1
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Johnson LA, Mart RJ, Allemann RK. A Photoresponsive Homing Endonuclease for Programmed DNA Cleavage. ACS Synth Biol 2024; 13:195-205. [PMID: 38061193 PMCID: PMC10804406 DOI: 10.1021/acssynbio.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 01/23/2024]
Abstract
Homing endonucleases are used in a wide range of biotechnological applications including gene editing, in gene drive systems, and for the modification of DNA structures, arrays, and prodrugs. However, controlling nuclease activity and sequence specificity remain key challenges when developing new tools. Here a photoresponsive homing endonuclease was engineered for optical control of DNA cleavage by partitioning DNA binding and nuclease domains of the monomeric homing endonuclease I-TevI into independent polypeptide chains. Use of the Aureochrome1a light-oxygen-voltage domain delivered control of dimerization with light. Illumination reduced the concentration needed to achieve 50% cleavage of the homing target site by 6-fold when compared to the dark state, resulting in an up to 9-fold difference in final yields between cleavage products. I-TevI nucleases with and without a native I-TevI zinc finger motif displayed different nuclease activity and sequence preference impacting the promiscuity of the nuclease domain. By harnessing an alternative DNA binding domain, target preference was reprogrammed only when the nuclease lacked the I-TevI zinc finger motif. This work establishes a first-generation photoresponsive platform for spatiotemporal activation of DNA cleavage.
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Affiliation(s)
- Luke A. Johnson
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
| | | | - Rudolf K. Allemann
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
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2
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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3
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Teufel M, Klein CA, Mager M, Sobetzko P. A multifunctional system for genome editing and large-scale interspecies gene transfer. Nat Commun 2022; 13:3430. [PMID: 35701417 PMCID: PMC9198041 DOI: 10.1038/s41467-022-30843-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 05/23/2022] [Indexed: 11/09/2022] Open
Abstract
CRISPR SWAPnDROP extends the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates species specific adaptation to confer genome editing in various species. In this study, we show the implementation of the CRISPR SWAPnDROP concept for the model organism Escherichia coli, the fast growing Vibrio natriegens and the plant pathogen Dickeya dadantii. We demonstrate the excision, transfer and integration of large chromosomal regions between E. coli, V. natriegens and D. dadantii without size-limiting intermediate DNA extraction. CRISPR SWAPnDROP also provides common genome editing approaches comprising scarless, marker-free, iterative and parallel insertions and deletions. The modular character facilitates DNA library applications, and recycling of standardized parts. Its multi-color scarless co-selection system significantly improves editing efficiency and provides visual quality controls throughout the assembly and editing process.
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Affiliation(s)
- Marc Teufel
- Philipps Universität Marburg, Synthetic Microbiology Center Marburg (SYNMIKRO), Marburg, 35043, Germany
| | - Carlo A Klein
- Philipps Universität Marburg, Synthetic Microbiology Center Marburg (SYNMIKRO), Marburg, 35043, Germany
| | - Maurice Mager
- Philipps Universität Marburg, Synthetic Microbiology Center Marburg (SYNMIKRO), Marburg, 35043, Germany
| | - Patrick Sobetzko
- Philipps Universität Marburg, Synthetic Microbiology Center Marburg (SYNMIKRO), Marburg, 35043, Germany.
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4
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Raza SHA, Hassanin AA, Pant SD, Bing S, Sitohy MZ, Abdelnour SA, Alotaibi MA, Al-Hazani TM, Abd El-Aziz AH, Cheng G, Zan L. Potentials, prospects and applications of genome editing technologies in livestock production. Saudi J Biol Sci 2022; 29:1928-1935. [PMID: 35531207 PMCID: PMC9072931 DOI: 10.1016/j.sjbs.2021.11.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years, significant progress has been achieved in genome editing applications using new programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9). These genome editing tools are capable of nicking DNA precisely by targeting specific sequences, and enable the addition, removal or substitution of nucleotides via double-stranded breakage at specific genomic loci. CRISPR/Cas system, one of the most recent genome editing tools, affords the ability to efficiently generate multiple genomic nicks in single experiment. Moreover, CRISPR/Cas systems are relatively easy and cost effective when compared to other genome editing technologies. This is in part because CRISPR/Cas systems rely on RNA-DNA binding, unlike other genome editing tools that rely on protein–DNA interactions, which affords CRISPR/Cas systems higher flexibility and more fidelity. Genome editing tools have significantly contributed to different aspects of livestock production such as disease resistance, improved performance, alterations of milk composition, animal welfare and biomedicine. However, despite these contributions and future potential, genome editing technologies also have inherent risks, and therefore, ethics and social acceptance are crucial factors associated with implementation of these technologies. This review emphasizes the impact of genome editing technologies in development of livestock breeding and production in numerous species such as cattle, pigs, sheep and goats. This review also discusses the mechanisms behind genome editing technologies, their potential applications, risks and associated ethics that should be considered in the context of livestock.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China.,National Beef Cattle Improvement Center, Northwest A&F University, 712100 Yangling, Shaanxi, PR China
| | - Abdallah A Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Sameer D Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650 Australia
| | - Sun Bing
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Mahmoud Z Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Sameh A Abdelnour
- Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | | | - Tahani Mohamed Al-Hazani
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box: 83, Al-Kharj 11940, Saudi Arabia
| | - Ayman H Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Daman Hour University, Damanhour, Egypt
| | - Gong Cheng
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Linsen Zan
- State Key Laboratory of Animal Genetics Breeding & Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, PR China.,National Beef Cattle Improvement Center, Northwest A&F University, 712100 Yangling, Shaanxi, PR China
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5
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Nawimanage R, Yuan Z, Casares M, Joshi R, Lohman JR, Gimble FS. Structure-function studies of two yeast homing endonucleases that evolved to cleave identical targets with dissimilar rates and specificities. J Mol Biol 2022; 434:167550. [DOI: 10.1016/j.jmb.2022.167550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
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6
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Lee KZ, Mechikoff MA, Parasa MK, Rankin TJ, Pandolfi P, Fitzgerald KS, Hillman ET, Solomon KV. Repurposing the Homing Endonuclease I-SceI for Positive Selection and Development of Gene-Editing Technologies. ACS Synth Biol 2022; 11:53-60. [PMID: 35007422 DOI: 10.1021/acssynbio.1c00340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prokaryote genomes encode diverse programmable DNA endonucleases with significant potential for biotechnology and gene editing. However, these endonucleases differ significantly in their properties, which must be screened and measured. While positive selection screens based on ccdB and barnase have been developed to evaluate such proteins, their high levels of toxicity make them challenging to use. Here, we develop and validate a more robust positive selection screen based on the homing endonuclease I-SceI. Candidate endonucleases target and cure the I-SceI expression plasmid preventing induction of I-SceI-mediated double strand DNA breaks that lead to cell death in E. coli. We validated this screen to measure the relative activity of SpCas9, xCas9, and eSpCas9 and demonstrated an ability to enrich for more active endonuclease variants from a mixed population. This system may be applied in high throughput to rapidly characterize novel programmable endonucleases and be adapted for directed evolution of endonuclease function.
