608237 DOI: 10.1002/jgm.3020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Gene correction at specific target loci provides a powerful strategy for overcoming genetic diseases. In the present study, we aimed to use an in vitro model for canine hemophilia B containing a single point mutation in the catalytic domain of the canine coagulation factor IX (cFIX) gene. To correct the defective gene via homology-directed repair (HDR), we designed transcription-activator like effector nucleases and clustered regularly interspaced short palindromic repeats including Cas9 (CRISPR/Cas9) for introduction of double-strand breaks at the mutation site. METHODS To generate a stable cell line containing the mutated cFIX locus, a 2-kb genomic DNA fragment derived from a hemophilia B dog was amplified and integrated utilizing the phiC31 integrase system. Designer nucleases were assembled and cloned into vectors for constitutive and inducible expression. To detect mutations, insertions and deletions, and HDR events after nuclease treatment T7E1 assays, an amplification-refractory mutation system-quantitative polymerase chain reaction and pyrosequencing were performed. RESULTS To perform HDR correction experiments, we established a cell line carrying the mutated cFIX locus. In HDR approaches we either explored a wild-type or an optimized cFIX sequence and we found that our modified HDR cassette showed higher gene correction efficiencies of up to 6.4%. Furthermore, we compared inducible and constitutive designer nuclease expression systems and found that the inducible system resulted in comparable HDR efficiencies. CONCLUSIONS In conclusion, the present study demonstrates the potential of this strategy for gene therapeutic approaches in vitro and in a canine model for hemophilia B.
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Affiliation(s)
- Thorsten Bergmann
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Eric Ehrke-Schulz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Jian Gao
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Maren Schiwon
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Verena Schildgen
- Institute of Molecular Pathology, Hospital Merheim, Clinics of Cologne, Witten/Herdecke University, Cologne, Germany
| | - Stephan David
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Oliver Schildgen
- Institute of Molecular Pathology, Hospital Merheim, Clinics of Cologne, Witten/Herdecke University, Cologne, Germany
| | - Anja Ehrhardt
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
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21
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Abstract
Serine integrases catalyze precise rearrangement of DNA through site-specific recombination of small sequences of DNA called attachment (att) sites. Unlike other site-specific recombinases, the recombination reaction driven by serine integrases is highly directional and can only be reversed in the presence of an accessory protein called a recombination directionality factor (RDF). The ability to control reaction directionality has led to the development of serine integrases as tools for controlled rearrangement and modification of DNA in synthetic biology, gene therapy, and biotechnology. This review discusses recent advances in serine integrase technologies focusing on their applications in genome engineering, DNA assembly, and logic and data storage devices.
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Affiliation(s)
- Christine A. Merrick
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
| | - Jia Zhao
- Novo
Nordisk (China) Pharmaceuticals Co., Ltd., Lei Shing Hong Center, Guangshunnan Avenue, Beijing 100102, China
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
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22
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Mariezcurrena A, Uhlmann F. Observation of DNA intertwining along authentic budding yeast chromosomes. Genes Dev 2017; 31:2151-2161. [PMID: 29208645 PMCID: PMC5749163 DOI: 10.1101/gad.305557.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
DNA replication of circular genomes generates physically interlinked or catenated sister DNAs. These are resolved through transient DNA fracture by type II topoisomerases to permit chromosome segregation during cell division. Topoisomerase II is similarly required for linear chromosome segregation, suggesting that linear chromosomes also remain intertwined following DNA replication. Indeed, chromosome resolution defects are a frequent cause of chromosome segregation failure and consequent aneuploidies. When and where intertwines arise and persist along linear chromosomes are not known, owing to the difficulty of demonstrating intertwining of linear DNAs. Here, we used excision of chromosomal regions as circular "loop outs" to convert sister chromatid intertwines into catenated circles. This revealed intertwining at replication termination and cohesin-binding sites, where intertwines are thought to arise and persist but not to a greater extent than elsewhere in the genome. Intertwining appears to spread evenly along chromosomes but is excluded from heterochromatin. We found that intertwines arise before replication termination, suggesting that replication forks rotate during replication elongation to dissipate torsion ahead of the forks. Our approach provides previously inaccessible insight into the topology of eukaryotic chromosomes and illuminates a process critical for successful chromosome segregation.