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Affiliation(s)
- Kok Zhi Lee
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Michael A. Mechikoff
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Drive, West Lafayette, Indiana 47907-2093, United States
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Tyler J. Rankin
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States
| | - Paula Pandolfi
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States
| | - Kevin S. Fitzgerald
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, 155 South Grant Street, West Lafayette, Indiana 47907, United States
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, Indiana 47907-2093, United States
- Department of Chemical & Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, 155 South Grant Street, West Lafayette, Indiana 47907, United States
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, Indiana 47907-2022, United States
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7
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Chen Y, Gong X, Gao Y, Shang Y, Shang J, Yu S, Li R, He S, Liu X, Wang F. Bioorthogonal regulation of DNA circuits for smart intracellular microRNA imaging. Chem Sci 2021; 12:15710-15718. [PMID: 35003602 PMCID: PMC8654030 DOI: 10.1039/d1sc05214d] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Catalytic DNA circuits represent a versatile toolbox for tracking intracellular biomarkers yet are constrained with low anti-interference capacity originating from their severe off-site activation. Herein, by introducing an unprecedented endogenous DNA repairing enzyme-powered pre-selection strategy, we develop a sequential and specific on-site activated catalytic DNA circuit for achieving the cancer cell-selective imaging of microRNA with high anti-interference capacity. Initially, the circuitry reactant is firmly caged by an elongated stabilizing duplex segment with a recognition/cleavage site of a cell-specific DNA repairing enzyme, which can prevent undesired signal leakage prior to its exposure to target cells. Then, the intrinsic DNA repairing enzyme of target cells can liberate the DNA probe for efficient intracellular microRNA imaging via the multiply guaranteed molecular recognition/activation procedures. This bioorthogonal regulated DNA circuit presents a modular and programmable amplification strategy for highly reliable assays of intracellular biomarkers, and provides a pivotal molecular toolbox for living systems. An on-site bioorthogonal regulated DNA circuit was developed by introducing an endogenous DNA repairing enzyme-mediated sequential activation strategy to achieve cancer cell-selective microRNA imaging with high anti-interference ability.![]()
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Affiliation(s)
- Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Yuhui Gao
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Yu Shang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China.,Research Institute of Shenzhen, Wuhan University Shenzhen 518057 P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 P. R. China.,Research Institute of Shenzhen, Wuhan University Shenzhen 518057 P. R. China
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8
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Lin Y, Yang Z, Lake RJ, Zheng C, Lu Y. Enzyme‐Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yao Lin
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
- Key Laboratory of Green Chemistry & TechnologyMinistry of EducationCollege of ChemistrySichuan University Chengdu Sichuan 610064 China
| | - Zhenglin Yang
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Ryan J. Lake
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & TechnologyMinistry of EducationCollege of ChemistrySichuan University Chengdu Sichuan 610064 China
| | - Yi Lu
- Department of ChemistryDepartment of BiochemistryUniversity of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
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9
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Lin Y, Yang Z, Lake RJ, Zheng C, Lu Y. Enzyme-Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells. Angew Chem Int Ed Engl 2019; 58:17061-17067. [PMID: 31529664 PMCID: PMC7174831 DOI: 10.1002/anie.201910343] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Indexed: 11/09/2022]
Abstract
Bioorthogonal control of metal-ion sensors for imaging metal ions in living cells is important for understanding the distribution and fluctuation of metal ions. Reported here is the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18-base pair recognition site of a homing endonuclease (I-SceI), which is found by chance only once in 7×1010 bp of genomic sequences, and can thus form a near bioorthogonal pair with I-SceI for DNAzyme activation with minimal effect on living cells. Once I-SceI is expressed inside cells, it cleaves at the recognition site, allowing the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg2+ to release the fluorophore-labeled DNA fragment and produce a fluorescent turn-on signal for Mg2+ . Thus I-SceI bioorthogonally activates the 10-23 DNAzyme for imaging of Mg2+ in HeLa cells.
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Affiliation(s)
- Yao Lin
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhenglin Yang
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ryan J. Lake
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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10
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Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR. Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease. Nucleic Acids Res 2019; 47:10830-10841. [PMID: 31602462 PMCID: PMC6847045 DOI: 10.1093/nar/gkz866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/17/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein-DNA covariation. Directed evolution experiments of one predicted pair, 227/+3, revealed variants with surprising shifts in I-OnuI substrate preference at the central 4 bases where cleavage occurs. Structural studies showed significant remodeling distant from the covarying position, including restructuring of an inter-hairpin loop, DNA distortions near the scissile phosphates, and new base-specific contacts. Our findings are consistent with a model whereby the functional impacts of covariation can be indirectly propagated to neighboring residues outside of direct contact range, allowing meganucleases to adapt to target site variation and indirectly expand the sequence space accessible for cleavage. We suggest that some engineered meganucleases may have unexpected cleavage profiles that were not rationally incorporated during the design process.
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Affiliation(s)
- Marc Laforet
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Thomas A McMurrough
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Michael Vu
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Christopher M Brown
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Kun Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Murray S Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
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11
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Paschon DE, Lussier S, Wangzor T, Xia DF, Li PW, Hinkley SJ, Scarlott NA, Lam SC, Waite AJ, Truong LN, Gandhi N, Kadam BN, Patil DP, Shivak DA, Lee GK, Holmes MC, Zhang L, Miller JC, Rebar EJ. Diversifying the structure of zinc finger nucleases for high-precision genome editing. Nat Commun 2019; 10:1133. [PMID: 30850604 PMCID: PMC6408524 DOI: 10.1038/s41467-019-08867-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 01/28/2019] [Indexed: 12/27/2022] Open
Abstract
Genome editing for therapeutic applications often requires cleavage within a narrow sequence window. Here, to enable such high-precision targeting with zinc-finger nucleases (ZFNs), we have developed an expanded set of architectures that collectively increase the configurational options available for design by a factor of 64. These new architectures feature the functional attachment of the FokI cleavage domain to the amino terminus of one or both zinc-finger proteins (ZFPs) in the ZFN dimer, as well as the option to skip bases between the target triplets of otherwise adjacent fingers in each zinc-finger array. Using our new architectures, we demonstrate targeting of an arbitrarily chosen 28 bp genomic locus at a density that approaches 1.0 (i.e., efficient ZFNs available for targeting almost every base step). We show that these new architectures may be used for targeting three loci of therapeutic significance with a high degree of precision, efficiency, and specificity.
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Affiliation(s)
- David E Paschon
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Stephanie Lussier
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Tenzin Wangzor
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Patrick W Li
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Sarah J Hinkley
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Nicholas A Scarlott
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Stephen C Lam
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Adam J Waite
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Lynn N Truong
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Nimisha Gandhi
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Bhakti N Kadam
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Deepak P Patil
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - David A Shivak
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Gary K Lee
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Michael C Holmes
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Lei Zhang
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA
| | - Edward J Rebar
- Sangamo Therapeutics, Inc., 501 Canal Boulevard, Suite A100, Richmond, California, 94804, USA.
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12
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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13
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Nelson CE, Robinson-Hamm JN, Gersbach CA. Genome engineering: a new approach to gene therapy for neuromuscular disorders. Nat Rev Neurol 2017; 13:647-661. [DOI: 10.1038/nrneurol.2017.126] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Renfer E, Technau U. Meganuclease-assisted generation of stable transgenics in the sea anemone Nematostella vectensis. Nat Protoc 2017; 12:1844-1854. [DOI: 10.1038/nprot.2017.075] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel 2017; 30:503-522. [PMID: 28873986 PMCID: PMC5914421 DOI: 10.1093/protein/gzx037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 11/14/2022] Open
Abstract
The combination of yeast surface display and flow cytometric analyses and selections is being used with increasing frequency to alter specificity of macromolecular recognition, including both protein-protein and protein-nucleic acid interactions. Here we describe the use of yeast surface display and cleavage-dependent flow cytometric assays to increase the specificity of an engineered meganuclease. The re-engineered meganuclease displays a significantly tightened specificity profile, while binding its cognate target site with a slightly lower, but still sub-nanomolar affinity. When incorporated into otherwise identical megaTAL protein scaffolds, these two nucleases display significantly different activity and toxicity profiles in cellulo. The structural basis for reprogrammed DNA cleavage specificity was further examined via high-resolution X-ray crystal structures of both enzymes. This analysis illustrated the altered protein-DNA contacts produced by mutagenesis and selection, that resulted both in altered readout of those based and a necessary reduction in DNA binding affinity that were necessary to improve specificity across the target site. The results of this study provide an illustrative example of the potential (and the challenges) associated with the use of surface display and flow cytometry for the retargeting and optimization of enzymes that act on nucleic acid substrates in a sequence-specific manner.
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Affiliation(s)
- Nixon Niyonzima
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Harshana De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
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16
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Grottesi A, Cecconi S, Molina R, D'abramo M. Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations. Biopolymers 2016; 105:898-904. [DOI: 10.1002/bip.22933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/28/2016] [Accepted: 08/08/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Alessandro Grottesi
- SuperComputing Applications and Innovations; CINECA; via dei Tizii 6 Rome 00185 Italy
| | - Simone Cecconi
- Department of Chemistry; Sapienza University of Rome; P.le A. Moro, 5 Rome 00185 Italy
| | - Rafael Molina
- Department of Crystallography and Structural Biology; Inst. Química-Física “Rocasolano”, CSIC; Serrano 119 Madrid 28006 Spain
| | - Marco D'abramo
- Department of Chemistry; Sapienza University of Rome; P.le A. Moro, 5 Rome 00185 Italy
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17
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Abstract
The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineering is the development of safe and effective delivery vehicles. A large body of work has applied genome engineering to genetic modification in vitro, and clinical trials have begun using cells modified by genome editing. Now, promising preclinical work is beginning to apply these tools in vivo. This article summarizes the development of genome engineering platforms, including meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas9, and their flexibility for precise genetic modifications. The prospects for the development of safe and effective viral and nonviral delivery vehicles for genome editing are reviewed, and promising advances in particular therapeutic applications are discussed.
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Affiliation(s)
- Christopher E Nelson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina 27708
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina 27708
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina 27708;
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18
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Yee JK. Off-target effects of engineered nucleases. FEBS J 2016; 283:3239-48. [PMID: 27208701 DOI: 10.1111/febs.13760] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/09/2016] [Accepted: 05/18/2016] [Indexed: 12/26/2022]
Abstract
Recent advances in gene editing with engineered nucleases have transformed our ability to manipulate the genome from diverse organisms for applications ranging from biomedical research to disease treatment. A major complication with these engineered nucleases is the binding of the nuclease to unintended genomic sites that share sequence homology with the on-target site. Cleavage of these off-target sites followed by DNA repair using normal cellular DNA repair mechanisms can cause gene mutation or gross chromosome rearrangement. Identification of nuclease-generated off-target sites is a daunting task due to the size and complexity of the mammalian genome. Five unbiased, genome-wide strategies have been developed to detect the off-target cleavage. Some of these strategies reach the sensitivity near the detection limit of directed deep sequencing and have sufficient precision and resolution to objectively assessing the off-target effect of any engineered nuclease. Significant progress has also been made recently to boost the nuclease targeting specificity by protein engineering to modify the structure of the nuclease and alter the interaction with its genomic target. In several studied cases, the off-target effect generated by the modified nuclease is completely eliminated. These modified nucleases significantly improve the overall fidelity of gene editing. These developments will enable gene editing tools to be applied more broadly and safely in basic research and disease treatment.
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Affiliation(s)
- Jiing-Kuan Yee
- Department of Diabetes and Metabolic Diseases Research, City of Hope National Medical Center, Duarte, CA, USA
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19
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Molina R, Besker N, Marcaida MJ, Montoya G, Prieto J, D’Abramo M. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics. ACS Chem Biol 2016; 11:1401-7. [PMID: 26909878 DOI: 10.1021/acschembio.5b00730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome these limitations is to unambiguously identify the key structural players involved in catalysis. Here, we report the E117A I-DmoI mutant crystal structure at 2.2 Å resolution that, together with the wt and Q42A/K120M constructs, is combined with computational approaches to shed light on protein cleavage activity. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved and noncleaved DNA strands when the ions and water molecules are correctly positioned for the nucleophilic attack that initiates the cleavage reaction, in line with experimental enzymatic activity. The proposed approach paves the way for an effective, general, and reliable procedure to analyze the enzymatic activity of endonucleases from a very limited data set, i.e., structure and dynamics.