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Affiliation(s)
- Ainhoa Mariezcurrena
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
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23
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Gupta K, Sharp R, Yuan JB, Li H, Van Duyne GD. Coiled-coil interactions mediate serine integrase directionality. Nucleic Acids Res 2017; 45:7339-7353. [PMID: 28549184 PMCID: PMC5499577 DOI: 10.1093/nar/gkx474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/15/2017] [Indexed: 11/14/2022] Open
Abstract
Serine integrases are bacteriophage enzymes that carry out site-specific integration and excision of their viral genomes. The integration reaction is highly directional; recombination between the phage attachment site attP and the host attachment site attB to form the hybrid sites attL and attR is essentially irreversible. In a recent model, extended coiled-coil (CC) domains in the integrase subunits are proposed to interact in a way that favors the attPxattB reaction but inhibits the attLxattR reaction. Here, we show for the Listeria innocua integrase (LI Int) system that the CC domain promotes self-interaction in isolated Int and when Int is bound to attachment sites. Three independent crystal structures of the CC domain reveal the molecular nature of the CC dimer interface. Alanine substitutions of key residues in the interface support the functional significance of the structural model and indicate that the same interaction is responsible for promoting integration and for inhibiting excision. An updated model of a LI Int•attL complex that incorporates the high resolution CC dimer structure provides insights that help to explain the unusual CC dimer structure and potential sources of stability in Int•attL and Int•attR complexes. Together, the data provide a molecular basis for understanding serine integrase directionality.
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MESH Headings
- Amino Acid Sequence
- Attachment Sites, Microbiological
- Bacteriophages/genetics
- Bacteriophages/metabolism
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Integrases/chemistry
- Integrases/genetics
- Integrases/metabolism
- Kinetics
- Listeria/genetics
- Listeria/metabolism
- Listeria/virology
- Models, Molecular
- Mutagenesis, Insertional
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombination, Genetic
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine/chemistry
- Serine/metabolism
- Substrate Specificity
- Thermodynamics
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - Robert Sharp
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - Jimmy B. Yuan
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - Huiguang Li
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - Gregory D. Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 10104, USA
- To whom correspondence should be addressed. Tel: +1 215 898 3058;
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24
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Vazquez-Vilar M, Quijano-Rubio A, Fernandez-Del-Carmen A, Sarrion-Perdigones A, Ochoa-Fernandez R, Ziarsolo P, Blanca J, Granell A, Orzaez D. GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Res 2017; 45:2196-2209. [PMID: 28053117 PMCID: PMC5389719 DOI: 10.1093/nar/gkw1326] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022] Open
Abstract
Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module.
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Affiliation(s)
- Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Asun Fernandez-Del-Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rocio Ochoa-Fernandez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Peio Ziarsolo
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - José Blanca
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
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25
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Tomimatsu K, Kokura K, Nishida T, Yoshimura Y, Kazuki Y, Narita M, Oshimura M, Ohbayashi T. Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome. FEBS Open Bio 2017; 7:306-317. [PMID: 28286726 PMCID: PMC5337897 DOI: 10.1002/2211-5463.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/17/2016] [Accepted: 11/24/2016] [Indexed: 01/21/2023] Open
Abstract
The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site-specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross-reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering.
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Affiliation(s)
- Kosuke Tomimatsu
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
- Japan Society for the Promotion of ScienceTokyoJapan
| | - Kenji Kokura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Division of Human Genome ScienceDepartment of Molecular and Cellular BiologySchool of Life SciencesFaculty of MedicineTottori UniversityYonagoJapan
| | - Tadashi Nishida
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
| | - Yuki Yoshimura
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
- Central Institute for Experimental AnimalsKawasakiJapan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeUK
| | - Mitsuo Oshimura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
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26
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Evolutionary variation in neural gene expression in the developing sense organs of the crustacean Daphnia magna. Dev Biol 2017; 424:50-61. [PMID: 28238736 DOI: 10.1016/j.ydbio.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/21/2016] [Accepted: 02/17/2017] [Indexed: 11/23/2022]
Abstract
Arthropods have numerous sense organs, which are adapted to their habitat. While some sense organs are similar in structure and function in all arthropod groups, structural differences in functionally related sense organs have been described, as well as the absence of particular sense organ subtypes in individual arthropod groups. Here we address the question of how the diverse structures of arthropod sense organs have evolved by analysing the underlying molecular developmental processes in a crustacean, an arthropod group that has been neglected so far. We have investigated the development of four types of chemo- and mechanosensory sense organs in the branchiopod Daphnia magna (Cladocera) that either cannot be found in arthropods other than crustaceans or represent adaptations to an aquatic environment. The formation of the sensory organ precursors shows greater similarity to the arthropod taxa Chelicerata and Myriapoda than to the more closely related insects. All analysed sense organ types co-express the proneural genes ASH and atonal regardless of their structure and function. In contrast, in Drosophila melanogaster, ASH and atonal expression does not overlap and the genes confer different sense organ subtype identities. We performed experimental co-expression studies in D. melanogaster and found that the combinatorial expression of ato and ASH can change the external structure of sense organs. Our results indicate a central role for ASH and Atonal family members in the emergence of structural variations in arthropod sense organs.