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Affiliation(s)
- Rafael Molina
- Structural
Biology and Biocomputing Programme, Macromolecular Crystallography
Group, Spanish National Cancer Research Centre (CNIO), c/Melchor
Fdez. Almagro 3, 28029 Madrid, Spain
| | - Neva Besker
- CINECA, SuperComputing Applications and Innovations, via dei Tizii 6, 00185 Rome, Italy
| | - Maria Jose Marcaida
- Structural
Biology and Biocomputing Programme, Macromolecular Crystallography
Group, Spanish National Cancer Research Centre (CNIO), c/Melchor
Fdez. Almagro 3, 28029 Madrid, Spain
| | - Guillermo Montoya
- Structural
Biology and Biocomputing Programme, Macromolecular Crystallography
Group, Spanish National Cancer Research Centre (CNIO), c/Melchor
Fdez. Almagro 3, 28029 Madrid, Spain
- Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jesús Prieto
- Structural
Biology and Biocomputing Programme, Macromolecular Crystallography
Group, Spanish National Cancer Research Centre (CNIO), c/Melchor
Fdez. Almagro 3, 28029 Madrid, Spain
| | - Marco D’Abramo
- Department
of Chemistry, University of Rome “La Sapienza”, p.le
A. Moro, 5, 00185 Rome, Italy
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20
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Jasin M, Haber JE. The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair. DNA Repair (Amst) 2016; 44:6-16. [PMID: 27261202 DOI: 10.1016/j.dnarep.2016.05.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA double-strand breaks (DSBs) are dangerous lesions that if not properly repaired can lead to genomic change or cell death. Organisms have developed several pathways and have many factors devoted to repairing DSBs, which broadly occurs by homologous recombination, which relies on an identical or homologous sequence to template repair, or nonhomologous end-joining. Much of our understanding of these repair mechanisms has come from the study of induced DNA cleavage by site-specific endonucleases. In addition to their biological role, these cellular pathways can be co-opted for gene editing to study gene function or for gene therapy or other applications. While the first gene editing experiments were done more than 20 years ago, the recent discovery of RNA-guided endonucleases has simplified approaches developed over the years to make gene editing an approach that is available to the entire biomedical research community. Here, we review DSB repair mechanisms and site-specific cleavage systems that have provided insight into these mechanisms and led to the current gene editing revolution.
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Affiliation(s)
- Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 02454-9110, USA.
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21
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Liu Y, Yang M, Chen J, Yan D, Cheng W, Wang Y, Thygesen A, Chen R, Xing J, Wang Q, Ma Y. PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in Escherichia coli. PLoS One 2016; 11:e0149762. [PMID: 27019283 PMCID: PMC4809717 DOI: 10.1371/journal.pone.0149762] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/04/2016] [Indexed: 11/18/2022] Open
Abstract
Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double-strand breakage (DSB) via replication fork reactivation. First, cat-sacB cassette flanked by tandem repeat sequence was integrated into target site in chromosome assisted by Red enzymes. Then, for the excision of the cat-sacB cassette, only subculturing is needed. The developed method was successfully applied for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli.
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Affiliation(s)
- Yilan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Maohua Yang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jinjin Chen
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Daojiang Yan
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Wanwan Cheng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yanyan Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Anders Thygesen
- Center of Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Ruonan Chen
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
- * E-mail: (JX); (QW)
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
- * E-mail: (JX); (QW)
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
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22
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Reid W, O'Brochta DA. Applications of genome editing in insects. CURRENT OPINION IN INSECT SCIENCE 2016; 13:43-54. [PMID: 27436552 DOI: 10.1016/j.cois.2015.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/14/2023]
Abstract
Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in insects to date have been technical in nature but this is rapidly changing. Functional genomics and genetics-based insect control efforts will be major beneficiaries of the application of contemporary gene editing technologies. Engineered endonucleases like Cas9 make it possible to create powerful and effective gene drive systems that could be used to reduce or even eradicate specific insect populations. 'Best practices' for using Cas9-based editing are beginning to emerge making it easier and more effective to design and use but gene editing technologies still require traditional means of delivery in order to introduce them into somatic and germ cells of insects-microinjection of developing embryos. This constrains the use of these technologies by insect scientists. Insects created using editing technologies challenge existing governmental regulatory structures designed to manage genetically modified organisms.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, Department of Entomology, University of Maryland, College Park, 9600 Gudelsky Drive, Rockville, MD 20850, United States.
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23
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Weninger A, Killinger M, Vogl T. Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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25
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Vogl T, Ahmad M, Krainer FW, Schwab H, Glieder A. Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. Microb Cell Fact 2015; 14:103. [PMID: 26169367 PMCID: PMC4501187 DOI: 10.1186/s12934-015-0293-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Tagging proteins is a standard method facilitating protein detection, purification or targeting. When tagging a certain protein of interest, it is challenging to predict which tag will give optimal results and will not interfere with protein folding, activity or yields. Ideally, multiple tags and positions are tested which however complicates molecular cloning and expression vector generation. In conventional cloning, tags are either added on PCR primers (requiring a distinct primer and PCR product per tag) or provided on the vector (typically leaving a restriction site scar). RESULTS Here we report a vector family of 40 plasmids allowing simple, seamless fusions of a single PCR product with various N- and C-terminal tags, signal sequences and promoters. The restriction site free cloning (RSFC) strategy presented in this paper relies on seamless cloning using type IIS restriction endonucleases. After cutting out a stuffer (placeholder) fragment from the vectors, a single PCR product can be directly inserted in frame into all 40 plasmids using blunt end or TA ligations, requiring only verification of the orientation. We have established a RSFC vector family for the commonly used protein expression host Pichia pastoris and demonstrated the system with the secretory expression of horseradish peroxidase (HRP). HRP fusions to four tags (Myc, FLAG, His, Strep) and two fusion proteins (GFP and MBP) showed a 31-fold difference in volumetric activities. C-terminal tagging caused in some cases almost a complete loss of function, whereas N-terminal tags showed moderate differences. CONCLUSIONS The RSFC vectors provide an unprecedented toolbox for expression optimization in P. pastoris. The results obtained with HRP underline the importance of comparing different tags to maximize activities of fusion proteins. In a similar fashion the RSFC strategy can be applied in other expression hosts to screen for optimal promoters, signal sequences or to facilitate the evaluation of (iso-) enzyme families.
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Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria. .,Queensland University of Technology, 2 George St., Brisbane, QLD, 4000, Australia.
| | - Mudassar Ahmad
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Florian W Krainer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Helmut Schwab
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
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26
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Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales APW, Li Z, Peterson RT, Yeh JRJ, Aryee MJ, Joung JK. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 2015; 523:481-5. [PMID: 26098369 PMCID: PMC4540238 DOI: 10.1038/nature14592] [Citation(s) in RCA: 1163] [Impact Index Per Article: 129.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
Although CRISPR-Cas9 nucleases are widely used for genome editing1, 2, the range of sequences that Cas9 can recognize is constrained by the need for a specific protospacer adjacent motif (PAM)3–6. As a result, it can often be difficult to target double-stranded breaks (DSBs) with the precision that is necessary for various genome editing applications. The ability to engineer Cas9 derivatives with purposefully altered PAM specificities would address this limitation. Here we show that the commonly used Streptococcus pyogenes Cas9 (SpCas9) can be modified to recognize alternative PAM sequences using structural information, bacterial selection-based directed evolution, and combinatorial design. These altered PAM specificity variants enable robust editing of endogenous gene sites in zebrafish and human cells not currently targetable by wild-type SpCas9, and their genome-wide specificities are comparable to wild-type SpCas9 as judged by GUIDE-Seq analysis7. In addition, we identified and characterized another SpCas9 variant that exhibits improved specificity in human cells, possessing better discrimination against off-target sites with non-canonical NAG and NGA PAMs and/or mismatched spacers. We also found that two smaller-size Cas9 orthologues, Streptococcus thermophilus Cas9 (St1Cas9) and Staphylococcus aureus Cas9 (SaCas9), function efficiently in the bacterial selection systems and in human cells, suggesting that our engineering strategies could be extended to Cas9s from other species. Our findings provide broadly useful SpCas9 variants and, more importantly, establish the feasibility of engineering a wide range of Cas9s with altered and improved PAM specificities.
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Affiliation(s)
- Benjamin P Kleinstiver
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michelle S Prew
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Shengdar Q Tsai
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ved V Topkar
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Nhu T Nguyen
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Zongli Zheng
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Andrew P W Gonzales
- 1] Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Zhuyun Li
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Randall T Peterson
- 1] Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Jing-Ruey Joanna Yeh
- 1] Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Martin J Aryee
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - J Keith Joung
- 1] Molecular Pathology Unit &Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
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27
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Abstract
Molecular scissors (MS), incl. Zinc Finger Nucleases (ZFN), Transcription-activator like endoncleases (TALENS) and meganucleases possess long recognition sites and are thus capable of cutting DNA in a very specific manner. These molecular scissors mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination based gene targeting, MS can increase the targeting rate 10,000-fold, and gene disruption via mutagenic DNA repair is stimulated at a similar frequency. The successful application of different MS has been shown in different organisms, including insects, amphibians, plants, nematodes, and mammals, including humans. Recently, another novel class of molecular scissors was described that uses RNAs to target a specific genomic site. The CRISPR/Cas9 system is capable of targeting even multiple genomic sites in one shot and thus could be superior to ZFNs or TALEN, especially by its easy design. MS can be successfully employed for improving the understanding of complex physiological systems, producing transgenic animals, incl. creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on molecular scissors, their underlying mechanism and focuses on new opportunities for generating genetically modified farm animals.
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28
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Petersen B, Niemann H. Molecular scissors and their application in genetically modified farm animals. Transgenic Res 2015; 24:381-96. [DOI: 10.1007/s11248-015-9862-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/02/2015] [Indexed: 11/21/2022]
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29
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Takeuchi R, Choi M, Stoddard BL. Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization. Methods Mol Biol 2015; 1239:105-132. [PMID: 25408403 PMCID: PMC4416406 DOI: 10.1007/978-1-4939-1862-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
LAGLIDADG homing endonucleases (also referred to as "meganucleases") are compact DNA cleaving enzymes that specifically recognize long target sequences (approximately 20 base pairs), and thus serve as useful tools for therapeutic genome engineering. While stand-alone meganucleases are sufficiently active to introduce targeted genome modification, they can be fused to additional sequence-specific DNA binding domains in order to improve their performance in target cells. In this chapter, we describe an approach to retarget meganucleases to DNA targets of interest (such as sequences found in genes and cis regulatory regions), which is feasible in an academic laboratory environment. A combination of two selection systems, in vitro compartmentalization and two-plasmid cleavage assay in bacteria, allow for efficient engineering of meganucleases that specifically cleave a wide variety of DNA sequences.
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Affiliation(s)
- Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., A3-025, Seattle, WA, 98109-1024, USA
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30
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Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res 2014; 42:13839-52. [PMID: 25389263 PMCID: PMC4267613 DOI: 10.1093/nar/gku1096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity screening in a bacterial selection system. We characterized the substrate specificity and kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The endonuclease specificities revealed by these experiments can be partially recapitulated using 3D structure-based computational models. Analysis of these models together with genome sequence data provide insights into how alternative endonuclease specificities were generated during natural evolution.
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Affiliation(s)
- Summer B Thyme
- Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Mindy D Szeto
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lara Kusak
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Philip Bradley
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
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31
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Homing endonuclease target site specificity defined by sequential enrichment and next-generation sequencing of highly complex target site libraries. Methods Mol Biol 2014. [PMID: 24510267 DOI: 10.1007/978-1-62703-968-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Homing endonucleases (HEs) are DNA sequence-specific enzymes that recognize and cleave long target sites (14-40 bp) to generate double-strand breaks (DSBs). Their high site recognition specificity and tight coupling of binding and cleavage make HEs attractive reagents for targeted genome manipulation. In order to delineate the target site specificity of HEs and facilitate HE engineering, we have developed a method for comprehensive target site profiling of HEs cleavage specificity using partially randomized target site libraries and high-throughput DNA sequencing.
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Zaslavskiy M, Bertonati C, Duchateau P, Duclert A, Silva GH. Efficient design of meganucleases using a machine learning approach. BMC Bioinformatics 2014; 15:191. [PMID: 24934562 PMCID: PMC4065607 DOI: 10.1186/1471-2105-15-191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/03/2014] [Indexed: 01/09/2023] Open
Abstract
Background Meganucleases are important tools for genome engineering, providing an efficient way to generate DNA double-strand breaks at specific loci of interest. Numerous experimental efforts, ranging from in vivo selection to in silico modeling, have been made to re-engineer meganucleases to target relevant DNA sequences. Results Here we present a novel in silico method for designing custom meganucleases that is based on the use of a machine learning approach. We compared it with existing in silico physical models and high-throughput experimental screening. The machine learning model was used to successfully predict active meganucleases for 53 new DNA targets. Conclusions This new method shows competitive performance compared with state-of-the-art in silico physical models, with up to a fourfold increase in terms of the design success rate. Compared to experimental high-throughput screening methods, it reduces the number of screening experiments needed by a factor of more than 100 without affecting final performance.
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Affiliation(s)
| | | | - Philippe Duchateau
- Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris 75013, France.