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27
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Fan HF, Hsieh TS, Ma CH, Jayaram M. Single-molecule analysis of ϕC31 integrase-mediated site-specific recombination by tethered particle motion. Nucleic Acids Res 2016; 44:10804-10823. [PMID: 27986956 PMCID: PMC5159548 DOI: 10.1093/nar/gkw861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/11/2016] [Accepted: 09/22/2016] [Indexed: 11/14/2022] Open
Abstract
Serine and tyrosine site-specific recombinases (SRs and YRs, respectively) provide templates for understanding the chemical mechanisms and conformational dynamics of strand cleavage/exchange between DNA partners. Current evidence suggests a rather intriguing mechanism for serine recombination, in which one half of the cleaved synaptic complex undergoes a 180° rotation relative to the other. The 'small' and 'large' SRs contain a compact amino-terminal catalytic domain, but differ conspicuously in their carboxyl-terminal domains. So far, only one serine recombinase has been analyzed using single substrate molecules. We now utilized single-molecule tethered particle motion (TPM) to follow step-by-step recombination catalyzed by a large SR, phage ϕC31 integrase. The integrase promotes unidirectional DNA exchange between attB and attP sites to integrate the phage genome into the host chromosome. The recombination directionality factor (RDF; ϕC31 gp3) activates the excision reaction (attL × attR). From integrase-induced changes in TPM in the presence or absence of gp3, we delineated the individual steps of recombination and their kinetic features. The gp3 protein appears to regulate recombination directionality by selectively promoting or excluding active conformations of the synapse formed by specific att site partners. Our results support a 'gated rotation' of the synaptic complex between DNA cleavage and joining.
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Affiliation(s)
- Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 112, Taiwan
- Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, 112, Taiwan
| | - Tao-Shih Hsieh
- Institute of Cellular and Organismic Biology Academia Sinica, 115, Taiwan
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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28
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Bowyer J, Zhao J, Subsoontorn P, Wong W, Rosser S, Bates D. Mechanistic Modeling of a Rewritable Recombinase Addressable Data Module. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2016; 10:1161-1170. [PMID: 27244749 DOI: 10.1109/tbcas.2016.2526668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Many of the most important applications predicted to arise from Synthetic Biology will require engineered cellular memory with the capability to store data in a rewritable and reversible manner upon induction by transient stimuli. DNA recombination provides an ideal platform for cellular data storage and has allowed the development of a rewritable recombinase addressable data (RAD) module, capable of efficient data storage within a chromosome. Here, we develop the first detailed mechanistic model of DNA recombination, and validate it against a new set of in vitro data on recombination efficiencies across a range of different concentrations of integrase and gp3. Investigation of in vivo recombination dynamics using our model reveals the importance of fully accounting for all mechanistic features of DNA recombination in order to accurately predict the effect of different switching strategies on RAD module performance, and highlights its usefulness as a design tool for building future synthetic circuitry.
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29
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Pokhilko A, Zhao J, Ebenhöh O, Smith MCM, Stark WM, Colloms SD. The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Res 2016; 44:7360-72. [PMID: 27387286 PMCID: PMC5009753 DOI: 10.1093/nar/gkw616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/28/2016] [Indexed: 02/04/2023] Open
Abstract
Serine integrases, DNA site-specific recombinases used by bacteriophages for integration and excision of their DNA to and from their host genomes, are increasingly being used as tools for programmed rearrangements of DNA molecules for biotechnology and synthetic biology. A useful feature of serine integrases is the simple regulation and unidirectionality of their reactions. Recombination between the phage attP and host attB sites is promoted by the serine integrase alone, giving recombinant attL and attR sites, whereas the ‘reverse’ reaction (between attL and attR) requires an additional protein, the recombination directionality factor (RDF). Here, we present new experimental data on the kinetics and regulation of recombination reactions mediated by ϕC31 integrase and its RDF, and use these data as the basis for a mathematical model of the reactions. The model accounts for the unidirectionality of the attP × attB and attL × attR reactions by hypothesizing the formation of structurally distinct, kinetically stable integrase–DNA product complexes, dependent on the presence or absence of RDF. The model accounts for all the available experimental data, and predicts how mutations of the proteins or alterations of reaction conditions might increase the conversion efficiency of recombination.
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Affiliation(s)
- Alexandra Pokhilko
- Institute of Molecular, Cell and Systems Biology, Bower Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jia Zhao
- Institute of Molecular, Cell and Systems Biology, Bower Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Oliver Ebenhöh
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany Institute for Complex Systems and Mathematical Biology, University of Aberdeen, AB24 3UE, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, Bower Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, Bower Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
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30
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Shi Z, Vickers CE. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metab Eng Commun 2016; 3:173-186. [PMID: 29468123 PMCID: PMC5779711 DOI: 10.1016/j.meteno.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023] Open
Abstract
Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. MCDS is an all-in-one in silico design, simulation and management platform. MCDS supports the design, simulation management of most cloning and recombineering technologies. MCDS has a novel interactive flowchart that allows simpler and more precise transactions. MCDS enables complete information integrity and consistency by keeping all details in one file.
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Affiliation(s)
- Zhenyu Shi
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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31
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Abstract
The large serine recombinases (LSRs) are a family of enzymes, encoded in temperate phage genomes or on mobile elements, that precisely cut and recombine DNA in a highly controllable and predictable way. In phage integration, the LSRs act at specific sites, the attP site in the phage and the attB site in the host chromosome, where cleavage and strand exchange leads to the integrated prophage flanked by the recombinant sites attL and attR. The prophage can excise by recombination between attL and attR but this requires a phage-encoded accessory protein, the recombination directionality factor (RDF). Although the LSRs can bind specifically to all the recombination sites, only specific integrase-bound sites can pair in a synaptic complex prior to strand exchange. Recent structural information has led to a breakthrough in our understanding of the mechanism of the LSRs, notably how the LSRs bind to their substrates and how LSRs display this site-selectivity. We also understand that the RDFs exercise control over the LSRs by protein-protein interactions. Other recent work with the LSRs have contributed to our understanding of how all serine recombinases undergo strand exchange subunit rotation, facilitated by surfaces that resemble a molecular bearing.
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Srivastava V, Thomson J. Gene stacking by recombinases. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:471-82. [PMID: 26332944 DOI: 10.1111/pbi.12459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 05/09/2023]
Abstract
Efficient methods of stacking genes into plant genomes are needed to expedite transfer of multigenic traits to crop varieties of diverse ecosystems. Over two decades of research has identified several DNA recombinases that carryout efficient cis and trans recombination between the recombination sites artificially introduced into the plant chromosome. The specificity and efficiency of recombinases make them extremely attractive for genome engineering. In plant biotechnology, recombinases have mostly been used for removing selectable marker genes and have rarely been extended to more complex applications. The reversibility of recombination, a property of the tyrosine family of recombinases, does not lend itself to gene stacking approaches that involve rounds of transformation for integrating genes into the engineered sites. However, recent developments in the field of recombinases have overcome these challenges and paved the way for gene stacking. Some of the key advancements include the application of unidirectional recombination systems, modification of recombination sites and transgene site modifications to allow repeated site-specific integrations into the selected site. Gene stacking is relevant to agriculturally important crops, many of which are difficult to transform; therefore, development of high-efficiency gene stacking systems will be important for its application on agronomically important crops, and their elite varieties. Recombinases, by virtue of their specificity and efficiency in plant cells, emerge as powerful tools for a variety of applications including gene stacking.
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Affiliation(s)
- Vibha Srivastava
- Department of Crop, Soil & Environmental Science, University of Arkansas, Fayetteville, AR, USA
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34
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Fernandez-Rodriguez J, Yang L, Gorochowski TE, Gordon DB, Voigt CA. Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability. ACS Synth Biol 2015; 4:1361-72. [PMID: 26548807 DOI: 10.1021/acssynbio.5b00170] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic memory can be implemented using enzymes that catalyze DNA inversions, where each orientation corresponds to a "bit". Here, we use two DNA invertases (FimE and HbiF) that reorient DNA irreversibly between two states with opposite directionality. First, we construct memory that is set by FimE and reset by HbiF. Next, we build a NOT gate where the input promoter drives FimE and in the absence of signal the reverse state is maintained by the constitutive expression of HbiF. The gate requires ∼3 h to turn on and off. The evolutionary stabilities of these circuits are measured by passaging cells while cycling function. The memory switch is stable over 400 h (17 days, 14 state changes); however, the gate breaks after 54 h (>2 days) due to continuous invertase expression. Genome sequencing reveals that the circuit remains intact, but the host strain evolves to reduce invertase expression. This work highlights the need to evaluate the evolutionary robustness and failure modes of circuit designs, especially as more complex multigate circuits are implemented.