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33
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Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues. Proc Natl Acad Sci U S A 2014; 111:E2376-83. [PMID: 24912189 DOI: 10.1073/pnas.1322352111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The active sites of enzymes consist of residues necessary for catalysis and structurally important noncatalytic residues that together maintain the architecture and function of the active site. Examples of evolutionary interactions between catalytic and noncatalytic residues have been difficult to define and experimentally validate due to a general intolerance of these residues to substitution. Here, using computational methods to predict coevolving residues, we identify a network of positions consisting of two catalytic metal-binding residues and two adjacent noncatalytic residues in LAGLIDADG homing endonucleases (LHEs). Distinct combinations of the four residues in the network map to distinct LHE subfamilies, with a striking distribution of the metal-binding Asp (D) and Glu (E) residues. Mutation of these four positions in three LHEs--I-LtrI, I-OnuI, and I-HjeMI--indicate that the combinations of residues tolerated are specific to each enzyme. Kinetic analyses under single-turnover conditions revealed that I-LtrI activity could be modulated over an ∼100-fold range by mutation of residues in the coevolving network. I-LtrI catalytic site variants with low activity could be rescued by compensatory mutations at adjacent noncatalytic sites that restore an optimal coevolving network and vice versa. Our results demonstrate that LHE activity is constrained by an evolutionary barrier of residues with strong context-dependent effects. Creation of optimal coevolving active-site networks is therefore an important consideration in engineering of LHEs and other enzymes.
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34
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Hafez M, Guha TK, Hausner G. I-OmiI and I-OmiII: two intron-encoded homing endonucleases within the Ophiostoma minus rns gene. Fungal Biol 2014; 118:721-31. [PMID: 25110134 DOI: 10.1016/j.funbio.2014.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022]
Abstract
The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively). Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand) of the intron insertion site generating 4 nucleotide 3' overhangs. The endonuclease activity of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was difficult, thus the endonuclease activity of this protein was tested via in vivo assays. Overall this study showed that there are many native forms of functional homing endonucleases yet to be discovered among fungal mtDNA genomes.
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Affiliation(s)
- Mohamed Hafez
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Botany, Faculty of Science, Suez University, Suez, Egypt
| | - Tuhin Kumar Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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35
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Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proc Natl Acad Sci U S A 2014; 111:4061-6. [PMID: 24591643 DOI: 10.1073/pnas.1321030111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
LAGLIDADG homing endonucleases (meganucleases) are sequence-specific DNA cleavage enzymes used for genome engineering. Recently, meganucleases fused to transcription activator-like effectors have been demonstrated to efficiently introduce targeted genome modifications. However, retargeting meganucleases to genomic sequences of interest remains challenging because it usually requires extensive alteration of a large number of amino acid residues that are situated in and near the DNA interface. Here we describe an effective strategy to extensively redesign such an extensive biomolecular interface. Well-characterized meganucleases are computationally screened to identify the best candidate enzyme to target a genomic region; that protein is then redesigned using iterative rounds of in vitro selections within compartmentalized aqueous droplets, which enable screening of extremely large numbers of protein variants at each step. The utility of this approach is illustrated by engineering three different meganucleases to cleave three human genomic sites (found in two exons and one flanking intron in two clinically relevant genes) and a fourth endonuclease that discriminates between single-nucleotide polymorphism variants of one of those targets. Fusion with transcription activator-like effector DNA binding domains significantly enhances targeted modification induced by meganucleases engineered in this study. Simultaneous expression of two such fusion endonucleases results in efficient excision of a defined genomic region.
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36
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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37
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Carlson JC, Badran AH, Guggiana-Nilo DA, Liu DR. Negative selection and stringency modulation in phage-assisted continuous evolution. Nat Chem Biol 2014; 10:216-22. [PMID: 24487694 PMCID: PMC3977541 DOI: 10.1038/nchembio.1453] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022]
Abstract
Phage-assisted continuous evolution (PACE) uses a modified filamentous bacteriophage life cycle to dramatically accelerate laboratory evolution experiments. In this work we expand the scope and capabilities of the PACE method with two key advances that enable the evolution of biomolecules with radically altered or highly specific new activities. First, we implemented small molecule-controlled modulation of selection stringency that enables otherwise inaccessible activities to be evolved directly from inactive starting libraries through a period of evolutionary drift. Second, we developed a general negative selection that enables continuous counter-selection against undesired activities. We integrated these developments to continuously evolve mutant T7 RNA polymerase enzymes with ∼10,000-fold altered, rather than merely broadened, substrate specificities during a single three-day PACE experiment. The evolved enzymes exhibit specificity for their target substrate that exceeds that of wild-type RNA polymerases for their cognate substrates, while maintaining wild-type-like levels of activity.
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Affiliation(s)
- Jacob C Carlson
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Ahmed H Badran
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | | | - David R Liu
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
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38
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Ito K, Shigi N, Komiyama M. An artificial restriction DNA cutter for site-selective gene insertion in human cells. Chem Commun (Camb) 2014; 49:6764-6. [PMID: 23778429 DOI: 10.1039/c3cc43261k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With the use of a chemistry-based artificial restriction DNA cutter (combination of Ce(IV)-EDTA and a pair of pcPNA), both an antibiotic-resistance gene and a fluorescent reporter protein gene were incorporated into the targeted site through homologous recombination in human cells.
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Affiliation(s)
- Kenichiro Ito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo 153-8904, Japan
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39
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Epinat JC. A yeast-based recombination assay for homing endonuclease activity. Methods Mol Biol 2014; 1123:105-26. [PMID: 24510264 DOI: 10.1007/978-1-62703-968-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Homing endonucleases (HEs) are natural enzymes that cleave long DNA target with a high specificity and trigger homologous recombination at the exact site of the break. Such mechanisms can thus be used for all the applications covered today by the generic name of "genome engineering": targeted sequence insertion, removal, or editing. However, before being able to address those applications, the engineering of HEs must be mastered so that any potential target would be efficiently and specifically recognized and cleaved. Working on the I-CreI model, we have developed a very powerful platform to generate HEs with new tailored specificity. We have put in place the first in vivo, functional, high throughput assay to generate I-CreI variants and measure their activity. We use semi-rational design combined with proprietary in silico predictions to design and synthesize I-CreI mutants that are tested for their capacity to induce homologous recombination in a yeast cell. The process has been standardized and robotized so that we can generate thousands of I-CreI derivatives, characterize their cleavage profile, and deliver them for further applications in the research, therapeutic, or agrobusiness fields.