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Affiliation(s)
- Jesus Fernandez-Rodriguez
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lei Yang
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas E. Gorochowski
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - D. Benjamin Gordon
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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35
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Bosch P, Forcato DO, Alustiza FE, Alessio AP, Fili AE, Olmos Nicotra MF, Liaudat AC, Rodríguez N, Talluri TR, Kues WA. Exogenous enzymes upgrade transgenesis and genetic engineering of farm animals. Cell Mol Life Sci 2015; 72:1907-29. [PMID: 25636347 PMCID: PMC11114025 DOI: 10.1007/s00018-015-1842-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 01/14/2023]
Abstract
Transgenic farm animals are attractive alternative mammalian models to rodents for the study of developmental, genetic, reproductive and disease-related biological questions, as well for the production of recombinant proteins, or the assessment of xenotransplants for human patients. Until recently, the ability to generate transgenic farm animals relied on methods of passive transgenesis. In recent years, significant improvements have been made to introduce and apply active techniques of transgenesis and genetic engineering in these species. These new approaches dramatically enhance the ease and speed with which livestock species can be genetically modified, and allow to performing precise genetic modifications. This paper provides a synopsis of enzyme-mediated genetic engineering in livestock species covering the early attempts employing naturally occurring DNA-modifying proteins to recent approaches working with tailored enzymatic systems.
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Affiliation(s)
- Pablo Bosch
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Diego O. Forcato
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Fabrisio E. Alustiza
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Ana P. Alessio
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Alejandro E. Fili
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - María F. Olmos Nicotra
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Ana C. Liaudat
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Nancy Rodríguez
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Thirumala R. Talluri
- Friedrich-Loeffler-Institute, Institute of Farm Animal Genetics, Biotechnology, 31535 Neustadt, Germany
| | - Wilfried A. Kues
- Friedrich-Loeffler-Institute, Institute of Farm Animal Genetics, Biotechnology, 31535 Neustadt, Germany
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Richier B, Salecker I. Versatile genetic paintbrushes: Brainbow technologies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:161-80. [PMID: 25491327 PMCID: PMC4384809 DOI: 10.1002/wdev.166] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/15/2014] [Indexed: 11/07/2022]
Abstract
UNLABELLED Advances in labeling technologies are instrumental to study the developmental mechanisms that control organ formation and function at the cellular level. Until recently, genetic tools relied on the expression of single markers to visualize individual cells or lineages in developing and adult animals. Exploiting the expanding color palette of fluorescent proteins and the power of site-specific recombinases in rearranging DNA fragments, the development of Brainbow strategies in mice made it possible to stochastically label many cells in different colors within the same sample. Over the past years, these pioneering approaches have been adapted for other experimental model organisms, including Drosophila melanogaster, zebrafish, and chicken. Balancing the distinct requirements of single cell and clonal analyses, adjustments were made that both enhance and expand the functionality of these tools. Multicolor cell labeling techniques have been successfully applied in studies analyzing the cellular components of neural circuits and other tissues, and the compositions and interactions of lineages. While being continuously refined, Brainbow technologies have thus found a firm place in the genetic toolboxes of developmental and neurobiologists. For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Benjamin Richier
- MRC National Institute for Medical Research, Division of Molecular NeurobiologyLondon, UK
| | - Iris Salecker
- MRC National Institute for Medical Research, Division of Molecular NeurobiologyLondon, UK
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37
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Chen C, Zhao X, Jin Y, Zhao Z(K, Suh JW. Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments. Plasmid 2014; 76:79-86. [DOI: 10.1016/j.plasmid.2014.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 11/28/2022]
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Wang H, Li Y, Truong LN, Shi LZ, Hwang PYH, He J, Do J, Cho MJ, Li H, Negrete A, Shiloach J, Berns MW, Shen B, Chen L, Wu X. CtIP maintains stability at common fragile sites and inverted repeats by end resection-independent endonuclease activity. Mol Cell 2014; 54:1012-1021. [PMID: 24837675 PMCID: PMC4105207 DOI: 10.1016/j.molcel.2014.04.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/04/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022]
Abstract
Chromosomal rearrangements often occur at genomic loci with DNA secondary structures, such as common fragile sites (CFSs) and palindromic repeats. We developed assays in mammalian cells that revealed CFS-derived AT-rich sequences and inverted Alu repeats (Alu-IRs) are mitotic recombination hotspots, requiring the repair functions of carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) and the Mre11/Rad50/Nbs1 complex (MRN). We also identified an endonuclease activity of CtIP that is dispensable for end resection and homologous recombination (HR) at I-SceI-generated "clean" double-strand breaks (DSBs) but is required for repair of DSBs occurring at CFS-derived AT-rich sequences. In addition, CtIP nuclease-defective mutants are impaired in Alu-IRs-induced mitotic recombination. These studies suggest that an end resection-independent CtIP function is important for processing DSB ends with secondary structures to promote HR. Furthermore, our studies uncover an important role of MRN, CtIP, and their associated nuclease activities in protecting CFSs in mammalian cells.
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Affiliation(s)
- Hailong Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yongjiang Li
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lan N Truong
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linda Z Shi
- The Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Patty Yi-Hwa Hwang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jing He
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Johnny Do
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Jeffrey Cho
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Alejandro Negrete
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michael W Berns
- The Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Department of Biomedical Engineering, Beckman Laser Institute, University of California at Irvine, Irvine, CA 92612, USA
| | - Binghui Shen
- Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Longchuan Chen
- Department of Pathology, Veterans Affairs Medical Center, Long Beach, CA 90822, USA
| | - Xiaohua Wu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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39
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Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. New applications for phage integrases. J Mol Biol 2014; 426:2703-16. [PMID: 24857859 PMCID: PMC4111918 DOI: 10.1016/j.jmb.2014.05.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision. The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors. Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro. Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers. Serine integrases are increasingly being exploited for synthetic biology applications.
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Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Sean Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh EH9 3JR, UK
| | - Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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40
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Unusual site-specific DNA integration into the highly active pseudo-attB of the Streptomyces albus J1074 genome. Appl Microbiol Biotechnol 2014; 98:5095-104. [PMID: 24566921 DOI: 10.1007/s00253-014-5605-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 10/25/2022]
Abstract
The φC31-encoded recombination system has become a widely used tool for genetic analysis of streptomycetes, gene therapy and generation of transgenic animals. However, the application of this system, even in the context of its natural host genus, Streptomyces, may require a specific approach for each species. In this study, we have identified a novel pseudo-attB site, called pseB4, for integration of vectors using the φC31 system. More than 90 % of clones contained two copies of pSET152- or pOJ436-based cosmids, after their introduction into S. albus. The efficiency of the integration of φC31-based vectors into pseB4 is therefore comparable to that of the integration into attB. Moreover, in contrast with integration into the native attB, integration into pseB4 is not polar and does not require a complementary sequence in the TT-core region. Furthermore, an analysis of conjugation frequency revealed mutual inhibition of plasmid integration into either site when both the attB and pseB4 sites were present in the genome.
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41
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Rutherford K, Van Duyne GD. The ins and outs of serine integrase site-specific recombination. Curr Opin Struct Biol 2014; 24:125-31. [PMID: 24509164 DOI: 10.1016/j.sbi.2014.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/27/2013] [Accepted: 01/08/2014] [Indexed: 11/19/2022]
Abstract
Serine integrases catalyze the integration and excision of phage genomes into and out of bacterial chromosomes in a highly specific and directional manner, making these proteins powerful tools for genome engineering. In 2013, the first structure of a serine integrase-DNA complex was reported. This work revealed how the phage attP sequence is recognized by the integrase and provided important clues about how serine integrases bind to other attachment site sequences. The resulting structural models indicate that distinct spatial arrangements of integrase domains are present for each attachment site complex. Here we describe how serine integrases may exploit this site-dependent domain arrangement to regulate the direction of recombination. We also discuss how phage-encoded recombination directionality factors could change this directionality by altering the nature of inter-subunit interactions.
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Affiliation(s)
- Karen Rutherford
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States.