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40
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Abstract
The rapid development of programmable site-specific endonucleases has led to a dramatic increase in genome engineering activities for research and therapeutic purposes. Specific loci of interest in the genomes of a wide range of organisms including mammals can now be modified using zinc-finger nucleases, transcription activator-like effectornucleases, and CRISPR-associated Cas9 endonucleases in a site-specific manner, in some cases requiring relatively modest effort for endonuclease design, construction, and application. While these technologies have made genome engineering widely accessible, the ability of programmable nucleases to cleave off-target sequences can limit their applicability and raise concerns about therapeutic safety. In this chapter, we review methods to evaluate and improve the DNA cleavage activity of programmable site-specific endonucleases and describe a procedure for a comprehensive off-target profiling method based on the in vitro selection of very large (~10(12)-membered) libraries of potential nuclease substrates.
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41
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Abstract
Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols. At this time, the computational methods are most useful for designing endonuclease variants that can accommodate small numbers of target site substitutions. Attempts to engineer for more extensive interface changes will likely benefit from an approach that uses the computational design results in conjunction with a high-throughput directed evolution or screening procedure. The family of enzymes presents an engineering challenge because their interfaces are highly integrated and there is significant coordination between the binding and catalysis events. Future developments in the computational algorithms depend on experimental feedback to improve understanding and modeling of these complex enzymatic features. This chapter presents both the basic method of design that has been successfully used to modulate specificity and more advanced procedures that incorporate DNA flexibility and other properties that are likely necessary for reliable modeling of more extensive target site changes.
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Affiliation(s)
- Summer Thyme
- Department of Biological Sciences, University of Washington, Seattle, WA, USA
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42
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Joshi R, Gimble FS. A bacterial one-hybrid system to isolate homing endonuclease variants with altered DNA target specificities. Methods Mol Biol 2014; 1114:221-36. [PMID: 24557906 DOI: 10.1007/978-1-62703-761-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chromosomal cleavage near the site of mutations that cause disease can facilitate the targeted repair of the locus. Gene therapy protocols therefore require the engineering of DNA endonucleases that target specific genomic loci. Here, we describe a bacterial one-hybrid selection system that has been used to isolate derivatives of the I-SceI homing endonuclease from combinatorial libraries that display altered DNA recognition specificities. The construction of plasmid expression libraries, the development of reporter strains, and the utilization of these components in the bacterial one-hybrid system are detailed.
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Affiliation(s)
- Rakesh Joshi
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
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43
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Djukanovic V, Smith J, Lowe K, Yang M, Gao H, Jones S, Nicholson MG, West A, Lape J, Bidney D, Carl Falco S, Jantz D, Alexander Lyznik L. Male-sterile maize plants produced by targeted mutagenesis of the cytochrome P450-like gene (MS26) using a re-designed I-CreI homing endonuclease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:888-99. [PMID: 24112765 DOI: 10.1111/tpj.12335] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 05/22/2023]
Abstract
The I-CreI homing endonuclease from Chlamydomonas reinhardti has been used as a molecular tool for creating DNA double-strand breaks and enhancing DNA recombination reactions in maize cells. The DNA-binding properties of this protein were re-designed to recognize a 22 bp target sequence in the 5th exon of MS26, a maize fertility gene. Three versions of a single-chain endonuclease, called Ems26, Ems26+ and Ems26++, cleaved their intended DNA site within the context of a reporter assay in a mammalian cell line. When the Ems26++ version was delivered to maize Black Mexican Sweet cells by Agrobacterium-mediated transformation, the cleavage resulted in mutations at a co-delivered extra-chromosomal ms26-site in up to 8.9% of the recovered clones. Delivery of the same version of Ems26 to immature embryos resulted in mutations at the predicted genomic ms26-site in 5.8% of transgenic T(0) plants. This targeted mutagenesis procedure yielded small deletions and insertions at the Ems26 target site consistent with products of double-strand break repair generated by non-homologous end joining. One of 21 mutagenized T(0) plants carried two mutated alleles of the MS26 gene. As expected, the bi-allelic mutant T(0) plant and the T(1) progeny homozygous for the ms26 mutant alleles were male-sterile. This paper described the second maize chromosomal locus (liguless-1 being the first one) mutagenized by a re-designed I-CreI-based endonuclease, demonstrating the general utility of these molecules for targeted mutagenesis in plants.
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Affiliation(s)
- Vesna Djukanovic
- DuPont/Pioneer Agricultural Biotechnology, 8305 N.W. 62nd Avenue, Johnston, IA, 50131, USA
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44
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Thyme SB, Boissel SJS, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res 2013; 42:2564-76. [PMID: 24270794 PMCID: PMC3936771 DOI: 10.1093/nar/gkt1212] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE variants with novel DNA cleavage specificities using an integrated experimental and computational approach. Using computational modeling and an improved selection strategy, which optimizes specificity in addition to activity, we engineered an endonuclease to cleave in a gene associated with Anopheles sterility and another to cleave near a mutation that causes pyruvate kinase deficiency. In the course of this work we observed unanticipated context-dependence between bases which will need to be mechanistically understood for reprogramming of specificity to succeed more generally.
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Affiliation(s)
- Summer B Thyme
- Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA, Graduate Program in Biomolecular Structure and Design, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA, Graduate Program in Molecular and Cellular Biology, University of Washington, UW Box 357275, 1959 NE Pacific St., Seattle, WA 98195, USA, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, Imperial College Road, London SW7 2AZ, UK, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB1 3QA, UK, Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA and Howard Hughes Medical Institute, University of Washington, UW Box 357350, 1705 NE Pacific St., Seattle, WA 98195, USA
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45
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Aryan A, Anderson MAE, Myles KM, Adelman ZN. Germline excision of transgenes in Aedes aegypti by homing endonucleases. Sci Rep 2013; 3:1603. [PMID: 23549343 PMCID: PMC3615334 DOI: 10.1038/srep01603] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/22/2013] [Indexed: 01/24/2023] Open
Abstract
Aedes (Ae.) aegypti is the primary vector for dengue viruses (serotypes1–4) and chikungunya virus. Homing endonucleases (HEs) are ancient selfish elements that catalyze double-stranded DNA breaks (DSB) in a highly specific manner. In this report, we show that the HEs Y2-I-AniI, I-CreI and I-SceI are all capable of catalyzing the excision of genomic segments from the Ae. aegypti genome in a heritable manner. Y2-I-AniI demonstrated the highest efficiency at two independent genomic targets, with 20–40% of Y2-I-AniI-treated individuals producing offspring that had lost the target transgene. HE-induced DSBs were found to be repaired via the single-strand annealing (SSA) and non-homologous end-joining (NHEJ) pathways in a manner dependent on the availability of direct repeat sequences in the transgene. These results support the development of HE-based gene editing and gene drive strategies in Ae. aegypti, and confirm the utility of HEs in the manipulation and modification of transgenes in this important vector.