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42
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Iterative marker excision system. Appl Microbiol Biotechnol 2014; 98:4557-70. [DOI: 10.1007/s00253-014-5523-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/03/2014] [Accepted: 01/05/2014] [Indexed: 10/25/2022]
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43
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Kanca O, Caussinus E, Denes AS, Percival-Smith A, Affolter M. Raeppli: a whole-tissue labeling tool for live imaging of Drosophila development. Development 2013; 141:472-80. [PMID: 24335257 DOI: 10.1242/dev.102913] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Observation of how cells divide, grow, migrate and form different parts of a developing organism is crucial for understanding developmental programs. Here, we describe a multicolor imaging tool named Raeppli (after the colorful confetti used at the carnival in Basel). Raeppli allows whole-tissue labeling such that the descendants of the majority of cells in a single organ are labeled and can be followed simultaneously relative to one another. We tested the use of Raeppli in the Drosophila melanogaster wing imaginal disc. Induction of Raeppli during larval stages irreversibly labels >90% of the cells with one of four spectrally separable, bright fluorescent proteins with low bias of selection. To understand the global growth characteristics of imaginal discs better, we induced Raeppli at various stages of development, imaged multiple fixed discs at the end of their larval development and estimated the size of their pouch primordium at those developmental stages. We also imaged the same wing disc through the larval cuticle at different stages of its development; the clones marked by Raeppli provide landmarks that can be correlated between multiple time points. Finally, we used Raeppli for continuous live imaging of prepupal eversion of the wing disc.
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Affiliation(s)
- Oguz Kanca
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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44
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Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MCM, Osbourn A, Keasling JD, Rosser SJ. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res 2013; 42:e23. [PMID: 24225316 PMCID: PMC3936721 DOI: 10.1093/nar/gkt1101] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
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Affiliation(s)
- Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK, Department of Metabolic Biology, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK, Joint BioEnergy Institute, Emeryville, CA 94608, USA, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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45
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Singh S, Rockenbach K, Dedrick RM, VanDemark AP, Hatfull GF. Cross-talk between diverse serine integrases. J Mol Biol 2013; 426:318-31. [PMID: 24161951 DOI: 10.1016/j.jmb.2013.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 01/06/2023]
Abstract
Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (<50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.
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Affiliation(s)
- Shweta Singh
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Kate Rockenbach
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15241, USA.
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46
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Van Duyne GD, Rutherford K. Large serine recombinase domain structure and attachment site binding. Crit Rev Biochem Mol Biol 2013; 48:476-91. [PMID: 23980849 DOI: 10.3109/10409238.2013.831807] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Large serine recombinases (LSRs) catalyze the movement of DNA elements into and out of bacterial chromosomes using site-specific recombination between short DNA "attachment sites". The LSRs that function as bacteriophage integrases carry out integration between attachment sites in the phage (attP) and in the host (attB). This process is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded recombination directionality factor, nor does recombination typically occur between other pairings of attachment sites. Although the mechanics of strand exchange are reasonably well understood through studies of the closely related resolvase and invertase serine recombinases, many of the fundamental aspects of the LSR reactions have until recently remained poorly understood on a structural level. In this review, we discuss the results of several years worth of biochemical and molecular genetic studies of LSRs in light of recently described structural models of LSR-DNA complexes. The focus is understanding LSR domain structure, how LSRs bind to the attP and attB attachment sites, and the differences between attP-binding and attB-binding modes. The simplicity, site-selectivity and strong directionality of the LSRs has led to their use as important tools in a number of genetic engineering applications in a wide variety of organisms. Given the important potential role of LSR enzymes in genetic engineering and gene therapy, understanding the structure and DNA-binding properties of LSRs is of fundamental importance for those seeking to enhance or alter specificity and functionality in these systems.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia , USA
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47
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Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD. Attachment site recognition and regulation of directionality by the serine integrases. Nucleic Acids Res 2013; 41:8341-56. [PMID: 23821671 PMCID: PMC3783163 DOI: 10.1093/nar/gkt580] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between ‘attachment sites’ in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP × attB synaptic complexes to initiate recombination, and how attL × attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.
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Affiliation(s)
- Karen Rutherford
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
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48
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Kobelt D, Schleef M, Schmeer M, Aumann J, Schlag PM, Walther W. Performance of high quality minicircle DNA for in vitro and in vivo gene transfer. Mol Biotechnol 2013; 53:80-9. [PMID: 22467123 DOI: 10.1007/s12033-012-9535-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmid DNA is frequently used particularly for nonviral gene therapy. Conventional plasmid DNA contains bacterial backbone and resistance gene sequences, as well as immunogenic CpG motifs. These components are not required for transgene expression. They represent a potential risk for safe clinical application and reduce gene transfer rates as well as transgene expression. To overcome these drawbacks, the minicircle technology is removing such sequences, to improve performance and also to reduce DNA size. Here, we show the effective production of luciferase, GFP, or lacZ-carrying minicircle DNA with high yield and reproducible high quality. They are used for lipofection or electroporation gene transfer into human melanoma and colon carcinoma cell lines. Comparison of respective parental plasmid and minicircle-mediated luciferase gene transfer shows improved luciferase expression by minicircle in all cell lines. This is not associated with increase in intracellular minicircle copy numbers after lipofection or electroporation. The minicircles rather mediate enhanced transgene mRNA transcription compared to their parental plasmids. In addition, FACS analysis revealed increase in counts of GFP positive cells after minicircle gene transfer, indicating higher gene transfer rates. Furthermore, minicircle showed also improved performance in vivo after jet-injection gene transfer. Therefore, availability of minicircles with reproducible high quality and sufficient amount makes them an applicable and effective alternative to conventional plasmid gene vectors.
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Affiliation(s)
- Dennis Kobelt
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany.
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49
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Misiura A, Pigli YZ, Boyle-Vavra S, Daum RS, Boocock MR, Rice PA. Roles of two large serine recombinases in mobilizing the methicillin-resistance cassette SCCmec. Mol Microbiol 2013; 88:1218-29. [PMID: 23651464 DOI: 10.1111/mmi.12253] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2013] [Indexed: 01/11/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) emerged via acquisition of a mobile element, staphylococcal cassette chromosome mec (SCCmec). Integration and excision of SCCmec is mediated by an unusual site-specific recombination system. Most variants of SCCmec encode two recombinases, CcrA and CcrB, that belong to the large serine family. Since CcrA and CcrB are always found together, we sought to address their specific roles. We show here that CcrA and CcrB can carry out both excisive and integrative recombination in Escherichia coli in the absence of any host-specific or SCCmec-encoded cofactors. CcrA and CcrB are promiscuous in their substrate choice: they act on many non-canonical pairs of recombination sites in addition to the canonical ones, which may explain tandem insertions into the SCCmec attachment site. Moreover, CcrB is always required, but CcrA is only required if one of the four half-sites is present. Recombinational activity correlates with DNA binding: CcrA recognizes only that half-site, which overlaps a conserved coding frame on the host chromosome. Therefore, we propose that CcrA serves as a specificity factor that emerged through modular evolution to enable recognition of a bacterial recombination site that is not an inverted repeat.
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Affiliation(s)
- Agnieszka Misiura
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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50
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Attachment site selection and identity in Bxb1 serine integrase-mediated site-specific recombination. PLoS Genet 2013; 9:e1003490. [PMID: 23658531 PMCID: PMC3642061 DOI: 10.1371/journal.pgen.1003490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/18/2013] [Indexed: 11/20/2022] Open
Abstract
Phage-encoded serine integrases mediate directionally regulated site-specific recombination between short attP and attB DNA sites without host factor requirements. These features make them attractive for genome engineering and synthetic genetics, although the basis for DNA site selection is poorly understood. Here we show that attP selection is determined through multiple proofreading steps that reject non-attP substrates, and that discrimination of attP and attB involves two critical site features: the outermost 5–6 base pairs of attP that are required for Int binding and recombination but antagonize attB function, and the “discriminators” at positions −15/+15 that determine attB identity but also antagonize attP function. Thus, although the attachment sites differ in length and sequence, only two base changes are needed to convert attP to attL, and just two more from attL to attB. The opposing effect of site identifiers ensures that site schizophrenia with dual identities does not occur. Site-specific recombinases catalyze recombination between two specific DNA sites to generate the products of recombination. The Integrase encoded by mycobacteriophage Bxb1 is a member of the serine-recombinase family and catalyzes strand exchange between attP and attB, the attachment sites for the phage and bacterial host, respectively. Although the DNA sites are relatively small (<50 bp), the reaction is highly selective for these sites and is also strongly directional. Here, we address the question of what sequences within attP are required for it to act as an attP site and identify the key sequence features that are required not just for Integrase binding but also for synapsis and post-synapsis events. We also have identified the key determinants of attP and attB identity, and although the sites are different in sequence and length, they can be interconverted with just two base changes in each of the half sites.
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