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Affiliation(s)
- Azadeh Aryan
- Fralin Life Science Institute and Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA
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46
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Abstract
PURPOSE OF REVIEW Recent clinical research suggests that an HIV-infected patient with lymphoma who was transplanted with bone marrow homozygous for a disrupted mutant CCR5 allele has no remaining HIV replication and is effectively cured of HIV. Here, we discuss the approaches of disrupting host and viral genes involved in HIV replication and pathogenesis with the aim of curing patients with HIV. RECENT FINDINGS Data from the 'Berlin patient' suggest that targeted gene disruption can lead to an HIV cure. This review discusses the recent advances in the field of gene disruption toward the development of an anti-HIV therapy. We will introduce the strategies to disrupt host and viral genes using precise disruptions, imprecise disruptions, or site-specific recombination. Furthermore, the production of engineered rare-cutting endonucleases (zinc finger nucleases, TAL effector nucleases, and homing endonucleases) and recombinases that can recognize specific DNA target sequences and facilitate gene disruption will be discussed. SUMMARY The discovery of a gene disruption approach that would cure or efficiently confine HIV infection could have broad implications for the treatment of millions of people infected with HIV. An efficient 'one-shot' curative therapy not only would give infected patients hope of a drug-free or treatment-free future, but also could reduce the huge financial burden faced by many countries because of widespread administration of highly active antiretroviral therapy.
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47
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Chan YS, Takeuchi R, Jarjour J, Huen DS, Stoddard BL, Russell S. The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive. PLoS One 2013; 8:e74254. [PMID: 24040217 PMCID: PMC3769382 DOI: 10.1371/journal.pone.0074254] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 07/26/2013] [Indexed: 01/20/2023] Open
Abstract
The homing endonuclease gene (HEG) drive system, a promising genetic approach for controlling arthropod populations, utilises engineered nucleases to spread deleterious mutations that inactivate individual genes throughout a target population. Previous work with a naturally occurring LAGLIDADG homing endonuclease (I-SceI) demonstrated its feasibility in both Drosophila and Anopheles. Here we report on the next stage of this strategy: the redesign of HEGs with customized specificity in order to drive HEG-induced ‘homing’ in vivo via break-induced homologous recombination. Variants targeting a sequence within the Anopheles AGAP004734 gene were created from the recently characterized I-OnuI endonuclease, and tested for cleavage activity and frequency of homing using a model Drosophila HEG drive system. We observed cleavage and homing at an integrated reporter for all endonuclease variants tested, demonstrating for the first time that engineered HEGs can cleave their target site in insect germline cells, promoting targeted mutagenesis and homing. However, in comparison to our previously reported work with I-SceI, the engineered I-OnuI variants mediated homing with a reduced frequency, suggesting that site-specific cleavage activity is insufficient by itself to ensure efficient homing. Taken together, our experiments take a further step towards the development of a viable HEG-based population control strategy for insects.
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Affiliation(s)
- Yuk-Sang Chan
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Ryo Takeuchi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Northwest Genome Engineering Consortium, Seattle, Washington, United States of America
| | - Jordan Jarjour
- Pregenen Inc., Seattle, Washington, United States of America
| | - David S. Huen
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
- * E-mail:
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Northwest Genome Engineering Consortium, Seattle, Washington, United States of America
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
- Cambridge Systems Biology Centre, Cambridge, Cambridgeshire, United Kingdom
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48
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Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 2013; 31:839-43. [PMID: 23934178 PMCID: PMC3782611 DOI: 10.1038/nbt.2673] [Citation(s) in RCA: 1088] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022]
Abstract
The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA at sites complementary to a 20-base-pair guide RNA. The Cas9 system has been used to modify genomes in multiple cells and organisms, demonstrating its potential as a facile genome-engineering tool. We used in vitro selection and high-throughput sequencing to determine the propensity of eight guide-RNA:Cas9 complexes to cleave each of 10(12) potential off-target DNA sequences. The selection results predicted five off-target sites in the human genome that were confirmed to undergo genome cleavage in HEK293T cells upon expression of one of two guide-RNA:Cas9 complexes. In contrast to previous models, our results show that guide-RNA:Cas9 specificity extends past a 7- to 12-base-pair seed sequence. Our results also suggest a tradeoff between activity and specificity both in vitro and in cells as a shorter, less-active guide RNA is more specific than a longer, more-active guide RNA. High concentrations of guide-RNA:Cas9 complexes can cleave off-target sites containing mutations near or within the PAM that are not cleaved when enzyme concentrations are limiting.
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Affiliation(s)
- Vikram Pattanayak
- Department of Chemistry & Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
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49
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Abstract
Buried within the genomes of many microorganisms are genetic elements that encode rare-cutting homing endonucleases that assist in the mobility of the elements that encode them, such as the self-splicing group I and II introns and in some cases inteins. There are several different families of homing endonucleases and their ability to initiate and target specific sequences for lateral transfers makes them attractive reagents for gene targeting. Homing endonucleases have been applied in promoting DNA modification or genome editing such as gene repair or "gene knockouts". This review examines the categories of homing endonucleases that have been described so far and their possible applications to biotechnology. Strategies to engineer homing endonucleases to alter target site specificities will also be addressed. Alternatives to homing endonucleases such as zinc finger nucleases, transcription activator-like effector nucleases, triplex forming oligonucleotide nucleases, and targetrons are also briefly discussed.
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Affiliation(s)
- Mohamed Hafez
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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50
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Sun N, Abil Z, Zhao H. Recent advances in targeted genome engineering in mammalian systems. Biotechnol J 2012; 7:1074-87. [PMID: 22777886 DOI: 10.1002/biot.201200038] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/22/2012] [Accepted: 06/15/2012] [Indexed: 12/21/2022]
Abstract
Targeted genome engineering enables researchers to disrupt, insert, or replace a genomic sequence precisely at a predetermined locus. One well-established technology to edit a mammalian genome is known as gene targeting, which is based on the homologous recombination (HR) mechanism. However, the low HR frequency in mammalian cells (except for mice) prevents its wide application. To address this limitation, a custom-designed nuclease is used to introduce a site-specific DNA double-strand break (DSB) on the chromosome and the subsequent repair of the DSB by the HR mechanism or the non-homologous end joining mechanism results in efficient targeted genome modifications. Engineered homing endonucleases (also called meganucleases), zinc finger nucleases, and transcription activator-like effector nucleases represent the three major classes of custom-designed nucleases that have been successfully applied in many different organisms for targeted genome engineering. This article reviews the recent developments of these genome engineering tools and highlights a few representative applications in mammalian systems. Recent advances in gene delivery strategies of these custom-designed nucleases are also briefly discussed.
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Affiliation(s)
- Ning Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 61801, USA
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